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Sample records for human gut ecosystem

  1. Gut microbiota diversity and human diseases: should we reintroduce key predators in our ecosystem?

    Directory of Open Access Journals (Sweden)

    Alexis eMosca

    2016-03-01

    Full Text Available Most of the Human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota. The Western way of life, with a wide use of antibiotics and other environmental triggers, may reduce the number of bacterial predators leading to a decrease in microbial diversity of the Human gut. We argue that this phenomenon is similar to the process of ecosystem impoverishment in macro ecology where human activity decreases ecological niches, the size of predator populations and finally the biodiversity. Such pauperization is fundamental since it reverses the evolution processes, drives life backward into diminished complexity, stability and adaptability. A simple therapeutic approach could thus be to reintroduce bacterial predators and restore a bacterial diversity of the host microbiota.

  2. Gut ecosystem: how microbes help us.

    Science.gov (United States)

    Martín, R; Miquel, S; Ulmer, J; Langella, P; Bermúdez-Humarán, L G

    2014-09-01

    The human gut houses one of the most complex and abundant ecosystems composed of up to 1013-1014 microorganisms. Although the anthropocentric concept of life has concealed the function of microorganisms inside us, the important role of gut bacterial community in human health is well recognised today. Moreover, different microorganims, which are commonly present in a large diversity of food products, transit through our gut every day adding in some cases a beneficial effect to our health (probiotics). This crosstalk is concentrated mainly in the intestinal epithelium, where microbes provide the host with essential nutrients and modulation of the immune system. Furthermore, microorganisms also display antimicrobial activities maintaining a gut ecosystem stable. This review summarises some of the recent findings on the interaction of both commensal and probiotic bacteria with each other and with the host. The aim is to highlight the cooperative status found in healthy individuals as well as the importance of this crosstalk in the maintenance of human homeostasis.

  3. Healthy human gut phageome

    NARCIS (Netherlands)

    Manrique, Pilar; Bolduc, Benjamin; Walk, Seth T.; Oost, van der John; Vos, de Willem M.; Young, Mark J.

    2016-01-01

    The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of

  4. Healthy human gut phageome

    NARCIS (Netherlands)

    Manrique, Pilar; Bolduc, Benjamin; Walk, Seth T.; Oost, van der John; Vos, de Willem M.; Young, Mark J.

    2016-01-01

    The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of hu

  5. Impacts of Gut Bacteria on Human Health and Diseases

    Directory of Open Access Journals (Sweden)

    Yu-Jie Zhang

    2015-04-01

    Full Text Available Gut bacteria are an important component of the microbiota ecosystem in the human gut, which is colonized by 1014 microbes, ten times more than the human cells. Gut bacteria play an important role in human health, such as supplying essential nutrients, synthesizing vitamin K, aiding in the digestion of cellulose, and promoting angiogenesis and enteric nerve function. However, they can also be potentially harmful due to the change of their composition when the gut ecosystem undergoes abnormal changes in the light of the use of antibiotics, illness, stress, aging, bad dietary habits, and lifestyle. Dysbiosis of the gut bacteria communities can cause many chronic diseases, such as inflammatory bowel disease, obesity, cancer, and autism. This review summarizes and discusses the roles and potential mechanisms of gut bacteria in human health and diseases.

  6. The human gut virome: a multifaceted majority

    Directory of Open Access Journals (Sweden)

    Lesley Ann Ogilvie

    2015-09-01

    Full Text Available Here we outline our current understanding of the human gut virome, in particular the phage component of this ecosystem, highlighting progress and challenges in viral discovery in this arena. We reveal how developments in high-throughput sequencing technologies and associated data analysis methodologies are helping to illuminate this abundant ‘biological dark matter’. Current evidence suggests that the human gut virome is a highly individual but temporally stable collective, dominated by phage exhibiting a temperate lifestyle. This viral community also appears to encode a surprisingly rich functional repertoire that confers a range of attributes to their bacterial hosts, ranging from bacterial virulence and pathogenesis to maintaining host-microbiome stability and community resilience. Despite the significant advances in our understanding of the gut virome in recent years, it is clear that we remain in a period of discovery and revelation, as new methods and technologies begin to provide deeper understanding of the inherent ecological characteristics of this viral ecosystem. As our understanding increases, the nature of the multi-partite interactions occurring between host and microbiome will become clearer, helping us to more rationally define the concepts and principles that will underpin approaches to using human gut virome components for medical or biotechnological applications.

  7. The Human Gut Microbiota

    NARCIS (Netherlands)

    Harmsen, Hermie J. M.; de Goffau, Marcus. C.; Schwiertz, A

    2016-01-01

    The microbiota in our gut performs many different essential functions that help us to stay healthy. These functions include vitamin production, regulation of lipid metabolism and short chain fatty acid production as fuel for epithelial cells and regulation of gene expression. There is a very numerou

  8. The Human Gut Microbiota

    NARCIS (Netherlands)

    Harmsen, Hermie J. M.; de Goffau, Marcus. C.; Schwiertz, A

    2016-01-01

    The microbiota in our gut performs many different essential functions that help us to stay healthy. These functions include vitamin production, regulation of lipid metabolism and short chain fatty acid production as fuel for epithelial cells and regulation of gene expression. There is a very

  9. Human gut microbiota: repertoire and variations

    Directory of Open Access Journals (Sweden)

    Jean-Christophe eLagier

    2012-11-01

    Full Text Available The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.

  10. Gut Low Density Array (GULDA), a novel qPCR approach to the study of the intestinal microbial ecosystem

    DEFF Research Database (Denmark)

    Bergström, Anders; Andersen, Jens Bo; Licht, Tine Rask

    Causal relationships between the vast numbers of bacterial species present in the human intestines contain a lot of potential information on the regulation of the gut in the healthy as well as in diseased states. Based on the hypothesis that the human gut microbiota constitutes a dynamic ecosystem...

  11. Collective unconscious: how gut microbes shape human behavior.

    Science.gov (United States)

    Dinan, Timothy G; Stilling, Roman M; Stanton, Catherine; Cryan, John F

    2015-04-01

    The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.

  12. Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach.

    Science.gov (United States)

    Aw, Wanping; Fukuda, Shinji

    2015-01-01

    Recent advances in DNA sequencing and mass spectrometry technologies have allowed us to collect more data on microbiome and metabolome to assess the influence of the gut microbiota on human health at a whole-systems level. Major advances in metagenomics and metabolomics technologies have shown that the gut microbiota contributes to host overall health status to a large extent. As such, the gut microbiota is often likened to a measurable and functional organ consisting of prokaryotic cells, which creates the unique gut ecosystem together with the host eukaryotic cells. In this review, we discuss in detail the relationship between gut microbiota and its metabolites like choline, bile acids, phenols, and short-chain fatty acids in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. By integrating metagenomic and metabolomic information on a systems biology-wide approach, we would be better able to understand this interplay between gut microbiome and host metabolism. Integration of the microbiome, metatranscriptome, and metabolome information will pave the way toward an improved holistic understanding of the complex mammalian superorganism. Through the modeling of metabolic interactions between lifestyle, diet, and microbiota, integrated omics-based understanding of the gut ecosystem is the new avenue, providing exciting novel therapeutic approaches for optimal host health.

  13. Metagenomic Analysis of the Human Gut Microbiome

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha

    Understanding the link between the human gut microbiome and human health is one of the biggest scientific challenges in our decade. Because 90% of our cells are bacteria, and the microbial genome contains 200 times more genes than the human genome, the study of the human microbiome has...... the potential to impact many areas of our health. This PhD thesis is the first study to generate a large amount of experimental data on the DNA and RNA of the human gut microbiome. This was made possible by our development of a human gut microbiome array capable of profiling any human gut microbiome. Analysis...... of our results changes the way we link the gut microbiome with diseases. Our results indicate that inflammatory diseases will affect the ecological system of the human gut microbiome, reducing its diversity. Classification analysis of healthy and unhealthy individuals demonstrates that unhealthy...

  14. Maintaining gut ecosystems for health: Are transitory food bugs stowaways or part of the crew?

    Science.gov (United States)

    Plé, Coline; Breton, Jérôme; Daniel, Catherine; Foligné, Benoît

    2015-11-20

    Do food ecosystems feed gut ecosystems? And if so… fuel the immune system? Recent developments in metagenomics have provided researchers tools to open the "black box" of microbiome science. These novel technologies have enabled the establishment of correlations between dysbiotic microbial communities and many diseases. The complex interaction of the commensal microbiota with the immune system is a topic of substantial interest due to its relevance to health. The human gastrointestinal tract is composed of an immense number of resident and transient microorganisms. Both may play a direct and vital role in the maintenance of human health and well-being. An understanding of the interactions and mechanisms through which commensal and food-derived microbes shape host immunity and metabolism may yield new insights into the pathogenesis of many immune-mediated diseases. Consequently, by manipulating the contribution of food microbiota to the functionality of the gut ecosystem, there is great hope for development of new prophylactic and therapeutic interventions. This paper presents some insights and comments on the possible impact of exogenous fermented food microbes on the gut homeostasis. We shed light on the similar features shared by both fermented food microbes and probiotics. In particular, the key role of microbial strains as part of food ecosystems for health and diseases is discussed through the prism of fermented dairy products and gut inflammation.

  15. Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

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    Chabé, Magali; Lokmer, Ana; Ségurel, Laure

    2017-09-01

    The importance of the gut microbiota for human health has sparked a strong interest in the study of the factors that shape its composition and diversity. Despite the growing evidence suggesting that helminths and protozoa significantly interact with gut bacteria, gut microbiome studies remain mostly focused on prokaryotes and on populations living in industrialized countries that typically have a low parasite burden. We argue that protozoa, like helminths, represent an important factor to take into account when studying the gut microbiome, and that their presence - especially considering their long coevolutionary history with humans - may be beneficial. From this perspective, we examine the relationship between the protozoa and their hosts, as well as their relevance for public health. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Gut Health in the era of the human gut microbiota: from metaphor to biovalue.

    Science.gov (United States)

    Baty, Vincent; Mougin, Bruno; Dekeuwer, Catherine; Carret, Gérard

    2014-11-01

    The human intestinal ecosystem, previously called the gut microflora is now known as the Human Gut Microbiota (HGM). Microbiome research has emphasized the potential role of this ecosystem in human homeostasis, offering unexpected opportunities in therapeutics, far beyond digestive diseases. It has also highlighted ethical, social and commercial concerns related to the gut microbiota. As diet factors are accepted to be the major regulator of the gut microbiota, the modulation of its composition, either by antibiotics or by food intake, should be regarded as a fascinating tool for improving the human health. Scientists, the food industry, consumers and policymakers alike are involved in this new field of nutrition. Defining how knowledge about the HGM is being translated into public perception has never been addressed before. This raises the question of metaphors associated with the HGM, and how they could be used to improve public understanding, and to influence individual decision-making on healthcare policy. This article suggests that a meeting of stakeholders from the social sciences, basic research and the food industry, taking an epistemological approach to the HGM, is needed to foster close, innovative partnerships that will help shape public perception and enable novel behavioural interventions that would benefit public health.

  17. Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

    Directory of Open Access Journals (Sweden)

    Nishat Tasnim

    2017-10-01

    Full Text Available Global comparisons reveal a decrease in gut microbiota diversity attributed to Western diets, lifestyle practices such as caesarian section, antibiotic use and formula-feeding of infants, and sanitation of the living environment. While gut microbial diversity is decreasing, the prevalence of chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma is on the rise in Westernized societies. Since the immune system development is influenced by microbial components, early microbial colonization may be a key factor in determining disease susceptibility patterns later in life. Evidence indicates that the gut microbiota is vertically transmitted from the mother and this affects offspring immunity. However, the role of the external environment in gut microbiome and immune development is poorly understood. Studies show that growing up in microbe-rich environments, such as traditional farms, can have protective health effects on children. These health-effects may be ablated due to changes in the human lifestyle, diet, living environment and environmental biodiversity as a result of urbanization. Importantly, if early-life exposure to environmental microbes increases gut microbiota diversity by influencing patterns of gut microbial assembly, then soil biodiversity loss due to land-use changes such as urbanization could be a public health threat. Here, we summarize key questions in environmental health research and discuss some of the challenges that have hindered progress toward a better understanding of the role of the environment on gut microbiome development.

  18. The human gut microbiome and body metabolism: implications for obesity and diabetes

    National Research Council Canada - National Science Library

    Devaraj, Sridevi; Hemarajata, Peera; Versalovic, James

    2013-01-01

    .... Recent advances in microbial DNA sequencing technologies have resulted in the widespread application of whole-genome sequencing technologies for metagenomic DNA analysis of complex ecosystems such as the human gut...

  19. The Bacterial Ecosystem of Mother’s Milk and Infant’s Mouth and Gut

    Directory of Open Access Journals (Sweden)

    Elena Biagi

    2017-06-01

    Full Text Available The progressive building of the infants’ gut microbiota is pivotal for educating their immune system. Human breast milk is among the first sources of microbes for the assembly of the infant’s microbiota, but research struggles to give a demonstration for the origin of bacteria in milk. Aiming at contributing to the knowledge on assembly of the mother’s milk and infant’s microbiome, here we characterized the oral, gut and milk ecosystems in a homogeneous cohort of 36 healthy mother–infants pairs, by 16S rRNA next-generation sequencing. A limited number of operational taxonomic units (OTUs was shared among the three ecosystems, including not only OTUs assigned to the well-known immune-modulating Bifidobacterium genus, but also specific Streptococcus and Staphylococcus OTUs, which were dominant in the infant’s mouth ecosystem. The high conservation of these OTUs among the three ecosystems seems to call for a worth exploring ecological role through targeted and/or culture-dependent techniques. Notwithstanding the limitations of a 16S rRNA gene-based molecular characterization, we might hypothesize that the baby’s mouth, being the transition point for the milk to reach the intestine, could play a role in both the gut microbiota assembly, via deglutition, and mother’s milk duct colonization, during suction.

  20. Insights from characterizing extinct human gut microbiomes.

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    Raul Y Tito

    Full Text Available In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites. To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (~8000 years B.P. in the southern United States, Caserones (1600 years B.P. in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.. Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.

  1. Introduction to the human gut microbiota

    Science.gov (United States)

    Thursby, Elizabeth

    2017-01-01

    The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host–microbe interactions. PMID:28512250

  2. Enterotypes of the human gut microbiome

    DEFF Research Database (Denmark)

    Arumugam, M.; Raes, J.; Pelletier, E.

    2011-01-01

    Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previou......Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries...

  3. Bioinformatics Approaches for Human Gut Microbiome Research

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    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  4. Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

    Directory of Open Access Journals (Sweden)

    Dragana Dobrijevic

    Full Text Available The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

  5. Enterotypes of the human gut microbiome

    DEFF Research Database (Denmark)

    Arumugam, M.; Raes, J.; Pelletier, E.

    2011-01-01

    Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries...

  6. The human gut microbiota and undernutrition.

    Science.gov (United States)

    Gordon, Jeffrey I; Dewey, Kathryn G; Mills, David A; Medzhitov, Ruslan M

    2012-06-06

    Childhood malnutrition is a global health problem that cannot be attributed to food insecurity alone. The gut microbiota may contribute to this devastating health disorder. In this Perspective, we call for the application of tools and concepts emerging from studies of the human gut microbiota to better understand the nutritional needs of infants and children and the role of the microbiota in the pathogenesis and treatment of undernutrition. This effort will require elucidation of the interrelationships between breast milk composition and the development of the microbiota and immune system in the context of the maternal-infant dyad.

  7. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

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    Marchesi Julian R

    2010-01-01

    Full Text Available Abstract Background Little is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome. Results Novel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90% to two plasmids (pTRACA10 and pTRACA22 were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria, but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division. Conclusions The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In

  8. From lifetime to evolution: timescales of human gut microbiota adaptation

    OpenAIRE

    2014-01-01

    Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The gut microbiota continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily varia...

  9. Metatranscriptomics of the human gut microbiome

    DEFF Research Database (Denmark)

    Sicheritz-Pontén, Thomas

    2011-01-01

    Our ‘other’ genome is the collective genetic information in all of the microorganisms that are living on and within us. Collectively known as the microbiome, these microbial cells outnumber human cells in the body by more than 10 to 1, and the genes carried by these organisms outnumber the genes...... in the human genome by more than 100 to 1. How these organisms contribute to and affect human health is poorly understood, but the emerging field of metagenomics promises a more comprehensive and complete understanding of the human microbiome. In the European-funded Metagenomics of the Human Intestinal Tract...... that there is a division of labor between the bacterial species in the human gut microbiome....

  10. Human gut microbiota: does diet matter?

    Science.gov (United States)

    Maukonen, Johanna; Saarela, Maria

    2015-02-01

    The human oro-gastrointestinal (GI) tract is a complex system, consisting of oral cavity, pharynx, oesophagus, stomach, small intestine, large intestine, rectum and anus, which all together with the accessory digestive organs constitute the digestive system. The function of the digestive system is to break down dietary constituents into small molecules and then absorb these for subsequent distribution throughout the body. Besides digestion and carbohydrate metabolism, the indigenous microbiota has an important influence on host physiological, nutritional and immunological processes, and commensal bacteria are able to modulate the expression of host genes that regulate diverse and fundamental physiological functions. The main external factors that can affect the composition of the microbial community in generally healthy adults include major dietary changes and antibiotic therapy. Changes in some selected bacterial groups have been observed due to controlled changes to the normal diet e.g. high-protein diet, high-fat diet, prebiotics, probiotics and polyphenols. More specifically, changes in the type and quantity of non-digestible carbohydrates in the human diet influence both the metabolic products formed in the lower regions of the GI tract and the bacterial populations detected in faeces. The interactions between dietary factors, gut microbiota and host metabolism are increasingly demonstrated to be important for maintaining homeostasis and health. Therefore the aim of this review is to summarise the effect of diet, and especially dietary interventions, on the human gut microbiota. Furthermore, the most important confounding factors (methodologies used and intrinsic human factors) in relation to gut microbiota analyses are elucidated.

  11. The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts

    Directory of Open Access Journals (Sweden)

    Michael C. Toh

    2015-01-01

    Full Text Available The human gut microbiota is a complex microbial ecosystem that contributes an important component towards the health of its host. This highly complex ecosystem has been underestimated in its importance until recently, when a realization of the enormous scope of gut microbiota function has been (and continues to be revealed. One of the more striking of these discoveries is the finding that the gut microbiota and the brain are connected, and thus there is potential for the microbiota in the gut to influence behavior and mental health. In this short review, we outline the link between brain and gut microbiota and urge the reader to consider the gut microbiota as an ecosystem ‘organ’ rather than just as a collection of microbes filling a niche, using the hypothesized role of the gut microbiota in autism spectrum disorder to illustrate the concept.

  12. The human gut microbiome, a taxonomic conundrum.

    Science.gov (United States)

    Sankar, Senthil Alias; Lagier, Jean-Christophe; Pontarotti, Pierre; Raoult, Didier; Fournier, Pierre-Edouard

    2015-06-01

    From culture to metagenomics, within only 130 years, our knowledge of the human microbiome has considerably improved. With >1000 microbial species identified to date, the gastro-intestinal microbiota is the most complex of human biotas. It is composed of a majority of Bacteroidetes and Firmicutes and, although exhibiting great inter-individual variations according to age, geographic origin, disease or antibiotic uptake, it is stable over time. Metagenomic studies have suggested associations between specific gut microbiota compositions and a variety of diseases, including irritable bowel syndrome, Crohn's disease, colon cancer, type 2 diabetes and obesity. However, these data remain method-dependent, as no consensus strategy has been defined to decipher the complexity of the gut microbiota. High-throughput culture-independent techniques have highlighted the limitations of culture by showing the importance of uncultured species, whereas modern culture methods have demonstrated that metagenomics underestimates the microbial diversity by ignoring minor populations. In this review, we highlight the progress and challenges that pave the way to a complete understanding of the human gastrointestinal microbiota and its influence on human health.

  13. The Human Neonatal Gut Microbiome: A Brief Review

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    Emily C. Gritz

    2015-03-01

    Full Text Available The field of genomics has expanded into subspecialties such as metagenomics over the course of the last decade and a half. The development of massively parallel sequencing capabilities has allowed for increasingly detailed study of the genome of the human microbiome, the microbial super organ that resides symbiotically within the mucosal tissues and integumentary system of the human host. The gut microbiome, and particularly the study of its origins in neonates, have become subtopics of great interest within the field of genomics. This brief review seeks to summarize recent literature regarding the origins and establishment of the neonatal gut microbiome, beginning in utero, and how it is affected by neonatal nutritional status (breastfed versus formula fed and gestational age (term versus preterm. We also explore the role of dysbiosis, a perturbation within the fragile ecosystem of the microbiome, and its role in the origin of select pathologic states, specifically, obesity and necrotizing enterocolitis in preterm infants. We discuss the evidence supporting enteral pre- and probiotic supplementation of commensal organisms such as Bifidobacterium and Lactobacillus in the neonatal period, and their role in the prevention and amelioration of necrotizing enterocolitis in premature infants. Finally, we review directions to consider for further research to promote human health within this field.

  14. Assessing the human gut microbiota in metabolic diseases.

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    Karlsson, Fredrik; Tremaroli, Valentina; Nielsen, Jens; Bäckhed, Fredrik

    2013-10-01

    Recent findings have demonstrated that the gut microbiome complements our human genome with at least 100-fold more genes. In contrast to our Homo sapiens-derived genes, the microbiome is much more plastic, and its composition changes with age and diet, among other factors. An altered gut microbiota has been associated with several diseases, including obesity and diabetes, but the mechanisms involved remain elusive. Here we discuss factors that affect the gut microbiome, how the gut microbiome may contribute to metabolic diseases, and how to study the gut microbiome. Next-generation sequencing and development of software packages have led to the development of large-scale sequencing efforts to catalog the human microbiome. Furthermore, the use of genetically engineered gnotobiotic mouse models may increase our understanding of mechanisms by which the gut microbiome modulates host metabolism. A combination of classical microbiology, sequencing, and animal experiments may provide further insights into how the gut microbiota affect host metabolism and physiology.

  15. Human gut microbiome viewed across age and geography

    Science.gov (United States)

    Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, we characterized bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy child...

  16. Elucidating the interactions between the human gut microbiota and its host through metabolic modeling

    Directory of Open Access Journals (Sweden)

    Saeed eShoaie

    2014-04-01

    Full Text Available Increased understanding of the interactions between the gut microbiota, diet and environmental effects may allow us to design efficient treatment strategies for addressing global health problems. Existence of symbiotic microorganisms in the human gut provides different functions for the host such as conversion of nutrients, training of the immune system and resistance to pathogens. The gut microbiome also plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of common disorders including obesity, type 2 diabetes and atherosclerosis. Due to the extreme complexity of such disorders, it is necessary to develop mathematical models for deciphering the role of its individual elements as well as the entire system and such models may assist in better understanding of the interactions between the bacteria in the human gut and the host by use of genome-scale metabolic models (GEMs. Recently, GEMs have been employed to explore the interactions between predominant bacteria in the gut ecosystems. Additionally, these models enabled analysis of the contribution of each species to the overall metabolism of the microbiota through the integration of omics data. The outcome of these studies can be used for proposing optimal conditions for desired microbiome phenotypes. Here, we review the recent progress and challenges for elucidating the interactions between the human gut microbiota and host through metabolic modeling. We discuss how these models may provide scaffolds for analyzing high throughput data, developing probiotics and prebiotics, evaluating the effects of probiotics and prebiotics and eventually designing clinical interventions.

  17. Human genetic variation and the gut microbiome in disease.

    Science.gov (United States)

    Hall, Andrew Brantley; Tolonen, Andrew C; Xavier, Ramnik J

    2017-08-21

    Taxonomic and functional changes to the composition of the gut microbiome have been implicated in multiple human diseases. Recent microbiome genome-wide association studies reveal that variants in many human genes involved in immunity and gut architecture are associated with an altered composition of the gut microbiome. Although many factors can affect the microbial organisms residing in the gut, a number of recent findings support the hypothesis that certain host genetic variants predispose an individual towards microbiome dysbiosis. This condition, in which the normal microbiome population structure is disturbed, is a key feature in disorders of metabolism and immunity.

  18. A human gut microbial gene catalogue established by metagenomic sequencing

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha; Sicheritz-Pontén, Thomas; Nielsen, Henrik Bjørn;

    2010-01-01

    To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence...... gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively....

  19. The gut microbiome, probiotics, bile acids axis, and human health.

    Science.gov (United States)

    Jones, Mitchell Lawrence; Tomaro-Duchesneau, Catherine; Prakash, Satya

    2014-06-01

    The human gut microbiome produces potent ligands to bile acid receptors, and probiotics could act as therapeutics of bile acid dysmetabolism. A recent study in Cell Reports demonstrates that probiotic VSL#3 affects bile acid deconjugation and excretion, as well as the gut-liver FXR-FGF15 axis.

  20. Richness of human gut microbiome correlates with metabolic markers

    DEFF Research Database (Denmark)

    Le Chatelier, Emmanuelle; Nielsen, Trine; Qin, Junjie

    2013-01-01

    We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus...

  1. Potential applications of gut microbiota to control human physiology.

    Science.gov (United States)

    Umu, Ozgün Candan Onarman; Oostindjer, Marije; Pope, Phillip B; Svihus, Birger; Egelandsdal, Bjørg; Nes, Ingolf F; Diep, Dzung B

    2013-11-01

    The microorganisms living in our gut have been a black box to us for a long time. However, with the recent advances in high throughput DNA sequencing technologies, it is now possible to assess virtually all microorganisms in our gut including non-culturable ones. With the use of powerful bioinformatics tools to deal with multivariate analyses of huge amounts of data from metagenomics, metatranscriptomics, metabolomics, we now start to gain some important insights into these tiny gut inhabitants. Our knowledge is increasing about who they are, to some extent, what they do and how they affect our health. Gut microbiota have a broad spectrum of possible effects on health, from preventing serious diseases, improving immune system and gut health to stimulating the brain centers responsible for appetite and food intake control. Further, we may be on the verge of being capable of manipulating the gut microbiota by diet control to possibly improve our health. Diets consisting of different components that are fermentable by microbiota are substrates for different kinds of microbes in the gut. Thus, diet control can be used to favor the growth of some selected gut inhabitants. Nowadays, the gut microbiota is taken into account as a separate organ in human body and their activities and metabolites in gut have many physiological and neurological effects. In this mini-review, we discuss the diversity of gut microbiota, the technologies used to assess them, factors that affect microbial composition and metabolites that affect human physiology, and their potential applications in satiety control via the gut-brain axis.

  2. Strain-level dissection of the contribution of the gut microbiome to human metabolic disease.

    Science.gov (United States)

    Zhang, Chenhong; Zhao, Liping

    2016-04-20

    The gut microbiota has been linked with metabolic diseases in humans, but demonstration of causality remains a challenge. The gut microbiota, as a complex microbial ecosystem, consists of hundreds of individual bacterial species, each of which contains many strains with high genetic diversity. Recent advances in genomic and metabolomic technologies are facilitating strain-level dissection of the contribution of the gut microbiome to metabolic diseases. Interventional studies and correlation analysis between variations in the microbiome and metabolome, captured by longitudinal sampling, can lead to the identification of specific bacterial strains that may contribute to human metabolic diseases via the production of bioactive metabolites. For example, high-quality draft genomes of prevalent gut bacterial strains can be assembled directly from metagenomic datasets using a canopy-based algorithm. Specific metabolites associated with a disease phenotype can be identified by nuclear magnetic resonance-based metabolomics of urine and other samples. Such multi-omics approaches can be employed to identify specific gut bacterial genomes that are not only correlated with detected metabolites but also encode the genes required for producing the precursors of those metabolites in the gut. Here, we argue that if a causative role can be demonstrated in follow-up mechanistic studies--for example, using gnotobiotic models--such functional strains have the potential to become biomarkers for diagnostics and targets for therapeutics.

  3. Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota

    OpenAIRE

    Mimee, Mark; Tucker, Alex C.; Voigt, Christopher A.; Lu, Timothy K.

    2015-01-01

    Engineering commensal organisms for challenging applications, such as modulating the gut ecosystem, is hampered by the lack of genetic parts. Here, we describe promoters, ribosome-binding sites, and inducible systems for use in the commensal bacterium Bacteroides thetaiotaomicron, a prevalent and stable resident of the human gut. We achieve up to 10,000-fold range in constitutive gene expression and 100-fold regulation of gene expression with inducible promoters and use these parts to record ...

  4. Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health.

    Science.gov (United States)

    Jost, Ted; Lacroix, Christophe; Braegger, Christian; Chassard, Christophe

    2015-07-01

    Neonatal gut microbiota establishment represents a crucial stage for gut maturation, metabolic and immunologic programming, and consequently short- and long-term health status. Human milk beneficially influences this process due to its dynamic profile of age-adapted nutrients and bioactive components and by providing commensal maternal bacteria to the neonatal gut. These include Lactobacillus spp., as well as obligate anaerobes such as Bifidobacterium spp., which may originate from the maternal gut via an enteromammary pathway as a novel form of mother-neonate communication. Additionally, human milk harbors a broad range of oligosaccharides that promote the growth and activity of specific bacterial populations, in particular, Bifidobacterium and Bacteroides spp. This review focuses on the diversity and origin of human milk bacteria, as well as on milk oligosaccharides that influence neonatal gut microbiota establishment. This knowledge can be used to develop infant formulae that more closely mimic nature's model and sustain a healthy gut microbiota. © The Author(s) 2015. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Challenges of metabolomics in human gut microbiota research.

    Science.gov (United States)

    Smirnov, Kirill S; Maier, Tanja V; Walker, Alesia; Heinzmann, Silke S; Forcisi, Sara; Martinez, Inés; Walter, Jens; Schmitt-Kopplin, Philippe

    2016-08-01

    The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine.

  6. Gut

    DEFF Research Database (Denmark)

    Muscogiuri, Giovanna; Balercia, Giancarlo; Barrea, Luigi

    2016-01-01

    The gut regulates glucose and energy homeostasis; thus, the presence of ingested nutrients into the gut activates sensing mechanisms that affect both glucose homeostasis and regulate food intake. Increasing evidence suggest that gut may also play a key role in the pathogenesis of type 2 diabetes...

  7. Integrating Human and Ecosystem Health Through Ecosystem Services Frameworks.

    Science.gov (United States)

    Ford, Adriana E S; Graham, Hilary; White, Piran C L

    2015-12-01

    The pace and scale of environmental change is undermining the conditions for human health. Yet the environment and human health remain poorly integrated within research, policy and practice. The ecosystem services (ES) approach provides a way of promoting integration via the frameworks used to represent relationships between environment and society in simple visual forms. To assess this potential, we undertook a scoping review of ES frameworks and assessed how each represented seven key dimensions, including ecosystem and human health. Of the 84 ES frameworks identified, the majority did not include human health (62%) or include feedback mechanisms between ecosystems and human health (75%). While ecosystem drivers of human health are included in some ES frameworks, more comprehensive frameworks are required to drive forward research and policy on environmental change and human health.

  8. Human Resource Ecosystem and its evolutionary rules

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The Paper,based on the concept and the elements of human resource ecosystem(HR Ecosystem),studies the function and structure of HR Ecosystem,introduces the entropy theory to define the content of entropy of HR Ecosystem,constructs the corresponding distinctive model to distinguish the direction of the evolution of HR Ecosystem and the evolutionary entropy model, and applies the models to demonstrate the evolutionary rules of HR Ecosystem.The study shows that the entropy theory can be well applied to the analysis on HR Ecosystem and that it opens up a new field in the research of human resource management and provides a new effective technical method.

  9. Obesity changes the human gut mycobiome.

    Science.gov (United States)

    Mar Rodríguez, M; Pérez, Daniel; Javier Chaves, Felipe; Esteve, Eduardo; Marin-Garcia, Pablo; Xifra, Gemma; Vendrell, Joan; Jové, Mariona; Pamplona, Reinald; Ricart, Wifredo; Portero-Otin, Manuel; Chacón, Matilde R; Fernández Real, José Manuel

    2015-10-12

    The human intestine is home to a diverse range of bacterial and fungal species, forming an ecological community that contributes to normal physiology and disease susceptibility. Here, the fungal microbiota (mycobiome) in obese and non-obese subjects was characterized using Internal Transcribed Spacer (ITS)-based sequencing. The results demonstrate that obese patients could be discriminated by their specific fungal composition, which also distinguished metabolically "healthy" from "unhealthy" obesity. Clusters according to genus abundance co-segregated with body fatness, fasting triglycerides and HDL-cholesterol. A preliminary link to metabolites such as hexadecanedioic acid, caproic acid and N-acetyl-L-glutamic acid was also found. Mucor racemosus and M. fuscus were the species more represented in non-obese subjects compared to obese counterparts. Interestingly, the decreased relative abundance of the Mucor genus in obese subjects was reversible upon weight loss. Collectively, these findings suggest that manipulation of gut mycobiome communities might be a novel target in the treatment of obesity.

  10. Gene expression profiling gut microbiota in different races of humans

    Science.gov (United States)

    Chen, Lei; Zhang, Yu-Hang; Huang, Tao; Cai, Yu-Dong

    2016-03-01

    The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. Its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. Several factors can affect the composition of the gut microbiome, such as eating habits, living environment, and antibiotic usage. Thus, various races are characterized by different gut microbiome characteristics. In this present study, we studied the gut microbiomes of three different races, including individuals of Asian, European and American races. The gut microbiome and the expression levels of gut microbiome genes were analyzed in these individuals. Advanced feature selection methods (minimum redundancy maximum relevance and incremental feature selection) and four machine-learning algorithms (random forest, nearest neighbor algorithm, sequential minimal optimization, Dagging) were employed to capture key differentially expressed genes. As a result, sequential minimal optimization was found to yield the best performance using the 454 genes, which could effectively distinguish the gut microbiomes of different races. Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome.

  11. From lifetime to evolution: timescales of human gut microbiota adaptation

    Directory of Open Access Journals (Sweden)

    Sara eQuercia

    2014-11-01

    Full Text Available Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The gut microbiota continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.

  12. How informative is the mouse for human gut microbiota research?

    Science.gov (United States)

    Nguyen, Thi Loan Anh; Vieira-Silva, Sara; Liston, Adrian; Raes, Jeroen

    2015-01-01

    The microbiota of the human gut is gaining broad attention owing to its association with a wide range of diseases, ranging from metabolic disorders (e.g. obesity and type 2 diabetes) to autoimmune diseases (such as inflammatory bowel disease and type 1 diabetes), cancer and even neurodevelopmental disorders (e.g. autism). Having been increasingly used in biomedical research, mice have become the model of choice for most studies in this emerging field. Mouse models allow perturbations in gut microbiota to be studied in a controlled experimental setup, and thus help in assessing causality of the complex host-microbiota interactions and in developing mechanistic hypotheses. However, pitfalls should be considered when translating gut microbiome research results from mouse models to humans. In this Special Article, we discuss the intrinsic similarities and differences that exist between the two systems, and compare the human and murine core gut microbiota based on a meta-analysis of currently available datasets. Finally, we discuss the external factors that influence the capability of mouse models to recapitulate the gut microbiota shifts associated with human diseases, and investigate which alternative model systems exist for gut microbiota research.

  13. How informative is the mouse for human gut microbiota research?

    Directory of Open Access Journals (Sweden)

    Thi Loan Anh Nguyen

    2015-01-01

    Full Text Available The microbiota of the human gut is gaining broad attention owing to its association with a wide range of diseases, ranging from metabolic disorders (e.g. obesity and type 2 diabetes to autoimmune diseases (such as inflammatory bowel disease and type 1 diabetes, cancer and even neurodevelopmental disorders (e.g. autism. Having been increasingly used in biomedical research, mice have become the model of choice for most studies in this emerging field. Mouse models allow perturbations in gut microbiota to be studied in a controlled experimental setup, and thus help in assessing causality of the complex host-microbiota interactions and in developing mechanistic hypotheses. However, pitfalls should be considered when translating gut microbiome research results from mouse models to humans. In this Special Article, we discuss the intrinsic similarities and differences that exist between the two systems, and compare the human and murine core gut microbiota based on a meta-analysis of currently available datasets. Finally, we discuss the external factors that influence the capability of mouse models to recapitulate the gut microbiota shifts associated with human diseases, and investigate which alternative model systems exist for gut microbiota research.

  14. Part 1: The Human Gut Microbiome in Health and Disease

    OpenAIRE

    Bull, Matthew J.; Plummer, Nigel T.

    2014-01-01

    The bacterial cells harbored within the human gastrointestinal tract (GIT) outnumber the host’s cells by a factor of 10 and the genes encoded by the bacteria resident within the GIT outnumber their host’s genes by more than 100 times. These human digestive-tract associated microbes are referred to as the gut microbiome. The human gut microbiome and its role in both health and disease has been the subject of extensive research, establishing its involvement in human metabolism, nutrition, physi...

  15. Molecular biological methods for studying the gut microbiota : the EU human gut flora project

    NARCIS (Netherlands)

    Blaut, M; Collins, MD; Welling, GW; Dore, J; van Loo, J; de Vos, W

    2002-01-01

    Seven European laboratories co-operated in a joint project (FAIR CT97-3035) to develop, refine and apply molecular methods towards facilitating elucidation of the complex composition of the human intestinal microflora and to devise robust methodologies for monitoring the gut flora in response to die

  16. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

    Energy Technology Data Exchange (ETDEWEB)

    Mahowald, Michael [Washington University, St. Louis; Rey, Frederico E. [Washington University, St. Louis; Seedorf, Henning [Washington University, St. Louis; Turnbaugh, Peter J. [Washington University, St. Louis; Fulton, Robert S. [Washington University, St. Louis; Wollam, Aye [Washington University, St. Louis; Shah, Neha [Washington University, St. Louis; Wang, Chunyan [Washington University, St. Louis; Magrini, Vincent [Washington University, St. Louis; Wilson, Richard K. [Washington University, St. Louis; Cantarel, Brandi L. [Centre National de la Recherche Scientifique, Unite Mixte de Recherche; Coutinho, Pedro M [Universite d' Aix-Marseille I & II; Henrissat, Bernard [Universite d' Aix-Marseille I & II; Crock, Lara W. [Washington University, St. Louis; Verberkmoes, Nathan C [ORNL; Hettich, Robert {Bob} L [ORNL; Erickson, Alison L [ORNL; Gordon, Jeffrey [Washington University, St. Louis

    2009-01-01

    The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial microbial and microbial host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

  17. Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis

    DEFF Research Database (Denmark)

    Travis, Anthony J.; Kelly, Denise; Flint, Harry J;

    2015-01-01

    We report here the complete genome sequence of the human gut symbiont Roseburia hominis A2-183(T) (= DSM 16839(T) = NCIMB 14029(T)), isolated from human feces. The genome is represented by a 3,592,125-bp chromosome with 3,405 coding sequences. A number of potential functions contributing to host-...

  18. Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.

    Science.gov (United States)

    Amato, Katherine R

    2016-01-01

    The mammalian gut is home to a diverse community of microbes. Advances in technology over the past two decades have allowed us to examine this community, the gut microbiota, in more detail, revealing a wide range of influences on host nutrition, health, and behavior. These host-gut microbe interactions appear to shape host plasticity and fitness in a variety of contexts, and therefore represent a key factor missing from existing models of human and non-human primate ecology and evolution. However, current studies of the gut microbiota tend to include limited contextual data or are clinical, making it difficult to directly test broad anthropological hypotheses. Here, I review what is known about the animal gut microbiota and provide examples of how gut microbiota research can be integrated into the study of human and non-human primate ecology and evolution with targeted data collection. Specifically, I examine how the gut microbiota may impact primate diet, energetics, disease resistance, and cognition. While gut microbiota research is proliferating rapidly, especially in the context of humans, there remain important gaps in our understanding of host-gut microbe interactions that will require an anthropological perspective to fill. Likewise, gut microbiota research will be an important tool for filling remaining gaps in anthropological research.

  19. Gut contents as direct indicators for trophic relationships in the Cambrian marine ecosystem.

    Science.gov (United States)

    Vannier, Jean

    2012-01-01

    Present-day ecosystems host a huge variety of organisms that interact and transfer mass and energy via a cascade of trophic levels. When and how this complex machinery was established remains largely unknown. Although exceptionally preserved biotas clearly show that Early Cambrian animals had already acquired functionalities that enabled them to exploit a wide range of food resources, there is scant direct evidence concerning their diet and exact trophic relationships. Here I describe the gut contents of Ottoia prolifica, an abundant priapulid worm from the middle Cambrian (Stage 5) Burgess Shale biota. I identify the undigested exoskeletal remains of a wide range of small invertebrates that lived at or near the water sediment interface such as hyolithids, brachiopods, different types of arthropods, polychaetes and wiwaxiids. This set of direct fossil evidence allows the first detailed reconstruction of the diet of a 505-million-year-old animal. Ottoia was a dietary generalist and had no strict feeding regime. It fed on both living individuals and decaying organic matter present in its habitat. The feeding behavior of Ottoia was remarkably simple, reduced to the transit of food through an eversible pharynx and a tubular gut with limited physical breakdown and no storage. The recognition of generalist feeding strategies, exemplified by Ottoia, reveals key-aspects of modern-style trophic complexity in the immediate aftermath of the Cambrian explosion. It also shows that the middle Cambrian ecosystem was already too complex to be understood in terms of simple linear dynamics and unique pathways.

  20. Gut contents as direct indicators for trophic relationships in the Cambrian marine ecosystem.

    Directory of Open Access Journals (Sweden)

    Jean Vannier

    Full Text Available Present-day ecosystems host a huge variety of organisms that interact and transfer mass and energy via a cascade of trophic levels. When and how this complex machinery was established remains largely unknown. Although exceptionally preserved biotas clearly show that Early Cambrian animals had already acquired functionalities that enabled them to exploit a wide range of food resources, there is scant direct evidence concerning their diet and exact trophic relationships. Here I describe the gut contents of Ottoia prolifica, an abundant priapulid worm from the middle Cambrian (Stage 5 Burgess Shale biota. I identify the undigested exoskeletal remains of a wide range of small invertebrates that lived at or near the water sediment interface such as hyolithids, brachiopods, different types of arthropods, polychaetes and wiwaxiids. This set of direct fossil evidence allows the first detailed reconstruction of the diet of a 505-million-year-old animal. Ottoia was a dietary generalist and had no strict feeding regime. It fed on both living individuals and decaying organic matter present in its habitat. The feeding behavior of Ottoia was remarkably simple, reduced to the transit of food through an eversible pharynx and a tubular gut with limited physical breakdown and no storage. The recognition of generalist feeding strategies, exemplified by Ottoia, reveals key-aspects of modern-style trophic complexity in the immediate aftermath of the Cambrian explosion. It also shows that the middle Cambrian ecosystem was already too complex to be understood in terms of simple linear dynamics and unique pathways.

  1. The Human Gut Phage Community and Its Implications for Health and Disease

    Science.gov (United States)

    Manrique, Pilar; Dills, Michael; Young, Mark J.

    2017-01-01

    In this review, we assess our current understanding of the role of bacteriophages infecting the human gut bacterial community in health and disease. In general, bacteriophages contribute to the structure of their microbial communities by driving host and viral diversification, bacterial evolution, and by expanding the functional diversity of ecosystems. Gut bacteriophages are an ensemble of unique and shared phages in individuals, which encompass temperate phages found predominately as prophage in gut bacteria (prophage reservoir) and lytic phages. In healthy individuals, only a small fraction of the prophage reservoir is activated and found as extracellular phages. Phage community dysbiosis is characterized by a shift in the activated prophage community or an increase of lytic phages, and has been correlated with disease, suggesting that a proper balance between lysis and lysogeny is needed to maintain health. Consequently, the concept of microbial dysbiosis might be extended to the phage component of the microbiome as well. Understanding the dynamics and mechanisms to restore balance after dysbiosis is an active area of research. The use of phage transplants to re-establish health suggests that phages can be used as disease treatment. Such advances represent milestones in our understanding of gut phages in human health and should fuel research on their role in health and disease. PMID:28594392

  2. Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota.

    Science.gov (United States)

    Mimee, Mark; Tucker, Alex C; Voigt, Christopher A; Lu, Timothy K

    2015-07-29

    Engineering commensal organisms for challenging applications, such as modulating the gut ecosystem, is hampered by the lack of genetic parts. Here, we describe promoters, ribosome-binding sites, and inducible systems for use in the commensal bacterium Bacteroides thetaiotaomicron, a prevalent and stable resident of the human gut. We achieve up to 10,000-fold range in constitutive gene expression and 100-fold regulation of gene expression with inducible promoters and use these parts to record DNA-encoded memory in the genome. We use CRISPR interference (CRISPRi) for regulated knockdown of recombinant and endogenous gene expression to alter the metabolic capacity of B. thetaiotaomicron and its resistance to antimicrobial peptides. Finally, we show that inducible CRISPRi and recombinase systems can function in B. thetaiotaomicron colonizing the mouse gut. These results provide a blueprint for engineering new chassis and a resource to engineer Bacteroides for surveillance of or therapeutic delivery to the gut microbiome.

  3. Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome.

    Directory of Open Access Journals (Sweden)

    Tanudeep Bhattacharya

    Full Text Available Carbohydrate Active enzyme (CAZyme families, encoded by human gut microflora, play a crucial role in breakdown of complex dietary carbohydrates into components that can be absorbed by our intestinal epithelium. Since nutritional wellbeing of an individual is dependent on the nutrient harvesting capability of the gut microbiome, it is important to understand how CAZyme repertoire in the gut is influenced by factors like age, geography and food habits.This study reports a comprehensive in-silico analysis of CAZyme profiles in the gut microbiomes of 448 individuals belonging to different geographies, using similarity searches of the corresponding gut metagenomic contigs against the carbohydrate active enzymes database. The study identifies a core group of 89 CAZyme families that are present across 85% of the gut microbiomes. The study detects several geography/age-specific trends in gut CAZyme repertoires of the individuals. Notably, a group of CAZymes having a positive correlation with BMI has been identified. Further this group of BMI-associated CAZymes is observed to be specifically abundant in the Firmicutes phyla. One of the major findings from this study is identification of three distinct groups of individuals, referred to as 'CAZotypes', having similar CAZyme profiles. Distinct taxonomic drivers for these CAZotypes as well as the probable dietary basis for such trends have also been elucidated. The results of this study provide a global view of CAZyme profiles across individuals of various geographies and age-groups. These results reiterate the need of a more precise understanding of the role of carbohydrate active enzymes in human nutrition.

  4. Effect of diet on the human gut microbiota

    DEFF Research Database (Denmark)

    Bahl, Martin Iain

    The gut microbiota plays an important role for humans in both health and disease. It is therefore important to understand how and to what extent choice of diet may influence the microbial community and the effects this has on the host. The variation in the normal human gut microbiota may however...... impede the discovery of correlations between dietary changes and compositional shifts in the microbiota by masking such effects. Although specific functional food ingredients, such as prebiotics, are known to have measurable effects on e.g. abundance of bifidobacteria, it is nevertheless clear...... that induced shifts in gut microbiota show large inter-individual variations. It thus seems plausible that knowing the microbiota composition could facilitate predictions as to how the community will react to dietary interventions thus moving towards some degree of personalised dietary recommendations. During...

  5. Starches, resistant starches, the gut microflora and human health.

    Science.gov (United States)

    Bird, A R; Brown, I L; Topping, D L

    2000-03-01

    Starches are important as energy sources for humans and also for their interactions with the gut microflora throughout the digestive tact. Largely, those interactions promote human health. In the mouth, less gelatinised starches may lower risk of cariogensis. In the large bowel, starches which have escaped small intestinal digestion (resistant starch), together with proteins, other undigested carbohydrates and endogenous secretions are fermented by the resident microflora. The resulting short chain fatty acids contribute substantially to the normal physiological functions of the viscera. Specific types of resistant starch (e.g. the chemically modified starches used in the food industry) may be used to manipulate the gut bacteria and their products (including short chain fatty acids) so as to optimise health. In the upper gut, these starches may assist in the transport of probiotic organisms thus promoting the immune response and suppressing potential pathogens. However, it appears unlikely that current probiotic organisms can be used to modulate large bowel short chain fatty acids in adults although resistant starch and other prebiotics can do so. Suggestions that starch may exacerbate certain conditions (such as ulcerative colitis) through stimulating the growth of certain pathogenic organisms appear to be unfounded. Short chain fatty acids may modulate tissue levels and effects of growth factors in the gut and so modify gut development and risk of serious disease, including colo-rectal cancer. However, information on the relationship between starches and the microflora is relatively sparse and substantial opportunities exist both for basic research and food product development.

  6. Shotgun metaproteomics of the human distal gut microbiota

    Energy Technology Data Exchange (ETDEWEB)

    VerBerkmoes, N.C.; Russell, A.L.; Shah, M.; Godzik, A.; Rosenquist, M.; Halfvarsson, J.; Lefsrud, M.G.; Apajalahti, J.; Tysk, C.; Hettich, R.L.; Jansson, Janet K.

    2008-10-15

    The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

  7. Shotgun Metaproteomics of the Human Distal Gut Microbiota

    Energy Technology Data Exchange (ETDEWEB)

    Verberkmoes, Nathan C [ORNL; Erickson, Alison L [ORNL; Shah, Manesh B [ORNL; Godzik, A [Burnham Institute for Medical Research, La Jolla, CA; Rosenquist, M [Swedish University of Agricultural Sciences, Upsalla, Sweden; Halfvarsson, J [Orebro University Hospital, Orebro, Sweden; Lefsrud, Mark G [McGill University, Montreal, Quebec; Apajalahti, J. [Alimetrics Ltd,; Hettich, Robert {Bob} L [ORNL; Jansson, J [Swedish University of Agricultural Sciences, Upsalla, Sweden

    2009-01-01

    The human gut contains a dense, complex, and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about what genes were expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production, and carbohydrate metabolism compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

  8. Application of metagenomics in the human gut microbiome.

    Science.gov (United States)

    Wang, Wei-Lin; Xu, Shao-Yan; Ren, Zhi-Gang; Tao, Liang; Jiang, Jian-Wen; Zheng, Shu-Sen

    2015-01-21

    There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.

  9. From lifetime to evolution: timescales of human gut microbiota adaptation

    Science.gov (United States)

    Quercia, Sara; Candela, Marco; Giuliani, Cristina; Turroni, Silvia; Luiselli, Donata; Rampelli, Simone; Brigidi, Patrizia; Franceschi, Claudio; Bacalini, Maria Giulia; Garagnani, Paolo; Pirazzini, Chiara

    2014-01-01

    Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies. PMID:25408692

  10. From lifetime to evolution: timescales of human gut microbiota adaptation.

    Science.gov (United States)

    Quercia, Sara; Candela, Marco; Giuliani, Cristina; Turroni, Silvia; Luiselli, Donata; Rampelli, Simone; Brigidi, Patrizia; Franceschi, Claudio; Bacalini, Maria Giulia; Garagnani, Paolo; Pirazzini, Chiara

    2014-01-01

    Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.

  11. In vitro fermentation of fructooligosaccharides with human gut bacteria.

    Science.gov (United States)

    Mao, Bingyong; Li, Dongyao; Zhao, Jianxin; Liu, Xiaoming; Gu, Zhennan; Chen, Yong Q; Zhang, Hao; Chen, Wei

    2015-03-01

    Fructooligosaccharides (FOS) are one of the most studied prebiotics, selectively stimulating the growth of health-promoting bacteria in the host. However, there is increasing evidence that commensal gut bacteria, such as Bacteroides fragilis, Clostridium butyricum, Enterobacter cloacae, and even the pathogenic Escherichia coli BEN2908, are also able to metabolize FOS in vitro, and in some cases, FOS displayed adverse effects. Therefore, it is necessary to identify FOS-metabolizing species that are present in the gut. Unlike previous studies focusing on individual strains, this study used the traditional culture method combined with an alignment search on the gut bacteria database established from the Human Microbiome Project (HMP). The alignment results showed that homologous proteins for FOS transporters and glycosidases were distributed in 237 of the 453 strains of gut bacteria. La506 msmK encoding the ATP-binding protein and Aec45 fosGH1 encoding glycoside hydrolase were most widely distributed, in 155 and 55 strains, respectively. Seven of eight strains with both transporters and glycosidases were proven to be capable of metabolizing FOS, while five strains without either transporters or glycosidases were not. Fifteen species isolated from human feces and 11 species from the alignment search were identified to be FOS-metabolizing, of which Cronobacter sakazakii, Marvinbryantia formatexigens, Ruminococcus gnavus, and Weissella paramesenteroides are reported here for the first time. Thus, alignment search combined with the culture method is an effective method for obtaining a global view of the FOS-metabolizing bacteria in the gut and will be helpful in further investigating the relationship between FOS and human gut bacteria.

  12. Human gut microbes impact host serum metabolome and insulin sensitivity

    DEFF Research Database (Denmark)

    Pedersen, Helle Krogh; Gudmundsdottir, Valborg; Nielsen, Henrik Bjørn

    2016-01-01

    -resistant individuals is characterized by increased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has an enriched biosynthetic potential for BCAAs and is deprived of genes encoding bacterial inward transporters for these amino acids. Prevotella copri and Bacteroides vulgatus......Insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals. The serum metabolome of insulin...

  13. Comparative (metagenomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14.

    Directory of Open Access Journals (Sweden)

    Lesley A Ogilvie

    Full Text Available Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (metagenomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14. In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored

  14. Comparative (Meta)genomic Analysis and Ecological Profiling of Human Gut-Specific Bacteriophage φB124-14

    Science.gov (United States)

    Ogilvie, Lesley A.; Caplin, Jonathan; Dedi, Cinzia; Diston, David; Cheek, Elizabeth; Bowler, Lucas; Taylor, Huw; Ebdon, James; Jones, Brian V.

    2012-01-01

    Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape

  15. Gut Low Density Array (GULDA), a novel qPCR approach to the study of the intestinal microbial ecosystem

    DEFF Research Database (Denmark)

    Bergström, Anders; Andersen, Jens Bo; Licht, Tine Rask

    developed GULDA; a qPCR low-density array with particular focus on bacteria of relevance to the human gut microbiota. The output is given as arbitrary bacterial quantities, which for large sample numbers allow for further characterization of the gut microbiota by uni- and multivariate statistical methods....

  16. Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

    Directory of Open Access Journals (Sweden)

    Isabelle Laforest-Lapointe

    2017-07-01

    Full Text Available Alterations in gut microbial colonization during early life have been reported in infants that later developed asthma, allergies, type 1 diabetes, as well as in inflammatory bowel disease patients, previous to disease flares. Mechanistic studies in animal models have established that microbial alterations influence disease pathogenesis via changes in immune system maturation. Strong evidence points to the presence of a window of opportunity in early life, during which changes in gut microbial colonization can result in immune dysregulation that predisposes susceptible hosts to disease. Although the ecological patterns of microbial succession in the first year of life have been partly defined in specific human cohorts, the taxonomic and functional features, and diversity thresholds that characterize these microbial alterations are, for the most part, unknown. In this review, we summarize the most important links between the temporal mosaics of gut microbial colonization and the age-dependent immune functions that rely on them. We also highlight the importance of applying ecology theory to design studies that explore the interactions between this complex ecosystem and the host immune system. Focusing research efforts on understanding the importance of temporally structured patterns of diversity, keystone groups, and inter-kingdom microbial interactions for ecosystem functions has great potential to enable the development of biologically sound interventions aimed at maintaining and/or improving immune system development and preventing disease.

  17. Dissecting the in vivo metabolic potential of two human gut acetogens.

    Science.gov (United States)

    Rey, Federico E; Faith, Jeremiah J; Bain, James; Muehlbauer, Michael J; Stevens, Robert D; Newgard, Christopher B; Gordon, Jeffrey I

    2010-07-16

    Fermenting microbial communities generate hydrogen; its removal through the production of acetate, methane, or hydrogen sulfide modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers than components for methanogenesis or sulfate reduction and subsequently analyzed the metabolic potential of two sequenced human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally applicable method for multiplex sequencing of expressed microbial mRNAs (microbial RNA-Seq) and, together with mass spectrometry of metabolites, showed that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents, thereby maintaining a high NAD(+)/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest.

  18. Antimicrobial Use, Human Gut Microbiota and Clostridium difficile Colonization and Infection

    Directory of Open Access Journals (Sweden)

    Caroline Vincent

    2015-07-01

    Full Text Available Clostridium difficile infection (CDI is the most important cause of nosocomial diarrhea. Broad-spectrum antimicrobials have profound detrimental effects on the structure and diversity of the indigenous intestinal microbiota. These alterations often impair colonization resistance, allowing the establishment and proliferation of C. difficile in the gut. Studies involving animal models have begun to decipher the precise mechanisms by which the intestinal microbiota mediates colonization resistance against C. difficile and numerous investigations have described gut microbiota alterations associated with C. difficile colonization or infection in human subjects. Fecal microbiota transplantation (FMT is a highly effective approach for the treatment of recurrent CDI that allows the restoration of a healthy intestinal ecosystem via infusion of fecal material from a healthy donor. The recovery of the intestinal microbiota after FMT has been examined in a few reports and work is being done to develop custom bacterial community preparations that could be used as a replacement for fecal material.

  19. Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human gut.

    Directory of Open Access Journals (Sweden)

    Sudarshan Anand Shetty

    Full Text Available With increasing number of novel bacteria being isolated from the human gut ecosystem, there is a greater need to study their role in the gut ecosystem and their effect on the host health. In the present study, we carried out in silico genome-wide analysis of two novel Megasphaera sp. isolates NM10 (DSM25563 and BL7 (DSM25562, isolated from feces of two healthy individuals and validated the key features by in vitro studies. The analysis revealed the general metabolic potential, adaptive features and the potential effects of these isolates on the host. The comparative genome analysis of the two human gut isolates NM10 and BL7 with ruminal isolate Megasphaera elsdenii (DSM20460 highlighted the differential adaptive features for their survival in human gut. The key findings include features like bile resistance, presence of various sensory and regulatory systems, stress response systems, membrane transporters and resistance to antibiotics. Comparison of the "glycobiome" based on the genomes of the ruminal isolate with the human gut isolates NM10 and BL revealed the presence of diverse and unique sets of Carbohydrate-Active enzymes (CAZymes amongst these isolates, with a higher collection of CAZymes in the human gut isolates. This could be attributed to the difference in host diet and thereby the environment, consequently suggesting host specific adaptation in these isolates. In silico analysis of metabolic potential predicted the ability of these isolates to produce important metabolites like short chain fatty acids (butyrate, acetate, formate, and caproate, vitamins and essential amino acids, which was further validated by in vitro experiments. The ability of these isolates to produce important metabolites advocates for a potential healthy influence on the host. Further in vivo studies including transcriptomic and proteomic analysis will be required for better understanding the role and impact of these Megasphaera sp. isolates NM10 and BL7 on the

  20. Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans

    Science.gov (United States)

    David, Lawrence A.; Weil, Ana; Ryan, Edward T.; Calderwood, Stephen B.; Harris, Jason B.; Chowdhury, Fahima; Begum, Yasmin; Qadri, Firdausi

    2015-01-01

    ABSTRACT Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these bacterial communities respond to diarrheal disease and its treatment. Here, we report that after Vibrio cholerae infection, the human gut microbiota undergoes an orderly and reproducible succession that features transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli (ETEC) infection. Our metagenomic analyses suggest that multiple mechanisms drive microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure but is driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea. PMID:25991682

  1. Diet rapidly and reproducibly alters the human gut microbiome.

    Science.gov (United States)

    David, Lawrence A; Maurice, Corinne F; Carmody, Rachel N; Gootenberg, David B; Button, Julie E; Wolfe, Benjamin E; Ling, Alisha V; Devlin, A Sloan; Varma, Yug; Fischbach, Michael A; Biddinger, Sudha B; Dutton, Rachel J; Turnbaugh, Peter J

    2014-01-23

    Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

  2. Variations in the post-weaning human gut metagenome profile as result of Bifidobacterium acquisition in the Western microbiome

    Directory of Open Access Journals (Sweden)

    Matteo Soverini

    2016-07-01

    Full Text Available Studies of the gut microbiome variation among human populations revealed the existence of robust compositional and functional layouts matching the three subsistence strategies that describe a trajectory of changes across our recent evolutionary history: hunting and gathering, rural agriculture, and urban post-industrialized agriculture. In particular, beside the overall reduction of ecosystem diversity, the gut microbiome of Western industrial populations is typically characterized by the loss of Treponema and the acquisition of Bifidobacterium as an abundant inhabitant of the post-weaning gut microbial ecosystem. In order to advance the hypothesis about the possible adaptive nature of this exchange, here we explore specific functional attributes that correspond to the mutually exclusive presence of Treponema and Bifidobacterium using publically available gut metagenomic data from Hadza hunter-gatherers and urban industrial Italians. According to our findings, Bifidobacterium provides the enteric ecosystem with a diverse panel of saccharolytic functions, well suited to the array of gluco- and galacto-based saccharides that abound in the Western diet. On the other hand, the metagenomic functions assigned to Treponema are more predictive of a capacity to incorporate complex polysaccharides, such as those found in unrefined plant foods, which are consistently incorporated in the Hadza diet. Finally, unlike Treponema, the Bifidobacterium metagenome functions include genes that permit the establishment of microbe-host immunological cross-talk, suggesting recent co-evolutionary events between the human immune system and Bifidobacterium that are adaptive in the context of agricultural subsistence and sedentary societies.

  3. Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale.

    Science.gov (United States)

    Cockburn, Darrell W; Orlovsky, Nicole I; Foley, Matthew H; Kwiatkowski, Kurt J; Bahr, Constance M; Maynard, Mallory; Demeler, Borries; Koropatkin, Nicole M

    2015-01-01

    Eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. Starch is one of the most abundant glycans in the human diet, and E. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. Here we present the results of a quantitative proteomics study in which we identify two glycoside hydrolase 13 family enzymes, and three ABC transporter solute-binding proteins that are abundant during growth on starch and, we hypothesize, work together at the cell surface to degrade starch and capture the released maltooligosaccharides. EUR_21100 is a multidomain cell wall anchored amylase that preferentially targets starch polysaccharides, liberating maltotetraose, whereas the membrane-associated maltogenic amylase EUR_01860 breaks down maltooligosaccharides longer than maltotriose. The three solute-binding proteins display a range of glycan-binding specificities that ensure the capture of glucose through maltoheptaose and some α1,6-branched glycans. Taken together, we describe a pathway for starch utilization by E. rectale DSM 17629 that may be conserved among other starch-degrading Clostridium cluster XIVa organisms in the human gut.

  4. Superresolution imaging captures carbohydrate utilization dynamics in human gut symbionts.

    Science.gov (United States)

    Karunatilaka, Krishanthi S; Cameron, Elizabeth A; Martens, Eric C; Koropatkin, Nicole M; Biteen, Julie S

    2014-11-11

    Gut microbes play a key role in human health and nutrition by catabolizing a wide variety of glycans via enzymatic activities that are not encoded in the human genome. The ability to recognize and process carbohydrates strongly influences the structure of the gut microbial community. While the effects of diet on the microbiota are well documented, little is known about the molecular processes driving metabolism. To provide mechanistic insight into carbohydrate catabolism in gut symbionts, we studied starch processing in real time in the model Bacteroides thetaiotaomicron starch utilization system (Sus) by single-molecule fluorescence. Although previous studies have explored Sus protein structure and function, the transient interactions, assembly, and collaboration of these outer membrane proteins have not yet been elucidated in live cells. Our live-cell superresolution imaging reveals that the polymeric starch substrate dynamically recruits Sus proteins, serving as an external scaffold for bacterial membrane assembly of the Sus complex, which may promote efficient capturing and degradation of starch. Furthermore, by simultaneously localizing multiple Sus outer membrane proteins on the B. thetaiotaomicron cell surface, we have characterized the dynamics and stoichiometry of starch-induced Sus complex assembly on the molecular scale. Finally, based on Sus protein knockout strains, we have discerned the mechanism of starch-induced Sus complex assembly in live anaerobic cells with nanometer-scale resolution. Our insights into the starch-induced outer membrane protein assembly central to this conserved nutrient uptake mechanism pave the way for the development of dietary or pharmaceutical therapies to control Bacteroidetes in the intestinal tract to enhance human health and treat disease. In this study, we used nanometer-scale superresolution imaging to reveal dynamic interactions between the proteins involved in starch processing by the prominent human gut symbiont

  5. Genomic variation landscape of the human gut microbiome

    DEFF Research Database (Denmark)

    Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi

    2013-01-01

    Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal...... metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous...... polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates...

  6. Prostaglandin H synthase immunoreactivity in human gut. An immunohistochemical study

    DEFF Research Database (Denmark)

    Mikkelsen, H B; Rumessen, J J; Qvortrup, Klaus

    1991-01-01

    Prostaglandins exhibit a variety of actions on intestinal smooth muscle depending upon the type, dose and muscle layer studied. As the cellular origin of prostaglandin H (PGH) synthase has not been established with certainty in the human gut wall, we studied the localization of PGH synthase...... in the human duodenum, jejunum, ileum and colon by immunohistochemistry. PGH synthase immunoreactivity appeared to be similar in all segments of the intestine. Most smooth muscle cells seemed to contain PGH synthase; however, the reaction in the lamina muscularis mucosae was much stronger than...... in the longitudinal and circular muscle layers. Endothelial cells in capillaries and larger vessels showed a positive reaction. In addition, unidentified cells in subserosa, at the level of Auerbach's plexus and in the submucosa were stained. We concluded that the smooth muscle cells of the human gut has a rather...

  7. Human gut microbes use multiple transporters to distinguish vitamin B12 analogs and compete in the gut

    Science.gov (United States)

    Degnan, Patrick H.; Barry, Natasha A.; Mok, Kenny C.; Taga, Michiko E.; Goodman, Andrew L.

    2014-01-01

    Summary Genomic and metagenomic sequencing efforts, including human microbiome projects, reveal that microbes often encode multiple systems that appear to accomplish the same task. Whether these predictions reflect actual functional redundancies is unclear. We report that the prominent human gut symbiont Bacteroides thetaiotaomicron employs three functional, homologous vitamin B12 transporters that in at least two cases confer a competitive advantage in the presence of distinct B12 analogs (corrinoids). In the mammalian gut, microbial fitness can be determined by the presence or absence of a single transporter. The total number of distinct corrinoid transporter families in the human gut microbiome likely exceeds those observed in B. thetaiotaomicron by an order of magnitude. These results demonstrate that human gut microbes use elaborate mechanisms to capture and differentiate corrinoids in vivo and that apparent redundancies observed in these genomes can instead reflect hidden specificities that determine whether a microbe will colonize its host. PMID:24439897

  8. Human-modified ecosystems and future evolution

    OpenAIRE

    2001-01-01

    Our global impact is finally receiving the scientific attention it deserves. The outcome will largely determine the future course of evolution. Human-modified ecosystems are shaped by our activities and their side effects. They share a common set of traits including simplified food webs, landscape homogenization, and high nutrient and energy inputs. Ecosystem simplification is the ecological hallmark of humanity and the reason for our evolutionary success. However, the...

  9. Two dynamic regimes in the human gut microbiome

    Science.gov (United States)

    Smillie, Chris S.; Alm, Eric J.

    2017-01-01

    The gut microbiome is a dynamic system that changes with host development, health, behavior, diet, and microbe-microbe interactions. Prior work on gut microbial time series has largely focused on autoregressive models (e.g. Lotka-Volterra). However, we show that most of the variance in microbial time series is non-autoregressive. In addition, we show how community state-clustering is flawed when it comes to characterizing within-host dynamics and that more continuous methods are required. Most organisms exhibited stable, mean-reverting behavior suggestive of fixed carrying capacities and abundant taxa were largely shared across individuals. This mean-reverting behavior allowed us to apply sparse vector autoregression (sVAR)—a multivariate method developed for econometrics—to model the autoregressive component of gut community dynamics. We find a strong phylogenetic signal in the non-autoregressive co-variance from our sVAR model residuals, which suggests niche filtering. We show how changes in diet are also non-autoregressive and that Operational Taxonomic Units strongly correlated with dietary variables have much less of an autoregressive component to their variance, which suggests that diet is a major driver of microbial dynamics. Autoregressive variance appears to be driven by multi-day recovery from frequent facultative anaerobe blooms, which may be driven by fluctuations in luminal redox. Overall, we identify two dynamic regimes within the human gut microbiota: one likely driven by external environmental fluctuations, and the other by internal processes. PMID:28222117

  10. Microbial ecology: human gut microbes associated with obesity.

    Science.gov (United States)

    Ley, Ruth E; Turnbaugh, Peter J; Klein, Samuel; Gordon, Jeffrey I

    2006-12-21

    Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes. Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet. Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications.

  11. A human gut microbial gene catalogue established by metagenomic sequencing

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha; Sicheritz-Pontén, Thomas; Nielsen, Henrik Bjørn

    2010-01-01

    , from faecal samples of 124 European individuals. The gene set, ,150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes......To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence...

  12. The Extended Nutrigenomics - Understanding the Interplay between the Genomes of Food, Gut Microbes, and Human Host.

    Science.gov (United States)

    Kussmann, Martin; Van Bladeren, Peter J

    2011-01-01

    Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well as specific bioactives, with those genes coding for bioactive proteins and peptides being of central interest. The human gut microbiota encompasses a complex ecosystem in the intestine with profound impact on host metabolism. It is being studied at genomic and, more recently, also at proteomic and metabonomic level. Humans are being characterized at the level of genetic pre-disposition and inter-individual variability in terms of (i) response to nutritional interventions and direction of health trajectories; (ii) epigenetic, metabolic programming at certain life stages with health consequences later in life and even for subsequent generations; and (iii) acute genomic expression as a holistic response to diet, monitored at gene transcript, protein and metabolite level. Modern nutrition science explores health-related aspects of bioactive food components, thereby promoting health, preventing, or delaying the onset of disease, optimizing performance and assessing benefits and risks in individuals and subpopulations. Personalized nutrition means adapting food to individual needs, depending on the human host's life stage, -style, and -situation. Traditionally, nutrigenomics and nutri(epi)genetics are seen as the key sciences to understand human variability in preferences and requirements for diet as well as responses to nutrition. This article puts the three nutrition and health-relevant genomes into perspective, namely the food, the gut microbial and the human host's genome, and calls for an "extended nutrigenomics" approach in order to build the future tools for personalized nutrition, health maintenance, and disease prevention. We discuss examples of these genomes

  13. Phylogeny, culturing, and metagenomics of the human gut microbiota.

    Science.gov (United States)

    Walker, Alan W; Duncan, Sylvia H; Louis, Petra; Flint, Harry J

    2014-05-01

    The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.

  14. Human seroreactivity to gut microbiota antigens.

    Science.gov (United States)

    Christmann, Benjamin S; Abrahamsson, Thomas R; Bernstein, Charles N; Duck, L Wayne; Mannon, Peter J; Berg, Göran; Björkstén, Bengt; Jenmalm, Maria C; Elson, Charles O

    2015-11-01

    Although immune responses directed against antigens from the intestinal microbiota are observed in certain diseases, the normal human adaptive immune response to intestinal microbiota is poorly defined. Our goal was to assess the adaptive immune response to the intestinal microbiota present in 143 healthy adults and compare this response with the response observed in 52 children and their mothers at risk of having allergic disease. Human serum was collected from adults and children followed from birth to 7 years of age, and the serum IgG response to a panel of intestinal microbiota antigens was assessed by using a novel protein microarray. Nearly every subject tested, regardless of health status, had serum IgG that recognized a common set of antigens. Seroreactivity to the panel of antigens was significantly lower in atopic adults. Healthy infants expressed the highest level of IgG seroreactivity to intestinal microbiota antigens. This adaptive response developed between 6 and 12 months of age and peaked around 2 years of age. Low IgG responses to certain clusters of microbiota antigens during infancy were associated with allergy development during childhood. There is an observed perturbation of the adaptive response to antigens from the microbiota in allergic subjects. These perturbations are observable even in childhood, suggesting that optimal stimulation of the adaptive immune system by the microbiota might be needed to prevent certain immune-mediated diseases. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  15. Human capital in the entrepreneurship ecosystem

    DEFF Research Database (Denmark)

    Østergaard, Annemarie; Marinova, Svetla Trifonova

    2017-01-01

    and activities when dealing with entrepreneurship and entrepreneurs. Along these lines, this paper focuses on an in-depth investigation of the domain of human capital in Isenberg's entrepreneurship ecosystem. It captures the entrepreneurial mindset of the highly complex individual as a requisite...... for entrepreneurial success and ultimately, for business growth and development. The increasing literature debating human capital confirms the relevance of locating and refining the factors for entrepreneurial success. Consequently, this paper improves the roadmap of entrepreneurship ecosystems by adding the innate...

  16. Human Gut Microbiota: Toward an Ecology of Disease

    Science.gov (United States)

    Selber-Hnatiw, Susannah; Rukundo, Belise; Ahmadi, Masoumeh; Akoubi, Hayfa; Al-Bizri, Hend; Aliu, Adelekan F.; Ambeaghen, Tanyi U.; Avetisyan, Lilit; Bahar, Irmak; Baird, Alexandra; Begum, Fatema; Ben Soussan, Hélène; Blondeau-Éthier, Virginie; Bordaries, Roxane; Bramwell, Helene; Briggs, Alicia; Bui, Richard; Carnevale, Matthew; Chancharoen, Marisa; Chevassus, Talia; Choi, Jin H.; Coulombe, Karyne; Couvrette, Florence; D'Abreau, Samantha; Davies, Meghan; Desbiens, Marie-Pier; Di Maulo, Tamara; Di Paolo, Sean-Anthony; Do Ponte, Sabrina; dos Santos Ribeiro, Priscyla; Dubuc-Kanary, Laure-Anne; Duncan, Paola K.; Dupuis, Frédérique; El-Nounou, Sara; Eyangos, Christina N.; Ferguson, Natasha K.; Flores-Chinchilla, Nancy R.; Fotakis, Tanya; Gado Oumarou H D, Mariam; Georgiev, Metodi; Ghiassy, Seyedehnazanin; Glibetic, Natalija; Grégoire Bouchard, Julien; Hassan, Tazkia; Huseen, Iman; Ibuna Quilatan, Marlon-Francis; Iozzo, Tania; Islam, Safina; Jaunky, Dilan B.; Jeyasegaram, Aniththa; Johnston, Marc-André; Kahler, Matthew R.; Kaler, Kiranpreet; Kamani, Cedric; Karimian Rad, Hessam; Konidis, Elisavet; Konieczny, Filip; Kurianowicz, Sandra; Lamothe, Philippe; Legros, Karina; Leroux, Sebastien; Li, Jun; Lozano Rodriguez, Monica E.; Luponio-Yoffe, Sean; Maalouf, Yara; Mantha, Jessica; McCormick, Melissa; Mondragon, Pamela; Narayana, Thivaedee; Neretin, Elizaveta; Nguyen, Thi T. T.; Niu, Ian; Nkemazem, Romeo B.; O'Donovan, Martin; Oueis, Matthew; Paquette, Stevens; Patel, Nehal; Pecsi, Emily; Peters, Jackie; Pettorelli, Annie; Poirier, Cassandra; Pompa, Victoria R.; Rajen, Harshvardhan; Ralph, Reginald-Olivier; Rosales-Vasquez, Josué; Rubinshtein, Daria; Sakr, Surya; Sebai, Mohammad S.; Serravalle, Lisa; Sidibe, Fily; Sinnathurai, Ahnjana; Soho, Dominique; Sundarakrishnan, Adithi; Svistkova, Veronika; Ugbeye, Tsolaye E.; Vasconcelos, Megan S.; Vincelli, Michael; Voitovich, Olga; Vrabel, Pamela; Wang, Lu; Wasfi, Maryse; Zha, Cong Y.; Gamberi, Chiara

    2017-01-01

    Composed of trillions of individual microbes, the human gut microbiota has adapted to the uniquely diverse environments found in the human intestine. Quickly responding to the variances in the ingested food, the microbiota interacts with the host via reciprocal biochemical signaling to coordinate the exchange of nutrients and proper immune function. Host and microbiota function as a unit which guards its balance against invasion by potential pathogens and which undergoes natural selection. Disturbance of the microbiota composition, or dysbiosis, is often associated with human disease, indicating that, while there seems to be no unique optimal composition of the gut microbiota, a balanced community is crucial for human health. Emerging knowledge of the ecology of the microbiota-host synergy will have an impact on how we implement antibiotic treatment in therapeutics and prophylaxis and how we will consider alternative strategies of global remodeling of the microbiota such as fecal transplants. Here we examine the microbiota-human host relationship from the perspective of the microbial community dynamics. PMID:28769880

  17. Fermentation of bioactive solid lipid nanoparticles by human gut microflora.

    Science.gov (United States)

    Madureira, Ana Raquel; Campos, Débora; Gullon, Beatriz; Marques, Cláudia; Rodríguez-Alcalá, Luís M; Calhau, Conceição; Alonso, Jose Luis; Sarmento, Bruno; Gomes, Ana Maria; Pintado, Manuela

    2016-01-01

    Solid lipid nanoparticles (SLNs) can be used for oral delivery of phenolic compounds in order to protect them from the harsh conditions of digestion and improve their bioavailability in the intestinal epithelium. Recently, the production and characterization of SLNs loaded with rosmarinic acid (RA) and herbal extracts was performed for future use as functional food ingredients. Diet components have been shown to have a huge impact on gut microbiota viability and metabolic activity. Hence, SLNs loaded with RA, sage and savoury extracts have been evaluated for their effect on intestinal microbiota growth and the metabolic products generated. Fermentations in anaerobic batch cultures using volunteer human faeces were performed during 24 h. Dynamic bacterial population changes were analysed using PCR-real time, as well as the generation of fatty acids and the quantification of phenolic compounds by analytical methods. Solid lipid nanoparticles released phenolic compounds at non-inhibitory bacterial growth concentrations. Released herbal extract phenolic compounds showed a beneficial effect on gut microbiota growth (e.g. bifidogenic effects) and were used as substrates. Acetate, formate, lactate and butyrate were produced in higher concentrations. The released phenolic compounds also induced PUFA and trans fatty acids metabolic activity, the production of saturated fatty acids, as well of potential beneficial conjugated linoleic acid isomers. Solid lipid nanoparticles modulate gut microbiota and metabolic activities.

  18. Connections between the human gut microbiome and gestational diabetes mellitus.

    Science.gov (United States)

    Kuang, Ya-Shu; Lu, Jin-Hua; Li, Sheng-Hui; Li, Jun-Hua; Yuan, Ming-Yang; He, Jian-Rong; Chen, Nian-Nian; Xiao, Wan-Qing; Shen, Song-Ying; Qiu, Lan; Wu, Ying-Fang; Hu, Cui-Yue; Wu, Yan-Yan; Li, Wei-Dong; Chen, Qiao-Zhu; Deng, Hong-Wen; Papasian, Christopher J; Xia, Hui-Min; Qiu, Xiu

    2017-08-01

    The human gut microbiome can modulate metabolic health and affect insulin resistance, and it may play an important role in the etiology of gestational diabetes mellitus (GDM). Here, we compared the gut microbial composition of 43 GDM patients and 81 healthy pregnant women via whole-metagenome shotgun sequencing of their fecal samples, collected at 21-29 weeks, to explore associations between GDM and the composition of microbial taxonomic units and functional genes. A metagenome-wide association study identified 154 837 genes, which clustered into 129 metagenome linkage groups (MLGs) for species description, with significant relative abundance differences between the 2 cohorts. Parabacteroides distasonis, Klebsiella variicola, etc., were enriched in GDM patients, whereas Methanobrevibacter smithii, Alistipes spp., Bifidobacterium spp., and Eubacterium spp. were enriched in controls. The ratios of the gross abundances of GDM-enriched MLGs to control-enriched MLGs were positively correlated with blood glucose levels. A random forest model shows that fecal MLGs have excellent discriminatory power to predict GDM status. Our study discovered novel relationships between the gut microbiome and GDM status and suggests that changes in microbial composition may potentially be used to identify individuals at risk for GDM. © The Author 2017. Published by Oxford University Press.

  19. An integrated catalog of reference genes in the human gut microbiome

    DEFF Research Database (Denmark)

    Li, Junhua; Jia, Huijue; Cai, Xianghang

    2014-01-01

    Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly...... signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease....

  20. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

    National Research Council Canada - National Science Library

    Wu, Meng; McNulty, Nathan P; Rodionov, Dmitry A; Khoroshkin, Matvei S; Griffin, Nicholas W; Cheng, Jiye; Latreille, Phil; Kerstetter, Randall A; Terrapon, Nicolas; Henrissat, Bernard; Osterman, Andrei L; Gordon, Jeffrey I

    2015-01-01

    Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice...

  1. Interior Design Research: A Human Ecosystem Model.

    Science.gov (United States)

    Guerin, Denise A.

    1992-01-01

    The interior ecosystems model illustrates effects on the human organism of the interaction of the natural, behavioral, and built environment. Examples of interior lighting and household energy consumption show the model's flexibility for organizing study variables in interior design research. (SK)

  2. Interior Design Research: A Human Ecosystem Model.

    Science.gov (United States)

    Guerin, Denise A.

    1992-01-01

    The interior ecosystems model illustrates effects on the human organism of the interaction of the natural, behavioral, and built environment. Examples of interior lighting and household energy consumption show the model's flexibility for organizing study variables in interior design research. (SK)

  3. Higher prevalence and abundance of Bdellovibrio bacteriovorus in the human gut of healthy subjects.

    Directory of Open Access Journals (Sweden)

    Valerio Iebba

    Full Text Available INTRODUCTION: Members of the human intestinal microbiota are key players in maintaining human health. Alterations in the composition of gut microbial community (dysbiosis have been linked with important human diseases. Understanding the underlying processes that control community structure, including the bacterial interactions within the microbiota itself, is essential. Bdellovibrio bacteriovorus is a gram-negative bacterium that preys other gram-negative species for survival, acting as a population-balancer. It was found in terrestrial/aquatic ecosystems, and in animal intestines, postulating its presence also in the human gut. METHODS: The present study was aimed to evaluate, by end-point PCR and qPCR, the presence of B. bacteriovorus in intestinal and faecal biopsy specimens from 92 paediatric healthy subjects and patients, suffering from Inflammatory Bowel Diseases (IBD, Celiac disease and Cystic fibrosis (CF. RESULTS: i B. bacteriovorus was present and abundant only in healthy individuals, while it was heavily reduced in patients, as in the case of IBD and Celiac, while in CF patients and relative controls we observed comparable results; ii B. bacteriovorus seemed to be mucosa-associated, because all IBD and Celiac biopsies (and related controls were treated with mucus-removing agents, leaving only the mucosa-attached microflora; iii B. bacteriovorus abundance was district-dependent, with a major preponderance in duodenum, and gradually decreasing up to rectum; iv B. bacteriovorus levels significantly dropped in disease status, in duodenum and ileum. CONCLUSIONS: Results obtained in this study could represent the first step for new therapeutic strategies aimed to restore a balance in the intestinal ecosystem, utilizing Bdellovibrio as a probiotic.

  4. Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

    DEFF Research Database (Denmark)

    Shoaie, Saeed; Ghaffari, Pouyan; Kovatcheva-Datchary, Petia

    2015-01-01

    The human gut microbiome is known to be associated with various human disorders, but a major challenge is to go beyond association studies and elucidate causalities. Mathematical modeling of the human gut microbiome at a genome scale is a useful tool to decipher microbe-microbe, diet-microbe and ...

  5. Iron supplementation promotes gut microbiota metabolic activity but not colitis markers in human gut microbiota-associated rats.

    Science.gov (United States)

    Dostal, Alexandra; Lacroix, Christophe; Pham, Van T; Zimmermann, Michael B; Del'homme, Christophe; Bernalier-Donadille, Annick; Chassard, Christophe

    2014-06-28

    The global prevalence of Fe deficiency is high and a common corrective strategy is oral Fe supplementation, which may affect the commensal gut microbiota and gastrointestinal health. The aim of the present study was to investigate the impact of different dietary Fe concentrations on the gut microbiota and gut health of rats inoculated with human faecal microbiota. Rats (8 weeks old, n 40) were divided into five (n 8 each) groups and fed diets differing only in Fe concentration during an Fe-depletion period (12 weeks) and an Fe-repletion period (4 weeks) as follows: (1) Fe-sufficient diet throughout the study period; (2) Fe-sufficient diet followed by 70 mg Fe/kg diet; (3) Fe-depleted diet throughout the study period; (4) Fe-depleted diet followed by 35 mg Fe/kg diet; (5) Fe-depleted diet followed by 70 mg Fe/kg diet. Faecal and caecal samples were analysed for gut microbiota composition (quantitative PCR and pyrosequencing) and bacterial metabolites (HPLC), and intestinal tissue samples were investigated histologically. Fe depletion did not significantly alter dominant populations of the gut microbiota and did not induce Fe-deficiency anaemia in the studied rats. Provision of the 35 mg Fe/kg diet after feeding an Fe-deficient diet significantly increased the abundance of dominant bacterial groups such as Bacteroides spp. and Clostridium cluster IV members compared with that of an Fe-deficient diet. Fe supplementation increased gut microbial butyrate concentration 6-fold compared with Fe depletion and did not affect histological colitis scores. The present results suggest that Fe supplementation enhances the concentration of beneficial gut microbiota metabolites and thus may contribute to gut health.

  6. Individuality and temporal stability of the human gut microbiome

    Directory of Open Access Journals (Sweden)

    Shinichi Sunagawa

    2014-03-01

    Full Text Available Introduction: The breakthrough of next generation sequencing-technologies has enabled large-scale studies of natural microbial communities and the 16S rRNA genes have been widely used as a phylogenetic marker to study community structure. However, major limitations of this approach are that neither strain-level resolution nor genomic context of microorganisms can be provided. This information, however, is crucial to answer fundamental questions about the temporal stability and distinctiveness of natural microbial communities.Material and methods: We developed a methodological framework for metagenomic single nucleotide polymorphism (SNP variation analysis and applied it to publicly available data from 252 human fecal samples from 207 European and North American individuals. We further analyzed samples from 43 healthy subjects that were sampled at least twice over time intervals of up to one year and measured population similarities of dominant gut species.Results: We detected 10.3 million SNPs in 101 species, which nearly amounts to the number identified in more than 1,000 humans. Conclusion: The most striking result was that host-specific strains appear to be retained over long time periods. This indicates that individual-specific strains are not easily exchanged with the environment and furthermore, that an individuals appear to have a unique metagenomic genotype. This, in turn, is linked to implications for human gut physiology, such as the stability of antibiotic resistance potential.

  7. Low calorie sweeteners: Evidence remains lacking for effects on human gut function.

    Science.gov (United States)

    Bryant, Charlotte; Mclaughlin, John

    2016-10-01

    The importance of nutrient induced gut-brain signalling in the regulation of human food intake has become an increasing focus of research. Much of the caloric excess consumed comes from dietary sugars, but our knowledge about the mechanisms mediating the physiological and appetitive effects of sweet tastants in the human gut and gut-brain axis is far from complete. The comparative effects of natural sugars vs low calorie sweeteners are also poorly understood. Research in animal and cellular models has suggested a key functional role in gut endocrine cells for the sweet taste receptors previously well described in oral taste. However human studies to date have very consistently failed to show that activation of the sweet taste receptor by low calorie sweeteners placed in the human gut fails to replicate any of the effects on gastric motility, gut hormones or appetitive responses evoked by caloric sugars. Copyright © 2016. Published by Elsevier Inc.

  8. Gut Bifidobacteria Populations in Human Health and Aging

    Science.gov (United States)

    Arboleya, Silvia; Watkins, Claire; Stanton, Catherine; Ross, R. Paul

    2016-01-01

    The intestinal microbiota has increasingly been shown to have a vital role in various aspects of human health. Indeed, several studies have linked alterations in the gut microbiota with the development of different diseases. Among the vast gut bacterial community, Bifidobacterium is a genus which dominates the intestine of healthy breast-fed infants whereas in adulthood the levels are lower but relatively stable. The presence of different species of bifidobacteria changes with age, from childhood to old age. Bifidobacterium longum, B. breve, and B. bifidum are generally dominant in infants, whereas B. catenulatum, B. adolescentis and, as well as B. longum are more prevalent in adults. Increasingly, evidence is accumulating which shows beneficial effects of supplementation with bifidobacteria for the improvement of human health conditions ranging from protection against infection to different extra- and intra-intestinal positive effects. Moreover, bifidobacteria have been associated with the production of a number of potentially health promoting metabolites including short chain fatty acids, conjugated linoleic acid and bacteriocins. The aim of this mini-review is to describe the bifidobacteria compositional changes associated with different stages in life, highlighting their beneficial role, as well as their presence or absence in many disease states. PMID:27594848

  9. Gut bifidobacteria populations in human health and aging

    Directory of Open Access Journals (Sweden)

    Silvia Arboleya

    2016-08-01

    Full Text Available The intestinal microbiota has increasingly been shown to have a vital role in various aspects of human health. Indeed, several studies have linked alterations in the gut microbiota with the development of different diseases. Among the vast gut bacterial community, Bifidobacterium is a genus which dominates the intestine of healthy breast-fed infants whereas in adulthood the levels are lower but relatively stable. The presence of different species of bifidobacteria changes with age, from the childhood to old age. Bifidobacterium longum, Bifidobacterium breve and Bifidobacterium bifidum are generally dominant in infants whereas Bifidobacterium catenulatum, Bifidobacterium adolescentis and, as well as B. longum are more dominant in adults. Increasingly, evidence is accumulating which shows beneficial effect of supplementation with bifidobacteria for the improvement of human health conditions ranging from protection against infection to different extra- and intra-intestinal positive effects. Moreover, bifidobacteria can be associated with the production of a number of potentially health promoting metabolites including short chain fatty acids, conjugated linoleic acid and bacteriocins. The aim of this mini-review is to describe the bifidobacteria composition changes associated with different stages in life, highlighting their beneficial role, as well as their presence in commonly known disease states.

  10. Short-term effect of antibiotics on human gut microbiota.

    Directory of Open Access Journals (Sweden)

    Suchita Panda

    Full Text Available From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002. At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016. Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04. The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.

  11. Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota

    NARCIS (Netherlands)

    Bello Gonzalez, T.D.G.; Passel, van M.W.J.; Tims, S.; Fuentes, S.; Vos, de W.M.; Smidt, H.; Belzer, C.

    2015-01-01

    The human intestinal microbiota is responsible for various health-related functions, and its diversity can be readily mapped with the 16S ribosomal RNA targeting Human Intestinal Tract (HIT) Chip. Here we characterise distal gut samples from chimpanzees, gorillas and marmosets, and compare them with

  12. Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota

    NARCIS (Netherlands)

    Bello Gonzalez, T.D.G.; Passel, van M.W.J.; Tims, S.; Fuentes, S.; Vos, de W.M.; Smidt, H.; Belzer, C.

    2015-01-01

    The human intestinal microbiota is responsible for various health-related functions, and its diversity can be readily mapped with the 16S ribosomal RNA targeting Human Intestinal Tract (HIT) Chip. Here we characterise distal gut samples from chimpanzees, gorillas and marmosets, and compare them with

  13. The gut microbiota in human energy homeostasis and obesity.

    Science.gov (United States)

    Rosenbaum, Michael; Knight, Rob; Leibel, Rudolph L

    2015-09-01

    Numerous studies of rodents suggest that the gut microbiota populations are sensitive to genetic and environmental influences, and can produce or influence afferent signals that directly or indirectly impinge on energy homeostatic systems affecting both energy balance (weight gain or loss) and energy stores. Fecal transplants from obese and lean human, and from mouse donors to gnotobiotic mice, result in adoption of the donor somatotype by the formerly germ-free rodents. Thus, the microbiota is certainly implicated in the development of obesity, adiposity-related comorbidities, and the response to interventions designed to achieve sustained weight reduction in mice. More studies are needed to determine whether the microbiota plays a similarly potent role in human body-weight regulation and obesity.

  14. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota

    NARCIS (Netherlands)

    Scanlan, P.D.; Stensvold, C.R.; Rajilic-Stojanovic, M.; Heilig, H.G.; Vos, de W.M.; O'Toole, P.W.; Cotter, P.D.

    2014-01-01

    To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the mi

  15. An integrated catalog of reference genes in the human gut microbiome

    NARCIS (Netherlands)

    Li, J.; Jia, H.; Cai, X.; Zhong, H.; Feng, Q.; Sunagawa, S.; Arumugam, M.; Kultima, J.R.; Prifti, E.; Nielsen, T.; Juncker, A.S.; Manichanh, C.; Chen, B.; Zhang, W.; Levenez, F.; Xu, X.; Xiao, L.; Liang, S.; Zhang, D.; Zhang, Z.; Chen, W.; Zhao, H.; Al-Aama, J.Y.; Edris, S.; Yang, H.; Hansen, H.; Nielsen, H.B.; Brunak, S.; Kristiansen, K.; Guarner, F.; Pedersen, O.; Doré, J.; Ehrlich, S.D.; Bork, P.; Wang, J.; Vos, de W.M.; Tims, S.; Zoetendal, E.G.; Kleerebezem, M.

    2014-01-01

    Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly

  16. Genome-Wide Association Studies of the Human Gut Microbiota.

    Directory of Open Access Journals (Sweden)

    Emily R Davenport

    Full Text Available The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host genetics plays in dictating the composition of bacteria living in the gut. In this study, we examined the association of ~200K host genotypes with the relative abundance of fecal bacterial taxa in a founder population, the Hutterites, during two seasons (n = 91 summer, n = 93 winter, n = 57 individuals collected in both. These individuals live and eat communally, minimizing variation due to environmental exposures, including diet, which could potentially mask small genetic effects. Using a GWAS approach that takes into account the relatedness between subjects, we identified at least 8 bacterial taxa whose abundances were associated with single nucleotide polymorphisms in the host genome in each season (at genome-wide FDR of 20%. For example, we identified an association between a taxon known to affect obesity (genus Akkermansia and a variant near PLD1, a gene previously associated with body mass index. Moreover, we replicate a previously reported association from a quantitative trait locus (QTL mapping study of fecal microbiome abundance in mice (genus Lactococcus, rs3747113, P = 3.13 x 10-7. Finally, based on the significance distribution of the associated microbiome QTLs in our study with respect to chromatin accessibility profiles, we identified tissues in which host genetic variation may be acting to influence bacterial abundance in the gut.

  17. Human impacts on Caribbean coral reef ecosystems

    OpenAIRE

    Hardt, Marah Justine

    2007-01-01

    Fishing is one of the oldest anthropogenic disturbances in the ocean, differing from other impacts in its direct removal of biomass from the ecosystem. Despite the centuries of fishing activities, there is much we still do not understand regarding the effects of fish removal on the benthic community. I use an interdisciplinary approach to investigate the affect of human disturbance, primarily the alteration of fish communities, on major functional groups of coral reefs, over extended temporal...

  18. Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans.

    Science.gov (United States)

    Pudlo, Nicholas A; Urs, Karthik; Kumar, Supriya Suresh; German, J Bruce; Mills, David A; Martens, Eric C

    2015-11-10

    Many symbiotic gut bacteria possess the ability to degrade multiple polysaccharides, thereby providing nutritional advantages to their hosts. Like microorganisms adapted to other complex nutrient environments, gut symbionts give different metabolic priorities to substrates present in mixtures. We investigated the responses of Bacteroides thetaiotaomicron, a common human intestinal bacterium that metabolizes more than a dozen different polysaccharides, including the O-linked glycans that are abundant in secreted mucin. Experiments in which mucin glycans were presented simultaneously with other carbohydrates show that degradation of these host carbohydrates is consistently repressed in the presence of alternative substrates, even by B. thetaiotaomicron previously acclimated to growth in pure mucin glycans. Experiments with media containing systematically varied carbohydrate cues and genetic mutants reveal that transcriptional repression of genes involved in mucin glycan metabolism is imposed by simple sugars and, in one example that was tested, is mediated through a small intergenic region in a transcript-autonomous fashion. Repression of mucin glycan-responsive gene clusters in two other human gut bacteria, Bacteroides massiliensis and Bacteroides fragilis, exhibited variable and sometimes reciprocal responses compared to those of B. thetaiotaomicron, revealing that these symbionts vary in their preference for mucin glycans and that these differences occur at the level of controlling individual gene clusters. Our results reveal that sensing and metabolic triaging of glycans are complex processes that vary among species, underscoring the idea that these phenomena are likely to be hidden drivers of microbiota community dynamics and may dictate which microorganisms preferentially commit to various niches in a constantly changing nutritional environment. Human intestinal microorganisms impact many aspects of health and disease, including digestion and the propensity to

  19. The human gut microbiome impacts health and disease.

    Science.gov (United States)

    Ehrlich, Stanislav Dusko

    2016-01-01

    The human gut microbiome can now be characterized in unprecedented detail by an approach based on high-throughput sequencing of total stool DNA, that we name quantitative metagenomics. Central to the approach is a catalog that lists all the genes of intestinal microbes that are known - 9.9 millions, identified by the analysis of 1267 stool samples. Beyond the gene list, genetic units that carry them begun to be known; many of these correspond to bacterial species that were never isolated and cultured yet. Quantitative metagenomics allows developing powerful algorithms to diagnose a disease, monitor patients and identify individuals at risk to progress towards a disease. This lays ground for developing new approaches to better restore and even preserve the health by modulation of the altered microbiome, which contributes to promote or aggravate a disease.

  20. Suggested alternative starch utilization system from the human gut bacterium Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Chaudet, Marcia M; Rose, David R

    2016-06-01

    The human digestive system is host to a highly populated ecosystem of bacterial species that significantly contributes to our assimilation of dietary carbohydrates. Bacteroides thetaiotaomicron is a member of this ecosystem, and participates largely in the role of the gut microbiome by breaking down dietary complex carbohydrates. This process of acquiring glycans from the colon lumen is predicted to rely on the mechanisms of proteins that are part of a classified system known as polysaccharide utilization loci (PUL). These loci are responsible for binding substrates at the cell outer membrane, internalizing them, and then hydrolyzing them within the periplasm into simple sugars. Here we report our investigation into specific components of a PUL, and suggest an alternative starch utilization system in B. thetaiotaomicron. Our analysis of an outer membrane binding protein, a SusD homolog, highlights its contribution to this PUL by acquiring starch-based sugars from the colon lumen. Through our structural characterization of two Family GH31 α-glucosidases, we reveal the flexibility of this bacterium with respect to utilizing a range of starch-derived glycans with an emphasis on branched substrates. With these results we demonstrate the predicted function of a gene locus that is capable of contributing to starch hydrolysis in the human colon.

  1. Human symbionts inject and neutralize antibacterial toxins to persist in the gut.

    Science.gov (United States)

    Wexler, Aaron G; Bao, Yiqiao; Whitney, John C; Bobay, Louis-Marie; Xavier, Joao B; Schofield, Whitman B; Barry, Natasha A; Russell, Alistair B; Tran, Bao Q; Goo, Young Ah; Goodlett, David R; Ochman, Howard; Mougous, Joseph D; Goodman, Andrew L

    2016-03-29

    The human gut microbiome is a dynamic and densely populated microbial community that can provide important benefits to its host. Cooperation and competition for nutrients among its constituents only partially explain community composition and interpersonal variation. Notably, certain human-associated Bacteroidetes--one of two major phyla in the gut--also encode machinery for contact-dependent interbacterial antagonism, but its impact within gut microbial communities remains unknown. Here we report that prominent human gut symbionts persist in the gut through continuous attack on their immediate neighbors. Our analysis of just one of the hundreds of species in these communities reveals 12 candidate antibacterial effector loci that can exist in 32 combinations. Through the use of secretome studies, in vitro bacterial interaction assays and multiple mouse models, we uncover strain-specific effector/immunity repertoires that can predict interbacterial interactions in vitro and in vivo, and find that some of these strains avoid contact-dependent killing by accumulating immunity genes to effectors that they do not encode. Effector transmission rates in live animals can exceed 1 billion events per minute per gram of colonic contents, and multiphylum communities of human gut commensals can partially protect sensitive strains from these attacks. Together, these results suggest that gut microbes can determine their interactions through direct contact. An understanding of the strategies human gut symbionts have evolved to target other members of this community may provide new approaches for microbiome manipulation.

  2. The Human Gut Antibiotic Resistome in the Metagenomic Era: Progress and Perspectives

    Directory of Open Access Journals (Sweden)

    Yongfei Hu

    2016-04-01

    Full Text Available The human gut is populated by a vast number of bacteria, which play a critical role in human health. In recent years, attention has focused on the gut bacteria as a reservoir of antibiotic resistance genes (ARGs. Both culture-dependent and culture-independent methods have been applied to investigate numerous ARGs, collectively called the antibiotic resistome, harbored by gut bacteria. This has led to an increased understanding of the overall profile of the gut antibiotic resistome, although it remains incompletely understood. In this review, we summarize the recent research findings on the human gut antibiotic resistome, with an emphasis on progress achieved using the culture-independent metagenomic strategy. We also describe the features of different available ARG databases used for annotation in metagenomic analysis, discuss the potential problems and limitations in current research, and suggest several directions for future investigation.

  3. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome

    NARCIS (Netherlands)

    Van den Abbeele, Pieter; Verstraete, Willy; El Aidy, Sahar; Geirnaert, Annelies; Van de Wiele, Tom

    2013-01-01

    Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) de

  4. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome

    NARCIS (Netherlands)

    Van den Abbeele, Pieter; Verstraete, Willy; El Aidy, Sahar; Geirnaert, Annelies; Van de Wiele, Tom

    2013-01-01

    Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) de

  5. Human Catestatin Alters Gut Microbiota Composition in Mice

    Science.gov (United States)

    Rabbi, Mohammad F.; Munyaka, Peris M.; Eissa, Nour; Metz-Boutigue, Marie-Hélène; Khafipour, Ehsan; Ghia, Jean Eric

    2017-01-01

    The mammalian intestinal tract is heavily colonized with a dense, complex, and diversified microbial populations. In healthy individuals, an array of epithelial antimicrobial agents is secreted in the gut to aid intestinal homeostasis. Enterochromaffin cells (EC) in the intestinal epithelium are a major source of chromogranin A (CgA), which is a pro-hormone and can be cleaved into many bioactive peptides that include catestatin (CST). This study was carried out to evaluate the possible impact of CST on gut microbiota in vivo using a mouse model. The CST (Human CgA352−372) or normal saline was intrarectally administered in C57BL/6 male mice for 6 days and then sacrificed. Feces and colonic mucosa tissue samples were collected, DNA was extracted, the V4 region of bacterial 16S rRNA gene was amplified and subjected to MiSeq Illumina sequencing. The α-diversity was calculated using Chao 1 and β-diversity was determined using QIIME. Differences at the genus level were determined using partial least square discriminant analysis (PLS-DA). Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to predict functional capacity of bacterial community. CST treatment did not modify bacterial richness in fecal and colonic mucosa-associated microbiota; however, treatment significantly modified bacterial community composition between the groups. Also, CST-treated mice had a significantly lower relative abundance of Firmicutes and higher abundance of Bacteroidetes, observed only in fecal samples. However, at lower phylogenetic levels, PLS-DA analysis revealed that some bacterial taxa were significantly associated with the CST-treated mice in both fecal and colonic mucosa samples. In addition, differences in predicted microbial functional pathways in both fecal and colonic mucosa samples were detected. The results support the hypothesis that CST treatment modulates gut microbiota composition under non-pathophysiological conditions

  6. Mucin glycan foraging in the human gut microbiome

    Science.gov (United States)

    Tailford, Louise E.; Crost, Emmanuelle H.; Kavanaugh, Devon; Juge, Nathalie

    2015-01-01

    The availability of host and dietary carbohydrates in the gastrointestinal (GI) tract plays a key role in shaping the structure-function of the microbiota. In particular, some gut bacteria have the ability to forage on glycans provided by the mucus layer covering the GI tract. The O-glycan structures present in mucin are diverse and complex, consisting predominantly of core 1-4 mucin-type O-glycans containing α- and β- linked N-acetyl-galactosamine, galactose and N-acetyl-glucosamine. These core structures are further elongated and frequently modified by fucose and sialic acid sugar residues via α1,2/3/4 and α2,3/6 linkages, respectively. The ability to metabolize these mucin O-linked oligosaccharides is likely to be a key factor in determining which bacterial species colonize the mucosal surface. Due to their proximity to the immune system, mucin-degrading bacteria are in a prime location to influence the host response. However, despite the growing number of bacterial genome sequences available from mucin degraders, our knowledge on the structural requirements for mucin degradation by gut bacteria remains fragmented. This is largely due to the limited number of functionally characterized enzymes and the lack of studies correlating the specificity of these enzymes with the ability of the strain to degrade and utilize mucin and mucin glycans. This review focuses on recent findings unraveling the molecular strategies used by mucin-degrading bacteria to utilize host glycans, adapt to the mucosal environment, and influence human health. PMID:25852737

  7. Green Infrastructure, Ecosystem Services, and Human Health.

    Science.gov (United States)

    Coutts, Christopher; Hahn, Micah

    2015-08-18

    Contemporary ecological models of health prominently feature the natural environment as fundamental to the ecosystem services that support human life, health, and well-being. The natural environment encompasses and permeates all other spheres of influence on health. Reviews of the natural environment and health literature have tended, at times intentionally, to focus on a limited subset of ecosystem services as well as health benefits stemming from the presence, and access and exposure to, green infrastructure. The sweeping influence of green infrastructure on the myriad ecosystem services essential to health has therefore often been underrepresented. This survey of the literature aims to provide a more comprehensive picture-in the form of a primer-of the many simultaneously acting health co-benefits of green infrastructure. It is hoped that a more accurately exhaustive list of benefits will not only instigate further research into the health co-benefits of green infrastructure but also promote consilience in the many fields, including public health, that must be involved in the landscape conservation necessary to protect and improve health and well-being.

  8. Prebiotics and gut microbial ecosystem%益生元与肠道微生态

    Institute of Scientific and Technical Information of China (English)

    沈定树; 郑静

    2013-01-01

    A prebiotic is "a non-digestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or the activity of one or a limited number of bacteria in the colon.",thereby,increase the body' s natural resistance to invading pathogens.The prebiotic carbohydrates that have been evaluated in humans at present largely consist of fructans or galactans.There is consistent evidence from in vitro and in vivo studies that these are not digested by normal human enzymes,but are readily fermented by anaerobic bacteria in the large intestine.There are no reports of faecal recovery of measurable quantities of prebiotic carbohydrates.Through fermentation in the large intestine,prebiotic carbohydrates yield short-chain fatty acids,stimulate the growth of many bacterial species in addition to the selective effects on lactobacilli and bifidobacteria.New methods are being applied extensively to human gut microbiology and promote the degree of reliability required to detect subtle changes in colonic microflora composition and to correlate such changes with health benefits.This paper reviewed the present status of studies concerning prebiotics,with emphasis on the mechanisms of selective growth stimulation,and physiologic effects.%益生元是一种非消化的成分,通过选择性的刺激肠道中一种或少数种益生菌的增长和/或活性而对宿主有利.具有抵抗致病菌侵入的天然功能.目前广泛研究的有果糖和半乳糖,体内与体外试验均表明不被正常人酶类所消化,在大肠中容易发酵,粪便内未能检出这种糖的成分.通过大肠细菌对益生元的发酵产生的短链脂肪酸是刺激双歧杆菌和乳杆菌增长的重要因素.应用现代技术获得了人肠道微生物细菌群的组成与种类的多样性.本文综述有关益生元的研究状况,强调益生元选择性刺激的机制和对人生理功能的影响.

  9. The mouse gut microbiome revisited: From complex diversity to model ecosystems.

    Science.gov (United States)

    Clavel, Thomas; Lagkouvardos, Ilias; Blaut, Michael; Stecher, Bärbel

    2016-08-01

    Laboratory mice are the most commonly used animal model in translational medical research. In recent years, the impact of the gut microbiota (i.e. communities of microorganisms in the intestine) on host physiology and the onset of diseases, including metabolic and neuronal disorders, cancers, gastrointestinal infections and chronic inflammation, became a focal point of interest. There is abundant evidence that mouse phenotypes in disease models vary greatly between animal facilities or commercial providers, and that this variation is associated with differences in the microbiota. Hence, there is a clear discrepancy between the widespread use of mouse models in research and the patchwork knowledge on the mouse gut microbiome. In the present manuscript, we summarize data pertaining to the diversity and functions of the mouse gut microbiota, review existing work on gnotobiotic mouse models, and discuss challenges and opportunities for current and future research in the field.

  10. Degradation of Marine Algae-Derived Carbohydrates by Bacteroidetes Isolated from Human Gut Microbiota.

    Science.gov (United States)

    Li, Miaomiao; Shang, Qingsen; Li, Guangsheng; Wang, Xin; Yu, Guangli

    2017-03-24

    Carrageenan, agarose, and alginate are algae-derived undigested polysaccharides that have been used as food additives for hundreds of years. Fermentation of dietary carbohydrates of our food in the lower gut of humans is a critical process for the function and integrity of both the bacterial community and host cells. However, little is known about the fermentation of these three kinds of seaweed carbohydrates by human gut microbiota. Here, the degradation characteristics of carrageenan, agarose, alginate, and their oligosaccharides, by Bacteroides xylanisolvens, Bacteroides ovatus, and Bacteroides uniforms, isolated from human gut microbiota, are studied.

  11. The role of gut microbiota in human metabolism

    NARCIS (Netherlands)

    Vrieze, A.

    2013-01-01

    This thesis supports the hypothesis that gut microbiota can be viewed as an ‘exteriorised organ’ that contributes to energy metabolism and the modulation of our immune system. Following Koch’s postulates, it has now been shown that gut microbiota are associated with metabolic disease and that these

  12. The role of gut microbiota in human metabolism

    NARCIS (Netherlands)

    Vrieze, A.

    2013-01-01

    This thesis supports the hypothesis that gut microbiota can be viewed as an ‘exteriorised organ’ that contributes to energy metabolism and the modulation of our immune system. Following Koch’s postulates, it has now been shown that gut microbiota are associated with metabolic disease and that these

  13. [The human gut microbiota: Interactions with the host and dysfunctions].

    Science.gov (United States)

    Lepage, P

    2017-05-12

    The human intestinal microbiota is composed of approximately 100,000 billion microorganisms with the average total number of different commensal bacterial species estimated at over 500 per individual. The human intestinal microbiota can be considered as an organ within another, which co-evolved with its host to achieve a symbiotic relationship leading to physiological homeostasis. The host provides an environment enriched in nutrients and the microbiota provides essential functions. Dysbiosis of the intestinal microbiota (changes in bacterial composition) has been associated with local dysfunctions of the gastrointestinal tract, such as inflammatory bowel disease or irritable bowel syndrome but also with obesity and metabolic diseases. However, a better understanding of the human intestinal ecosystem is still needed to understand the exact role of the microbiota in health and disease. Most intestinal bacteria are anaerobic and therefore, for the large majority, impossible to culture at present. Consequently, their function cannot be inferred from data on their composition. Today, with the help of a metagenomic approach, the bacterial genomic content of an ecosystem and the associated functions can be directly accessed from the environment without culture. Copyright © 2017 SPLF. Published by Elsevier Masson SAS. All rights reserved.

  14. The active human gut microbiota differs from the total microbiota.

    Directory of Open Access Journals (Sweden)

    Francesc Peris-Bondia

    Full Text Available The human gut microbiota is considered one of the most fascinating reservoirs of microbial diversity hosting between 400 to 1000 bacterial species distributed among nine phyla with Firmicutes, Bacteroidetes and Actinobacteria representing around 75% of the diversity. One of the most intriguing issues relates to understanding which microbial groups are active players in the maintenance of the microbiota homeostasis.Here, we describe the diversity of active microbial fractions compared with the whole community from raw human fecal samples. We studied four healthy volunteers by 16S rDNA gene pyrosequencing. The fractions were obtained by cell sorting based on bacterial RNA concentration. Bacterial families were observed to appear or disappear on applying a cell sorting method in which flow cytometry was used to evaluate the active cells by pyronin-Y staining of RNA. This method was able to detect active bacteria, indicating that the active players differed from that observed in raw fecal material. Generally, observations showed that in the active fractions, the number of reads related to Bacteroidetes decreased whereas several families from Clostridiales (Firmicutes were more highly represented. Moreover, a huge number of families appeared as part of the active fraction when cell sorting was applied, indicating reads that are simply statistically hidden by the total reads.

  15. Changes in human gut flora with age: an Indian familial study

    Directory of Open Access Journals (Sweden)

    Marathe Nachiket

    2012-09-01

    Full Text Available Abstract Background The gut micro flora plays vital role in health status of the host. The majority of microbes residing in the gut have a profound influence on human physiology and nutrition. Different human ethnic groups vary in genetic makeup as well as the environmental conditions they live in. The gut flora changes with genetic makeup and environmental factors and hence it is necessary to understand the composition of gut flora of different ethnic groups. Indian population is different in physiology from western population (YY paradox and thus the gut flora in Indian population is likely to differ from the extensively studied gut flora in western population. In this study we have investigated the gut flora of two Indian families, each with three individuals belonging to successive generations and living under the same roof. Results Denaturation gradient gel electrophoresis analysis showed age-dependant variation in gut microflora amongst the individuals within a family. Different bacterial genera were dominant in the individual of varying age in clone library analysis. Obligate anaerobes isolated from individuals within a family showed age related differences in isolation pattern, with 27% (6 out of 22 of the isolates being potential novel species based on 16S rRNA gene sequence. In qPCR a consistent decrease in Firmicutes number and increase in Bacteroidetes number with increasing age was observed in our subjects, this pattern of change in Firmicutes / Bacteroidetes ratio with age is different than previously reported in European population. Conclusion There is change in gut flora with age amongst the individuals within a family. The isolation of high percent of novel bacterial species and the pattern of change in Firmicutes /Bacteroidetes ratio with age suggests that the composition of gut flora in Indian individuals may be different than the western population. Thus, further extensive study is needed to define the gut flora in Indian

  16. Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model

    NARCIS (Netherlands)

    Aguirre, M.; Eck, A.; Koenen, M.E.; Savelkoul, P.H.M.; Budding, A.E.; Venema, K.

    2016-01-01

    The aim of this study was to screen how rapidly the human gut microbiota responds to diet in an in vitro model of the proximal colon (TIM-system). Two experimental diets were provided to the gut bacteria: a high carbohydrate and a high protein diet. The metabolic response and the composition of the

  17. Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model

    NARCIS (Netherlands)

    Aguirre, M.; Eck, A.; Koenen, M.E.; Savelkoul, P.H.M.; Budding, A.E.; Venema, K.

    2016-01-01

    The aim of this study was to screen how rapidly the human gut microbiota responds to diet in an in vitro model of the proximal colon (TIM-system). Two experimental diets were provided to the gut bacteria: a high carbohydrate and a high protein diet. The metabolic response and the composition of the

  18. Sex, Body Mass Index, and Dietary Fiber Intake Influence the Human Gut Microbiome

    Science.gov (United States)

    Dominianni, Christine; Sinha, Rashmi; Goedert, James J.; Pei, Zhiheng; Yang, Liying; Hayes, Richard B.; Ahn, Jiyoung

    2015-01-01

    Increasing evidence suggests that the composition of the human gut microbiome is important in the etiology of human diseases; however, the personal factors that influence the gut microbiome composition are poorly characterized. Animal models point to sex hormone-related differentials in microbiome composition. In this study, we investigated the relationship of sex, body mass index (BMI) and dietary fiber intake with the gut microbiome in 82 humans. We sequenced fecal 16S rRNA genes by 454 FLX technology, then clustered and classified the reads to microbial genomes using the QIIME pipeline. Relationships of sex, BMI, and fiber intake with overall gut microbiome composition and specific taxon abundances were assessed by permutational MANOVA and multivariate logistic regression, respectively. We found that sex was associated with the gut microbiome composition overall (p=0.001). The gut microbiome in women was characterized by a lower abundance of Bacteroidetes (p=0.03). BMI (>25 kg/m2 vs. Fiber from beans and from fruits and vegetables were associated, respectively, with greater abundance of Actinobacteria (p=0.006 and false discovery rate adjusted q=0.05) and Clostridia (p=0.009 and false discovery rate adjusted q=0.09). Our findings suggest that sex, BMI, and dietary fiber contribute to shaping the gut microbiome in humans. Better understanding of these relationships may have significant implications for gastrointestinal health and disease prevention. PMID:25874569

  19. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

    Science.gov (United States)

    Forslund, Kristoffer; Hildebrand, Falk; Nielsen, Trine; Falony, Gwen; Le Chatelier, Emmanuelle; Sunagawa, Shinichi; Prifti, Edi; Vieira-Silva, Sara; Gudmundsdottir, Valborg; Krogh Pedersen, Helle; Arumugam, Manimozhiyan; Kristiansen, Karsten; Voigt, Anita Yvonne; Vestergaard, Henrik; Hercog, Rajna; Igor Costea, Paul; Kultima, Jens Roat; Li, Junhua; Jørgensen, Torben; Levenez, Florence; Dore, Joël; Nielsen, H Bjørn; Brunak, Søren; Raes, Jeroen; Hansen, Torben; Wang, Jun; Ehrlich, S Dusko; Bork, Peer; Pedersen, Oluf

    2015-12-10

    In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication.

  20. Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

    DEFF Research Database (Denmark)

    Rettedal, Elizabeth; Gumpert, Heidi; Sommer, Morten

    2014-01-01

    The human gut microbiota is linked to a variety of human health issues and implicated in antibiotic resistance gene dissemination. Most of these associations rely on culture-independent methods, since it is commonly believed that gut microbiota cannot be easily or sufficiently cultured. Here, we...... show that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling. We use this approach to determine the phylogenetic distribution of antibiotic tolerance phenotypes for 16 antibiotics in the human gut...... microbiota. Based on the phenotypic mapping, we tailor antibiotic combinations to specifically select for previously uncultivated bacteria. Utilizing this method we cultivate and sequence the genomes of four isolates, one of which apparently belongs to the genus Oscillibacter; uncultivated Oscillibacter...

  1. Neonatal Gut Microbiota and Human Milk Glycans Cooperate to Attenuate Infection and Inflammation.

    Science.gov (United States)

    Newburg, David S; He, Yingying

    2015-12-01

    Glycans of the intestinal mucosa and oligosaccharides of human milk influence the early colonization of the infant gut and establishment of mucosal homeostasis, and differences in colonization of the gut influence the ontogeny of glycans on the surface of the intestinal mucosa, proinflammatory signaling, homeostasis, and resilience to insult. This interkingdom reciprocal interaction is typical of a mutualistic symbiotic relationship. The period in which the infant gut most needs protection from hypersensitive inflammation overlaps with the recommended period of exclusive nursing; electively substituting artificial formula that lacks human milk protective glycans seems ill advised, especially for premature infants.

  2. Human gut microbiota in obesity and after gastric bypass.

    Science.gov (United States)

    Zhang, Husen; DiBaise, John K; Zuccolo, Andrea; Kudrna, Dave; Braidotti, Michele; Yu, Yeisoo; Parameswaran, Prathap; Crowell, Michael D; Wing, Rod; Rittmann, Bruce E; Krajmalnik-Brown, Rosa

    2009-02-17

    Recent evidence suggests that the microbial community in the human intestine may play an important role in the pathogenesis of obesity. We examined 184,094 sequences of microbial 16S rRNA genes from PCR amplicons by using the 454 pyrosequencing technology to compare the microbial community structures of 9 individuals, 3 in each of the categories of normal weight, morbidly obese, and post-gastric-bypass surgery. Phylogenetic analysis demonstrated that although the Bacteria in the human intestinal community were highly diverse, they fell mainly into 6 bacterial divisions that had distinct differences in the 3 study groups. Specifically, Firmicutes were dominant in normal-weight and obese individuals but significantly decreased in post-gastric-bypass individuals, who had a proportional increase of Gammaproteobacteria. Numbers of the H(2)-producing Prevotellaceae were highly enriched in the obese individuals. Unlike the highly diverse Bacteria, the Archaea comprised mainly members of the order Methanobacteriales, which are H(2)-oxidizing methanogens. Using real-time PCR, we detected significantly higher numbers of H(2)-utilizing methanogenic Archaea in obese individuals than in normal-weight or post-gastric-bypass individuals. The coexistence of H(2)-producing bacteria with relatively high numbers of H(2)-utilizing methanogenic Archaea in the gastrointestinal tract of obese individuals leads to the hypothesis that interspecies H(2) transfer between bacterial and archaeal species is an important mechanism for increasing energy uptake by the human large intestine in obese persons. The large bacterial population shift seen in the post-gastric-bypass individuals may reflect the double impact of the gut alteration caused by the surgical procedure and the consequent changes in food ingestion and digestion.

  3. Degradation of Marine Algae-Derived Carbohydrates by Bacteroidetes Isolated from Human Gut Microbiota

    OpenAIRE

    Li, Miaomiao; Shang, Qingsen; Li, Guangsheng; Wang, Xin; Yu, Guangli

    2017-01-01

    Carrageenan, agarose, and alginate are algae-derived undigested polysaccharides that have been used as food additives for hundreds of years. Fermentation of dietary carbohydrates of our food in the lower gut of humans is a critical process for the function and integrity of both the bacterial community and host cells. However, little is known about the fermentation of these three kinds of seaweed carbohydrates by human gut microbiota. Here, the degradation characteristics of carrageenan, agaro...

  4. Dietary modulation of the human gut microflora using prebiotics.

    Science.gov (United States)

    Gibson, G R

    1998-10-01

    The human colonic flora has both beneficial and pathogenic potentials with respect to host health. There is now much interest in manipulation of the microbiota composition in order to improve the potentially beneficial aspects. The prebiotic approach dictates that non-viable food components are specifically fermented in the colon by indigenous bacteria thought to be of positive value, e.g. bifidobacteria, lactobacilli. Any food ingredient that enters the large intestine is a candidate prebiotic. However, to be effective, selectivity of the fermentation is essential. Most current attention and success has been derived using non-digestible oligosaccharides. Types primarily being looked at include those which contain fructose, xylose, soya, galactose, glucose and mannose. In particular, fructose-containing oligosaccharides, which occur naturally in a variety of plants such as onion, asparagus, chicory, banana and artichoke, fulfil the prebiotic criteria. Various data have shown that fructo-oligosaccharides (FOS) are specifically fermented by bifidobacteria. During controlled feeding studies, ingestion of these prebiotics causes bifidobacteria to become numerically dominant in faeces. Recent studies have indicated that a FOS dose of 4 g/d is prebiotic. To exploit this concept more fully, there is a need for assessments of (a) improved determination of the gut microbiota composition and activity; (b) the use of molecular methodologies to assess accurately prebiotic identities and develop efficient bacterial probing strategies; (c) the prebiotic potential of raw and processed foods; and (d) the health consequences of dietary modulation.

  5. Alterations of the human gut microbiome in multiple sclerosis

    Science.gov (United States)

    Jangi, Sushrut; Gandhi, Roopali; Cox, Laura M.; Li, Ning; von Glehn, Felipe; Yan, Raymond; Patel, Bonny; Mazzola, Maria Antonietta; Liu, Shirong; Glanz, Bonnie L.; Cook, Sandra; Tankou, Stephanie; Stuart, Fiona; Melo, Kirsy; Nejad, Parham; Smith, Kathleen; Topçuolu, Begüm D.; Holden, James; Kivisäkk, Pia; Chitnis, Tanuja; De Jager, Philip L.; Quintana, Francisco J.; Gerber, Georg K.; Bry, Lynn; Weiner, Howard L.

    2016-01-01

    The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis. PMID:27352007

  6. Going beyond the Millennium Ecosystem Assessment: an index system of human dependence on ecosystem services.

    Science.gov (United States)

    Yang, Wu; Dietz, Thomas; Liu, Wei; Luo, Junyan; Liu, Jianguo

    2013-01-01

    The Millennium Ecosystem Assessment (MA) estimated that two thirds of ecosystem services on the earth have degraded or are in decline due to the unprecedented scale of human activities during recent decades. These changes will have tremendous consequences for human well-being, and offer both risks and opportunities for a wide range of stakeholders. Yet these risks and opportunities have not been well managed due in part to the lack of quantitative understanding of human dependence on ecosystem services. Here, we propose an index of dependence on ecosystem services (IDES) system to quantify human dependence on ecosystem services. We demonstrate the construction of the IDES system using household survey data. We show that the overall index and sub-indices can reflect the general pattern of households' dependences on ecosystem services, and their variations across time, space, and different forms of capital (i.e., natural, human, financial, manufactured, and social capitals). We support the proposition that the poor are more dependent on ecosystem services and further generalize this proposition by arguing that those disadvantaged groups who possess low levels of any form of capital except for natural capital are more dependent on ecosystem services than those with greater control of capital. The higher value of the overall IDES or sub-index represents the higher dependence on the corresponding ecosystem services, and thus the higher vulnerability to the degradation or decline of corresponding ecosystem services. The IDES system improves our understanding of human dependence on ecosystem services. It also provides insights into strategies for alleviating poverty, for targeting priority groups of conservation programs, and for managing risks and opportunities due to changes of ecosystem services at multiple scales.

  7. Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut

    DEFF Research Database (Denmark)

    Dantas, Gautam; Sommer, Morten; Degnan, Patrick H.

    2013-01-01

    The complex and intimate relationship between humans and their gut microbial communities is becoming less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-independent surveys of the composition and gene content of these communities.These studies build upon...... ofmicrobial genome and community profiling projects, and the loss-of-function and gain-of-function strategies long employed in model organisms are now being extended to microbial genes, species, and communities from the human gut. These developments promise to deepen our understanding of human gut host......–microbiota relationships and are readily applicable to other host-associated and free-living microbial communities....

  8. Metagenomics Study on the Polymorphism of Gut Microbiota and Their Function on Human Health

    DEFF Research Database (Denmark)

    Feng, Qiang

    ) were conducted to investigate the potential relationship between gut microbiome and diseases such as colorectal adenoma (CRA) and carcinoma (CRC), rheumatoid arthritis (RA) and coronary heart disease (CHD). Compared to the healthy individuals, CRA and CRC patients exhibited an enrichment of specificly...... abnormality in CHD patients. The extended integrated gene catalog of the human gut microbiome and the following association studies in a series of complex diseases highlight the strong connection between intestinal microorganisms and human health. These studies also shows a great potential of using microbiome...... diversity and functional complexity of the gut microbiome. Facilitated by the Next Generation Sequencing (NGS) technologies and the progress of bioinformatics in the past decade, we have acquired substantial achievements in metagenomic studies on human gut microbiome and established the fundamentals of our...

  9. Metagenomic insights into the human gut resistome and the forces that shape it.

    Science.gov (United States)

    Forslund, Kristoffer; Sunagawa, Shinichi; Coelho, Luis P; Bork, Peer

    2014-03-01

    We show how metagenomic analysis of the human gut antibiotic resistome, compared across large populations and against environmental or agricultural resistomes, suggests a strong anthropogenic cause behind increasing antibiotic resistance in bacteria. This area has been the subject of intense and polarized debate driven by economic and political concerns; therefore such recently available insights address an important need. We derive and compare antibiotic resistomes of human gut microbes from 832 individuals from ten different countries. We observe and describe significant differences between samples from these countries in the gut resistance potential, in line with expectations from antibiotic usage and exposure in medical and food production contexts. Our results imply roles for both of these sources in increased resistance among pathogens in recent history. In contrast, other available metadata such as age, body mass index, sex, or health status have little effect on the antibiotic resistance potential of human gut microbes. Also watch the Video Abstract.

  10. T Follicular Helper Cells Promote a Beneficial Gut Ecosystem for Host Metabolic Homeostasis by Sensing Microbiota-Derived Extracellular ATP

    Directory of Open Access Journals (Sweden)

    Lisa Perruzza

    2017-03-01

    Full Text Available The ATP-gated ionotropic P2X7 receptor regulates T follicular helper (Tfh cell abundance in the Peyer’s patches (PPs of the small intestine; deletion of P2rx7, encoding for P2X7, in Tfh cells results in enhanced IgA secretion and binding to commensal bacteria. Here, we show that Tfh cell activity is important for generating a diverse bacterial community in the gut and that sensing of microbiota-derived extracellular ATP via P2X7 promotes the generation of a proficient gut ecosystem for metabolic homeostasis. The results of this study indicate that Tfh cells play a role in host-microbiota mutualism beyond protecting the intestinal mucosa by induction of affinity-matured IgA and suggest that extracellular ATP constitutes an inter-kingdom signaling molecule important for selecting a beneficial microbial community for the host via P2X7-mediated regulation of B cell help.

  11. The Extended Nutrigenomics – Understanding the Interplay between the Genomes of Food, Gut Microbes and Human Host

    Directory of Open Access Journals (Sweden)

    Martin eKussmann

    2011-05-01

    Full Text Available Comprehensive investigation of nutritional health effects at molecular level requires understanding the interplay between three genomes, the food, the gut microbial and the human host genome. Food genomes are researched for exploitation of macro- and micronutrients as well as bioactives, with the genes coding for bioactive proteins and peptides being of central interest. The human gut microbiota encompasses a complex intestinal ecosystem with profound impact on host metabolism. It is studied at genomic, proteomic and metabolomic level. Humans are characterized at the level of: genetic predisposition and variability in terms of dietary response and direction of health trajectories; epigenetic, metabolic programming at certain life stages with health consequences later in life and for subsequent generations; and acute genomic expression as a holistic response to diet, monitored at gene transcript, protein and metabolite level.Modern nutrition science explores health aspects of bioactive food components, thereby promoting health, preventing or delaying the onset of disease, optimizing performance and assessing benefits and risks. Personalized nutrition means adapting food to individual needs, depending on the human host’s life stage, -style and -situation. Traditionally, nutrigenomics and nutri(epigenetics have been seen as the key sciences to understand human variability in preferences and requirements for diet as well as responses to nutrition. This article puts the three nutrition and health-relevant genomes into perspective, i.e. the food, the gut microbial and the human host’s genome, and calls for an extended nutrigenomics approach to build the future tools for personalized nutrition, health maintenance and disease prevention. We discuss examples of these genomes, proteomes, transcriptomes and metabolomes under the overarching term genomics that covers all Omics rather than the sole study of DNA and RNA.

  12. Ecological Interactions of Bacteria in the Human Gut

    Science.gov (United States)

    Falony, Gwen; de Vuyst, Luc

    The colon or large intestine is one of the most important organs of the human body (Macfarlane and Cummings, 1991). Moreover, its inhabitants, the colon microbiota, are the key elements of the human digestive ecosystem. The vast complexity of the human large-intestinal microbiota has inspired researchers to consider it as an organ itself, located inside the colon and acquired postnatally (Bäckhed et al., 2005; Zocco et al., 2007). From a physiologist's point of view, this image of the colon microbiota is relevant: like an organ, it is composed of different cell lineages that communicate with both one another and the host; it consumes, stores, and redistributes energy; it mediates physiologically important chemical transformations; and it is able to maintain and repair itself through self-replication (Bäckhed et al., 2005). As a microbial organ, the human colon community does not only broaden the digestive abilities of the host (Gill et al., 2006), but also influences body processes far beyond digestion (Roberfroid, 2005b; Turnbaugh et al., 2007).

  13. Dynamics and stabilization of the human gut microbiome during the first year of life

    DEFF Research Database (Denmark)

    Bäckhed, Gert Fredrik; Roswall, Josefine; Peng, Yangqing

    2015-01-01

    The gut microbiota is central to human health, but its establishment in early life has not been quantitatively and functionally examined. Applying metagenomic analysis on fecal samples from a large cohort of Swedish infants and their mothers, we characterized the gut microbiome during the first...... year of life and assessed the impact of mode of delivery and feeding on its establishment. In contrast to vaginally delivered infants, the gut microbiota of infants delivered by C-section showed significantly less resemblance to their mothers. Nutrition had a major impact on early microbiota...

  14. Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations.

    Directory of Open Access Journals (Sweden)

    Tatiana Shashkova

    Full Text Available Intestinal microbiota plays an important role in the human health. It is involved in the digestion and protects the host against external pathogens. Examination of the intestinal microbiome interactions is required for understanding of the community influence on host health. Studies of the microbiome can provide insight on methods of improving health, including specific clinical procedures for individual microbial community composition modification and microbiota correction by colonizing with new bacterial species or dietary changes.In this work we report an agent-based model of interactions between two bacterial species and between species and the gut. The model is based on reactions describing bacterial fermentation of polysaccharides to acetate and propionate and fermentation of acetate to butyrate. Antibiotic treatment was chosen as disturbance factor and used to investigate stability of the system. System recovery after antibiotic treatment was analyzed as dependence on quantity of feedback interactions inside the community, therapy duration and amount of antibiotics. Bacterial species are known to mutate and acquire resistance to the antibiotics. The ability to mutate was considered to be a stochastic process, under this suggestion ratio of sensitive to resistant bacteria was calculated during antibiotic therapy and recovery.The model confirms a hypothesis of feedbacks mechanisms necessity for providing functionality and stability of the system after disturbance. High fraction of bacterial community was shown to mutate during antibiotic treatment, though sensitive strains could become dominating after recovery. The recovery of sensitive strains is explained by fitness cost of the resistance. The model demonstrates not only quantitative dynamics of bacterial species, but also gives an ability to observe the emergent spatial structure and its alteration, depending on various feedback mechanisms. Visual version of the model shows that spatial

  15. Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions

    OpenAIRE

    Bijaya Upadhyaya; Lacey McCormack; Ali Reza Fardin-Kia; Robert Juenemann; Sailendra Nichenametla; Jeffrey Clapper; Bonny Specker; Moul Dey

    2016-01-01

    Dietary modulation of the gut microbiota impacts human health. Here we investigated the hitherto unknown effects of resistant starch type 4 (RS4) enriched diet on gut microbiota composition and short-chain fatty acid (SCFA) concentrations in parallel with host immunometabolic functions in twenty individuals with signs of metabolic syndrome (MetS). Cholesterols, fasting glucose, glycosylated haemoglobin, and proinflammatory markers in the blood as well as waist circumference and % body fat wer...

  16. Colonizing the embryonic zebrafish gut with anaerobic bacteria derived from the human gastrointestinal tract.

    Science.gov (United States)

    Toh, Michael C; Goodyear, Mara; Daigneault, Michelle; Allen-Vercoe, Emma; Van Raay, Terence J

    2013-06-01

    The zebrafish has become increasingly popular for microbiological research. It has been used as an infection model for a variety of pathogens, and is also emerging as a tool for studying interactions between a host and its resident microbial communities. The mouse microbiota has been transplanted into the zebrafish gut, but to our knowledge, there has been no attempt to introduce a bacterial community derived from the human gut. We explored two methods for colonizing the developing gut of 5-day-old germ-free zebrafish larvae with a defined anaerobic microbial community derived from a single human fecal sample. Both environmental exposure (static immersion) and direct microinjection into the gut resulted in the establishment of two species-Lactobacillus paracasei and Eubacterium limosum-from a community of 30 strains consisting of 22 anaerobic species. Of particular interest is E. limosum, which, as a strict anaerobe, represents a group of bacteria which until now have not been shown to colonize the developing zebrafish gut. Our success here indicates that further investigation of zebrafish as a tool for studying human gut microbial communities is warranted.

  17. Dynamics of the human gut microbiome in inflammatory bowel disease

    Energy Technology Data Exchange (ETDEWEB)

    Halfvarson, Jonas; Brislawn, Colin J.; Lamendella, Regina; Vázquez-Baeza, Yoshiki; Walters, William A.; Bramer, Lisa M.; D' Amato, Mauro; Bonfiglio, Ferdinando; McDonald, Daniel; Gonzalez, Antonio; McClure, Erin E.; Dunklebarger, Mitchell F.; Knight, Rob; Jansson, Janet K.

    2017-02-13

    Inflammatory bowel disease (IBD) is characterized by flares of inflammation with periodic need for increased medication and sometimes even surgery. IBD etiology is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD diseases, including ulcerative colitis (UC), colonic Crohn’s Disease (CCD), and ileal CD (ICD). Although IBD is dynamic, microbiome studies have primarily focused on single timepoints or few individuals. Here we dissect the long-term dynamic behavior of the gut microbiome in IBD and differentiate this from normal variation. Microbiomes of IBD subjects fluctuate more than healthy individuals, based on deviation from a newly-defined healthy plane (HP). ICD subjects deviated most from the HP, especially subjects with surgical resection. Intriguingly, the microbiomes of some IBD subjects periodically visited the HP then deviated away from it. Inflammation was not directly correlated with distance to the healthy plane, but there was some correlation between observed dramatic fluctuations in the gut microbiome and intensified medication due to a flare of the disease. These results help guide therapies that will re-direct the gut microbiome towards a healthy state and maintain remission in IBD.

  18. Elasticity in ecosystem services: exploring the variable relationship between ecosystems and human well-being

    Directory of Open Access Journals (Sweden)

    Tim M. Daw

    2016-06-01

    Full Text Available Although ecosystem services are increasingly recognized as benefits people obtain from nature, we still have a poor understanding of how they actually enhance multidimensional human well-being, and how well-being is affected by ecosystem change. We develop a concept of "ecosystem service elasticity" (ES elasticity that describes the sensitivity of human well-being to changes in ecosystems. ES Elasticity is a result of complex social and ecological dynamics and is context dependent, individually variable, and likely to demonstrate nonlinear dynamics such as thresholds and hysteresis. We present a conceptual framework that unpacks the chain of causality from ecosystem stocks through flows, goods, value, and shares to contribute to the well-being of different people. This framework builds on previous conceptualizations, but places multidimensional well-being of different people as the final element. This ultimately disaggregated approach emphasizes how different people access benefits and how benefits match their needs or aspirations. Applying this framework to case studies of individual coastal ecosystem services in East Africa illustrates a wide range of social and ecological factors that can affect ES elasticity. For example, food web and habitat dynamics affect the sensitivity of different fisheries ecosystem services to ecological change. Meanwhile high cultural significance, or lack of alternatives enhance ES elasticity, while social mechanisms that prevent access can reduce elasticity. Mapping out how chains are interlinked illustrates how different types of value and the well-being of different people are linked to each other and to common ecological stocks. We suggest that examining chains for individual ecosystem services can suggest potential interventions aimed at poverty alleviation and sustainable ecosystems while mapping out of interlinkages between chains can help to identify possible ecosystem service trade-offs and winners and

  19. Colonic transit time is related to bacterial metabolism and mucosal turnover in the human gut

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Hansen, Lea Benedicte Skov; Bahl, Martin Iain

    transit time and the gut microbial composition and metabolism, we assessed the colonic transit time of 98 subjects using radiopaque markers, and profiled their gut microbiota by16S rRNA gene sequencing and their urine metabolome by ultra performance liquid chromatography mass spectrometry. Based......Little is known about how colonic transit time relates to human colonic metabolism, and its importance for host health, although stool consistency, a proxy for colonic transit time, has recently been negatively associated with gut microbial richness. To address the relationships between colonic...... on correlation analyses, we show that colonic transit time is associated with overall gut microbial composition, diversity and metabolism. A relatively prolonged colonic transit time associates with high microbial species richness and a shift in colonic metabolism from carbohydrate fermentation to protein...

  20. Metagenomics Study on the Polymorphism of Gut Microbiota and Their Function on Human Health

    DEFF Research Database (Denmark)

    Feng, Qiang

    diversity and functional complexity of the gut microbiome. Facilitated by the Next Generation Sequencing (NGS) technologies and the progress of bioinformatics in the past decade, we have acquired substantial achievements in metagenomic studies on human gut microbiome and established the fundamentals of our...... and their mothers were collected and analyzed after parturition. In this study, we found that delivery methods (vaginally- or C-section-delivered) and feeding regime (breast-feeding or mixed feeding) had significant impacts on the gut microbiome of the infants. Moreover, metagenome-wide association studies (MGWAS...... low abundannce microbes in their gut, which were positively related to the red meat intake, while taxa associated with fruit and vegetable intake were depleted. Abundance changes in certain bacteria, such as Fusobacterium nucleatum and Parvimonas micra, were correlated with the different stages during...

  1. An integrated catalog of reference genes in the human gut microbiome.

    Science.gov (United States)

    Li, Junhua; Jia, Huijue; Cai, Xianghang; Zhong, Huanzi; Feng, Qiang; Sunagawa, Shinichi; Arumugam, Manimozhiyan; Kultima, Jens Roat; Prifti, Edi; Nielsen, Trine; Juncker, Agnieszka Sierakowska; Manichanh, Chaysavanh; Chen, Bing; Zhang, Wenwei; Levenez, Florence; Wang, Juan; Xu, Xun; Xiao, Liang; Liang, Suisha; Zhang, Dongya; Zhang, Zhaoxi; Chen, Weineng; Zhao, Hailong; Al-Aama, Jumana Yousuf; Edris, Sherif; Yang, Huanming; Wang, Jian; Hansen, Torben; Nielsen, Henrik Bjørn; Brunak, Søren; Kristiansen, Karsten; Guarner, Francisco; Pedersen, Oluf; Doré, Joel; Ehrlich, S Dusko; Bork, Peer; Wang, Jun

    2014-08-01

    Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.

  2. Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

    NARCIS (Netherlands)

    Heinken, Almut; Khan, M. Tanweer; Paglia, Giuseppe; Rodionov, Dmitry A.; Harmsen, Hermie J. M.; Thiele, Ines

    2014-01-01

    The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly charact

  3. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

    Science.gov (United States)

    Wu, Meng; McNulty, Nathan P.; Rodionov, Dmitry A.; Khoroshkin, Matvei S.; Griffin, Nicholas W.; Cheng, Jiye; Latreille, Phil; Kerstetter, Randall A.; Terrapon, Nicolas; Henrissat, Bernard; Osterman, Andrei L.; Gordon, Jeffrey I.

    2015-01-01

    Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in ordered sequence. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability and resilience, and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness. PMID:26430127

  4. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.

    Science.gov (United States)

    Wu, Meng; McNulty, Nathan P; Rodionov, Dmitry A; Khoroshkin, Matvei S; Griffin, Nicholas W; Cheng, Jiye; Latreille, Phil; Kerstetter, Randall A; Terrapon, Nicolas; Henrissat, Bernard; Osterman, Andrei L; Gordon, Jeffrey I

    2015-10-02

    Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness. Copyright © 2015, American Association for the Advancement of Science.

  5. Human gut microbiota changes reveal the progression of glucose intolerance.

    Science.gov (United States)

    Zhang, Xiuying; Shen, Dongqian; Fang, Zhiwei; Jie, Zhuye; Qiu, Xinmin; Zhang, Chunfang; Chen, Yingli; Ji, Linong

    2013-01-01

    To explore the relationship of gut microbiota with the development of type 2 diabetes (T2DM), we analyzed 121 subjects who were divided into 3 groups based on their glucose intolerance status: normal glucose tolerance (NGT; n = 44), prediabetes (Pre-DM; n = 64), or newly diagnosed T2DM (n = 13). Gut microbiota characterizations were determined with 16S rDNA-based high-throughput sequencing. T2DM-related dysbiosis was observed, including the separation of microbial communities and a change of alpha diversity between the different glucose intolerance statuses. To assess the correlation between metabolic parameters and microbiota diversity, clinical characteristics were also measured and a significant association between metabolic parameters (FPG, CRP) and gut microbiota was found. In addition, a total of 28 operational taxonomic units (OTUs) were found to be related to T2DM status by the Kruskal-Wallis H test, most of which were enriched in the T2DM group. Butyrate-producing bacteria (e.g. Akkermansia muciniphila ATCCBAA-835, and Faecalibacterium prausnitzii L2-6) had a higher abundance in the NGT group than in the pre-DM group. At genus level, the abundance of Bacteroides in the T2DM group was only half that of the NGT and Pre-DM groups. Previously reported T2DM-related markers were also compared with the data in this study, and some inconsistencies were noted. We found that Verrucomicrobiae may be a potential marker of T2DM as it had a significantly lower abundance in both the pre-DM and T2DM groups. In conclusion, this research provides further evidence of the structural modulation of gut microbiota in the pathogenesis of diabetes.

  6. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults

    DEFF Research Database (Denmark)

    Larsen, Nadja; Vogensen, Finn Kvist; van der Berg, Franciscus Winfried J;

    2010-01-01

    Background Recent evidence suggests that there is a link between metabolic diseases and bacterial populations in the gut. The aim of this study was to assess the differences between the composition of the intestinal microbiota in humans with type 2 diabetes and non-diabetic persons as control...... to control metabolic diseases by modifying the gut microbiota....... = 0.04). Conclusions The results of this study indicate that type 2 diabetes in humans is associated with compositional changes in intestinal microbiota. The level of glucose tolerance should be considered when linking microbiota with metabolic diseases such as obesity and developing strategies...

  7. Ecosystem Services Connect Environmental Change to Human Health Outcomes

    Energy Technology Data Exchange (ETDEWEB)

    Bayles, Brett R.; Brauman, Kate A.; Adkins, Joshua N.; Allan, Brian F.; Ellis, Alicia M.; Goldberg, Tony L.; Golden, Christopher D.; Grigsby-Toussaint, Diana S.; Myers, Samuel S.; Ofosky, Steven A.; Ricketts, Taylor H.; Ristaino, Jean B.

    2016-06-29

    Global environmental change, driven in large part by human activities, profoundly impacts the structure and functioning of Earth’s ecosystems (Millennium Ecosystem Assessment 2005). We are beginning to push beyond planetary boundaries (Steffan et al. 2015), and the consequences for human health remain largely unknown (Myers et al. 2013). Growing evidence suggests that ecological transformations can dramatically affect human health in ways that are both obvious and obscure (Myers and Patz 2009; Myers et al. 2013). The framework of ecosystem services, designed to evaluate the benefits that people derive from ecosystem products and processes, provides a compelling framework for integrating the many factors that influence the human health response to global change, as well as for integrating health impacts into broader analyses of the impacts of this change

  8. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

    DEFF Research Database (Denmark)

    Forslund, Kristoffer; Hildebrand, Falk ; Nielsen, Trine N.

    2015-01-01

    on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified......In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported1,2. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs...... for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment...

  9. The yin and yang of bacterial resilience in the human gut microbiota.

    Science.gov (United States)

    Gibson, Molly K; Pesesky, Mitchell W; Dantas, Gautam

    2014-11-25

    The human gut is home to trillions of microbes that form a symbiotic relationship with the human host. During health, the intestinal microbiota provides many benefits to the host and is generally resistant to colonization by new species; however, disruption of this complex community can lead to pathogen invasion, inflammation, and disease. Restoration and maintenance of a healthy gut microbiota composition requires effective therapies to reduce and prevent colonization of harmful bacteria (pathogens) while simultaneously promoting growth of beneficial bacteria (probiotics). Here we review the mechanisms by which the host modulates the gut community composition during health and disease, and we discuss prospects for antibiotic and probiotic therapy for restoration of a healthy intestinal community following disruption.

  10. Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

    Energy Technology Data Exchange (ETDEWEB)

    Koropatkin, Nicole M.; Martens, Eric C.; Gordon, Jeffrey I.; Smith, Thomas J. (WU); (Danforth)

    2009-01-12

    The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique {alpha}-helical protein contains an arc of aromatic residues that complements the natural helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.

  11. Neural Mechanisms of Exercise: Effects on Gut Miccrobiota and Depression.

    Science.gov (United States)

    Yuan, Ti-Fei; Ferreira Rocha, Nuno Barbosa; Paes, Flávia; Arias-Carrión, Oscar; Machado, Sergio; de Sá Filho, Alberto Souza

    2015-01-01

    Microbiota is a set of microorganisms resident in gut ecosystem that reacts to psychological stressful stimuli, and is involved in depressed or anxious status in both animals and human being. Interestingly, a series of studies have shown the effects of physical exercise on gut microbiota dynamics, suggesting that gut microbiota regulation might act as one mediator for the effects of exercise on the brain. Recent studies found that gut microbiota dynamics are also regulated by metabolism changes, such as through physical exercise or diet change. Interestingly, physical exercise modulates different population of gut bacteria in compared to food restriction or rich diet, and alleviates gut syndromes to toxin intake. Gut microbiota could as well contribute to the beneficial effects of exercise on cognition and emotion, either directly through serotonin signaling or indirectly by modulating metabolism and exercise performance.

  12. Comparative diversity analysis of gut microbiota in two different human flora-associated mouse strains.

    Science.gov (United States)

    Zhang, Xiaojing; Zeng, Benhua; Liu, Zhiwei; Liao, Zhenlin; Li, Wenxai; Wei, Hong; Fang, Xiang

    2014-09-01

    The Kunming (KM) mouse is a closed colony mouse strain widely used in Chinese pharmacology, toxicology, and microbiology research laboratories. However, few studies have examined human flora-associated (HFA) microbial communities in KM mice. In this study, HFA models were built from germ-free KM and C57BL/6J mouse strains, and gut microbial diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) and DNA sequencing. We found that the two strains of HFA mice were significantly different based on the UPGMA dendrogram and the Richness index, but dice similarity coefficients of mouse replicates were not significantly different between HFA-KM and HFA-C57BL/6J. Most of the dominant phyla of human gut microflora could be transferred into the guts of the two mouse strains. However, the predominant genus that formed in HFA-KM was Clostridium sp. and that in HFA-C57BL/6J was Blautia sp. These results imply that genotypes difference between the two mice strains is a critical factor in shaping the intestinal microflora. However, genetic differences of individuals within KM mouse populations failed to lead to individual difference in microflora. Successful generation of HFA-KM mice will facilitate studies examining how diet affects gut microbial structure, and will enable comparative studies for uncovering genetic factors that shape gut microbial communities.

  13. Mucin glycan foraging in the human gut microbiome

    OpenAIRE

    Tailford, Louise E; Crost, Emmanuelle H.; Kavanaugh, Devon; Juge, Nathalie

    2015-01-01

    The availability of host and dietary carbohydrates in the gastrointestinal (GI) tract plays a key role in shaping the structure-function of the microbiota. In particular, some gut bacteria have the ability to forage on glycans provided by the mucus layer covering the GI tract. The O-glycan structures present in mucin are diverse and complex, consisting predominantly of core 1-4 mucin-type O-glycans containing α- and β- linked N-acetyl-galactosamine, galactose and N-acetyl-glucosamine. These c...

  14. Human norovirus binding to select bacteria representative of the human gut microbiota

    Science.gov (United States)

    Almand, Erin A.; Outlaw, Janie; Jaykus, Lee-Ann

    2017-01-01

    Recent reports describe the ability of select bacterial strains to bind human norovirus, although the specificity of such interactions is unknown. The purpose of this work was to determine if a select group of bacterial species representative of human gut microbiota bind to human norovirus, and if so, to characterize the intensity and location of that binding. The bacteria screened included naturally occurring strains isolated from human stool (Klebsiella spp., Citrobacter spp., Bacillus spp., Enterococcus faecium and Hafnia alvei) and select reference strains (Staphylococcus aureus and Enterobacter cloacae). Binding in PBS was evaluated to three human norovirus strains (GII.4 New Orleans 2009 and Sydney 2012, GI.6) and two surrogate viruses (Tulane virus and Turnip Crinkle Virus (TCV)) using a suspension assay format linked to RT-qPCR for quantification. The impact of different overnight culture media prior to washing on binding efficiency in PBS was also evaluated, and binding was visualized using transmission electron microscopy. All bacteria tested bound the representative human norovirus strains with high efficiency (90% binding efficiency) (p>0.05); there was selective binding for Tulane virus and no binding observed for TCV. Binding efficiency was highest when bacteria were cultured in minimal media (90% bound), but notably decreased when cultured in enriched media (1–3 log10 unbound or 0.01 –structures, without apparent localization. The findings reported here further elucidate and inform the dynamics between human noroviruses and enteric bacteria with implications for norovirus pathogenesis. PMID:28257478

  15. The extended nutrigenomics - understanding the interplay between the genomes of food, gut microbes, and human host

    NARCIS (Netherlands)

    Kussmann, M.; Bladeren, van P.J.

    2011-01-01

    Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well

  16. Relationship between Human Gut Microbiota and Interleukin 6 Levels in Overweight and Obese Adults

    Science.gov (United States)

    Background: Gut microbial diversity and abundance can profoundly impact human health. Research has shown that obese individuals are likely to have altered microbiota compared to lean individuals. Obesity is often considered a pro-inflammatory state, however the relationship between microbiota and i...

  17. In vitro fermentation patterns of rice bran components by human gut microbiota

    Science.gov (United States)

    Rice bran is a rich source of bioactive components that can promote gastrointestinal health. However, bran is removed during polishing. Among those, feruloylated arabinoxylan oligosaccharides (FAXO) and rice bran polyphenolics (RBPP) are hypothesized to have positive impacts on human gut microbiota ...

  18. Different human gut models reveal the distinct fermentation patterns of arabinoxylan versus inulin

    NARCIS (Netherlands)

    Abbeele, P. van den; Venema, K.; Wiele, T. van de; Verstraete, W.; Possemiers, S.

    2013-01-01

    Different in vitro models have been developed to assess how food compounds affect the human gut microbiota. Using two such models (SHIME(R) and TIM-2), we compared how long-chain arabinoxylan (LC-AX), a wheat-derived potentially prebiotic fiber, and inulin (IN), a well-established prebiotic compound

  19. Transcriptional interactions suggest niche segregation among microorganisms in the human gut

    DEFF Research Database (Denmark)

    Plichta, Damian Rafal; Juncker, Agnieszka; dos Santos, Marcelo Bertalan Quintanilha

    2016-01-01

    The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species 1. Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect funct...

  20. Gut Microbiota: Impact of probiotics, prebiotics, synbiotics, pharmabiotics and postbiotics on human health

    Science.gov (United States)

    Multidisciplinary approaches enabled a better understanding of the connection between human gut microbes and health. This knowledge is rapidly changing how we think about probiotics and related –biotics (prebiotics, synbiotics, pharmabiotics and postbiotics). Functional –omics approaches are very im...

  1. The extended nutrigenomics - understanding the interplay between the genomes of food, gut microbes, and human host

    NARCIS (Netherlands)

    Kussmann, M.; Bladeren, van P.J.

    2011-01-01

    Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well

  2. Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron

    NARCIS (Netherlands)

    Lammerts van Bueren, Alicia; Mulder, Marieke; Leeuwen, Sander van; Dijkhuizen, Lubbert

    2017-01-01

    Galactooligosaccharides (GOS) are prebiotic carbohydrates that impart changes in the gut bacterial composition of formula-fed infants to more closely resemble that of breast-fed infants. Consuming human milk oligosaccharides (HMOs) provides specific bacterial strains with an advantage for colonizing

  3. A geographically-diverse collection of 418 human gut microbiome pathway genome databases

    KAUST Repository

    Hahn, Aria S.

    2017-04-11

    Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.

  4. The human gut microbiota as a reservoir for antimicrobial resistance genes

    NARCIS (Netherlands)

    Bülow, E.

    2015-01-01

    In the last decades, the emergence and spread of resistant opportunistic pathogens is compromising the effectiveness of antimicrobial therapies. Understanding the emergence and global spread of drug-resistant microorganisms is thus crucial to combat antimicrobial resistance. The human gut harbors a

  5. The human gut microbiota as a reservoir for antimicrobial resistance genes

    NARCIS (Netherlands)

    Bülow, E.

    2015-01-01

    In the last decades, the emergence and spread of resistant opportunistic pathogens is compromising the effectiveness of antimicrobial therapies. Understanding the emergence and global spread of drug-resistant microorganisms is thus crucial to combat antimicrobial resistance. The human gut harbors a

  6. Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans

    Directory of Open Access Journals (Sweden)

    Raoult Didier

    2008-12-01

    Full Text Available Abstract Background Recent studies of 16S rRNA genes in the mammalian gut microbiota distinguished a higher Firmicutes/Bacteroidetes ratio in obese individuals compared to lean individuals. This ratio was estimated using a clonal Sanger sequencing approach which is time-consuming and requires laborious data analysis. In contrast, new high-throughput pyrosequencing technology offers an inexpensive alternative to clonal Sanger sequencing and would significantly advance our understanding of obesity via the development of a clinical diagnostic method. Here we present a cost-effective method that combines 16S rRNA pyrosequencing and DNA barcodes of the Firmicutes and Bacteroidetes 16S rRNA genes to determine the Firmicutes/Bacteroidetes ratio in the gut microbiota of obese humans. Results The main result was the identification of DNA barcodes targeting the Firmicutes and Bacteroidetes phyla. These barcodes were validated using previously published 16S rRNA gut microbiota clone libraries. In addition, an accurate F/B ratio was found when the DNA barcodes were applied to short pyrosequencing reads of published gut metagenomes. Finally, the barcodes were utilized to define the F/B ratio of 16S rRNA pyrosequencing data generated from brain abscess pus and cystic fibrosis sputum. Conclusion Using DNA barcodes of Bacteroidetes and Firmicutes 16S rRNA genes combined with pyrosequencing is a cost-effective method for monitoring relevant changes in the relative abundance of Firmicutes and Bacteroidetes bacterial communities in microbial ecosystems.

  7. Colonic transit time relates to bacterial metabolism and mucosal turnover in the human gut

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Hansen, Lea Benedicte Skov; Bahl, Martin Iain

    transit time and the gut microbial composition and metabolism, we assessed the colonic transit time of 98 subjects using radiopaque markers, and profiled their gut microbiota by16S rRNA gene sequencingand their urine metabolome by ultra performance liquid chromatography mass spectrometry. Based......Little is known about how colonic transit time relates to human colonic metabolism, and its importance for host health, although stool consistency, a proxy for colonic transit time, has recently been negatively associated with gut microbial richness. To address the relationships between colonic...... on correlation analyses,we show that colonic transit time is associated with overall gutmicrobial composition, diversity and metabolism. A relatively prolonged colonic transit time associates with high microbial species richness and a shift in colonic metabolismfrom carbohydrate fermentation to protein...

  8. Teplizumab induces human gut-tropic regulatory cells in humanized mice and patients.

    Science.gov (United States)

    Waldron-Lynch, Frank; Henegariu, Octavian; Deng, Songyan; Preston-Hurlburt, Paula; Tooley, James; Flavell, Richard; Herold, Kevan C

    2012-01-25

    The development and optimization of immune therapies in patients has been hampered by the lack of preclinical models in which their effects on human immune cells can be studied. As a result, observations that have been made in preclinical studies have suggested mechanisms of drug action in murine models that have not been confirmed in clinical studies. Here, we used a humanized mouse reconstituted with human hematopoietic stem cells to study the mechanism of action of teplizumab, an Fc receptor nonbinding humanized monoclonal antibody to CD3 being tested in clinical trials for the treatment of patients with type 1 diabetes mellitus. In this model, human gut-tropic CCR6(+) T cells exited the circulation and secondary lymph organs and migrated to the small intestine. These cells then produced interleukin-10 (IL-10), a regulatory cytokine, in quantities that could be detected in the peripheral circulation. Blocking T cell migration to the small intestine with natalizumab, which prevents cellular adhesion by inhibiting α(4) integrin binding, abolished the treatment effects of teplizumab. Moreover, IL-10 expression by CD4(+)CD25(high)CCR6(+)FoxP3 cells returning to the peripheral circulation was increased in patients with type 1 diabetes treated with teplizumab. These findings demonstrate that humanized mice may be used to identify novel immunologic mechanisms that occur in patients treated with immunomodulators.

  9. The Effect of Pomegranate (Punica granatum L.) Byproducts and Ellagitannins on the Growth of Human Gut Bacteria

    Science.gov (United States)

    The consumption of pomegranate products leads to a significant accumulation of ellagitannins in the large intestines, where they interact with complex gut microflora. This study investigated the effect of pomegranate tannin constituents on the growth of various species of human gut bacteria. Our r...

  10. Study of the aminoglycoside subsistence phenotype of bacteria residing in the gut of humans and zoo animals

    NARCIS (Netherlands)

    Bello Gonzalez, Teresita; Zuidema, Tina; Bor, Gerrit; Smidt, Hauke; Passel, van M.W.J.

    2016-01-01

    Recent studies indicate that next to antibiotic resistance, bacteria are able to subsist on antibiotics as a carbon source. Here we evaluated the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics. Nine gut isolates of Escherichia coli and Cellulosim

  11. Xylo-oligosaccharides and the gut micro-ecosystem%低聚木糖与肠道微生态研究进展

    Institute of Scientific and Technical Information of China (English)

    王俊丽; 聂国兴

    2011-01-01

    The human gastrointestinal microbiota is a complex micro-ecosystem. It influences a variety of intestinal functions and plays a key role in nutrition regulation, in maintaining the integrity of the epithelial barrier, and in the development of mucosal immunity. In the normal gut the population structure of the microbiota is relatively stable and the relationship between the microbiota and the host is mutually beneficial. The complex network of host-microbe interactions is thought to prohibit colonization by intruding pathogens and any disruption of the net may lead to the loss of the microecological balance which will bring about the relevant diseases. Xylo-oligosaccharides (XOS), an emerging food additive, cause prebiotic effects when ingested as part of the diet through the modulation of colonic microflora. XOS affect the gut health and remedy diseases related to intestinal microbe dysbiosis by promoting the growth of good bacteria and diminishing the growth of deleterious microorganisms.%人类胃肠微生物区系是一复杂的微生态系统,他影响肠道的多种生理功能,并对机体的营养调控、肠道上皮屏障完整性的维持和肠黏膜免疫的发育等方面起重要作用.正常情况下,微生物与宿主间互惠共生,形成一复杂的相互作用网络,共同维护微生物群落的相对稳定和抵御致病菌在肠道的定植和入侵.当肠道微生态平衡被打破时,就会造成肠道菌群失调,导致疾病的发生.低聚木糖(xylo-oligosaccharides,XOS)是近年发展起来的一种功能性食品添加剂,作为一种食物成分被摄入后,通过调节结肠微生物区系而发挥益生元作用.XOS通过选择性增殖肠道有益菌抑制有害菌而调节人和动物胃肠功能,纠正和治疗微生态失调相关性疾病.

  12. Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome

    Directory of Open Access Journals (Sweden)

    Yue-Dong Gao

    2014-01-01

    Full Text Available The recent high-throughput sequencing has enabled the composition of Escherichia coli strains in the human microbial community to be profiled en masse. However, there are two challenges to address: (1 exploring the genetic differences between E. coli strains in human gut and (2 dynamic responses of E. coli to diverse stress conditions. As a result, we investigated the E. coli strains in human gut microbiome using deep sequencing data and reconstructed genome-wide metabolic networks for the three most common E. coli strains, including E. coli HS, UTI89, and CFT073. The metabolic models show obvious strain-specific characteristics, both in network contents and in behaviors. We predicted optimal biomass production for three models on four different carbon sources (acetate, ethanol, glucose, and succinate and found that these stress-associated genes were involved in host-microbial interactions and increased in human obesity. Besides, it shows that the growth rates are similar among the models, but the flux distributions are different, even in E. coli core reactions. The correlations between human diabetes-associated metabolic reactions in the E. coli models were also predicted. The study provides a systems perspective on E. coli strains in human gut microbiome and will be helpful in integrating diverse data sources in the following study.

  13. Human activities change marine ecosystems by altering predation risk.

    Science.gov (United States)

    Madin, Elizabeth M P; Dill, Lawrence M; Ridlon, April D; Heithaus, Michael R; Warner, Robert R

    2016-01-01

    In ocean ecosystems, many of the changes in predation risk - both increases and decreases - are human-induced. These changes are occurring at scales ranging from global to local and across variable temporal scales. Indirect, risk-based effects of human activity are known to be important in structuring some terrestrial ecosystems, but these impacts have largely been neglected in oceans. Here, we synthesize existing literature and data to explore multiple lines of evidence that collectively suggest diverse human activities are changing marine ecosystems, including carbon storage capacity, in myriad ways by altering predation risk. We provide novel, compelling evidence that at least one key human activity, overfishing, can lead to distinct, cascading risk effects in natural ecosystems whose magnitude exceeds that of presumed lethal effects and may account for previously unexplained findings. We further discuss the conservation implications of human-caused indirect risk effects. Finally, we provide a predictive framework for when human alterations of risk in oceans should lead to cascading effects and outline a prospectus for future research. Given the speed and extent with which human activities are altering marine risk landscapes, it is crucial that conservation and management policy considers the indirect effects of these activities in order to increase the likelihood of success and avoid unfortunate surprises. © 2015 John Wiley & Sons Ltd.

  14. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota

    Science.gov (United States)

    Audebert, Christophe; Even, Gaël; Cian, Amandine; Safadi, Dima El; Certad, Gabriela; Delhaes, Laurence; Pereira, Bruno; Nourrisson, Céline; Poirier, Philippe; Wawrzyniak, Ivan; Delbac, Frédéric; Morelle, Christelle; Bastien, Patrick; Lachaud, Laurence; Bellanger, Anne-Pauline; Botterel, Françoise; Candolfi, Ermanno; Desoubeaux, Guillaume; Morio, Florent; Pomares, Christelle; Rabodonirina, Meja; Loywick, Alexandre; Merlin, Sophie; Viscogliosi, Eric; Chabé, Magali

    2016-01-01

    Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross-sectional study including 48 Blastocystis-colonized patients and 48 Blastocystis-free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis-associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract. PMID:27147260

  15. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts.

    Directory of Open Access Journals (Sweden)

    Eric C Martens

    2011-12-01

    Full Text Available Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target

  16. The role of gut microbiota in health and disease : In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut

    NARCIS (Netherlands)

    von Martels, Julius Z H; Sadaghian Sadabad, Mehdi; Bourgonje, Arno R; Blokzijl, Tjasso; Dijkstra, Gerard; Faber, Klaas Nico; Harmsen, Hermie J M

    2017-01-01

    The microbiota of the gut has many crucial functions in human health. Dysbiosis of the microbiota has been correlated to a large and still increasing number of diseases. Recent studies have mostly focused on analyzing the associations between disease and an aberrant microbiota composition. Functiona

  17. Early impairment of gut function and gut flora supporting a role for alteration of gastrointestinal mucosa in human immunodeficiency virus pathogenesis

    NARCIS (Netherlands)

    Gori, Andrea; Tincati, Camilla; Rizzardini, Giuliano; Torti, Carlo; Quirino, Tiziana; Haarman, Monique; Ben Amor, Kaouther; van Schaik, Jacqueline; Vriesema, Aldwin; Knol, Jan; Marchetti, Giulia; Welling, Gjalt; Clerici, Mario

    Our results show that impairment of the gastrointestinal tracts in human immunodeficiency virus (HIV)-positive patients is present in the early phases of HIV disease. This impairment is associated with alterations in gut microbiota and intestinal inflammatory parameters. These findings support the

  18. Early impairment of gut function and gut flora supporting a role for alteration of gastrointestinal mucosa in human immunodeficiency virus pathogenesis

    NARCIS (Netherlands)

    Gori, Andrea; Tincati, Camilla; Rizzardini, Giuliano; Torti, Carlo; Quirino, Tiziana; Haarman, Monique; Ben Amor, Kaouther; van Schaik, Jacqueline; Vriesema, Aldwin; Knol, Jan; Marchetti, Giulia; Welling, Gjalt; Clerici, Mario

    2008-01-01

    Our results show that impairment of the gastrointestinal tracts in human immunodeficiency virus (HIV)-positive patients is present in the early phases of HIV disease. This impairment is associated with alterations in gut microbiota and intestinal inflammatory parameters. These findings support the h

  19. A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation

    Directory of Open Access Journals (Sweden)

    Alessandro Tanca

    2015-09-01

    Full Text Available We present a human gut metaproteomic dataset deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001573. Ten aliquots of a single stool sample collected from a healthy human volunteer were either pretreated by differential centrifugation (DC; N=5 or not centrifuged (NC; N=5. Protein extracts were then processed by filter-aided sample preparation, single-run liquid chromatography and high-resolution mass spectrometry, and peptide identification was carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform. The dataset described here is also related to the research article entitled “Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota” published in Proteomics (Tanca et al., 2015, [1].

  20. Probiotics, gut microbiota and health.

    Science.gov (United States)

    Butel, M-J

    2014-01-01

    The human gut is a huge complex ecosystem where microbiota, nutrients, and host cells interact extensively, a process crucial for the gut homeostasis and host development with a real partnership. The various bacterial communities that make up the gut microbiota have many functions including metabolic, barrier effect, and trophic functions. Hence, any dysbiosis could have negative consequences in terms of health and many diseases have been associated to impairment of the gut microbiota. These close relationships between gut microbiota, health, and disease, have led to great interest in using probiotics (i.e. live micro-organisms), or prebiotics (i.e. non-digestible substrates) to positively modulate the gut microbiota to prevent or treat some diseases. This review focuses on probiotics, their mechanisms of action, safety, and major health benefits. Health benefits remain to be proven in some indications, and further studies on the best strain(s), dose, and algorithm of administration to be used are needed. Nevertheless, probiotic administration seems to have a great potential in terms of health that justifies more research. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  1. Validation of GUt Low Density Array (GULDA), a novel qPCR approach to the study of the intestinal microbial ecosystem

    DEFF Research Database (Denmark)

    Bergström, Anders; Licht, Tine Rask; Bahl, Martin Iain

    , interesting correlations between the presences of the given species should exist at any time. In order to analyze this, we have developed GULDA, a cheap, flexible, reliable and high throughput qPCR-based gut low-density array (GULDA), which simultaneously gives the quantities of approximately 40 different...... one standard qPCR program is used for ~40 primer sets, validation is important. We present here strategies involved in verification of GULDA as a valid tool for analysis of the human gut microbiota....

  2. Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice.

    Science.gov (United States)

    Smits, Samuel A; Marcobal, Angela; Higginbottom, Steven; Sonnenburg, Justin L; Kashyap, Purna C

    2016-01-01

    Diet plays an important role in shaping the structure and function of the gut microbiota. The microbes and microbial products in turn can influence various aspects of host physiology. One promising route to affect host function and restore health is by altering the gut microbiome using dietary intervention. The individuality of the microbiome may pose a significant challenge, so we sought to determine how different microbiotas respond to the same dietary intervention in a controlled setting. We modeled gut microbiotas from three healthy donors in germfree mice and defined compositional and functional alteration following a change in dietary microbiota-accessible carbohydrates (MACs). The three gut communities exhibited responses that differed markedly in magnitude and in the composition of microbiota-derived metabolites. Adjustments in community membership did not correspond to the magnitude of changes in the microbial metabolites, highlighting potential challenges in predicting functional responses from compositional data and the need to assess multiple microbiota parameters following dietary interventions. IMPORTANCE Dietary modification has long been used empirically to modify symptoms in inflammatory bowel disease, irritable bowel syndrome, and a diverse group of diseases with gastrointestinal symptoms. There is both anecdotal and scientific evidence to suggest that individuals respond quite differently to similar dietary changes, and the highly individualized nature of the gut microbiota makes it a prime candidate for these differences. To overcome the typical confounding factors of human dietary interventions, here we employ ex-germfree mice colonized by microbiotas of three different humans to test how different microbiotas respond to a defined change in carbohydrate content of diet by measuring changes in microbiota composition and function using marker gene-based next-generation sequencing and metabolomics. Our findings suggest that the same diet has very

  3. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

    Science.gov (United States)

    Tyakht, Alexander V; Popenko, Anna S; Belenikin, Maxim S; Altukhov, Ilya A; Pavlenko, Alexander V; Kostryukova, Elena S; Selezneva, Oksana V; Larin, Andrei K; Karpova, Irina Y; Alexeev, Dmitry G

    2012-12-07

    MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors' knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org). MALINA is made freely available on the web at http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

  4. Postmortem succession of gut microbial communities in deceased human subjects

    Directory of Open Access Journals (Sweden)

    Jennifer M. DeBruyn

    2017-06-01

    Full Text Available The human microbiome has demonstrated an importance for the health and functioning in living individuals. However, the fate of the microbiome after death is less understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI. The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449 while diversity decreased (rs =  − 0.701. The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides significantly declined while Clostridiales (Clostridium, Anaerosphaera and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.

  5. Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions.

    Science.gov (United States)

    Upadhyaya, Bijaya; McCormack, Lacey; Fardin-Kia, Ali Reza; Juenemann, Robert; Nichenametla, Sailendra; Clapper, Jeffrey; Specker, Bonny; Dey, Moul

    2016-06-30

    Dietary modulation of the gut microbiota impacts human health. Here we investigated the hitherto unknown effects of resistant starch type 4 (RS4) enriched diet on gut microbiota composition and short-chain fatty acid (SCFA) concentrations in parallel with host immunometabolic functions in twenty individuals with signs of metabolic syndrome (MetS). Cholesterols, fasting glucose, glycosylated haemoglobin, and proinflammatory markers in the blood as well as waist circumference and % body fat were lower post intervention in the RS4 group compared with the control group. 16S-rRNA gene sequencing revealed a differential abundance of 71 bacterial operational taxonomic units, including the enrichment of three Bacteroides species and one each of Parabacteroides, Oscillospira, Blautia, Ruminococcus, Eubacterium, and Christensenella species in the RS4 group. Gas chromatography-mass spectrometry revealed higher faecal SCFAs, including butyrate, propionate, valerate, isovalerate, and hexanoate after RS4-intake. Bivariate analyses showed RS4-specific associations of the gut microbiota with the host metabolic functions and SCFA levels. Here we show that dietary RS4 induced changes in the gut microbiota are linked to its biological activity in individuals with signs of MetS. These findings have potential implications for dietary guidelines in metabolic health management.

  6. Gut microbiota profiling: metabolomics based approach to unravel compounds affecting human health

    Directory of Open Access Journals (Sweden)

    Pamela Vernocchi

    2016-07-01

    Full Text Available Abstract The gut microbiota is composed of a huge number of different bacteria, which produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activity is affected by environmental stimuli leading to the generation of a wide number of compounds, which influence the host metabolome and human health. Indeed, metabolic profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.

  7. Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions

    Science.gov (United States)

    Upadhyaya, Bijaya; McCormack, Lacey; Fardin-Kia, Ali Reza; Juenemann, Robert; Nichenametla, Sailendra; Clapper, Jeffrey; Specker, Bonny; Dey, Moul

    2016-01-01

    Dietary modulation of the gut microbiota impacts human health. Here we investigated the hitherto unknown effects of resistant starch type 4 (RS4) enriched diet on gut microbiota composition and short-chain fatty acid (SCFA) concentrations in parallel with host immunometabolic functions in twenty individuals with signs of metabolic syndrome (MetS). Cholesterols, fasting glucose, glycosylated haemoglobin, and proinflammatory markers in the blood as well as waist circumference and % body fat were lower post intervention in the RS4 group compared with the control group. 16S-rRNA gene sequencing revealed a differential abundance of 71 bacterial operational taxonomic units, including the enrichment of three Bacteroides species and one each of Parabacteroides, Oscillospira, Blautia, Ruminococcus, Eubacterium, and Christensenella species in the RS4 group. Gas chromatography–mass spectrometry revealed higher faecal SCFAs, including butyrate, propionate, valerate, isovalerate, and hexanoate after RS4-intake. Bivariate analyses showed RS4-specific associations of the gut microbiota with the host metabolic functions and SCFA levels. Here we show that dietary RS4 induced changes in the gut microbiota are linked to its biological activity in individuals with signs of MetS. These findings have potential implications for dietary guidelines in metabolic health management. PMID:27356770

  8. Development of gut microbiota in pigs and the effect of diet, antibiotics and other environmental factors

    NARCIS (Netherlands)

    Zhang, J.

    2014-01-01

    The intestinal tract of humans and animals is colonized by trillions of microorganisms that constitute a community or ecosystem known as the gut microbiota. The gut microbiota undergoes remarkable alterations during early age, reaches a relative stable state in adulthood, and is driven by internal

  9. Romboutsia timonensis, a new species isolated from human gut

    Directory of Open Access Journals (Sweden)

    D. Ricaboni

    2016-07-01

    Full Text Available The exploration of the human microbiome was recently revolutionized by microbial culturomics and taxonogenomics. Thanks to this approach, we report here the main characteristics of Romboutsia timonensis strain Marseille-P326, a new bacterium isolated from the right human colon by colonoscopy in a 63-year-old French man with severe anaemia with melaena.

  10. Country-specific antibiotic use practices impact the human gut resistome

    DEFF Research Database (Denmark)

    Forslund, Kristoffer; Sunagawa, Shinichi; Kultima, Jens Roat;

    2013-01-01

    Despite increasing concerns over inappropriate use of antibiotics in medicine and food production, population-level resistance transfer into the human gut microbiota has not been demonstrated beyond individual case studies. To determine the "antibiotic resistance potential" for entire microbial...... in these statistics match the observed resistance potential differences. The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year....... communities, we employ metagenomic data and quantify the totality of known resistance genes in each community (its resistome) for 68 classes and subclasses of antibiotics. In 252 fecal metagenomes from three countries, we show that the most abundant resistance determinants are those for antibiotics also used...

  11. Biotransformation of aesculin by human gut bacteria and identification of its metabolites in rat urine

    Institute of Scientific and Technical Information of China (English)

    Wei-Jun Ding; Yun Deng; Hao Feng; Wei-Wei Liu; Rong Hu; Xiang Li; Zhe-Ming Gu; Xiao-Ping Dong

    2009-01-01

    AIM:To observe the biotransformation process of a Chinese compound, aesculin, by human gut bacteria, and to identify its metabolites in rat urine. METHODS:Representative human gut bacteria were collected from 20 healthy volunteers, and then utilized in vitro to biotransform aesculin under anaerobic conditions. At 0, 2, 4, 8, 12, 16, 24, 48 and 72 h postincubation, 10 mL of culture medium was collected. Metabolites of aesculin were extracted 3 × from rat urine with methanol and analyzed by HPLC. For in vivo metabolite analysis, aesculetin (100 mg/kg) was administered to rats via stomach gavage, rat urine was collected from 6 to 48 h post-administration, and metabolite analysis was performed by LC/ESI-MS and MS/MS in the positive and negative modes. RESULTS:Human gut bacteria could completely convert aesculin into aesculetin in vitro. The biotransformation process occurred from 8 to 24 h post-incubation, with its highest activity was seen from 8 to 12 h. The in vitro process was much slower than the in vivo process. In contrast to the in vitro model, six aesculetin metabolites were identified in rat urine, including 6-hydroxy-7-glucocoumarin (M1), 6-hydroxy-7-sulf-coumarin (M2), 6, 7-digluco- coumarin (M3), 6-glc-7-gluco-coumarin (M4), 6-O-methyl-7-gluco-coumarin (M5) and 6-O-methyl-7- sulf-coumarin (M6). Of which, M2 and M6 were novel metabolites. CONCLUSION:Aesculin can be transferred into aesculetin by human gut bacteria and is furth er modifiedby the host in vivo. The diverse metabolites of aesculin may explain its pleiotropic pharmaceutical effects.

  12. An ecosystem for Linked Humanities Data

    NARCIS (Netherlands)

    Hoekstra, Rinke; Meroño-Peñuela, A.; Zijdeman, Richard L.; Rijpma, Auke; Dentler, K.; Zandhuis, I.; Adamou, Alessandro; Daga, Enrico; Isaksen, Leif

    2016-01-01

    The main promise of the digital humanities is the ability to perform scholar studies at a much broader scale, and in a much more reusable fashion. The key enabler for such studies is the availability of sufficiently well described data. For the field of socio-economic history, data usually comes in

  13. An Ecosystem for Linked Humanities Data

    NARCIS (Netherlands)

    Hoekstra, R.; Meroño-Peñuela, A.; Dentler, K.; Rijpma, A.; Zijdeman, R.; Zandhuis, I.; Sack, H.; Rizzo, G.; Steinmetz, N.; Mladenić, D.; Auer, S.; Lange, C.

    2016-01-01

    The main promise of the digital humanities is the ability to perform scholarly studies at a much broader scale, and in a much more reusable fashion. The key enabler for such studies is the availability of sufficiently well described data. For the field of socio-economic history, data usually comes

  14. A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut

    OpenAIRE

    Karlsson, Fredrik H; Ussery, David,; Nielsen, Jens; Nookaew, Intawat

    2011-01-01

    The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chloro...

  15. Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393

    KAUST Repository

    Hong, Pei-Ying

    2014-01-24

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

  16. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota.

    Science.gov (United States)

    Scanlan, Pauline D; Stensvold, Christen R; Rajilić-Stojanović, Mirjana; Heilig, Hans G H J; De Vos, Willem M; O'Toole, Paul W; Cotter, Paul D

    2014-10-01

    To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the microbial eukaryote Blastocystis, which has been implicated in the aetiology of a range of different intestinal and extra-intestinal diseases. However, prevalence data from different studies are conflicting, and crucially, there is limited information on its incidence and diversity in healthy individuals. Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n = 105) using a sensitive PCR assay. Blastocystis was present in 56% of our sample set, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected, and Blastocystis was present in a subset of individuals sampled over a period of time between 6 and 10 years, indicating that it is capable of long-term host colonisation. These results show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  17. Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393

    Science.gov (United States)

    Hong, Pei-Ying; Iakiviak, Michael; Dodd, Dylan; Zhang, Meiling; Mackie, Roderick I.

    2014-01-01

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut. PMID:24463968

  18. A novel transcriptional regulator of L-arabinose utilization in human gut bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Changsoo; Tesar, Christine; Li, Xiaoqing; Kim, Youngchang; Rodionov, Dmitry A.; Joachimiak, Andrzej

    2015-12-02

    Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.

  19. Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.

    Science.gov (United States)

    Hong, Pei-Ying; Iakiviak, Michael; Dodd, Dylan; Zhang, Meiling; Mackie, Roderick I; Cann, Isaac

    2014-04-01

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

  20. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families.

    Directory of Open Access Journals (Sweden)

    Kyle Ellrott

    2010-06-01

    Full Text Available The microbes that inhabit particular environments must be able to perform molecular functions that provide them with a competitive advantage to thrive in those environments. As most molecular functions are performed by proteins and are conserved between related proteins, we can expect that organisms successful in a given environmental niche would contain protein families that are specific for functions that are important in that environment. For instance, the human gut is rich in polysaccharides from the diet or secreted by the host, and is dominated by Bacteroides, whose genomes contain highly expanded repertoire of protein families involved in carbohydrate metabolism. To identify other protein families that are specific to this environment, we investigated the distribution of protein families in the currently available human gut genomic and metagenomic data. Using an automated procedure, we identified a group of protein families strongly overrepresented in the human gut. These not only include many families described previously but also, interestingly, a large group of previously unrecognized protein families, which suggests that we still have much to discover about this environment. The identification and analysis of these families could provide us with new information about an environment critical to our health and well being.

  1. Members of the human gut microbiota involved in recovery from Vibrio cholerae infection

    Science.gov (United States)

    Hsiao, Ansel; Shamsir Ahmed, A.M.; Subramanian, Sathish; Griffin, Nicholas W.; Drewry, Lisa L.; Petri, William A.; Haque, Rashidul; Ahmed, Tahmeed; Gordon, Jeffrey I.

    2015-01-01

    Given the global burden of diarrheal diseases1, it is important to understand how members of the gut microbiota affect the risk for, course of, and recovery from disease in children and adults. The acute, voluminous diarrhea caused by Vibrio cholerae represents a dramatic example of enteropathogen invasion and gut microbial community disruption. We have conducted a detailed time-series metagenomic study of fecal microbiota collected during the acute diarrheal and recovery phases of cholera in a cohort of Bangladeshi adults living in an area with a high burden of disease2. We find that recovery is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of assembly/maturation of the gut microbiota in healthy Bangladeshi children3. To define underlying mechanisms, we introduced into gnotobiotic mice an artificial community that was composed of human gut bacterial species that directly correlate with recovery from cholera in adults and are indicative of normal microbiota maturation in healthy Bangladeshi children3. One of the species, Ruminococcus obeum, exhibited consistent increases in its relative abundance upon V. cholerae infection of the mice. Follow-up analyses, including mono- and co-colonization studies, established that R. obeum restricts V. cholerae colonization, that R. obeum luxS [autoinducer-2 (AI-2) synthase] expression and AI-2 production increase significantly with V. cholerae invasion, and that R. obeum AI-2 causes quorum-sensing mediated repression of several V. cholerae colonization factors. Co-colonization with V. cholerae mutants disclosed that R. obeum AI-2 reduces Vibrio colonization/pathogenicity through a novel pathway that does not depend on the V. cholerae AI-2 sensor, LuxP. The approach described can be used to mine the gut microbiota of Bangladeshi or other populations for members that use autoinducers and/or other mechanisms to limit colonization with V. cholerae, or conceivably other

  2. Members of the human gut microbiota involved in recovery from Vibrio cholerae infection.

    Science.gov (United States)

    Hsiao, Ansel; Ahmed, A M Shamsir; Subramanian, Sathish; Griffin, Nicholas W; Drewry, Lisa L; Petri, William A; Haque, Rashidul; Ahmed, Tahmeed; Gordon, Jeffrey I

    2014-11-20

    Given the global burden of diarrhoeal diseases, it is important to understand how members of the gut microbiota affect the risk for, course of, and recovery from disease in children and adults. The acute, voluminous diarrhoea caused by Vibrio cholerae represents a dramatic example of enteropathogen invasion and gut microbial community disruption. Here we conduct a detailed time-series metagenomic study of faecal microbiota collected during the acute diarrhoeal and recovery phases of cholera in a cohort of Bangladeshi adults living in an area with a high burden of disease. We find that recovery is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of assembly/maturation of the gut microbiota in healthy Bangladeshi children. To define the underlying mechanisms, we introduce into gnotobiotic mice an artificial community composed of human gut bacterial species that directly correlate with recovery from cholera in adults and are indicative of normal microbiota maturation in healthy Bangladeshi children. One of the species, Ruminococcus obeum, exhibits consistent increases in its relative abundance upon V. cholerae infection of the mice. Follow-up analyses, including mono- and co-colonization studies, establish that R. obeum restricts V. cholerae colonization, that R. obeum luxS (autoinducer-2 (AI-2) synthase) expression and AI-2 production increase significantly with V. cholerae invasion, and that R. obeum AI-2 causes quorum-sensing-mediated repression of several V. cholerae colonization factors. Co-colonization with V. cholerae mutants discloses that R. obeum AI-2 reduces Vibrio colonization/pathogenicity through a novel pathway that does not depend on the V. cholerae AI-2 sensor, LuxP. The approach described can be used to mine the gut microbiota of Bangladeshi or other populations for members that use autoinducers and/or other mechanisms to limit colonization with V. cholerae, or conceivably other enteropathogens.

  3. Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species.

    Science.gov (United States)

    Perez-Muñoz, Maria Elisa; Joglekar, Payal; Shen, Yi-Ju; Shen, Yi-Ji; Chang, Kuan Y; Peterson, Daniel A

    2015-01-01

    Host T cell reactivity toward gut bacterial epitopes has been recognized as part of disease pathogenesis. However, the specificity of T cells that recognize this vast number of epitopes has not yet been well described. After colonizing a C57BL/6J germ-free mouse with the human gut symbiotic bacteria Bacteroides thetaiotaomicron, we isolated a T cell that recognized these bacteria in vitro. Using this T cell, we mapped the first known non-carbohydrate T cell epitope within the phylum Bacteroidetes. The T cell also reacted to two other additional Bacteroides species. We identified the peptide that stimulated the T cell by using a genetic approach. Genomic data from the epitope-positive and epitope-negative bacteria explain the cross-reactivity of the T cell to multiple species. This epitope degeneracy should shape our understanding of the T cell repertoire stimulated by the complex microbiome residing in the gastrointestinal tract in both healthy and disease states.

  4. Crowdsourcing the human gut:Is crowdsourcing also 'citizen science'?

    OpenAIRE

    Del Savio, Lorenzo; Prainsack, Barbara; Buyx, Alena

    2016-01-01

    The participation of non-professionally trained people in so-called citizen science (CS) projects is a much discussed topic at the moment. Frequently, however, the contribution of citizens is limited to only a few narrow tasks. Focusing on an initiative dedicated to the study of the human microbiome, this paper describes such a case where citizen participation is limited to the provision of funding, samples, and personal data. Researchers opted for a crowdsourced approaches because other form...

  5. Human Gut-On-A-Chip Supports Polarized Infection of Coxsackie B1 Virus In Vitro

    Science.gov (United States)

    Papafragkou, Efstathia; Weaver, James C.; Ferrante, Thomas C.; Bahinski, Anthony; Elkins, Christopher A.; Kulka, Michael; Ingber, Donald E.

    2017-01-01

    Analysis of enterovirus infection is difficult in animals because they express different virus receptors than humans, and static cell culture systems do not reproduce the physical complexity of the human intestinal epithelium. Here, using coxsackievirus B1 (CVB1) as a prototype enterovirus strain, we demonstrate that human enterovirus infection, replication and infectious virus production can be analyzed in vitro in a human Gut-on-a-Chip microfluidic device that supports culture of highly differentiated human villus intestinal epithelium under conditions of fluid flow and peristalsis-like motions. When CVB1 was introduced into the epithelium-lined intestinal lumen of the device, virions entered the epithelium, replicated inside the cells producing detectable cytopathic effects (CPEs), and both infectious virions and inflammatory cytokines were released in a polarized manner from the cell apex, as they could be detected in the effluent from the epithelial microchannel. When the virus was introduced via a basal route of infection (by inoculating virus into fluid flowing through a parallel lower ‘vascular’ channel separated from the epithelial channel by a porous membrane), significantly lower viral titers, decreased CPEs, and delayed caspase-3 activation were observed; however, cytokines continued to be secreted apically. The presence of continuous fluid flow through the epithelial lumen also resulted in production of a gradient of CPEs consistent with the flow direction. Thus, the human Gut-on-a-Chip may provide a suitable in vitro model for enteric virus infection and for investigating mechanisms of enterovirus pathogenesis. PMID:28146569

  6. Human Gut-On-A-Chip Supports Polarized Infection of Coxsackie B1 Virus In Vitro.

    Science.gov (United States)

    Villenave, Remi; Wales, Samantha Q; Hamkins-Indik, Tiama; Papafragkou, Efstathia; Weaver, James C; Ferrante, Thomas C; Bahinski, Anthony; Elkins, Christopher A; Kulka, Michael; Ingber, Donald E

    2017-01-01

    Analysis of enterovirus infection is difficult in animals because they express different virus receptors than humans, and static cell culture systems do not reproduce the physical complexity of the human intestinal epithelium. Here, using coxsackievirus B1 (CVB1) as a prototype enterovirus strain, we demonstrate that human enterovirus infection, replication and infectious virus production can be analyzed in vitro in a human Gut-on-a-Chip microfluidic device that supports culture of highly differentiated human villus intestinal epithelium under conditions of fluid flow and peristalsis-like motions. When CVB1 was introduced into the epithelium-lined intestinal lumen of the device, virions entered the epithelium, replicated inside the cells producing detectable cytopathic effects (CPEs), and both infectious virions and inflammatory cytokines were released in a polarized manner from the cell apex, as they could be detected in the effluent from the epithelial microchannel. When the virus was introduced via a basal route of infection (by inoculating virus into fluid flowing through a parallel lower 'vascular' channel separated from the epithelial channel by a porous membrane), significantly lower viral titers, decreased CPEs, and delayed caspase-3 activation were observed; however, cytokines continued to be secreted apically. The presence of continuous fluid flow through the epithelial lumen also resulted in production of a gradient of CPEs consistent with the flow direction. Thus, the human Gut-on-a-Chip may provide a suitable in vitro model for enteric virus infection and for investigating mechanisms of enterovirus pathogenesis.

  7. Capturing One of the Human Gut Microbiome's Most Wanted

    DEFF Research Database (Denmark)

    Jeraldo, Patricio; Hernandez, Alvaro; Nielsen, Henrik Bjørn

    2016-01-01

    The role of the microbiome in health and disease is attracting great attention, yet we still know little about some of the most prevalent microorganisms inside our bodies. Several years ago, Human Microbiome Project (HMP) researchers generated a list of "most wanted" taxa: bacteria both prevalent...... allowed us to assemble "most wanted" genomes from metagenomic data collected from four stool samples. Using a combination of both de novo and guided assembly methods, we assembled and binned over 100 genomes from an initial data set of over 1,300 Gbp. One of these genome bins, which met HMP's criteria...

  8. The Gut Microbiota and Irritable Bowel Syndrome: Friend or Foe?

    OpenAIRE

    2012-01-01

    Progress in the understanding of the pathophysiology of irritable bowel syndrome (IBS), once thought to be a purely psychosomatic disease, has advanced considerably and low-grade inflammation and changes in the gut microbiota now feature as potentially important. The human gut harbours a huge microbial ecosystem, which is equipped to perform a variety of functions such as digestion of food, metabolism of drugs, detoxification of toxic compounds, production of essential vitamins, prevention of...

  9. [Ecosystem services supply and consumption and their relationships with human well-being].

    Science.gov (United States)

    Wang, Da-Shang; Zheng, Hua; Ouyang, Zhi-Yun

    2013-06-01

    Sustainable ecosystem services supply is the basis of regional sustainable development, and human beings can satisfy and improve their well-being through ecosystem services consumption. To understand the relationships between ecosystem services supply and consumption and human well-being is of vital importance for coordinating the relationships between the conservation of ecosystem services and the improvement of human well-being. This paper summarized the diversity, complexity, and regionality of ecosystem services supply, the diversity and indispensability of ecosystem services consumption, and the multi-dimension, regionality, and various evaluation indices of human well-being, analyzed the uncertainty and multi-scale correlations between ecosystem services supply and consumption, and elaborated the feedback and asynchronous relationships between ecosystem services and human well-being. Some further research directions for the relationships between ecosystem services supply and consumption and human well-being were recommended.

  10. ESTIMATING SUSTAINABILITY OF A SIMPLE HUMAN SOCIETY AND ITS ASSOCIATED ECOSYSTEM USING RESILIENCE AND FISHER INFORMATION

    Science.gov (United States)

    Sustainability applies to integrated systems comprising humans and the rest of nature. To be considered sustainable, human components (society, economy, law, etc.) that interact with ecosystems cannot decrease the resilience of ecosystem structures and functions (trophic linkage...

  11. ESTIMATING SUSTAINABILITY OF A SIMPLE HUMAN SOCIETY AND ITS ASSOCIATED ECOSYSTEM USING RESILIENCE AND FISHER INFORMATION

    Science.gov (United States)

    Sustainability applies to integrated systems comprising humans and the rest of nature. To be considered sustainable, human components (society, economy, law, etc.) that interact with ecosystems cannot decrease the resilience of ecosystem structures and functions (trophic linkage...

  12. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes.

    Science.gov (United States)

    Larsbrink, Johan; Rogers, Theresa E; Hemsworth, Glyn R; McKee, Lauren S; Tauzin, Alexandra S; Spadiut, Oliver; Klinter, Stefan; Pudlo, Nicholas A; Urs, Karthik; Koropatkin, Nicole M; Creagh, A Louise; Haynes, Charles A; Kelly, Amelia G; Cederholm, Stefan Nilsson; Davies, Gideon J; Martens, Eric C; Brumer, Harry

    2014-02-27

    A well-balanced human diet includes a significant intake of non-starch polysaccharides, collectively termed 'dietary fibre', from the cell walls of diverse fruits and vegetables. Owing to the paucity of alimentary enzymes encoded by the human genome, our ability to derive energy from dietary fibre depends on the saccharification and fermentation of complex carbohydrates by the massive microbial community residing in our distal gut. The xyloglucans (XyGs) are a ubiquitous family of highly branched plant cell wall polysaccharides whose mechanism(s) of degradation in the human gut and consequent importance in nutrition have been unclear. Here we demonstrate that a single, complex gene locus in Bacteroides ovatus confers XyG catabolism in this common colonic symbiont. Through targeted gene disruption, biochemical analysis of all predicted glycoside hydrolases and carbohydrate-binding proteins, and three-dimensional structural determination of the vanguard endo-xyloglucanase, we reveal the molecular mechanisms through which XyGs are hydrolysed to component monosaccharides for further metabolism. We also observe that orthologous XyG utilization loci (XyGULs) serve as genetic markers of XyG catabolism in Bacteroidetes, that XyGULs are restricted to a limited number of phylogenetically diverse strains, and that XyGULs are ubiquitous in surveyed human metagenomes. Our findings reveal that the metabolism of even highly abundant components of dietary fibre may be mediated by niche species, which has immediate fundamental and practical implications for gut symbiont population ecology in the context of human diet, nutrition and health.

  13. The Impact of Diet and Lifestyle on Gut Microbiota and Human Health

    Directory of Open Access Journals (Sweden)

    Michael A. Conlon

    2014-12-01

    Full Text Available There is growing recognition of the role of diet and other environmental factors in modulating the composition and metabolic activity of the human gut microbiota, which in turn can impact health. This narrative review explores the relevant contemporary scientific literature to provide a general perspective of this broad area. Molecular technologies have greatly advanced our understanding of the complexity and diversity of the gut microbial communities within and between individuals. Diet, particularly macronutrients, has a major role in shaping the composition and activity of these complex populations. Despite the body of knowledge that exists on the effects of carbohydrates there are still many unanswered questions. The impacts of dietary fats and protein on the gut microbiota are less well defined. Both short- and long-term dietary change can influence the microbial profiles, and infant nutrition may have life-long consequences through microbial modulation of the immune system. The impact of environmental factors, including aspects of lifestyle, on the microbiota is particularly poorly understood but some of these factors are described. We also discuss the use and potential benefits of prebiotics and probiotics to modify microbial populations. A description of some areas that should be addressed in future research is also presented.

  14. HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats.

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    Phoebe Lin

    Full Text Available The HLA-B27 gene is a major risk factor for clinical diseases including ankylosing spondylitis, acute anterior uveitis, reactive arthritis, and psoriatic arthritis, but its mechanism of risk enhancement is not completely understood. The gut microbiome has recently been shown to influence several HLA-linked diseases. However, the role of HLA-B27 in shaping the gut microbiome has not been previously investigated. In this study, we characterize the differences in the gut microbiota mediated by the presence of the HLA-B27 gene. We identified differences in the cecal microbiota of Lewis rats transgenic for HLA-B27 and human β2-microglobulin (hβ2m, compared with wild-type Lewis rats, using biome representational in situ karyotyping (BRISK and 16S rRNA gene sequencing. 16S sequencing revealed significant differences between transgenic animals and wild type animals by principal coordinates analysis. Further analysis of the data set revealed an increase in Prevotella spp. and a decrease in Rikenellaceae relative abundance in the transgenic animals compared to the wild type animals. By BRISK analysis, species-specific differences included an increase in Bacteroides vulgatus abundance in HLA-B27/hβ2m and hβ2m compared to wild type rats. The finding that HLA-B27 is associated with altered cecal microbiota has not been shown before and can potentially provide a better understanding of the clinical diseases associated with this gene.

  15. Eden in Peril: Impact of Humans on Pacific Island Ecosystems

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    Moshe Rapaport

    2006-05-01

    Full Text Available Islands have often been cited as models of human impact upon the environment. With high rates of endemism and other unique characteristics, island ecosystems are subject to dramatic perturbation. The arrival of humans in Near Oceania during the Pleistocene led swiftly to a series of fauna extinctions. In the New Guinea Highlands clearing and tending of wild plants gave rise to tree and root crop agriculture, intensive cultivation technology, and anthropogenic grasslands. By 3600 BP (Before Present, Lapita settlers had reached Remote Oceania, leading to deforestation and declines in birds and other species. European contact introduced new biota and new technology, with significant consequences for island environments and societies. Questions have been raised concerning the impact of climate change on island ecosystems. Population growth plays a significant role in environmental degradation, though not necessarily as a proximate cause. The Tikopian arboriculture system provides one of several Oceanic models of sustainability.

  16. Understanding Complex Human Ecosystems: The Case of Ecotourism on Bonaire

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    Thomas Abel

    2003-12-01

    Full Text Available It is suggested that ecotourism development on the island of Bonaire can be productively understood as a perturbation of a complex human ecosystem. Inputs associated with ecotourism have fueled transformations of the island ecology and sociocultural system. The results of this study indicate that Bonaire's social and economic hierarchy is approaching a new, stable systems state following a 50-yr transition begun by government and industry that stabilized with the appearance of ecotourism development and population growth. Ecotourism can be understood to have "filled in" the middle of the production hierarchy of Bonaire. Interpreted from this perspective, population growth has completed the transformation by expanding into production niches at smaller scales in the production hierarchy. Both a consequence and a cause, ecotourism has transformed the island's social structure and demography. The theory and methods applied in this case study of interdisciplinary research in the field of human ecosystems are also presented.

  17. Pantoea intestinalis sp. nov., isolated from the human gut.

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    Prakash, Om; Nimonkar, Yogesh; Vaishampayan, Ankita; Mishra, Mrinal; Kumbhare, Shreyas; Josef, Neetha; Shouche, Yogesh S

    2015-10-01

    A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on trypticase soy agar and showed optimum growth at 35 °C. Strain 29Y89BT showed highest 16S rRNA gene sequence similarity to Pantoea gaviniae A18/07T (98.4 %) followed by Pantoea calida 1400/07T (97.2 %). Multi-locus sequence analysis using atpD (ATP synthase β subunit), gyrB (DNA gyrase), infB (initiation translation factor 2) and rpoB (RNA polymerase β subunit) genes also supported the result of 16S rRNA gene sequence based phylogeny. Strain 29Y89BT showed 62 and 40.7 % DNA-DNA relatedness with P. calida DSM 22759T and P. gaviniae DSM 22758T. Strain 29Y89BT contained C17  : 0 cyclo, C19  : 0 cyclo ω8c, C16 : 0, C14 : 0 and C12 : 0 as predominant fatty acids. In addition, strain 29Y89BT showed physiological and phenotypic differences from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T. The polar lipid profile mainly comprised phospholipids. The DNA G+C content was 59.1 mol%. Thus, based on the findings of the current study, strain 29Y89BT showed clear delineations from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T, and is thus considered to represent a novel species of the genus Pantoea, for which the name Pantoea intestinalis sp. nov. is proposed. The type strain is 29Y89BT ( = DSM 28113T = MCC 2554T).

  18. In vitro fermentation of alginate and its derivatives by human gut microbiota.

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    Li, Miaomiao; Li, Guangsheng; Shang, Qingsen; Chen, Xiuxia; Liu, Wei; Pi, Xiong'e; Zhu, Liying; Yin, Yeshi; Yu, Guangli; Wang, Xin

    2016-06-01

    Alginate (Alg) has a long history as a food ingredient in East Asia. However, the human gut microbes responsible for the degradation of alginate and its derivatives have not been fully understood yet. Here, we report that alginate and the low molecular polymer derivatives of mannuronic acid oligosaccharides (MO) and guluronic acid oligosaccharides (GO) can be completely degraded and utilized at various rates by fecal microbiota obtained from six Chinese individuals. However, the derivative of propylene glycol alginate sodium sulfate (PSS) was not hydrolyzed. The bacteria having a pronounced ability to degrade Alg, MO and GO were isolated from human fecal samples and were identified as Bacteroides ovatus, Bacteroides xylanisolvens, and Bacteroides thetaiotaomicron. Alg, MO and GO can increase the production level of short chain fatty acids (SCFA), but GO generates the highest level of SCFA. Our data suggest that alginate and its derivatives could be degraded by specific bacteria in the human gut, providing the basis for the impacts of alginate and its derivates as special food additives on human health. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Urban transitions: on urban resilience and human-dominated ecosystems.

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    Ernstson, Henrik; van der Leeuw, Sander E; Redman, Charles L; Meffert, Douglas J; Davis, George; Alfsen, Christine; Elmqvist, Thomas

    2010-12-01

    Urbanization is a global multidimensional process paired with increasing uncertainty due to climate change, migration of people, and changes in the capacity to sustain ecosystem services. This article lays a foundation for discussing transitions in urban governance, which enable cities to navigate change, build capacity to withstand shocks, and use experimentation and innovation in face of uncertainty. Using the three concrete case cities--New Orleans, Cape Town, and Phoenix--the article analyzes thresholds and cross-scale interactions, and expands the scale at which urban resilience has been discussed by integrating the idea from geography that cities form part of "system of cities" (i.e., they cannot be seen as single entities). Based on this, the article argues that urban governance need to harness social networks of urban innovation to sustain ecosystem services, while nurturing discourses that situate the city as part of regional ecosystems. The article broadens the discussion on urban resilience while challenging resilience theory when addressing human-dominated ecosystems. Practical examples of harnessing urban innovation are presented, paired with an agenda for research and policy.

  20. Comparative biogeochemistry-ecosystem-human interactions on dynamic continental margins

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    Levin, Lisa A.; Liu, Kon-Kee; Emeis, Kay-Christian; Breitburg, Denise L.; Cloern, James; Deutsch, Curtis; Giani, Michele; Goffart, Anne; Hofmann, Eileen E.; Lachkar, Zouhair; Limburg, Karin; Liu, Su-Mei; Montes, Enrique; Naqvi, Wajih; Ragueneau, Olivier; Rabouille, Christophe; Sarkar, Santosh Kumar; Swaney, Dennis P.; Wassman, Paul; Wishner, Karen F.

    2014-01-01

    The ocean’s continental margins face strong and rapid change, forced by a combination of direct human activity, anthropogenic CO2-induced climate change, and natural variability. Stimulated by discussions in Goa, India at the IMBER IMBIZO III, we (1) provide an overview of the drivers of biogeochemical variation and change on margins, (2) compare temporal trends in hydrographic and biogeochemical data across different margins (3) review ecosystem responses to these changes, (4) highlight the importance of margin time series for detecting and attributing change and (5) examine societal responses to changing margin biogeochemistry and ecosystems. We synthesize information over a wide range of margin settings in order to identify the commonalities and distinctions among continental margin ecosystems. Key drivers of biogeochemical variation include long-term climate cycles, CO2-induced warming, acidification, and deoxygenation, as well as sea level rise, eutrophication, hydrologic and water cycle alteration, changing land use, fishing, and species invasion. Ecosystem responses are complex and impact major margin services including primary production, fisheries production, nutrient cycling, shoreline protection, chemical buffering, and biodiversity. Despite regional differences, the societal consequences of these changes are unarguably large and mandate coherent actions to reduce, mitigate and adapt to multiple stressors on continental margins.

  1. Direct sequencing of human gut virome fractions obtained by flow cytometry

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    Mária eDžunková

    2015-09-01

    Full Text Available The sequence assembly of the human gut virome encounters several difficulties. A high proportion of human and bacterial matches is detected in purified viral samples. Viral DNA extraction results in a low DNA concentration, which does not reach the minimal limit required for sequencing library preparation. Therefore, the viromes are usually enriched by whole genome amplification, which is, however, prone to the development of chimeras and amplification bias. In addition, as there is a very wide diversity of gut viral species, very extensive sequencing efforts must be made for the assembling of whole viral genomes. We present an approach to improve human gut virome assembly by employing a more precise preparation of a viral sample before sequencing. Particles present in a virome previously filtered through 0.2 µm pores were further divided into groups in accordance with their size and DNA content by fluorescence activated cell sorting (FACS. One selected viral fraction was sequenced excluding the whole genome amplification step, so that unbiased sequences with high reliability were obtained.The DNA extracted from the 314 viral particles of the selected fraction was assembled into 34 contigs longer than 1,000 bp. This represents an increase to the number of assembled long contigs per sequenced Gb in comparison with other studies where non-fractioned viromes are sequenced. Seven of these contigs contained open reading frames (ORFs with explicit matches to proteins related to bacteriophages. The remaining contigs also possessed uncharacterized ORFs with bacteriophage-related domains. When the particles that are present in the filtered viromes are sorted into smaller groups by FACS, large pieces of viral genomes can be recovered easily. This approach has several advantages over the conventional sequencing of non-fractioned viromes: non-viral contamination is reduced and the sequencing efforts required for viral assembly are minimised.

  2. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression.

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    Fisher, Charles K; Mehta, Pankaj

    2014-01-01

    Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1) a correlation between the abundances of two species does not imply that those species are interacting, 2) the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3) errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called "errors-in-variables". Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct "keystone species", Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in the human gut

  3. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression.

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    Charles K Fisher

    Full Text Available Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1 a correlation between the abundances of two species does not imply that those species are interacting, 2 the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3 errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called "errors-in-variables". Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS, that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct "keystone species", Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in

  4. Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

    Science.gov (United States)

    Fisher, Charles K.; Mehta, Pankaj

    2014-01-01

    Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1) a correlation between the abundances of two species does not imply that those species are interacting, 2) the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3) errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called “errors-in-variables”. Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct “keystone species”, Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in the human

  5. Modulation of the human gut microbiota by dietary fibres occurs at the species level.

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    Chung, Wing Sun Faith; Walker, Alan W; Louis, Petra; Parkhill, Julian; Vermeiren, Joan; Bosscher, Douwina; Duncan, Sylvia H; Flint, Harry J

    2016-01-11

    Dietary intake of specific non-digestible carbohydrates (including prebiotics) is increasingly seen as a highly effective approach for manipulating the composition and activities of the human gut microbiota to benefit health. Nevertheless, surprisingly little is known about the global response of the microbial community to particular carbohydrates. Recent in vivo dietary studies have demonstrated that the species composition of the human faecal microbiota is influenced by dietary intake. There is now potential to gain insights into the mechanisms involved by using in vitro systems that produce highly controlled conditions of pH and substrate supply. We supplied two alternative non-digestible polysaccharides as energy sources to three different human gut microbial communities in anaerobic, pH-controlled continuous-flow fermentors. Community analysis showed that supply of apple pectin or inulin resulted in the highly specific enrichment of particular bacterial operational taxonomic units (OTUs; based on 16S rRNA gene sequences). Of the eight most abundant Bacteroides OTUs detected, two were promoted specifically by inulin and six by pectin. Among the Firmicutes, Eubacterium eligens in particular was strongly promoted by pectin, while several species were stimulated by inulin. Responses were influenced by pH, which was stepped up, and down, between 5.5, 6.0, 6.4 and 6.9 in parallel vessels within each experiment. In particular, several experiments involving downshifts to pH 5.5 resulted in Faecalibacterium prausnitzii replacing Bacteroides spp. as the dominant sequences observed. Community diversity was greater in the pectin-fed than in the inulin-fed fermentors, presumably reflecting the differing complexity of the two substrates. We have shown that particular non-digestible dietary carbohydrates have enormous potential for modifying the gut microbiota, but these modifications occur at the level of individual strains and species and are not easily predicted a priori

  6. Complementary methodologies to investigate human gut microbiota in host health, working towards integrative systems biology.

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    Méndez-García, Celia; Barbas, Coral; Ferrer, Manuel; Rojo, David

    2017-09-05

    In 1680, Antonie van Leewenhoek noted compositional differences in his oral and fecal microbiota, pioneering the study of the diversity of the human microbiome. From Leewenhoek to modern successful attempts of changing the gut microbiota landscape to cure disease, there has been an exponential increase in the recognition of our resident microbes as part of ourselves. Thus, the human host and microbiome have evolved in parallel to configure a balanced system in which microbes survive in homeostasis with our innate and acquired immune system, unless disease occurs. A growing number of studies have demonstrated a correlation between the presence/absence of microbial taxa, and some of their functional molecules (i.e. genes, proteins, and metabolites), with health and disease states. Nevertheless, misleading experimental design on human subjects, and the cost and lack of standardized animal models pose challenges to answering the question of whether changes in the microbiome composition are cause or consequence of a certain biological state. In this review, we evaluate the state of the art of methodologies that enable the study of the gut microbiome, encouraging a change in broadly used analytic strategies by choosing effector molecules (proteins, metabolites) in combination with coding nucleic acids. We further explore microbial and effector microbial products imbalances that relate to disease and health. Copyright © 2017 American Society for Microbiology.

  7. Different human gut models reveal the distinct fermentation patterns of Arabinoxylan versus inulin.

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    Van den Abbeele, Pieter; Venema, Koen; Van de Wiele, Tom; Verstraete, Willy; Possemiers, Sam

    2013-10-16

    Different in vitro models have been developed to assess how food compounds affect the human gut microbiota. Using two such models (SHIME(R) and TIM-2), we compared how long-chain arabinoxylan (LC-AX), a wheat-derived potentially prebiotic fiber, and inulin (IN), a well-established prebiotic compound, modulate SCFA production and bifidobacteria composition. While both the SHIME and TIM-2 differ in experimental design, they both demonstrated that LC-AX and IN specifically increased the health-promoting metabolites propionate and butyrate, respectively. Furthermore, LC-AX stimulated Bifidobacterium longum, while IN stimulated other bifidobacteria including Bifidobacterium adolescentis. The SHIME experiment also revealed that effects of LC-AX were more persistent during the 2-week wash-out period. These results confirm a recent in vivo study, during which humanized rats were treated with the same LC-AX/IN. In conclusion, results from different human gut models suggest that, besides IN, LC-AX are promising prebiotic candidates with high specificity toward Bifidobacterium longum and a selective propionate increase.

  8. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria.

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    Cecchini, Davide A; Laville, Elisabeth; Laguerre, Sandrine; Robe, Patrick; Leclerc, Marion; Doré, Joël; Henrissat, Bernard; Remaud-Siméon, Magali; Monsan, Pierre; Potocki-Véronèse, Gabrielle

    2013-01-01

    The human intestine hosts a complex bacterial community that plays a major role in nutrition and in maintaining human health. A functional metagenomic approach was used to explore the prebiotic breakdown potential of human gut bacteria, including non-cultivated ones. Two metagenomic libraries, constructed from ileum mucosa and fecal microbiota, were screened for hydrolytic activities on the prebiotic carbohydrates inulin, fructo-oligosaccharides, xylo-oligosaccharides, galacto-oligosaccharides and lactulose. The DNA inserts of 17 clones, selected from the 167 hits that were identified, were pyrosequenced in-depth, yielding in total 407, 420 bp of metagenomic DNA. From these sequences, we discovered novel prebiotic degradation pathways containing carbohydrate transporters and hydrolysing enzymes, for which we provided the first experimental proof of function. Twenty of these proteins are encoded by genes that are also present in the gut metagenome of at least 100 subjects, whatever are their ages or their geographical origin. The sequence taxonomic assignment indicated that still unknown bacteria, for which neither culture conditions nor genome sequence are available, possess the enzymatic machinery to hydrolyse the prebiotic carbohydrates tested. The results expand the vision on how prebiotics are metabolized along the intestine, and open new perspectives for the design of functional foods.

  9. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria.

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    Davide A Cecchini

    Full Text Available The human intestine hosts a complex bacterial community that plays a major role in nutrition and in maintaining human health. A functional metagenomic approach was used to explore the prebiotic breakdown potential of human gut bacteria, including non-cultivated ones. Two metagenomic libraries, constructed from ileum mucosa and fecal microbiota, were screened for hydrolytic activities on the prebiotic carbohydrates inulin, fructo-oligosaccharides, xylo-oligosaccharides, galacto-oligosaccharides and lactulose. The DNA inserts of 17 clones, selected from the 167 hits that were identified, were pyrosequenced in-depth, yielding in total 407, 420 bp of metagenomic DNA. From these sequences, we discovered novel prebiotic degradation pathways containing carbohydrate transporters and hydrolysing enzymes, for which we provided the first experimental proof of function. Twenty of these proteins are encoded by genes that are also present in the gut metagenome of at least 100 subjects, whatever are their ages or their geographical origin. The sequence taxonomic assignment indicated that still unknown bacteria, for which neither culture conditions nor genome sequence are available, possess the enzymatic machinery to hydrolyse the prebiotic carbohydrates tested. The results expand the vision on how prebiotics are metabolized along the intestine, and open new perspectives for the design of functional foods.

  10. Susceptibility and tolerance of human gut culturable aerobic microbiota to wine polyphenols.

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    Cueva, Carolina; Bartolomé, Begoña; Moreno-Arribas, M Victoria; Bustos, Irene; Requena, Teresa; González-Manzano, Susana; Santos-Buelga, Celestino; Turrientes, María-Carmen; del Campo, Rosa

    2015-02-01

    Diet is one of the main factors that could affect quantitatively and qualitatively the stability of the gut microbiota. Polyphenols are abundantly present in the human diet and have an antimicrobial effect inducing selective changes in the microbiota composition, with potential beneficial effects for the human health. Our aim was to determine the human gut microbiota susceptibility toward wine polyphenols. Susceptibility to two commercial wine phenolic extracts (Vitaflavan(®) and Provinols™) was determined in isolates from fecal samples from 36 gastrointestinal healthy volunteers. To select the polyphenol-resistant isolates, feces were seeded in plates containing 1 mg/ml of phenolic extract. The minimal inhibitory concentration to polyphenols in the collected isolates was assessed by the agar dilution method. Overall results showed that Gram-negative isolates are most tolerant to the presence of both grape seed and red wine extracts. Furthermore, we purified to homogeneity the phenolic fractions by high-performance liquid chromatography (HPLC) to determine their antimicrobial effect and their influence on bacterial growth in four selected ATCC strains using the BioScreen apparatus. Results showed that the antimicrobial activity of the wine polyphenols is the result of the interaction of both the flavan-3-ol type and the bacteria. Bacterial Intraspecies differences in the phenolic susceptibility suggest the existence of polyphenol-resistant mechanisms that are uncharacterized as yet.

  11. Country-specific antibiotic use practices impact the human gut resistome.

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    Forslund, Kristoffer; Sunagawa, Shinichi; Kultima, Jens Roat; Mende, Daniel R; Arumugam, Manimozhiyan; Typas, Athanasios; Bork, Peer

    2013-07-01

    Despite increasing concerns over inappropriate use of antibiotics in medicine and food production, population-level resistance transfer into the human gut microbiota has not been demonstrated beyond individual case studies. To determine the "antibiotic resistance potential" for entire microbial communities, we employ metagenomic data and quantify the totality of known resistance genes in each community (its resistome) for 68 classes and subclasses of antibiotics. In 252 fecal metagenomes from three countries, we show that the most abundant resistance determinants are those for antibiotics also used in animals and for antibiotics that have been available longer. Resistance genes are also more abundant in samples from Spain, Italy, and France than from Denmark, the United States, or Japan. Where comparable country-level data on antibiotic use in both humans and animals are available, differences in these statistics match the observed resistance potential differences. The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year.

  12. Complexity of human and ecosystem interactions in an agricultural landscape

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    Coupe, Richard H.; Barlow, Jeannie R.; Capel, Paul D.

    2012-01-01

    The complexity of human interaction in the commercial agricultural landscape and the resulting impacts on the ecosystem services of water quality and quantity is largely ignored by the current agricultural paradigm that maximizes crop production over other ecosystem services. Three examples at different spatial scales (local, regional, and global) are presented where human and ecosystem interactions in a commercial agricultural landscape adversely affect water quality and quantity in unintended ways in the Delta of northwestern Mississippi. In the first example, little to no regulation of groundwater use for irrigation has caused declines in groundwater levels resulting in loss of baseflow to streams and threatening future water supply. In the second example, federal policy which subsidizes corn for biofuel production has encouraged many producers to switch from cotton to corn, which requires more nutrients and water, counter to national efforts to reduce nutrient loads to the Gulf of Mexico and exacerbating groundwater level declines. The third example is the wholesale adoption of a system for weed control that relies on a single chemical, initially providing many benefits and ultimately leading to the widespread occurrence of glyphosate and its degradates in Delta streams and necessitating higher application rates of glyphosate as well as the use of other herbicides due to increasing weed resistance. Although these examples are specific to the Mississippi Delta, analogous situations exist throughout the world and point to the need for change in how we grow our food, fuel, and fiber, and manage our soil and water resources.

  13. Perception, acquisition and use of ecosystem services: human behavior, and ecosystem management and policy implications

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    Stanley T. Asah; Anne D. Guerry; Dale J. Blahna; Joshua J. Lawler

    2014-01-01

    Ecosystem services, fundamental to livelihoods and well-being, are reshaping environmental management and policy. However, the behavioral dimensions of ecosystem services and the responses of ordinary people to the management of those services, is less well understood. The ecosystem services framework lends itself to understanding the relationship between ecosystems...

  14. Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults.

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    Theresa Wan-Chen Yap

    Full Text Available Accumulating evidence shows that Helicobacter pylori protects against some metabolic and immunological diseases in which the development of these diseases coincide with temporal or permanent dysbiosis. The aim of this study was to assess the effect of H. pylori eradication on the human gut microbiome.As part of the currently on-going ESSAY (Eradication Study in Stable Adults/Youths study, we collected stool samples from 17 H. pylori-positive young adult (18-30 years-old volunteers. The same cohort was followed up 6, 12 and 18 months-post H. pylori eradication. The impact of H. pylori on the human gut microbiome pre- and post-eradication was investigated using high throughput 16S rRNA gene (V3-V4 region sequencing using the Illumina Miseq followed by data analysis using Qiime pipeline.We compared the composition and diversity of bacterial communities in the fecal microbiome of the H. pylori-positive volunteers, before and after H. pylori eradication therapy. The 16S rRNA gene was sequenced at an average of 150,000-170,000 reads/sample. The microbial diversity were similar pre- and post-H. pylori eradication with no significant differences in richness and evenness of bacterial species. Despite that the general profile of the gut microbiome was similar pre- and post-eradication, some changes in the bacterial communities at the phylum and genus levels were notable, particularly the decrease in relative abundance of Bacterioidetes and corresponding increase in Firmicutes after H. pylori eradication. The significant increase of short-chain fatty acids (SCFA-producing bacteria genera could also be associated with increased risk of metabolic disorders.Our preliminary stool metagenomics study shows that eradication of H. pylori caused perturbation of the gut microbiome and may indirectly affect the health of human. Clinicians should be aware of the effect of broad spectrum antibiotics used in H. pylori eradication regimen and be cautious in the clinical

  15. Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome

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    Meehan Conor J

    2012-11-01

    Full Text Available Abstract Background Several links have been established between the human gut microbiome and conditions such as obesity and inflammatory bowel syndrome. This highlights the importance of understanding what properties of the gut microbiome can affect the health of the human host. Studies have been undertaken to determine the species composition of this microbiome and infer functional profiles associated with such host properties. However, lateral gene transfer (LGT between community members may result in misleading taxonomic attributions for the recipient organisms, thus making species-function links difficult to establish. Results We identified a peptides/nickel transport complex whose components differed in abundance based upon levels of host obesity, and assigned the encoded proteins to members of the microbial community. Each protein was assigned to several distinct taxonomic groups, with moderate levels of agreement observed among different proteins in the complex. Phylogenetic trees of these proteins produced clusters that differed greatly from taxonomic attributions and indicated that habitat-directed LGT of this complex is likely to have occurred, though not always between the same partners. Conclusions These findings demonstrate that certain membrane transport systems may be an important factor within an obese-associated gut microbiome and that such complexes may be acquired several times by different strains of the same species. Additionally, an example of individual proteins from different organisms being transferred into one operon was observed, potentially demonstrating a functional complex despite the donors of the subunits being taxonomically disparate. Our results also highlight the potential impact of habitat-directed LGT on the resident microbiota.

  16. Assessing the impact of protein extraction methods for human gut metaproteomics.

    Science.gov (United States)

    Zhang, Xu; Li, Leyuan; Mayne, Janice; Ning, Zhibin; Stintzi, Alain; Figeys, Daniel

    2017-07-10

    Metaproteomics is a promising methodology for the functional characterizations of the gut microbiome. However, the performance of metaproteomic analysis is affected by protein extraction protocols in terms of the amount of protein recovered and the relative abundance of different bacteria observed in microbiome. Currently, there is a lack of consistency on protein extraction methods in published metaproteomics studies. Here we evaluated the effects of different protein extraction methods on human fecal metaproteome characterizations. We found that sodium dodecyl sulfate (SDS)-based lysis buffer obtained higher protein yields and peptide/protein group identifications compared to urea and the non-ionic detergent-based B-Per buffer. The addition of bead beating to any of the extraction buffers increased both protein yields and protein identifications. As well, bead beating led to a significant increase of the relative abundances of Firmicutes and Actinobacteria. We also demonstrated that ultrasonication, another commonly used mechanical disruption approach, performed even better than bead beating for gut microbial protein extractions. Importantly, proteins of the basic metabolic pathways showed significantly higher relative abundances when using ultrasonication. Overall, these results demonstrate that protein extraction protocols markedly impact the metaproteomic results and recommend a protein extraction protocol with both SDS and ultrasonication for metaproteomic studies. The gut microbiome is emerging as an important factor influencing human health. Metaproteomics is promising for advancing the understanding of the functional roles of the microbiome in disease. However, metaproteomics suffers from a lack of consistent sample preparation procedures. In the present study, protein extraction protocols for fecal microbiome samples were evaluated for their effects on protein yields, peptide identifications, protein group identifications, taxonomic compositions and

  17. Unraveling the relationships between ecosystems and human wellbeing in Spain.

    Directory of Open Access Journals (Sweden)

    Fernando Santos-Martín

    Full Text Available National ecosystem assessments provide evidence on the status and trends of biodiversity, ecosystem conditions, and the delivery of ecosystem services to society. I this study, we analyze the complex relationships established between ecosystems and human systems in Spain through the combination of Driver-Pressure-State-Impact-Response framework and structural equation models. Firstly, to operationalize the framework, we selected 53 national scale indicators that provide accurate, long-term information on each of the components. Secondly, structural equation models were performed to understand the relationships among the components of the framework. Trend indicators have shown an overall progressive biodiversity loss, trade-offs between provisioning and cultural services associated with urban areas vs. regulating and cultural services associated with rural areas, a decoupling effect between material and non-material dimensions of human wellbeing, a rapid growing trend of conservation responses in recent years and a constant growing linear trend of direct or indirect drivers of change. Results also show that all the components analyzed in the model are strongly related. On one hand, the model shows that biodiversity erosion negatively affect the supply of regulating services, while it is positively related with the increase of provisioning service delivery. On the other hand, the most important relationship found in the model is the effect of pressures on biodiversity loss, indicating that response options for conserving nature cannot counteract the effect of the drivers of change. These results suggest that there is an insufficient institutional response to address the underlying causes (indirect drivers of change of biodiversity loos in Spain. We conclude that more structural changes are required in the Spanish institutional framework to reach 2020 biodiversity conservation international targets.

  18. Vegetable microbiomes: is there a connection among opportunistic infections, human health and our 'gut feeling'?

    Science.gov (United States)

    Berg, Gabriele; Erlacher, Armin; Smalla, Kornelia; Krause, Robert

    2014-11-01

    The highly diverse microbiomes of vegetables are reservoirs for opportunistic and emerging pathogens. In recent years, an increased consumption, larger scale production and more efficient distribution of vegetables together with an increased number of immunocompromised individuals resulted in an enhanced number of documented outbreaks of human infections associated with the consumption of vegetables. Here we discuss the occurrence of potential pathogens in vegetable microbiomes, the impact of farming and processing practices, and plant and human health issues. Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. Moreover, the potentially positive aspects of the vegetables microbiome for the gut microbiota and human health are presented.

  19. Rifaximin is a gut-specific human pregnane X receptor activator.

    Science.gov (United States)

    Ma, Xiaochao; Shah, Yatrik M; Guo, Grace L; Wang, Ting; Krausz, Kristopher W; Idle, Jeffrey R; Gonzalez, Frank J

    2007-07-01

    Rifaximin, a rifamycin analog approved for the treatment of travelers' diarrhea, is also beneficial in the treatment of multiple chronic gastrointestinal disorders. However, the mechanisms contributing to the effects of rifaximin on chronic gastrointestinal disorders are not fully understood. In the current study, rifaximin was investigated for its role in activation of the pregnane X receptor (PXR), a nuclear receptor that regulates genes involved in xenobiotic and limited endobiotic deposition and detoxication. PXR-humanized (hPXR), Pxr-null, and wild-type mice were treated orally with rifaximin, and rifampicin, a well characterized human PXR ligand. Rifaximin was highly concentrated in the intestinal tract compared with rifampicin. Rifaximin treatment resulted in significant induction of PXR target genes in the intestine of hPXR mice, but not in wild-type and Pxr-null mice. However, rifaximin treatment demonstrated no significant effect on hepatic PXR target genes in wild-type, Pxr-null, and hPXR mice. Consistent with the in vivo data, cell-based reporter gene assay revealed rifaximin-mediated activation of human PXR, but not the other xenobiotic nuclear receptors constitutive androstane receptor, peroxisome proliferator-activated receptor (PPAR)alpha, PPARgamma, and farnesoid X receptor. Pretreatment with rifaximin did not affect the pharmacokinetics of the CYP3A substrate midazolam, but it increased the C(max) and decreased T(max) of 1'-hydroxymidazolam. Collectively, the current study identified rifaximin as a gut-specific human PXR ligand, and it provided further evidence for the utility of hPXR mice as a critical tool for the study of human PXR activators. Further human studies are suggested to assess the potential role of rifaximin-mediated gut PXR activation in therapeutics of chronic gastrointestinal disorders.

  20. A conceptual framework for the study of human ecosystems in urban areas

    Science.gov (United States)

    Steward T.A. Pickett; William R. Burch; Shawn E. Dalton; Timothy W. Foresman; J. Morgan Grove; Rowan. Rowntree

    1997-01-01

    The need for integrated concepts, capable of satisfying natural and social scientists and supporting integrated research, motivates a conceptual framework for understanding the role of humans in ecosystems. The question is how to add humans to the ecological models used to understand urban ecosystems. The ecosystem concept can serve as the basis, but specific social...

  1. Preterm infant gut microbiota affects intestinal epithelial development in a humanized microbiome gnotobiotic mouse model.

    Science.gov (United States)

    Yu, Yueyue; Lu, Lei; Sun, Jun; Petrof, Elaine O; Claud, Erika C

    2016-09-01

    Development of the infant small intestine is influenced by bacterial colonization. To promote establishment of optimal microbial communities in preterm infants, knowledge of the beneficial functions of the early gut microbiota on intestinal development is needed. The purpose of this study was to investigate the impact of early preterm infant microbiota on host gut development using a gnotobiotic mouse model. Histological assessment of intestinal development was performed. The differentiation of four epithelial cell lineages (enterocytes, goblet cells, Paneth cells, enteroendocrine cells) and tight junction (TJ) formation was examined. Using weight gain as a surrogate marker for health, we found that early microbiota from a preterm infant with normal weight gain (MPI-H) induced increased villus height and crypt depth, increased cell proliferation, increased numbers of goblet cells and Paneth cells, and enhanced TJs compared with the changes induced by early microbiota from a poor weight gain preterm infant (MPI-L). Laser capture microdissection (LCM) plus qRT-PCR further revealed, in MPI-H mice, a higher expression of stem cell marker Lgr5 and Paneth cell markers Lyz1 and Cryptdin5 in crypt populations, along with higher expression of the goblet cell and mature enterocyte marker Muc3 in villus populations. In contrast, MPI-L microbiota failed to induce the aforementioned changes and presented intestinal characteristics comparable to a germ-free host. Our data demonstrate that microbial communities have differential effects on intestinal development. Future studies to identify pioneer settlers in neonatal microbial communities necessary to induce maturation may provide new insights for preterm infant microbial ecosystem therapeutics. Copyright © 2016 the American Physiological Society.

  2. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

    Science.gov (United States)

    Tailford, Louise E.; Owen, C. David; Walshaw, John; Crost, Emmanuelle H.; Hardy-Goddard, Jemma; Le Gall, Gwenaelle; de Vos, Willem M.; Taylor, Garry L.; Juge, Nathalie

    2015-07-01

    The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease.

  3. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.

    Directory of Open Access Journals (Sweden)

    Christian Hoffmann

    Full Text Available Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.

  4. Dietary Fiber and the Human Gut Microbiota: Application of Evidence Mapping Methodology

    Directory of Open Access Journals (Sweden)

    Caleigh M. Sawicki

    2017-02-01

    Full Text Available Interest is rapidly growing around the role of the human gut microbiota in facilitating beneficial health effects associated with consumption of dietary fiber. An evidence map of current research activity in this area was created using a newly developed database of dietary fiber intervention studies in humans to identify studies with the following broad outcomes: (1 modulation of colonic microflora; and/or (2 colonic fermentation/short-chain fatty acid concentration. Study design characteristics, fiber exposures, and outcome categories were summarized. A sub-analysis described oligosaccharides and bacterial composition in greater detail. One hundred eighty-eight relevant studies were identified. The fiber categories represented by the most studies were oligosaccharides (20%, resistant starch (16%, and chemically synthesized fibers (15%. Short-chain fatty acid concentration (47% and bacterial composition (88% were the most frequently studied outcomes. Whole-diet interventions, measures of bacterial activity, and studies in metabolically at-risk subjects were identified as potential gaps in the evidence. This evidence map efficiently captured the variability in characteristics of expanding research on dietary fiber, gut microbiota, and physiological health benefits, and identified areas that may benefit from further research. We hope that this evidence map will provide a resource for researchers to direct new intervention studies and meta-analyses.

  5. Dietary Fiber and the Human Gut Microbiota: Application of Evidence Mapping Methodology.

    Science.gov (United States)

    Sawicki, Caleigh M; Livingston, Kara A; Obin, Martin; Roberts, Susan B; Chung, Mei; McKeown, Nicola M

    2017-02-10

    Interest is rapidly growing around the role of the human gut microbiota in facilitating beneficial health effects associated with consumption of dietary fiber. An evidence map of current research activity in this area was created using a newly developed database of dietary fiber intervention studies in humans to identify studies with the following broad outcomes: (1) modulation of colonic microflora; and/or (2) colonic fermentation/short-chain fatty acid concentration. Study design characteristics, fiber exposures, and outcome categories were summarized. A sub-analysis described oligosaccharides and bacterial composition in greater detail. One hundred eighty-eight relevant studies were identified. The fiber categories represented by the most studies were oligosaccharides (20%), resistant starch (16%), and chemically synthesized fibers (15%). Short-chain fatty acid concentration (47%) and bacterial composition (88%) were the most frequently studied outcomes. Whole-diet interventions, measures of bacterial activity, and studies in metabolically at-risk subjects were identified as potential gaps in the evidence. This evidence map efficiently captured the variability in characteristics of expanding research on dietary fiber, gut microbiota, and physiological health benefits, and identified areas that may benefit from further research. We hope that this evidence map will provide a resource for researchers to direct new intervention studies and meta-analyses.

  6. Dietary Fiber and the Human Gut Microbiota: Application of Evidence Mapping Methodology

    Science.gov (United States)

    Sawicki, Caleigh M.; Livingston, Kara A.; Obin, Martin; Roberts, Susan B.; Chung, Mei; McKeown, Nicola M.

    2017-01-01

    Interest is rapidly growing around the role of the human gut microbiota in facilitating beneficial health effects associated with consumption of dietary fiber. An evidence map of current research activity in this area was created using a newly developed database of dietary fiber intervention studies in humans to identify studies with the following broad outcomes: (1) modulation of colonic microflora; and/or (2) colonic fermentation/short-chain fatty acid concentration. Study design characteristics, fiber exposures, and outcome categories were summarized. A sub-analysis described oligosaccharides and bacterial composition in greater detail. One hundred eighty-eight relevant studies were identified. The fiber categories represented by the most studies were oligosaccharides (20%), resistant starch (16%), and chemically synthesized fibers (15%). Short-chain fatty acid concentration (47%) and bacterial composition (88%) were the most frequently studied outcomes. Whole-diet interventions, measures of bacterial activity, and studies in metabolically at-risk subjects were identified as potential gaps in the evidence. This evidence map efficiently captured the variability in characteristics of expanding research on dietary fiber, gut microbiota, and physiological health benefits, and identified areas that may benefit from further research. We hope that this evidence map will provide a resource for researchers to direct new intervention studies and meta-analyses. PMID:28208609

  7. Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis.

    Science.gov (United States)

    Cameron, Elizabeth A; Kwiatkowski, Kurt J; Lee, Byung-Hoo; Hamaker, Bruce R; Koropatkin, Nicole M; Martens, Eric C

    2014-09-09

    To compete for the dynamic stream of nutrients flowing into their ecosystem, colonic bacteria must respond rapidly to new resources and then catabolize them efficiently once they are detected. The Bacteroides thetaiotaomicron starch utilization system (Sus) is a model for nutrient acquisition by symbiotic gut bacteria, which harbor thousands of related Sus-like systems. Structural investigation of the four Sus outer membrane proteins (SusD, -E, -F, and -G) revealed that they contain a total of eight starch-binding sites that we demonstrated, using genetic and biochemical approaches, to play distinct roles in starch metabolism in vitro and in vivo in gnotobiotic mice. SusD, whose homologs are abundant in the human microbiome, is critical for the initial sensing of available starch, allowing sus transcriptional activation at much lower concentrations than without this function. In contrast, seven additional binding sites across SusE, -F, and -G are dispensable for sus activation. However, they optimize the rate of growth on starch in a manner dependent on the expression of the bacterial polysaccharide capsule, suggesting that they have evolved to offset the diffusion barrier created by this structure. These findings demonstrate how proteins with similar biochemical behavior can serve orthogonal functions during different stages of cellular adaptation to nutrients. Finally, we demonstrated in gnotobiotic mice fed a starch-rich diet that the Sus binding sites confer a competitive advantage to B. thetaiotaomicron in vivo in a manner that is dependent on other colonizing microbes. This study reveals how numerically dominant families of carbohydrate-binding proteins in the human microbiome fulfill separate and sometimes cooperative roles to optimize gut commensal bacteria for nutrient acquisition. Our intestinal tract harbors trillions of symbiotic microbes. A critical function contributed by this microbial community is the ability to degrade most of the complex

  8. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults

    DEFF Research Database (Denmark)

    Larsen, Nadja; Vogensen, Finn Kvist; van der Berg, Franciscus Winfried J

    2010-01-01

    Background Recent evidence suggests that there is a link between metabolic diseases and bacterial populations in the gut. The aim of this study was to assess the differences between the composition of the intestinal microbiota in humans with type 2 diabetes and non-diabetic persons as control....... Methods and Findings The study included 36 male adults with a broad range of age and body-mass indices (BMIs), among which 18 subjects were diagnosed with diabetes type 2. The fecal bacterial composition was investigated by real-time quantitative PCR (qPCR) and in a subgroup of subjects (N = 20) by tag...... = 0.04). Conclusions The results of this study indicate that type 2 diabetes in humans is associated with compositional changes in intestinal microbiota. The level of glucose tolerance should be considered when linking microbiota with metabolic diseases such as obesity and developing strategies...

  9. Novel Probiotics and Prebiotics: How Can They Help in Human Gut Microbiota Dysbiosis?

    Directory of Open Access Journals (Sweden)

    Carlos Gómez Gallego

    2016-03-01

    Full Text Available Background and Objectives: Novel probiotics and prebiotics designed to modulate the gut microbiota for improving health outcomes are in demand as the importance of the gut microbiota in human health is revealed. A review of the scientific literature regarding the current knowledge and novel species and novel oligosaccharides for the treatment of dysbiosis-associated diseases has been carried out due to their growing interest. Results and Conclusions: The regulations governing introduction of novel probiotics and prebiotics vary by geographical region. Novel foods and foods with health claims fall under specific regulations in several countries. In European Union (EU, safety is assessed by novel food approval process and by the European Food Safety Authority (EFSA established Quantitative Presumption of Safety (QPS system for bacteria and other biologicals. Any messages on health benefits are covered by the European Regulation on Health Claims (ERHC, also assessed by EFSA. Examples of recent novel probiotics in EU include Clostridium butyricum, and Bacteroides xylanisolvens and examples of novel prebiotics include human milk oligosaccharides such as Lacto-N-neotetraose. Yacon root is an example on a previously novel prebiotic food which is allowed due to the reported existing cultivation and use in EU prior to the novel food regulation. Potential future candidates include further human milk oligosaccharides and bacteria such Faecalibacterium prausnitzii and Akkermasia muciniphila. Increasing knowledge on human intestinal microbiota and microbiota development enables the design of new more specific and hitherto unknown probiotics and prebiotics. Also understanding the microbe and microbe host interactions facilitates the search for novel probiotics and prebiotics.

  10. Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air.

    Directory of Open Access Journals (Sweden)

    M Tanweer Khan

    Full Text Available The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far precluded its clinical application in the treatment of patients with inflammatory bowel diseases. The present studies were therefore aimed at developing a strategy to keep F. prausnitzii alive at ambient air. Our previous research showed that F. prausnitzii can survive in moderately oxygenized environments like the gut mucosa by transfer of electrons to oxygen. For this purpose, the bacterium exploits extracellular antioxidants, such as riboflavin and cysteine, that are abundantly present in the gut. We therefore tested to what extent these antioxidants can sustain the viability of F. prausnitzii at ambient air. The present results show that cysteine can facilitate the survival of F. prausnitzii upon exposure to air, and that this effect is significantly enhanced the by addition of riboflavin and the cryoprotectant inulin. The highly oxygen-sensitive gut bacterium F. prausnitzii can be kept alive at ambient air for 24 h when formulated with the antioxidants cysteine and riboflavin plus the cryoprotectant inulin. Improved formulations were obtained by addition of the bulking agents corn starch and wheat bran. Our present findings pave the way towards the biomedical exploitation of F. prausnitzii in redox-based therapeutics for treatment of dysbiosis-related inflammatory disorders of the human gut.

  11. Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron

    Science.gov (United States)

    Lammerts van Bueren, Alicia; Mulder, Marieke; Leeuwen, Sander van; Dijkhuizen, Lubbert

    2017-01-01

    Galactooligosaccharides (GOS) are prebiotic carbohydrates that impart changes in the gut bacterial composition of formula-fed infants to more closely resemble that of breast-fed infants. Consuming human milk oligosaccharides (HMOs) provides specific bacterial strains with an advantage for colonizing the infant intestine. These same effects are seen in infants after GOS consumption, however GOS are very complex mixtures and the underlying molecular mechanisms of how GOS mimic HMOs are relatively unknown. Here we studied the effects of GOS utilization on a prominent gut symbiont, Bacteroides thetaiotaomicron, which has been previously shown to consume HMOs via mucin O-glycan degradation pathways. We show that several pathways for targeting O-mucin glycans are activated in B. thetaiotaomicron by GOS, as well as the galactan utilization sytem. Characterization of the endo-galactanase from this system identified activity on various longer GOS substrates while a subset of GOS compounds were identified as potential activators of mucin glycan metabolism in B. thetaiotaomicron. Our results show that GOS functions as an inducer of mucin-glycan pathways while providing a nutrient source in the form of β-(1 → 4)-galactan. These metabolic features of GOS mixtures may serve to explain the beneficial effects that are seen for GOS supplemented infant formula. PMID:28091546

  12. Persistence of Bacillus thuringiensis bioinsecticides in the gut of human-flora-associated rats.

    Science.gov (United States)

    Wilcks, Andrea; Hansen, Bjarne Munk; Hendriksen, Niels Bohse; Licht, Tine Rask

    2006-12-01

    The capability of two bioinsecticide strains of Bacillus thuringiensis (ssp. israelensis and ssp. kurstaki) to germinate and persist in vivo in the gastrointestinal tract of human-flora-associated rats was studied. Rats were dosed either with vegetative cells or spores of the bacteria for 4 consecutive days. In animals fed spores, B. thuringiensis cells were detected in faecal and intestinal samples of all animals, whereas vegetative cells only poorly survived the gastric passage. Heat-treatment of intestinal samples, which kills vegetative cells, revealed that B. thuringiensis spores were capable of germination in the gastrointestinal tract. In one animal fed spores of B. thuringiensis ssp. kurstaki, these bacteria were detected at high density (10(3)-10(4) CFU g(-1) faecal and intestinal samples) even 2 weeks after the last dosage. In the same animal, passage of B. thuringiensis ssp. kurstaki to the spleen was observed; however, no other adverse effects were observed. Denaturing gradient gel electrophoresis of PCR-amplified bacterial 16S rRNA genes in faecal samples revealed no major effect of B. thuringiensis on the composition of the indigenous gut bacteria. Additionally, no cytotoxic effect was detectable in gut samples by Vero cell assay.

  13. Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Lammerts van Bueren, Alicia; Mulder, Marieke; Leeuwen, Sander van; Dijkhuizen, Lubbert

    2017-01-16

    Galactooligosaccharides (GOS) are prebiotic carbohydrates that impart changes in the gut bacterial composition of formula-fed infants to more closely resemble that of breast-fed infants. Consuming human milk oligosaccharides (HMOs) provides specific bacterial strains with an advantage for colonizing the infant intestine. These same effects are seen in infants after GOS consumption, however GOS are very complex mixtures and the underlying molecular mechanisms of how GOS mimic HMOs are relatively unknown. Here we studied the effects of GOS utilization on a prominent gut symbiont, Bacteroides thetaiotaomicron, which has been previously shown to consume HMOs via mucin O-glycan degradation pathways. We show that several pathways for targeting O-mucin glycans are activated in B. thetaiotaomicron by GOS, as well as the galactan utilization sytem. Characterization of the endo-galactanase from this system identified activity on various longer GOS substrates while a subset of GOS compounds were identified as potential activators of mucin glycan metabolism in B. thetaiotaomicron. Our results show that GOS functions as an inducer of mucin-glycan pathways while providing a nutrient source in the form of β-(1 → 4)-galactan. These metabolic features of GOS mixtures may serve to explain the beneficial effects that are seen for GOS supplemented infant formula.

  14. Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species.

    Directory of Open Access Journals (Sweden)

    Maria Elisa Perez-Muñoz

    Full Text Available Host T cell reactivity toward gut bacterial epitopes has been recognized as part of disease pathogenesis. However, the specificity of T cells that recognize this vast number of epitopes has not yet been well described. After colonizing a C57BL/6J germ-free mouse with the human gut symbiotic bacteria Bacteroides thetaiotaomicron, we isolated a T cell that recognized these bacteria in vitro. Using this T cell, we mapped the first known non-carbohydrate T cell epitope within the phylum Bacteroidetes. The T cell also reacted to two other additional Bacteroides species. We identified the peptide that stimulated the T cell by using a genetic approach. Genomic data from the epitope-positive and epitope-negative bacteria explain the cross-reactivity of the T cell to multiple species. This epitope degeneracy should shape our understanding of the T cell repertoire stimulated by the complex microbiome residing in the gastrointestinal tract in both healthy and disease states.

  15. Time course production of urolithins from ellagic acid by human gut microbiota.

    Science.gov (United States)

    García-Villalba, Rocío; Beltrán, David; Espín, Juan Carlos; Selma, María Victoria; Tomás-Barberán, Francisco A

    2013-09-18

    Ellagic acid (EA) is converted to urolithins by gut microbiota. Urolithins have beneficial biological effects in humans, but differences in urolithin production capacity among individuals have been shown. Therefore, the identification of the urolithin production pathways and the microorganisms implicated is of high interest. EA was incubated with gut microbiota from two volunteers able to produce urolithins but with different in vivo urolithin profiles (urolithin A and isourolithin A producers). The metabolic capabilities observed in vivo were retained in vitro. Both individuals showed a much higher abundance of Clostridium leptum group of Firmicutes phylum than Bacteroides / Prevotella . EA was either dissolved in DMSO or suspended in water. DMSO increased EA solubility but decreased urolithin production rate due to a delay in growth of some microbial groups, principally, Clostridium coccoides . This allowed the detection of catabolic intermediates [urolithins M-5, M-6, M-7, C, and 2,3,8,10-tetrahydroxy urolithin (urolithin E)]. Bacteria from C. coccoides group (or genera co-occurring in vivo with this group) seem to be involved in production of different urolithins.

  16. Progress and Challenges in Developing Metabolic Footprints from Diet in Human Gut Microbial Cometabolism12

    Science.gov (United States)

    Duffy, Linda C; Raiten, Daniel J; Hubbard, Van S; Starke-Reed, Pamela

    2015-01-01

    Homo sapiens harbor trillions of microbes, whose microbial metagenome (collective genome of a microbial community) using omic validation interrogation tools is estimated to be at least 100-fold that of human cells, which comprise 23,000 genes. This article highlights some of the current progress and open questions in nutrition-related areas of microbiome research. It also underscores the metabolic capabilities of microbial fermentation on nutritional substrates that require further mechanistic understanding and systems biology approaches of studying functional interactions between diet composition, gut microbiota, and host metabolism. Questions surrounding bacterial fermentation and degradation of dietary constituents (particularly by Firmicutes and Bacteroidetes) and deciphering how microbial encoding of enzymes and derived metabolites affect recovery of dietary energy by the host are more complex than previously thought. Moreover, it is essential to understand to what extent the intestinal microbiota is subject to dietary control and to integrate these data with functional metabolic signatures and biomarkers. Many lines of research have demonstrated the significant role of the gut microbiota in human physiology and disease. Probiotic and prebiotic products are proliferating in the market in response to consumer demand, and the science and technology around these products are progressing rapidly. With high-throughput molecular technologies driving the science, studying the bidirectional interactions of host-microbial cometabolism, epithelial cell maturation, shaping of innate immune development, normal vs. dysfunctional nutrient absorption and processing, and the complex signaling pathways involved is now possible. Substantiating the safety and mechanisms of action of probiotic/prebiotic formulations is critical. Beneficial modulation of the human microbiota by using these nutritional and biotherapeutic strategies holds considerable promise as next

  17. Gut microbiota and obesity.

    Science.gov (United States)

    Gérard, Philippe

    2016-01-01

    The human intestine harbors a complex bacterial community called the gut microbiota. This microbiota is specific to each individual despite the existence of several bacterial species shared by the majority of adults. The influence of the gut microbiota in human health and disease has been revealed in the recent years. Particularly, the use of germ-free animals and microbiota transplant showed that the gut microbiota may play a causal role in the development of obesity and associated metabolic disorders, and lead to identification of several mechanisms. In humans, differences in microbiota composition, functional genes and metabolic activities are observed between obese and lean individuals suggesting a contribution of the gut microbiota to these phenotypes. Finally, the evidence linking gut bacteria to host metabolism could allow the development of new therapeutic strategies based on gut microbiota modulation to treat or prevent obesity.

  18. Amidated joining peptide in the human pituitary, gut, adrenal gland and bronchial carcinoids. Immunocytochemical and immunochemical evidence

    DEFF Research Database (Denmark)

    Bjartell, A; Fenger, M; Ekman, R;

    1990-01-01

    The distribution of the proopiomelanocortin-derivated amidated joining peptide (JP-N) was examined in the human pituitary gland, adrenal gland, gut and in three bronchial carcinoids. Double immunostaining showed coexistence of immunoreactive JP-N and other proopiomelanocortin derivatives, e...

  19. A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut

    DEFF Research Database (Denmark)

    Karlsson, Fredrik H.; Ussery, David; Nielsen, Jens;

    2011-01-01

    The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacte...... of members of the Bacteroidetes/Chlorobi phylum by whole genome comparison. Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for diet digestion.......The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105...... Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number...

  20. The migration and loss of human primordial germ stem cells from the hind gut epithelium towards the gonadal ridge

    DEFF Research Database (Denmark)

    Mamsen, Linn Salto; Brøchner, Christian Beltoft; Byskov, Anne Grete

    2012-01-01

    Human primordial germ cells (PGCs) can be recognized in the yolk sac wall, from 3-4 weeks post conception (wpc), in the hind gut epithelium from week 4 and in the gonadal area from early week 5. The objective of this study was to map the migration route of PGCs and elucidate the role of the nervous...

  1. Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health

    NARCIS (Netherlands)

    Kelder, T.; Stroeve, J.H.M.; Bijlsma, S.; Radonjic, M.; Roeselers, G.

    2014-01-01

    BACKGROUND: Recent evidence suggests that the gut microbiota plays an important role in human metabolism and energy homeostasis and is therefore a relevant factor in the assessment of metabolic health and flexibility. Understanding of these host–microbiome interactions aids the design of nutritional

  2. Tolevamer is not efficacious in the neutralization of cytotoxin in a human gut model of Clostridium difficile infection.

    Science.gov (United States)

    Baines, Simon D; Freeman, Jane; Wilcox, Mark H

    2009-05-01

    The efficacy of tolevamer, a nonantimicrobial styrene derivative toxin-binding agent, in treating simulated Clostridium difficile infection in an in vitro human gut model was investigated. Tolevamer reduced neither the duration nor magnitude of cytotoxin activity by C. difficile, reflecting poor efficacy observed in recent phase III clinical trials.

  3. Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air

    NARCIS (Netherlands)

    Khan, M. Tanweer; van Dijl, Jan Maarten; Harmsen, Hermie J M

    2014-01-01

    The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far precl

  4. Mining the human gut microbiota for effector strains that shape the immune system.

    Science.gov (United States)

    Ahern, Philip P; Faith, Jeremiah J; Gordon, Jeffrey I

    2014-06-19

    The gut microbiota codevelops with the immune system beginning at birth. Mining the microbiota for bacterial strains responsible for shaping the structure and dynamic operations of the innate and adaptive arms of the immune system represents a formidable combinatorial problem but one that needs to be overcome to advance mechanistic understanding of microbial community and immune system coregulation and to develop new diagnostic and therapeutic approaches that promote health. Here, we discuss a scalable, less biased approach for identifying effector strains in complex microbial communities that impact immune function. The approach begins by identifying uncultured human fecal microbiota samples that transmit immune phenotypes to germ-free mice. Clonally arrayed sequenced collections of bacterial strains are constructed from representative donor microbiota. If the collection transmits phenotypes, effector strains are identified by testing randomly generated subsets with overlapping membership in individually housed germ-free animals. Detailed mechanistic studies of effector strain-host interactions can then be performed.

  5. Structure of the gut microbiome following colonization with human feces determines colonic tumor burden.

    Science.gov (United States)

    Baxter, Nielson T; Zackular, Joseph P; Chen, Grace Y; Schloss, Patrick D

    2014-01-01

    A growing body of evidence indicates that the gut microbiome plays a role in the development of colorectal cancer (CRC). Patients with CRC harbor gut microbiomes that are structurally distinct from those of healthy individuals; however, without the ability to track individuals during disease progression, it has not been possible to observe changes in the microbiome over the course of tumorigenesis. Mouse models have demonstrated that these changes can further promote colonic tumorigenesis. However, these models have relied upon mouse-adapted bacterial populations and so it remains unclear which human-adapted bacterial populations are responsible for modulating tumorigenesis. We transplanted fecal microbiota from three CRC patients and three healthy individuals into germ-free mice, resulting in six structurally distinct microbial communities. Subjecting these mice to a chemically induced model of CRC resulted in different levels of tumorigenesis between mice. Differences in the number of tumors were strongly associated with the baseline microbiome structure in mice, but not with the cancer status of the human donors. Partitioning of baseline communities into enterotypes by Dirichlet multinomial mixture modeling resulted in three enterotypes that corresponded with tumor burden. The taxa most strongly positively correlated with increased tumor burden were members of the Bacteroides, Parabacteroides, Alistipes, and Akkermansia, all of which are Gram-negative. Members of the Gram-positive Clostridiales, including multiple members of Clostridium Group XIVa, were strongly negatively correlated with tumors. Analysis of the inferred metagenome of each community revealed a negative correlation between tumor count and the potential for butyrate production, and a positive correlation between tumor count and the capacity for host glycan degradation. Despite harboring distinct gut communities, all mice underwent conserved structural changes over the course of the model. The

  6. Effects of Antibiotics on Bacterial Species Composition and Metabolic Activities in Chemostats Containing Defined Populations of Human Gut Microorganisms

    Science.gov (United States)

    Newton, Dorothy F.; Macfarlane, George T.

    2013-01-01

    The composition and metabolic activities of the human colonic microbiota are modulated by a number of external factors, including diet and antibiotic therapy. Changes in the structure and metabolism of the gut microbiota may have long-term consequences for host health. The large intestine harbors a complex microbial ecosystem comprising several hundreds of different bacterial species, which complicates investigations on intestinal physiology and ecology. To facilitate such studies, a highly simplified microbiota consisting of 14 anaerobic and facultatively anaerobic organisms (Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bifidobacterium longum, Bifidobacterium infantis, Bifidobacterium pseudolongum, Bifidobacterium adolescentis, Clostridium butyricum, C. perfringens, C. bifermentans, C. innocuum, Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Lactobacillus acidophilus) was used in this investigation. Ampicillin [9.2 μg (ml culture)−1] was added to two chemostats operated at different dilution rates (D; 0.10 h−1 and 0.21 h−1), and metronidazole [76.9 μg (ml culture)−1] was added to a third vessel (D = 0.21 h−1). Perturbations in bacterial physiology and metabolism were sampled over a 48-h period. Lactobacillus acidophilus and C. bifermentans populations did not establish in the fermentors under the imposed growth conditions. Ampicillin resulted in substantial reductions in bacteroides and C. perfringens populations at both dilution rates. Metronidazole strongly affected bacteroides communities but had no effect on bifidobacterial communities. The bacteriostatic effect of ampicillin on bifidobacterial species was growth rate dependent. Several metabolic activities were affected by antibiotic addition, including fermentation product formation and enzyme synthesis. The growth of antibiotic-resistant bifidobacteria in the large bowel may enable them to occupy ecological niches left vacant after antibiotic administration, preventing

  7. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

    Science.gov (United States)

    Lozupone, Catherine; Faust, Karoline; Raes, Jeroen; Faith, Jeremiah J.; Frank, Daniel N.; Zaneveld, Jesse; Gordon, Jeffrey I.; Knight, Rob

    2012-01-01

    We lack a deep understanding of genetic and metabolic attributes specializing in microbial consortia for initial and subsequent waves of colonization of our body habitats. Here we show that phylogenetically interspersed bacteria in Clostridium cluster XIVa, an abundant group of bacteria in the adult human gut also known as the Clostridium coccoides or Eubacterium rectale group, contains species that have evolved distribution patterns consistent with either early successional or stable gut communities. The species that specialize to the infant gut are more likely to associate with systemic infections and can reach high abundances in individuals with Inflammatory Bowel Disease (IBD), indicating that a subset of the microbiota that have adapted to pioneer/opportunistic lifestyles may do well in both early development and with disease. We identified genes likely selected during adaptation to pioneer/opportunistic lifestyles as those for which early succession association and not phylogenetic relationships explain genomic abundance. These genes reveal potential mechanisms by which opportunistic gut bacteria tolerate osmotic and oxidative stress and potentially important aspects of their metabolism. These genes may not only be biomarkers of properties associated with adaptation to early succession and disturbance, but also leads for developing therapies aimed at promoting reestablishment of stable gut communities following physiologic or pathologic disturbances. PMID:22665442

  8. Human transformations of the Wadden Sea ecosystem through time : a synthesis

    NARCIS (Netherlands)

    Lotze, H.K.; Reise, K; Worm, B.; van Beusekom, J.; Busch, M.; Ehlers, A.; Heinrich, D.; Hoffman, R.C.; Holm, P.; Jensen, C.; Knottnerus, O.S.; Langhanki, N.; Prummel, W.; Vollmer, M.; Wolff, W.J.

    Todays Wadden Sea is a heavily human-altered ecosystem. Shaped by natural forces since its origin 7,500 years ago, humans gradually gained dominance in influencing ecosystem structure and functioning. Here, we reconstruct the timeline of human impacts and the history of ecological changes in the

  9. Human transformations of the Wadden Sea ecosystem through time : a synthesis

    NARCIS (Netherlands)

    Lotze, HK; Reise, K; Worm, B; van Beusekom, J; Busch, M; Ehlers, A; Heinrich, D; Hoffmann, RC; Holm, P; Jensen, C; Knottnerus, OS; Langhanki, N; Prummel, W; Vollmer, M; Wolff, WJ

    2005-01-01

    Todays Wadden Sea is a heavily human-altered ecosystem. Shaped by natural forces since its origin 7,500 years ago, humans gradually gained dominance in influencing ecosystem structure and functioning. Here, we reconstruct the timeline of human impacts and the history of ecological changes in the Wad

  10. Production of α-galactosylceramide by a prominent member of the human gut microbiota.

    Directory of Open Access Journals (Sweden)

    Laura C Wieland Brown

    2013-07-01

    Full Text Available While the human gut microbiota are suspected to produce diffusible small molecules that modulate host signaling pathways, few of these molecules have been identified. Species of Bacteroides and their relatives, which often comprise >50% of the gut community, are unusual among bacteria in that their membrane is rich in sphingolipids, a class of signaling molecules that play a key role in inducing apoptosis and modulating the host immune response. Although known for more than three decades, the full repertoire of Bacteroides sphingolipids has not been defined. Here, we use a combination of genetics and chemistry to identify the sphingolipids produced by Bacteroides fragilis NCTC 9343. We constructed a deletion mutant of BF2461, a putative serine palmitoyltransferase whose yeast homolog catalyzes the committed step in sphingolipid biosynthesis. We show that the Δ2461 mutant is sphingolipid deficient, enabling us to purify and solve the structures of three alkaline-stable lipids present in the wild-type strain but absent from the mutant. The first compound was the known sphingolipid ceramide phosphorylethanolamine, and the second was its corresponding dihydroceramide base. Unexpectedly, the third compound was the glycosphingolipid α-galactosylceramide (α-GalCer(Bf, which is structurally related to a sponge-derived sphingolipid (α-GalCer, KRN7000 that is the prototypical agonist of CD1d-restricted natural killer T (iNKT cells. We demonstrate that α-GalCer(Bf has similar immunological properties to KRN7000: it binds to CD1d and activates both mouse and human iNKT cells both in vitro and in vivo. Thus, our study reveals BF2461 as the first known member of the Bacteroides sphingolipid pathway, and it indicates that the committed steps of the Bacteroides and eukaryotic sphingolipid pathways are identical. Moreover, our data suggest that some Bacteroides sphingolipids might influence host immune homeostasis.

  11. Production of α-Galactosylceramide by a Prominent Member of the Human Gut Microbiota

    Science.gov (United States)

    Kashyap, Purna C.; Williams, Brianna B.; Clardy, Jon; Kronenberg, Mitchell; Sonnenburg, Justin L.; Comstock, Laurie E.; Bluestone, Jeffrey A.; Fischbach, Michael A.

    2013-01-01

    While the human gut microbiota are suspected to produce diffusible small molecules that modulate host signaling pathways, few of these molecules have been identified. Species of Bacteroides and their relatives, which often comprise >50% of the gut community, are unusual among bacteria in that their membrane is rich in sphingolipids, a class of signaling molecules that play a key role in inducing apoptosis and modulating the host immune response. Although known for more than three decades, the full repertoire of Bacteroides sphingolipids has not been defined. Here, we use a combination of genetics and chemistry to identify the sphingolipids produced by Bacteroides fragilis NCTC 9343. We constructed a deletion mutant of BF2461, a putative serine palmitoyltransferase whose yeast homolog catalyzes the committed step in sphingolipid biosynthesis. We show that the Δ2461 mutant is sphingolipid deficient, enabling us to purify and solve the structures of three alkaline-stable lipids present in the wild-type strain but absent from the mutant. The first compound was the known sphingolipid ceramide phosphorylethanolamine, and the second was its corresponding dihydroceramide base. Unexpectedly, the third compound was the glycosphingolipid α-galactosylceramide (α-GalCerBf), which is structurally related to a sponge-derived sphingolipid (α-GalCer, KRN7000) that is the prototypical agonist of CD1d-restricted natural killer T (iNKT) cells. We demonstrate that α-GalCerBf has similar immunological properties to KRN7000: it binds to CD1d and activates both mouse and human iNKT cells both in vitro and in vivo. Thus, our study reveals BF2461 as the first known member of the Bacteroides sphingolipid pathway, and it indicates that the committed steps of the Bacteroides and eukaryotic sphingolipid pathways are identical. Moreover, our data suggest that some Bacteroides sphingolipids might influence host immune homeostasis. PMID:23874157

  12. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults.

    Directory of Open Access Journals (Sweden)

    Nadja Larsen

    Full Text Available BACKGROUND: Recent evidence suggests that there is a link between metabolic diseases and bacterial populations in the gut. The aim of this study was to assess the differences between the composition of the intestinal microbiota in humans with type 2 diabetes and non-diabetic persons as control. METHODS AND FINDINGS: The study included 36 male adults with a broad range of age and body-mass indices (BMIs, among which 18 subjects were diagnosed with diabetes type 2. The fecal bacterial composition was investigated by real-time quantitative PCR (qPCR and in a subgroup of subjects (N = 20 by tag-encoded amplicon pyrosequencing of the V4 region of the 16S rRNA gene. The proportions of phylum Firmicutes and class Clostridia were significantly reduced in the diabetic group compared to the control group (P = 0.03. Furthermore, the ratios of Bacteroidetes to Firmicutes as well as the ratios of Bacteroides-Prevotella group to C. coccoides-E. rectale group correlated positively and significantly with plasma glucose concentration (P = 0.04 but not with BMIs. Similarly, class Betaproteobacteria was highly enriched in diabetic compared to non-diabetic persons (P = 0.02 and positively correlated with plasma glucose (P = 0.04. CONCLUSIONS: The results of this study indicate that type 2 diabetes in humans is associated with compositional changes in intestinal microbiota. The level of glucose tolerance should be considered when linking microbiota with metabolic diseases such as obesity and developing strategies to control metabolic diseases by modifying the gut microbiota.

  13. Gut microbial ecosystem and colonization resistance%肠道微生态与定植抗力

    Institute of Scientific and Technical Information of China (English)

    沈定树; 陈素云

    2012-01-01

    Recently developed molecular biology approaches indicate that gut microbiota is dominated by relatively few divisions that are highly diversity at the strain/subspecies level. The microbiota and host select each other to form a superorgan-ism. As gut microbiota is made up by many kinds cell line, there is capability of message communication. It is an important effect in nutrient, immunity and metabolism of host. The mechanistic basis of CR is incompletely defined. At least three mechanisms seem to contribute: (1) direct inhibition of pathogen growth by microbiota-derived substances, (2) nutrient depletion by microbiota growth, and (3) microbiota-induced stimulation of innate and adaptive immune responses.%分子生物学技术的研究表明,肠道微生物群落无论是亚种或菌株水平有极大的多样性,宿主与微生物之间相互选择,构成了一个相对稳定的超级生物体.由于微生物群落是由多种细胞系组成,细胞间或细胞与宿主之间有信息交流能力,在宿主的营养、免疫和代谢中有重作用.肠道微生物定植抗力机制还未完全清楚,但至少有三种机制认为:(1)正常肠道微生物的代谢物可直接抑制致病菌的生长;(2)正常肠道微生物的生长可以竟争性的消耗掉致病菌所需的营养物质;(3)正常肠道微生物可诱导或刺激宿主的先天和后于的免疫反应.

  14. Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health.

    Science.gov (United States)

    Wasielewski, Helen; Alcock, Joe; Aktipis, Athena

    2016-05-01

    Diet has been known to play an important role in human health since at least the time period of the ancient Greek physician Hippocrates. In the last decade, research has revealed that microorganisms inhabiting the digestive tract, known as the gut microbiota, are critical factors in human health. This paper draws on concepts of cooperation and conflict from ecology and evolutionary biology to make predictions about host-microbiota interactions involving nutrients. To optimally extract energy from some resources (e.g., fiber), hosts require cooperation from microbes. Other nutrients can be utilized by both hosts and microbes (e.g., simple sugars, iron) in their ingested form, which may lead to greater conflict over these resources. This framework predicts that some negative health effects of foods are driven by the direct effects of these foods on human physiology and by indirect effects resulting from microbiome-host competition and conflict (e.g., increased invasiveness and inflammation). Similarly, beneficial effects of some foods on host health may be enhanced by resource sharing and other cooperative behaviors between host and microbes that may downregulate inflammation and virulence. Given that some foods cultivate cooperation between hosts and microbes while others agitate conflict, host-microbe interactions may be novel targets for interventions aimed at improving nutrition and human health.

  15. Natural and human impacts on ecosystem services in Guanzhong - Tianshui economic region of China.

    Science.gov (United States)

    Li, Jing; Zhou, Z X

    2016-04-01

    Due to the accelerated growth of society, the gaps between the capacity of ecosystems to provide services and human needs are steadily widening. Natural, semi-natural, or managed ecosystems had been able to provide ecosystem services to meet the needs of social development. Four agricultural ecosystem services (net primary production (NPP), carbon sequestration and oxygen production (CSOP), water interception, soil conservation and agriculture production) were quantified in Guanzhong-Tianshui economic region. Estimates of ecosystem services were obtained from the analysis of satellite imagery and the use of well-known models. Based on the ecological services in Guanzhong-Tianshui economic region, this study mainly analysed the driving mechanism of the changes from the two aspects of natural drivers and human drivers. Natural drivers (climate, soil, elevation, land cover) had incentive to the ecological services. Human activity was quantified by an integrated human activity index (HAI) based on population density, farmland ratio, and the influence of road networks and residential areas. We found relationships between ecosystem services, human activities and many natural factors, however these varied according to the service studied. Human activities were mostly negatively related to each ecosystem services, while population and residential land ware positively related to agricultural production. Land use change had made a contribution to ecosystem services. Based on the selected ecosystem services and HAI, we provided sustainable ecosystem management suggestions.

  16. Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans : A Randomized Double-Blind Placebo-Controlled Trial

    NARCIS (Netherlands)

    Reijnders, Dorien; Goossens, Gijs H.; Hermes, Gerben D. A.; Neis, Evelien P. J. G.; van der Beek, Christina M.; Most, Jasper; Holst, Jens J.; Lenaerts, Kaatje; Kootte, Ruud S.; Nieuwdorp, Max; Groen, Albert K.; Damink, Steven W. M. Olde; Boekschoten, Mark V.; Smidt, Hauke; Zoetendal, Erwin G.; Dejong, Cornelis H. C.; Blaak, Ellen E.

    2016-01-01

    The gut microbiota has been implicated in obesity and cardiometabolic diseases, although evidence in humans is scarce. We investigated how gut microbiota manipulation by antibiotics (7-day administration of amoxicillin, vancomycin, or placebo) affects host metabolism in 57 obese, prediabetic men.

  17. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism

    OpenAIRE

    Douglas J. Morrison; Preston, Tom

    2016-01-01

    ABSTRACT The formation of SCFA is the result of a complex interplay between diet and the gut microbiota within the gut lumen environment. The discovery of receptors, across a range of cell and tissue types for which short chain fatty acids SCFA appear to be the natural ligands, has led to increased interest in SCFA as signaling molecules between the gut microbiota and the host. SCFA represent the major carbon flux from the diet through the gut microbiota to the host and evidence is emerging f...

  18. Pyrene metabolites in the hepatopancreas and gut of the isopod Porcellio scaber, a new biomarker for polycyclic aromatic hydrocarbon exposure in terrestrial ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Stroomberg, G.J.; Knecht, J.A. de; Ariese, F.; Gestel, C.A.M. Van; Velthorst, N.H.

    1999-10-01

    The object of this study was to investigate the formation of pyrene metabolites by the isopod Porcellio scaber as a possible tool in the environmental risk assessment of polycyclic aromatic hydrocarbon (PAH) exposure in terrestrial ecosystems. The formation of pyrene metabolites was studied after either pulse exposure to a single high dose, or prolonged exposure (14 d) to a lower dosage. Exposure studies were carried out with unlabeled or radiolabeled pyrene, ion pair chromatography was used for analysis, and reference conjugates were synthesized. The authors also measured pyrene metabolites in field-exposed animals, to explore their use as biomarkers of PAH exposure. Analysis of the hepatopancreas and gut of single isopods revealed the formation of five products, one of which was 1-hydroxypyrene. Four of the remaining products were identified as phase 2 metabolites of 1-hydroxypyrene, with UV absorption and fluorescence characteristics similar to that of pyrene. One metabolite was identified as pyrene-1-glucoside, which is in accordance with high rates of glucosidation, reported for these isopods. Another conjugate was identified as pyrene-1-sulfate. None of the metabolites coeluted with a pyrene-1-glucuronide reference obtained from fish bile. A fifth metabolite detected by on-line scintillation detection did not exhibit any absorption at 340 nm, possibly because one of the aromatic rings of pyrene had lost its aromatic character. Although pyrene is not known for its toxicity, it usually co-occurs with other PAHs that are transformed into toxic products. Investigating the metabolism of pyrene can provide information with regard to the biotransformation capacity of invertebrate species and uptake and elimination kinetics. Because pyrene is one of the most predominant PAHs in the environment, analysis of its metabolites provides an extra tool for the environmental risk assessment of ecosystems with regard to PAH exposure, bioavailability, and biotransformation.

  19. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota

    Energy Technology Data Exchange (ETDEWEB)

    Hibberd, Matthew C. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Research; Wu, Meng [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology; Rodionov, Dmitry A. [Russian Academy of Sciences (RAS), Moscow (Russian Federation). A.A. Kharkevich Inst. for Information Transmission Problems; Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States); Li, Xiaoqing [Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States); Cheng, Jiye [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc; Griffin, Nicholas W. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc; Barratt, Michael J. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc; Giannone, Richard J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division; Hettich, Robert L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division; Osterman, Andrei L. [Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States); Gordon, Jeffrey I. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc

    2017-05-17

    Micronutrient deficiencies afflict two billion people. And while the impact of these imbalances on host biology has been studied extensively, much less is known about their effects on the developing or adult gut microbiota. Thus, we established a community of 44 cultured, sequenced human gut-derived bacterial species in gnotobiotic mice and fed the animals a defined, micronutrient-sufficient diet, followed by a derivative diet devoid of vitamin A, folate, iron or zinc, followed by return to the sufficient diet. Acute vitamin A deficiency had the largest effect on community structure and meta-transcriptome, with Bacteroides vulgatus, a prominent responder, increasing its abundance in the absence of vitamin A, and manifesting transcriptional changes involving various metabolic pathways. Applying retinol selection to a library of 30,300 B. vulgatus transposon mutants revealed that disruption of acrR abrogated retinol sensitivity. Genetic complementation studies, microbial RNA-Seq, and transcription factor binding assays disclosed that AcrR functions as a repressor of an adjacent AcrAB-TolC efflux system plus other members of its regulon. Retinol efflux measurements in wild-type, acrR-mutant, and complemented acrR mutant strains, plus treatment with a pharmacologic inhibitor of the efflux system, revealed that AcrAB-TolC is a determinant of retinol and bile acid sensitivity. We associated acute vitamin A deficiency with altered bile acid metabolism in vivo, raising the possibility that retinol, bile acid metabolites, and AcrAB-TolC interact to influence the fitness of B. vulgatus and perhaps other microbiota members. This type of preclinical model can help develop mechanistic insights about and more effective treatment strategies for micronutrient deficiencies.

  20. Characterization of functional properties of Enterococcus faecium strains isolated from human gut.

    Science.gov (United States)

    İspirli, Hümeyra; Demirbaş, Fatmanur; Dertli, Enes

    2015-11-01

    The aim of this work was to characterize the functional properties of Enterococcus faecium strains identified after isolation from human faeces. Of these isolates, strain R13 showed the best resistance to low pH, bile salts, and survival in the simulated in vitro digestion assay, and demonstrated an important level of adhesion to hexadecane as a potential probiotic candidate. Analysis of the antibiotic resistance of E. faecium strains indicated that in general these isolates were sensitive to the tested antibiotics and no strain appeared to be resistant to vancomycin. Examination of the virulence determinants for E. faecium strains demonstrated that all strains contained the virulence genes common in gut- and food-originated enterococci, and strain R13 harboured the lowest number of virulence genes. Additionally, no strain contained the genes related to cytolysin metabolism and showed hemolytic activity. The antimicrobial role of E. faecium strains was tested against several pathogens, in which different levels of inhibitory effects were observed, and strain R13 was inhibitory to all tested pathogens. PCR screening of genes encoding enterocin A and B indicated the presence of these genes in E. faecium strains. Preliminary characterization of bacteriocins revealed that their activity was lost after proteolytic enzyme treatments, but no alteration in antimicrobial activity was observed at different pHs (3.5 to 9.5) and after heat treatments. In conclusion, this study revealed the functional characteristics of E. faecium R13 as a gut isolate, and this strain could be developed as a new probiotic after further tests.

  1. Recent advances and remaining gaps in our knowledge of associations between gut microbiota and human health

    Institute of Scientific and Technical Information of China (English)

    Volker Mai; Peter V Draganov

    2009-01-01

    The complex gut microbial flora harbored by individuals (microbiota) has long been proposed to contribute to intestinal health as well as disease. Pre- and probiotic products aimed at improving health by modifying microbiota composition have already become widely available and acceptance of these products appears to be on the rise. However, although required for the development of effective microbiota based interventions, our basic understanding of microbiota variation on a population level and its dynamics within individuals is still rudimentary. Powerful new parallel sequence technologies combined with other efficient molecular microbiota analysis methods now allow for comprehensive analysis of microbiota composition in large human populations. Recent findings in the field strongly suggest that microbiota contributes to the development of obesity, atopic diseases, inflammatory bowel diseases and intestinal cancers. Through the ongoing National Institutes of Health Roadmap 'Human of the world, a large coordinated effort is currently underway to study how microbiota can impact human health. Translating findings from these studies into effective interventions that can improve health,possibly personalized based on an individuals existing microbiota, will be the task for the next decade(s).

  2. Ecosystem Functions Connecting Contributions from Ecosystem Services to Human Wellbeing in a Mangrove System in Northern Taiwan.

    Science.gov (United States)

    Hsieh, Hwey-Lian; Lin, Hsing-Juh; Shih, Shang-Shu; Chen, Chang-Po

    2015-06-09

    The present study examined a mangrove ecosystem in northern Taiwan to determine how the various components of ecosystem function, ecosystem services and human wellbeing are connected. The overall contributions of mangrove services to specific components of human wellbeing were also assessed. A network was developed and evaluated by an expert panel consisting of hydrologists, ecologists, and experts in the field of culture, landscape or architecture. The results showed that supporting habitats was the most important function to human wellbeing, while water quality, habitable climate, air quality, recreational opportunities, and knowledge systems were services that were strongly linked to human welfare. Security of continuous supply of services appeared to be the key to a comfortable life. From a bottom-up and top-down perspective, knowledge systems (a service) were most supported by ecosystem functions, while the security of continuous supply of services (wellbeing) had affected the most services. In addition, the overall benefits of mangrove services to human prosperity concentrated on mental health, security of continuous supply of services, and physical health.

  3. Gut pathogens: invaders and turncoats in a complex cosmos.

    Science.gov (United States)

    Hermon-Taylor, John

    2009-02-03

    Intestinal infections and diarrhoeal diseases of humans are under-reported yet each account worldwide for more deaths than those from Tuberculosis. For external gut pathogens to do this they have to penetrate, survive and prosper in an established and defended ecosystem comprising the human gut with a massive immune system, a structured tight mucosal lining and a lumen densely occupied by a huge community of diverse bacteria adapted to their environment and optimised in a balanced and mutually beneficial relationship with its host.

  4. Gut pathogens: invaders and turncoats in a complex cosmos

    Directory of Open Access Journals (Sweden)

    Hermon-Taylor John

    2009-02-01

    Full Text Available Abstract Intestinal infections and diarrhoeal diseases of humans are under-reported yet each account worldwide for more deaths than those from Tuberculosis. For external gut pathogens to do this they have to penetrate, survive and prosper in an established and defended ecosystem comprising the human gut with a massive immune system, a structured tight mucosal lining and a lumen densely occupied by a huge community of diverse bacteria adapted to their environment and optimised in a balanced and mutually beneficial relationship with its host.

  5. Gut does not contribute to systemic ammonia release in humans without portosystemic shunting

    NARCIS (Netherlands)

    van de Poll, Marcel C. G.; Ligthart-Melis, Gerdien C.; Damink, Steven W. M. Olde; van Leeuwen, Paul A. M.; Beets-Tan, Regina G. H.; Deutz, Nicolaas E. P.; Wigmore, Stephen J.; Soeters, Peter B.; Dejong, Cornelis H. C.

    2008-01-01

    The gut is classically seen as the main source of circulating ammonia. However, the contribution of the intestines to systemic ammonia production may be limited by hepatic extraction of portal-derived ammonia. Recent data suggest that the kidney may be more important than the gut for systemic ammoni

  6. Impact of the gut microbiota on inflammation, obesity, and metabolic disease.

    Science.gov (United States)

    Boulangé, Claire L; Neves, Ana Luisa; Chilloux, Julien; Nicholson, Jeremy K; Dumas, Marc-Emmanuel

    2016-04-20

    The human gut harbors more than 100 trillion microbial cells, which have an essential role in human metabolic regulation via their symbiotic interactions with the host. Altered gut microbial ecosystems have been associated with increased metabolic and immune disorders in animals and humans. Molecular interactions linking the gut microbiota with host energy metabolism, lipid accumulation, and immunity have also been identified. However, the exact mechanisms that link specific variations in the composition of the gut microbiota with the development of obesity and metabolic diseases in humans remain obscure owing to the complex etiology of these pathologies. In this review, we discuss current knowledge about the mechanistic interactions between the gut microbiota, host energy metabolism, and the host immune system in the context of obesity and metabolic disease, with a focus on the importance of the axis that links gut microbes and host metabolic inflammation. Finally, we discuss therapeutic approaches aimed at reshaping the gut microbial ecosystem to regulate obesity and related pathologies, as well as the challenges that remain in this area.

  7. The Role of the Gut Microbiota in Childhood Obesity

    DEFF Research Database (Denmark)

    Pihl, Andreas Friis; Fonvig, Cilius Esmann; Stjernholm, Theresa

    2016-01-01

    BACKGROUND: Childhood and adolescent obesity has reached epidemic proportions worldwide. The pathogenesis of obesity is complex and multifactorial, in which genetic and environmental contributions seem important. The gut microbiota is increasingly documented to be involved in the dysmetabolism...... associated with obesity. METHODS: We conducted a systematic search for literature available before October 2015 in the PubMed and Scopus databases, focusing on the interplay between the gut microbiota, childhood obesity, and metabolism. RESULTS: The review discusses the potential role of the bacterial...... component of the human gut microbiota in childhood and adolescent-onset obesity, with a special focus on the factors involved in the early development of the gut bacterial ecosystem, and how modulation of this microbial community might serve as a basis for new therapeutic strategies in combating childhood...

  8. A simulation of microbial competition in the human colonic ecosystem.

    Science.gov (United States)

    Coleman, M E; Dreesen, D W; Wiegert, R G

    1996-10-01

    Many investigations of the interactions of microbial competitors in the gastrointestinal tract used continuous-flow anaerobic cultures. The simulation reported here was a deterministic 11-compartment model coded by using the C programming language and based on parameters from published in vitro studies and assumptions were data were unavailable. The resource compartments were glucose, lactose and sucrose, starch, sorbose, and serine. Six microbial competitors included indigenous nonpathogenic colonizers of the human gastrointestinal tract (Escherichia coli, Enterobacter aerogenes, Bacteroids ovatus, Fusobacterium varium, and Enterococcus faecalis) and the potential human enteropathogen Salmonella typhimurium. Flows of carbon from the resources to the microbes were modified by resource and space controls. Partitioning of resources to the competitors that could utilize them was calculated at each iteration on the basis of availability of all resources by feeding preference functions. Resources did not accumulate during iterations of the model. The results of the computer simulation of microbial competition model and for various modifications of the model. The results were based on few measured parameters but may be useful in the design of user-friendly software to aid researchers in defining and manipulating the microbial ecology of colonic ecosystems as relates to food-borne disease.

  9. Human-derived gut microbiota modulates colonic secretion in mice by regulating 5-HT3 receptor expression via acetate production.

    Science.gov (United States)

    Bhattarai, Yogesh; Schmidt, Bradley A; Linden, David R; Larson, Eric D; Grover, Madhusudan; Beyder, Arthur; Farrugia, Gianrico; Kashyap, Purna C

    2017-07-01

    Serotonin [5-hydroxytryptamine (5-HT)], an important neurotransmitter and a paracrine messenger in the gastrointestinal tract, regulates intestinal secretion by its action primarily on 5-HT3 and 5-HT4 receptors. Recent studies highlight the role of gut microbiota in 5-HT biosynthesis. In this study, we determine whether human-derived gut microbiota affects host secretory response to 5-HT and 5-HT receptor expression. We used proximal colonic mucosa-submucosa preparation from age-matched Swiss Webster germ-free (GF) and humanized (HM; ex-GF colonized with human gut microbiota) mice. 5-HT evoked a significantly greater increase in short-circuit current (ΔIsc) in GF compared with HM mice. Additionally, 5-HT3 receptor mRNA and protein expression was significantly higher in GF compared with HM mice. Ondansetron, a 5-HT3 receptor antagonist, inhibited 5-HT-evoked ΔIsc in GF mice but not in HM mice. Furthermore, a 5-HT3 receptor-selective agonist, 2-methyl-5-hydroxytryptamine hydrochloride, evoked a significantly higher ΔIsc in GF compared with HM mice. Immunohistochemistry in 5-HT3A-green fluorescent protein mice localized 5-HT3 receptor expression to enterochromaffin cells in addition to nerve fibers. The significant difference in 5-HT-evoked ΔIsc between GF and HM mice persisted in the presence of tetrodotoxin (TTX) but was lost after ondansetron application in the presence of TTX. Application of acetate (10 mM) significantly lowered 5-HT3 receptor mRNA in GF mouse colonoids. We conclude that host secretory response to 5-HT may be modulated by gut microbiota regulation of 5-HT3 receptor expression via acetate production. Epithelial 5-HT3 receptor may function as a mediator of gut microbiota-driven change in intestinal secretion.NEW & NOTEWORTHY We found that gut microbiota alters serotonin (5-HT)-evoked intestinal secretion in a 5-HT3 receptor-dependent mechanism and gut microbiota metabolite acetate alters 5-HT3 receptor expression in colonoids.View this article

  10. The Gut Microbiota and Human Health with an Emphasis on the Use of Microencapsulated Bacterial Cells

    Directory of Open Access Journals (Sweden)

    Satya Prakash

    2011-01-01

    Full Text Available The gut microbiota plays a crucial role in maintaining health. Alterations of the gut bacterial population have been associated with a number of diseases. Past and recent studies suggest that one can positively modify the contents of the gut microbiota by introducing prebiotics, probiotics, synbiotics, and other therapeutics. This paper focuses on probiotic modulation of the gut microbiota by their delivery to the lower gastrointestinal tract (GIT. There are numerous obstacles to overcome before microorganisms can be utilized as therapeutics. One important limitation is the delivery of viable cells to the lower GIT without a significant loss of cell viability and metabolic features through the harsh conditions of the upper GIT. Microencapsulation has been shown to overcome this, with various types of microcapsules available for resolving this limitation. This paper discusses the gut microbiota and its role in disease, with a focus on microencapsulated probiotics and their potentials and limitations.

  11. A human volunteer study to assess the impact of confectionery sweeteners on the gut microbiota composition.

    Science.gov (United States)

    Beards, Emma; Tuohy, Kieran; Gibson, Glenn

    2010-09-01

    Sweeteners are being sourced to lower the energetic value of confectionery including chocolates. Some, especially non-digestible carbohydrates, may possess other benefits for human health upon their fermentation by the colonic microbiota. The present study assessed non-digestible carbohydrate sweeteners, selected for use in low-energy chocolates, for their ability to beneficially modulate faecal bacterial profiles in human volunteers. Forty volunteers consumed a test chocolate (low-energy or experimental chocolate) containing 22.8 g of maltitol (MTL), MTL and polydextrose (PDX), or MTL and resistant starch for fourteen consecutive days. The dose of the test chocolates was doubled every 2 weeks over a 6-week period. Numbers of faecal bifidobacteria significantly increased with all the three test treatments. Chocolate containing the PDX blend also significantly increased faecal lactobacilli (P = 0.00 001) after the 6 weeks. The PDX blend also showed significant increases in faecal propionate and butyrate (P = 0.002 and 0.006, respectively). All the test chocolates were well tolerated with no significant change in bowel habit or intestinal symptoms even at a daily dose of 45.6 g of non-digestible carbohydrate sweetener. This is of importance not only for giving manufacturers a sugar replacement that can reduce energetic content, but also for providing a well-tolerated means of delivering high levels of non-digestible carbohydrates into the colon, bringing about improvements in the biomarkers of gut health.

  12. Bifidobacteria and Their Role as Members of the Human Gut Microbiota.

    Science.gov (United States)

    O'Callaghan, Amy; van Sinderen, Douwe

    2016-01-01

    Members of the genus Bifidobacterium are among the first microbes to colonize the human gastrointestinal tract and are believed to exert positive health benefits on their host. Due to their purported health-promoting properties, bifidobacteria have been incorporated into many functional foods as active ingredients. Bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract, such as the human oral cavity, the insect gut and sewage. To be able to survive in these particular ecological niches, bifidobacteria must possess specific adaptations to be competitive. Determination of genome sequences has revealed genetic attributes that may explain bifidobacterial ecological fitness, such as metabolic abilities, evasion of the host adaptive immune system and colonization of the host through specific appendages. However, genetic modification is crucial toward fully elucidating the mechanisms by which bifidobacteria exert their adaptive abilities and beneficial properties. In this review we provide an up to date summary of the general features of bifidobacteria, whilst paying particular attention to the metabolic abilities of this species. We also describe methods that have allowed successful genetic manipulation of bifidobacteria.

  13. Effects of almond and pistachio consumption on gut microbiota composition in a randomised cross-over human feeding study.

    Science.gov (United States)

    Ukhanova, Maria; Wang, Xiaoyu; Baer, David J; Novotny, Janet A; Fredborg, Marlene; Mai, Volker

    2014-06-28

    The modification of microbiota composition to a 'beneficial' one is a promising approach for improving intestinal as well as overall health. Natural fibres and phytochemicals that reach the proximal colon, such as those present in various nuts, provide substrates for the maintenance of healthy and diverse microbiota. The effects of increased consumption of specific nuts, which are rich in fibre as well as various phytonutrients, on human gut microbiota composition have not been investigated to date. The objective of the present study was to determine the effects of almond and pistachio consumption on human gut microbiota composition. We characterised microbiota in faecal samples collected from volunteers in two separate randomised, controlled, cross-over feeding studies (n 18 for the almond feeding study and n 16 for the pistachio feeding study) with 0, 1·5 or 3 servings/d of the respective nuts for 18 d. Gut microbiota composition was analysed using a 16S rRNA-based approach for bacteria and an internal transcribed spacer region sequencing approach for fungi. The 16S rRNA sequence analysis of 528 028 sequence reads, retained after removing low-quality and short-length reads, revealed various operational taxonomic units that appeared to be affected by nut consumption. The effect of pistachio consumption on gut microbiota composition was much stronger than that of almond consumption and included an increase in the number of potentially beneficial butyrate-producing bacteria. Although the numbers of bifidobacteria were not affected by the consumption of either nut, pistachio consumption appeared to decrease the number of lactic acid bacteria (Ppistachios appears to be an effective means of modifying gut microbiota composition.

  14. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow.

    Science.gov (United States)

    Kim, Hyun Jung; Huh, Dongeun; Hamilton, Geraldine; Ingber, Donald E

    2012-06-21

    Development of an in vitro living cell-based model of the intestine that mimics the mechanical, structural, absorptive, transport and pathophysiological properties of the human gut along with its crucial microbial symbionts could accelerate pharmaceutical development, and potentially replace animal testing. Here, we describe a biomimetic 'human gut-on-a-chip' microdevice composed of two microfluidic channels separated by a porous flexible membrane coated with extracellular matrix (ECM) and lined by human intestinal epithelial (Caco-2) cells that mimics the complex structure and physiology of living intestine. The gut microenvironment is recreated by flowing fluid at a low rate (30 μL h(-1)) producing low shear stress (0.02 dyne cm(-2)) over the microchannels, and by exerting cyclic strain (10%; 0.15 Hz) that mimics physiological peristaltic motions. Under these conditions, a columnar epithelium develops that polarizes rapidly, spontaneously grows into folds that recapitulate the structure of intestinal villi, and forms a high integrity barrier to small molecules that better mimics whole intestine than cells in cultured in static Transwell models. In addition, a normal intestinal microbe (Lactobacillus rhamnosus GG) can be successfully co-cultured for extended periods (>1 week) on the luminal surface of the cultured epithelium without compromising epithelial cell viability, and this actually improves barrier function as previously observed in humans. Thus, this gut-on-a-chip recapitulates multiple dynamic physical and functional features of human intestine that are critical for its function within a controlled microfluidic environment that is amenable for transport, absorption, and toxicity studies, and hence it should have great value for drug testing as well as development of novel intestinal disease models.

  15. A primary human macrophage-enteroid co-culture model to investigate mucosal gut physiology and host-pathogen interactions

    Science.gov (United States)

    Noel, Gaelle; Baetz, Nicholas W.; Staab, Janet F.; Donowitz, Mark; Kovbasnjuk, Olga; Pasetti, Marcela F.; Zachos, Nicholas C.

    2017-01-01

    Integration of the intestinal epithelium and the mucosal immune system is critical for gut homeostasis. The intestinal epithelium is a functional barrier that secludes luminal content, senses changes in the gut microenvironment, and releases immune regulators that signal underlying immune cells. However, interactions between epithelial and innate immune cells to maintain barrier integrity and prevent infection are complex and poorly understood. We developed and characterized a primary human macrophage-enteroid co-culture model for in-depth studies of epithelial and macrophage interactions. Human intestinal stem cell-derived enteroid monolayers co-cultured with human monocyte-derived macrophages were used to evaluate barrier function, cytokine secretion, and protein expression under basal conditions and following bacterial infection. Macrophages enhanced barrier function and maturity of enteroid monolayers as indicated by increased transepithelial electrical resistance and cell height. Communication between the epithelium and macrophages was demonstrated through morphological changes and cytokine production. Intraepithelial macrophage projections, efficient phagocytosis, and stabilized enteroid barrier function revealed a coordinated response to enterotoxigenic and enteropathogenic E. coli infections. In summary, we have established the first primary human macrophage-enteroid co-culture system, defined conditions that allow for a practical and reproducible culture model, and demonstrated its suitability to study gut physiology and host responses to enteric pathogens. PMID:28345602

  16. Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip.

    Science.gov (United States)

    Kim, Hyun Jung; Li, Hu; Collins, James J; Ingber, Donald E

    2016-01-05

    A human gut-on-a-chip microdevice was used to coculture multiple commensal microbes in contact with living human intestinal epithelial cells for more than a week in vitro and to analyze how gut microbiome, inflammatory cells, and peristalsis-associated mechanical deformations independently contribute to intestinal bacterial overgrowth and inflammation. This in vitro model replicated results from past animal and human studies, including demonstration that probiotic and antibiotic therapies can suppress villus injury induced by pathogenic bacteria. By ceasing peristalsis-like motions while maintaining luminal flow, lack of epithelial deformation was shown to trigger bacterial overgrowth similar to that observed in patients with ileus and inflammatory bowel disease. Analysis of intestinal inflammation on-chip revealed that immune cells and lipopolysaccharide endotoxin together stimulate epithelial cells to produce four proinflammatory cytokines (IL-8, IL-6, IL-1β, and TNF-α) that are necessary and sufficient to induce villus injury and compromise intestinal barrier function. Thus, this human gut-on-a-chip can be used to analyze contributions of microbiome to intestinal pathophysiology and dissect disease mechanisms in a controlled manner that is not possible using existing in vitro systems or animal models.

  17. Predicting Drug Extraction in the Human Gut Wall: Assessing Contributions from Drug Metabolizing Enzymes and Transporter Proteins using Preclinical Models.

    Science.gov (United States)

    Peters, Sheila Annie; Jones, Christopher R; Ungell, Anna-Lena; Hatley, Oliver J D

    2016-06-01

    Intestinal metabolism can limit oral bioavailability of drugs and increase the risk of drug interactions. It is therefore important to be able to predict and quantify it in drug discovery and early development. In recent years, a plethora of models-in vivo, in situ and in vitro-have been discussed in the literature. The primary objective of this review is to summarize the current knowledge in the quantitative prediction of gut-wall metabolism. As well as discussing the successes of current models for intestinal metabolism, the challenges in the establishment of good preclinical models are highlighted, including species differences in the isoforms; regional abundances and activities of drug metabolizing enzymes; the interplay of enzyme-transporter proteins; and lack of knowledge on enzyme abundances and availability of empirical scaling factors. Due to its broad specificity and high abundance in the intestine, CYP3A is the enzyme that is frequently implicated in human gut metabolism and is therefore the major focus of this review. A strategy to assess the impact of gut wall metabolism on oral bioavailability during drug discovery and early development phases is presented. Current gaps in the mechanistic understanding and the prediction of gut metabolism are highlighted, with suggestions on how they can be overcome in the future.

  18. Spatial Assessment of Forest Ecosystem Functions and Services using Human Relating Factors for SDG

    Science.gov (United States)

    Song, C.; Lee, W. K.; Jeon, S. W.; Kim, T.; Lim, C. H.

    2015-12-01

    Application of ecosystem service concept in environmental related decision making could be numerical and objective standard for policy maker between preserving and developing perspective of environment. However, pursuing maximum benefit from natural capital through ecosystem services caused failure by losing ecosystem functions through its trade-offs. Therefore, difference between ecosystem functions and services were demonstrated and would apply human relating perspectives. Assessment results of ecosystem functions and services can be divided 3 parts. Tree growth per year set as the ecosystem function factor and indicated through so called pure function map. After that, relating functions can be driven such as water conservation, air pollutant purification, climate change regulation, and timber production. Overall process and amount are numerically quantified. These functional results can be transferred to ecosystem services by multiplying economic unit value, so function reflecting service maps can be generated. On the other hand, above services, to implement more reliable human demand, human reflecting service maps are also be developed. As the validation, quantified ecosystem functions are compared with former results through pixel based analysis. Three maps are compared, and through comparing difference between ecosystem function and services and inversed trends in function based and human based service are analysed. In this study, we could find differences in PF, FRS, and HRS in relation to based ecosystem conditions. This study suggests that the differences in PF, FRS, and HRS should be understood in the decision making process for sustainable management of ecosystem services. Although the analysis is based on in sort existing process separation, it is important to consider the possibility of different usage of ecosystem function assessment results and ecosystem service assessment results in SDG policy making. Furthermore, process based functional approach

  19. Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

    National Research Council Canada - National Science Library

    McNulty, Nathan P; Wu, Meng; Erickson, Alison R; Pan, Chongle; Erickson, Brian K; Martens, Eric C; Pudlo, Nicholas A; Muegge, Brian D; Henrissat, Bernard; Hettich, Robert L; Gordon, Jeffrey I

    2013-01-01

    The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet...

  20. Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome: e1001637

    National Research Council Canada - National Science Library

    Nathan P McNulty; Meng Wu; Alison R Erickson; Chongle Pan; Brian K Erickson; Eric C Martens; Nicholas A Pudlo; Brian D Muegge; Bernard Henrissat; Robert L Hettich; Jeffrey I Gordon

    2013-01-01

      The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet...

  1. Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level

    National Research Council Canada - National Science Library

    Despres, Jordane; Forano, Evelyne; Lepercq, Pascale; Comtet-Marre, Sophie; Jubelin, Gregory; Chambon, Christophe; Yeoman, Carl J; Berg Miller, Margaret E; Fields, Christopher J; Martens, Eric; Terrapon, Nicolas; Henrissat, Bernard; White, Bryan A; Mosoni, Pascale

    2016-01-01

    .... In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1A...

  2. Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level

    National Research Council Canada - National Science Library

    Despres, Jordane; Forano, Evelyne; Lepercq, Pascale; Comtet-Marre, Sophie; Jubelin, Gregory; Chambon, Christophe; Yeoman, Carl J; Berg Miller, Margaret E; Fields, Christopher J; Martens, Eric; Terrapon, Nicolas; Henrissat, Bernard; White, Bryan A; Mosoni, Pascale

    2016-01-01

    .... In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Transcriptomic analyses...

  3. Impact of the gut microbiota, prebiotics, and probiotics on human health and disease.

    Science.gov (United States)

    Lin, Chuan-Sheng; Chang, Chih-Jung; Lu, Chia-Chen; Martel, Jan; Ojcius, David M; Ko, Yun-Fei; Young, John D; Lai, Hsin-Chih

    2014-01-01

    Recent studies have revealed that the gut microbiota regulates many physiological functions, ranging from energy regulation and cognitive processes to toxin neutralization and immunity against pathogens. Accordingly, alterations in the composition of the gut microbiota have been shown to contribute to the development of various chronic diseases. The main objectives of this review are to present recent breakthroughs in the study of the gut microbiota and show that intestinal bacteria play a critical role in the development of different disease conditions, including obesity, fatty liver disease, and lung infection. We also highlight the potential application of prebiotics and probiotics in maintaining optimal health and treating chronic inflammatory and immunity-related diseases.

  4. Rangeland Ecosystem Services: Nature's Supply and Human's Demands

    Science.gov (United States)

    Ecosystem services are the benefits that society receives from nature and they include the regulation of climate, the pollination of crops, the provisioning of intellectual inspiration and recreational environment, as well as many essential goods such as food, fiber, and wood. Rangeland ecosystem se...

  5. Conservation of gene cassettes among diverse viruses of the human gut.

    Directory of Open Access Journals (Sweden)

    Samuel Minot

    Full Text Available Viruses are a crucial component of the human microbiome, but large population sizes, high sequence diversity, and high frequencies of novel genes have hindered genomic analysis by high-throughput sequencing. Here we investigate approaches to metagenomic assembly to probe genome structure in a sample of 5.6 Gb of gut viral DNA sequence from six individuals. Tests showed that a new pipeline based on DeBruijn graph assembly yielded longer contigs that were able to recruit more reads than the equivalent non-optimized, single-pass approach. To characterize gene content, the database of viral RefSeq proteins was compared to the assembled viral contigs, generating a bipartite graph with functional cassettes linking together viral contigs, which revealed a high degree of connectivity between diverse genomes involving multiple genes of the same functional class. In a second step, open reading frames were grouped by their co-occurrence on contigs in a database-independent manner, revealing conserved cassettes of co-oriented ORFs. These methods reveal that free-living bacteriophages, while usually dissimilar at the nucleotide level, often have significant similarity at the level of encoded amino acid motifs, gene order, and gene orientation. These findings thus connect contemporary metagenomic analysis with classical studies of bacteriophage genomic cassettes. Software is available at https://sourceforge.net/projects/optitdba/.

  6. Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Lammerts van Bueren, Alicia; Saraf, Aakanksha; Martens, Eric C; Dijkhuizen, Lubbert

    2015-06-15

    Probiotic microorganisms are ingested as food or supplements and impart positive health benefits to consumers. Previous studies have indicated that probiotics transiently reside in the gastrointestinal tract and, in addition to modulating commensal species diversity, increase the expression of genes for carbohydrate metabolism in resident commensal bacterial species. In this study, it is demonstrated that the human gut commensal species Bacteroides thetaiotaomicron efficiently metabolizes fructan exopolysaccharide (EPS) synthesized by probiotic Lactobacillus reuteri strain 121 while only partially degrading reuteran and isomalto/malto-polysaccharide (IMMP) α-glucan EPS polymers. B. thetaiotaomicron metabolized these EPS molecules via the activation of enzymes and transport systems encoded by dedicated polysaccharide utilization loci specific for β-fructans and α-glucans. Reduced metabolism of reuteran and IMMP α-glucan EPS molecules may be due to reduced substrate binding by components of the starch utilization system (sus). This study reveals that microbial EPS substrates activate genes for carbohydrate metabolism in B. thetaiotaomicron and suggests that microbially derived carbohydrates provide a carbohydrate-rich reservoir for B. thetaiotaomicron nutrient acquisition in the gastrointestinal tract. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  7. Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

    Science.gov (United States)

    Ravcheev, Dmitry A.; Thiele, Ines

    2016-01-01

    Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM. PMID:26904004

  8. Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome.

    Science.gov (United States)

    Culligan, Eamonn P; Marchesi, Julian R; Hill, Colin; Sleator, Roy D

    2014-01-01

    In the current study, a number of salt-tolerant clones previously isolated from a human gut metagenomic library were screened using Phenotype MicroArray (PM) technology to assess their functional capacity. PM's can be used to study gene function, pathogenicity, metabolic capacity and identify drug targets using a series of specialized microtitre plate assays, where each well of the microtitre plate contains a different set of conditions and tests a different phenotype. Cellular respiration is monitored colorimetrically by the reduction of a tetrazolium dye. One clone, SMG 9, was found to be positive for utilization/transport of L-carnitine (a well-characterized osmoprotectant) in the presence of 6% w/v sodium chloride (NaCl). Subsequent experiments revealed a significant growth advantage in minimal media containing NaCl and L-carnitine. Fosmid sequencing revealed putative candidate genes responsible for the phenotype. Subsequent cloning of two genes did not replicate the L-carnitine-associated phenotype, although one of the genes, a σ(54)-dependent transcriptional regulator, did confer salt tolerance to Escherichia coli when expressed in isolation. The original clone, SMG 9, was subsequently found to have lost the original observed phenotype upon further investigation. Nevertheless, this study demonstrates the usefulness of a phenomic approach to assign a functional role to metagenome-derived clones.

  9. Transforming the Rockies: Human forces, settlement patterns, and ecosystem effects

    Science.gov (United States)

    Travis, William R.; Theobald, David M.; Fagre, Daniel B.

    2002-01-01

    The current ecological condition of the Rocky Mountains can be viewed from two somewhat opposing perspectives. The first is that human occupation has had relatively little effect on the Rockies: large natural, if not pristine, areas remain, and the region's open spaces provide wildlife habitat, majestic scenery, and a sense of wildness. Unlike the situation in, say, the Swiss Alps, where even high-elevation meadows have been mown and grazed intensively for as long as 500 years and many large mammals have been extirpated, most elements of Rocky Mountain landscapes and biota are reasonably unaltered. Even the presumption that Native Americans changed regional landscapes with deliberately set fires has been challenged by Baker and Ehle (2001) and others who think that most fires were lightning-caused or accidental ignitions. The second view is that humans have dramatically transformed the Rockies, at least since Euro-American settlement in the mid- to late 1800s. The slaughter of vast buffalo herds, the clearing of timber for railroad ties, and even the removal of whole hillsides in hydraulic placer mining represented substantial transformation. Ranch, resort, and residential development marks the latest incarnation of this transformation. Numerous, complex layers of land use have left landscape legacies, some of which may be unrecognized or underappreciated in modern assessments (Wohl 2001). Here we consider both perspectives because we are impressed with both the many effects of human use of the Rockies and the region's remaining wild landscapes. Ironically, much of the recent population growth and development in the Rockies is driven by the region's wild landscapes, which make the present widespread transformation seem all the more significant. It is, of course, the rapid clip of current human transformation—high population growth rates, pervasive rural residential development, and landscape fragmentation (Baron, Theobald, and Fagre 2000)—that worries

  10. “Lachnoclostridium touaregense,” a new bacterial species isolated from the human gut microbiota

    OpenAIRE

    M. Tidjani Alou; S. Khelaifia; B. La Scola; Cassir, N.

    2016-01-01

    We report the main characteristics of “Lachnoclostridium touaregense” strain Marseille-P2415T (= CSUR P2415 = DSM 102219), a new bacterial species isolated from the gut microbiota of a healthy young girl from Niger.

  11. ‘Lachnoclostridium massiliosenegalense’, a new bacterial species isolated from the human gut microbiota

    OpenAIRE

    M. Tidjani Alou; J.-C. Lagier; B. La Scola; Cassir, N.

    2016-01-01

    We report the main characteristics of ‘Lachnoclostridium massiliosenegalense’ strain mt23T (=CSUR P299 =DSM 102084), a new bacterial species isolated from the gut microbiota of a healthy young girl from Senegal.

  12. Arsenic Metabolism by Human Gut Microbiota upon In Vitro Digestion of Contaminated Soils

    Science.gov (United States)

    Background: Speciation analysis is essential when evaluating risks from arsenic (As) exposure. In an oral exposure scenario, the importance of presystemic metabolism by gut microorganisms has been evidenced with in vivo animal models and in vitro experiments with ...

  13. Arsenic Metabolism by Human Gut Microbiota upon In Vitro Digestion of Contaminated Soils

    Science.gov (United States)

    Background: Speciation analysis is essential when evaluating risks from arsenic (As) exposure. In an oral exposure scenario, the importance of presystemic metabolism by gut microorganisms has been evidenced with in vivo animal models and in vitro experiments with ...

  14. Human and rat gut microbiome composition is maintained following sleep restriction

    NARCIS (Netherlands)

    Zhang, Shirley L; Bai, Lei; Goel, Namni; Bailey, Aubrey; Jang, Christopher J; Bushman, Frederic D; Meerlo, Peter; Dinges, David F; Sehgal, Amita

    2017-01-01

    Insufficient sleep increasingly characterizes modern society, contributing to a host of serious medical problems. Loss of sleep is associated with metabolic diseases such as obesity and diabetes, cardiovascular disorders, and neurological and cognitive impairments. Shifts in gut microbiome compositi

  15. The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?

    Science.gov (United States)

    Doré, Joël; Multon, Marie-Christine; Béhier, Jehan-Michel

    2017-02-01

    From the moment of birth, each human being builds a microbe-host symbiosis which is key for the preservation of its health and well-being. This personal symbiotic coexistence is the result of progressive enrichments in microorganism diversity through external supplies. This diversity is nowadays massively overthrown by drastic changes related to clinical practice in birth management, environmental exposure, nutrition and healthcare behaviors. The last two generations have been the frame of massive modifications in life and food habits, with people being more and more sedentary, overfed and permeated with drugs and pollutants. We are now able to measure the impact of these changes on the gut microbiota diversity. Concomitantly, these modifications of lifestyle were associated with a dramatic increase in incidence of immune-mediated diseases including metabolic, allergic and inflammatory diseases and most likely neurodegenerative and psychiatric disorders. Microbiota is becoming a hot topic in the scientific community and in the mainstream media. The number of scientific publications increased by up to a factor three over the last five years, with gastrointestinal and metabolic diseases being the most productive areas. In the intellectual property landscape, the patent families on microbiota have more than doubled in the meantime. In parallel, funding either from National Institutes (e.g. from NIH which funds research mainly in the field of allergies, infections, cancer and cardiovascular diseases, from the White House which launched the national microbiome initiative) or by pharmaceutical companies follow the same trend, showing a boost and a strong support in the research field on microbiota. All major health players are investing in microbiome research as shown by the number of deals signed and by funding during 2015. The Giens round table addressed how the medicine of tomorrow, considering human beings as a human-microbe symbiotic supraorganism, could leverage

  16. Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species.

    Science.gov (United States)

    Chatzidaki-Livanis, Maria; Geva-Zatorsky, Naama; Comstock, Laurie E

    2016-03-29

    Type VI secretion systems (T6SSs) are multiprotein complexes best studied in Gram-negative pathogens where they have been shown to inhibit or kill prokaryotic or eukaryotic cells and are often important for virulence. We recently showed that T6SS loci are also widespread in symbiotic human gut bacteria of the order Bacteroidales, and that these T6SS loci segregate into three distinct genetic architectures (GA). GA1 and GA2 loci are present on conserved integrative conjugative elements (ICE) and are transferred and shared among diverse human gut Bacteroidales species. GA3 loci are not contained on conserved ICE and are confined to Bacteroides fragilis Unlike GA1 and GA2 T6SS loci, most GA3 loci do not encode identifiable effector and immunity proteins. Here, we studied GA3 T6SSs and show that they antagonize most human gut Bacteroidales strains analyzed, except for B. fragilis strains with the same T6SS locus. A combination of mutation analyses,trans-protection analyses, and in vitro competition assays, allowed us to identify novel effector and immunity proteins of GA3 loci. These proteins are not orthologous to known proteins, do not contain identified motifs, and most have numerous predicted transmembrane domains. Because the genes encoding effector and immunity proteins are contained in two variable regions of GA3 loci, GA3 T6SSs of the species B. fragilis are likely the source of numerous novel effector and immunity proteins. Importantly, we show that the GA3 T6SS of strain 638R is functional in the mammalian gut and provides a competitive advantage to this organism.

  17. Effect of oligosaccharides on the adhesion of gut bacteria to human HT-29 cells.

    Science.gov (United States)

    Altamimi, M; Abdelhay, O; Rastall, R A

    2016-06-01

    The influence of five oligosaccharides (cellobiose, stachyose, raffinose, lactulose and chito-oligosaccharides) on the adhesion of eight gut bacteria (Bifidobacterium bifidum ATCC 29521, Bacteroides thetaiotaomicron ATCC 29148D-5, Clostridium leptum ATCC 29065, Blautia coccoides ATCC 29236, Faecalibacterium prausnitzii ATCC 27766, Bacteroides fragilis ATCC 23745, Clostridium difficile ATCC 43255 and Lactobacillus casei ATCC 393) to mucous secreting and non-mucous secreting HT-29 human epithelial cells, was investigated. In pure culture, the bacteria showed variations in their ability to adhere to epithelial cells. The effect of oligosaccharides diminished adhesion and the presence of mucus played a major factor in adhesion, likely due to high adhesiveness to mucins present in the native human mucus layer covering the whole cell surface. However, clostridia displayed almost the same level of adhesion either with or without mucus being present. Bl. coccoides adhesion was decreased by stachyose and cellobiose in non-mucus-secreting cells in pure culture, while in mixed faecal culture cellobiose displayed the highest antiadhesive activity with an overall average of 65% inhibition amongst tested oligomers and lactulose displayed the lowest with an average of 47.4%. Bifidobacteria, Bacteroides, lactobacilli and clostridia were inhibited within the following ranges 47-78%, 32-65%, 11.7-58% and 64-85% respectively. This means that clostridia were the most strongly influenced members of the microflora amongst the bacterial groups tested in mixed culture. In conclusion, introducing oligosaccharides which are candidate prebiotics into pure or mixed cultures has affected bacterial adhesion. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Targeting the ecology within: The role of the gut-brain axis and human microbiota in drug addiction.

    Science.gov (United States)

    Skosnik, Patrick D; Cortes-Briones, Jose A

    2016-08-01

    Despite major advances in our understanding of the brain using traditional neuroscience, reliable and efficacious treatments for drug addiction have remained elusive. Hence, the time has come to utilize novel approaches, particularly those drawing upon contemporary advances in fields outside of established neuroscience and psychiatry. Put another way, the time has come for a paradigm shift in the addiction sciences. Apropos, a revolution in the area of human health is underway, which is occurring at the nexus between enteric microbiology and neuroscience. It has become increasingly clear that the human microbiota (the vast ecology of bacteria residing within the human organism), plays an important role in health and disease. This is not surprising, as it has been estimated that bacteria living in the human body (approximately 1kg of mass, roughly equivalent to that of the human brain) outnumber human cells 10 to 1. While advances in the understanding of the role of microbiota in other areas of human health have yielded intriguing results (e.g., Clostridium difficile, irritable bowel syndrome, autism, etc.), to date, no systematic programs of research have examined the role of microbiota in drug addiction. The current hypothesis, therefore, is that gut dysbiosis plays a key role in addictive disorders. In the context of this hypothesis, this paper provides a rationale for future research to target the "gut-brain axis" in addiction. A brief background of the gut-brain axis is provided, along with a series of hypothesis-driven ideas outlining potential treatments for addiction via manipulations of the "ecology within." Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota.

    Science.gov (United States)

    Bai, Shaofeng; Chen, Huahai; Zhu, Liying; Liu, Wei; Yu, Hongwei D; Wang, Xin; Yin, Yeshi

    2017-01-01

    Alginates pertain to organic polysaccharides that have been extensively used in food- and medicine-related industries. The present study obtained alginates from an alginate overproducing Pseudomonas aeruginosa PAO1 mutant by screening transposon mutagenesis libraries. The interaction between bacterial and seaweed alginates and gut microbiota were further studied by using an in vitro batch fermentation system. Thin-layer chromatography (TLC) analysis indicated that both bacterial and seaweed alginates can be completely degraded by fecal bacteria isolated from study volunteers, indicating that a minor structural difference between bacterial and seaweed alginates (O-acetylation and lack of G-G blocks) didn't affect the digestion of alginates by human microbiota. Although, the digestion of bacterial and seaweed alginates was attributed to different Bacteroides xylanisolvens strains, they harbored similar alginate lyase genes. Genus Bacteroides with alginate-degrading capability were enriched in growth medium containing bacterial or seaweed alginates after in vitro fermentation. Short-chain fatty acid (SCFA) production in both bacterial and seaweed alginates was also comparable, but was significantly higher than the same medium using starch. In summary, the present study has isolated an alginate-overproducing P. aeruginosa mutant strain. Both seaweed and bacterial alginates were degraded by human gut microbiota, and their regulatory function on gut microbiota was similar.

  20. Integrated modelling for assessing the risk of groundwater contaminants to human health and surface water ecosystems

    DEFF Research Database (Denmark)

    McKnight, Ursula S.; Rasmussen, Jes; Funder, Simon G.;

    2010-01-01

    for evaluating the impact of a TCE groundwater plume, located in an area with protected drinking water interests, to human health and surface water ecosystems. This is accomplished by coupling the system dynamicsbased decision support system CARO-Plus to the aquatic ecosystem model AQUATOX via an analytical...

  1. Human activities cause distinct dissolved organic matter composition across freshwater ecosystems

    Science.gov (United States)

    Williams, Clayton J.; Frost, Paul C.; Morales-Williams, Ana M.; Larson, James H.; Richardson, William B.; Chiandet, Aisha S.; Xenopoulos, Marguerite A.

    2016-01-01

    Dissolved organic matter (DOM) composition in freshwater ecosystems is influenced by interactions between physical, chemical, and biological processes that are controlled, at one level, by watershed landscape, hydrology, and their connections. Against this environmental template, humans may strongly influence DOM composition. Yet, we lack a comprehensive understanding of DOM composition variation across freshwater ecosystems differentially affected by human activity. Using optical properties, we described DOM variation across five ecosystem groups of the Laurentian Great Lakes Region: large lakes, Kawartha Lakes, Experimental Lakes Area, urban stormwater ponds, and rivers (n = 184 sites). We determined how between ecosystem variation in DOM composition related to watershed size, land use and cover, water quality measures (conductivity, dissolved organic carbon (DOC), nutrient concentration, chlorophyll a), and human population density. The five freshwater ecosystem groups had distinctive DOM composition from each other. These significant differences were not explained completely through differences in watershed size nor spatial autocorrelation. Instead, multivariate partial least squares regression showed that DOM composition was related to differences in human impact across freshwater ecosystems. In particular, urban/developed watersheds with higher human population densities had a unique DOM composition with a clear anthropogenic influence that was distinct from DOM composition in natural land cover and/or agricultural watersheds. This nonagricultural, human developed impact on aquatic DOM was most evident through increased levels of a microbial, humic-like parallel factor analysis component (C6). Lotic and lentic ecosystems with low human population densities had DOM compositions more typical of clear water to humic-rich freshwater ecosystems but C6 was only present at trace to background levels. Consequently, humans are strongly altering the quality of DOM in

  2. Cross feeding of glucose metabolism byproducts of Escherichia coli human gut isolates and probiotic strains affect survival of Vibrio cholerae.

    Science.gov (United States)

    Sengupta, Chirantana; Ekka, Manjula; Arora, Saurabh; Dhaware, Prashant D; Chowdhury, Rukhsana; Raychaudhuri, Saumya

    2017-01-01

    Vibrio cholerae converts glucose into either acid or the neutral end product acetoin and its survival in carbohydrate enriched media is linked to the nature of the byproducts produced. It has been demonstrated in this study that Escherichia coli strain isolated from the gut of healthy human volunteers and the commonly used probiotic E. coli Nissle strain that metabolize glucose to acidic byproducts drastically reduce the survival of V. cholerae strains irrespective of their glucose sensitivity and acetoin production status. Accordingly, E. coli glucose transport mutants that produce lower amounts of acidic metabolites had little effect on the survival of V. cholerae in cocultures. Thus, cross feeding of byproducts of glucose metabolism by heterologous bacteria modulates the survival of V. cholerae in glucose rich medium suggesting that composition of the gut microbiota could influence the outcome of V. cholerae infection especially when glucose based ORS is administered.

  3. 肠道微生物与人体健康综述%The Review of Gut Microbiota and Human Health

    Institute of Scientific and Technical Information of China (English)

    颜晓庆; 陈宏运; 吴彬彬; 刘春花; 梁岩

    2015-01-01

    人体肠道中含有大量的微生物。研究表明,肠道微生物的群落结构在人体的许多生理功能上发挥重要作用,如机体物质代谢、能量吸收、胃肠道功能的完善及免疫功能的调节等。人体的许多慢性疾病,比如肥胖症、与肥胖相关的炎症反应、炎症性肠病、抑郁症等都与胃肠道微生物的群落结构失衡有关。肠道微生物与人体相互作用关系的研究对许多慢性病的预防和治疗,以及保持人体健康具有一定的指导意义。%The human gut is densely populated by the gut microbiota. There are accumulating evidences indicating that the gut microbiota plays a signiifcant role in the function of the body, which including the metabolism and energy absorption, the development in the function of gastrointestinal, the modulation of immune system and so on. Many chronic diseases, such as obesity, obesity-associated inlfammation, inlfammatory bowel disease and depression, are related to gut microbiota dysbiosis. The research of the interaction between intestinal bacteria and human body is instructive to the prevention or treatment of many chronic diseases and maintaining health.

  4. Prebiotic Potential of a Maize-Based Soluble Fibre and Impact of Dose on the Human Gut Microbiota.

    Directory of Open Access Journals (Sweden)

    Adele Costabile

    Full Text Available Dietary management of the human gut microbiota towards a more beneficial composition is one approach that may improve host health. To date, a large number of human intervention studies have demonstrated that dietary consumption of certain food products can result in significant changes in the composition of the gut microbiota i.e. the prebiotic concept. Thus the prebiotic effect is now established as a dietary approach to increase beneficial gut bacteria and it has been associated with modulation of health biomarkers and modulation of the immune system. Promitor™ Soluble Corn Fibre (SCF is a well-known maize-derived source of dietary fibre with potential selective fermentation properties. Our aim was to determine the optimum prebiotic dose of tolerance, desired changes to microbiota and fermentation of SCF in healthy adult subjects. A double-blind, randomised, parallel study was completed where volunteers (n = 8/treatment group consumed 8, 14 or 21 g from SCF (6, 12 and 18 g/fibre delivered respectively over 14-d. Over the range of doses studied, SCF was well tolerated Numbers of bifidobacteria were significantly higher for the 6 g/fibre/day compared to 12 g and 18 g/fibre delivered/day (mean 9.25 and 9.73 Log10 cells/g fresh faeces in the pre-treatment and treatment periods respectively. Such a numerical change of 0.5 Log10 bifidobacteria/g fresh faeces is consistent with those changes observed for inulin-type fructans, which are recognised prebiotics. A possible prebiotic effect of SCF was therefore demonstrated by its stimulation of bifidobacteria numbers in the overall gut microbiota during a short-term intervention.

  5. Prebiotic Potential of a Maize-Based Soluble Fibre and Impact of Dose on the Human Gut Microbiota.

    Science.gov (United States)

    Costabile, Adele; Deaville, Eddie R; Morales, Agustin Martin; Gibson, Glenn R

    2016-01-01

    Dietary management of the human gut microbiota towards a more beneficial composition is one approach that may improve host health. To date, a large number of human intervention studies have demonstrated that dietary consumption of certain food products can result in significant changes in the composition of the gut microbiota i.e. the prebiotic concept. Thus the prebiotic effect is now established as a dietary approach to increase beneficial gut bacteria and it has been associated with modulation of health biomarkers and modulation of the immune system. Promitor™ Soluble Corn Fibre (SCF) is a well-known maize-derived source of dietary fibre with potential selective fermentation properties. Our aim was to determine the optimum prebiotic dose of tolerance, desired changes to microbiota and fermentation of SCF in healthy adult subjects. A double-blind, randomised, parallel study was completed where volunteers (n = 8/treatment group) consumed 8, 14 or 21 g from SCF (6, 12 and 18 g/fibre delivered respectively) over 14-d. Over the range of doses studied, SCF was well tolerated Numbers of bifidobacteria were significantly higher for the 6 g/fibre/day compared to 12 g and 18 g/fibre delivered/day (mean 9.25 and 9.73 Log10 cells/g fresh faeces in the pre-treatment and treatment periods respectively). Such a numerical change of 0.5 Log10 bifidobacteria/g fresh faeces is consistent with those changes observed for inulin-type fructans, which are recognised prebiotics. A possible prebiotic effect of SCF was therefore demonstrated by its stimulation of bifidobacteria numbers in the overall gut microbiota during a short-term intervention.

  6. Oceans and Human Health: Linking Ocean, Organism, and Human Health for Sustainable Management of Coastal Ecosystems

    Science.gov (United States)

    Sandifer, P. A.; Trtanj, J.; Collier, T. K.

    2012-12-01

    Scientists and policy-makers are increasingly recognizing that sustainable coastal communities depend on healthy and resilient economies, ecosystems, and people, and that the condition or "health" of the coastal ocean and humans are intimately and inextricably connected. A wealth of ecosystem services provided by ocean and coastal environments are crucial for human survival and well being. Nonetheless, the health of coastal communities, their economies, connected ecosystems and ecosystem services, and people are under increasing threats from health risks associated with environmental degradation, climate change, and unwise land use practices, all of which contribute to growing burdens of naturally-occurring and introduced pathogens, noxious algae, and chemical contaminants. The occurrence, frequency, intensity, geographic range, and number and kinds of ocean health threats are increasing, with concomitant health and economic effects and eroding public confidence in the safety and wholesomeness of coastal environments and resources. Concerns in the research and public health communities, many summarized in the seminal 1999 NRC Report, From Monsoons to Microbes and the 2004 final report of the US Commission on Ocean Policy, resulted in establishment of a new "meta-discipline" known as Oceans and Human Health (OHH). OHH brings together practitioners in oceanography, marine biology, ecology, biomedical science, medicine, economics and other social sciences, epidemiology, environmental management, and public health to focus on water- and food-borne causes of human and animal illnesses associated with ocean and coastal systems and on health benefits of seafood and other marine products. It integrates information across multiple disciplines to increase knowledge of ocean health risks and benefits and communicate such information to enhance public safety. Recognizing the need for a comprehensive approach to ocean health threats and benefits, Congress passed the Oceans and

  7. Evaluation of an oral subchronic exposure of deoxynivalenol on the composition of human gut microbiota in a model of human microbiota-associated rats.

    Directory of Open Access Journals (Sweden)

    Manuel J Saint-Cyr

    Full Text Available BACKGROUND: Deoxynivalenol (DON, a mycotoxin produced by Fusarium species, is one of the most prevalent mycotoxins present in cereal crops worldwide. Due to its toxic properties, high stability and prevalence, the presence of DON in the food chain represents a health risk for both humans and animals. The gastrointestinal microbiota represents potentially the first target for these food contaminants. Thus, the effects of mycotoxins on the human gut microbiota is clearly an issue that needs to be addressed in further detail. Using a human microbiota-associated rat model, the aim of the present study was to evaluate the impact of a chronic exposure of DON on the composition of human gut microbiota. METHODOLOGY/PRINCIPAL FINDINGS: Four groups of 5 germ free male rats each, housed in 4 sterile isolators, were inoculated with a different fresh human fecal flora. Rats were then fed daily by gavage with a solution of DON at 100 µg/kg bw for 4 weeks. Fecal samples were collected at day 0 before the beginning of the treatment; days 7, 16, 21, and 27 during the treatment; and 10 days after the end of the treatment at day 37. DON effect was assessed by real-time PCR quantification of dominant and subdominant bacterial groups in feces. Despite a different intestinal microbiota in each isolator, similar trends were generally observed. During oral DON exposure, a significant increase of 0.5 log10 was observed for the Bacteroides/Prevotella group during the first 3 weeks of administration. Concentration levels for Escherichia coli decreased at day 27. This significant decrease (0.9 log10 CFU/g remained stable until the end of the experiment. CONCLUSIONS/SIGNIFICANCE: We have demonstrated an impact of oral DON exposure on the human gut microbiota composition. These findings can serve as a template for risk assessment studies of food contaminants on the human gut microbiota.

  8. Multicompartment ecosystem mass balances as a tool for understanding and managing the biogeochemical cycles of human ecosystems.

    Science.gov (United States)

    Baker, L A; Hope, D; Xu, Y; Edmonds, J

    2001-10-09

    Nitrogen remains a ubiquitous pollutant in surface and groundwater throughout the United States, despite 30 years of pollution control efforts. A detailed multicompartment N balance for the Central Arizona-Phoenix ecosystem is used to illustrate how an ecosystem-level approach can be used to develop improved N management strategies. The N balance is used to demonstrate how nitrate in pumped groundwater used for crop irrigation could be used to reduce inputs of commercial fertilizer and decrease N leaching to aquifers. Effectively managing N pollution also will require an understanding of the complex factors that control the N balance, including targeted regulations, individual human behavior, land-use conversion, and other ecosystem management practices that affect the N balance. These sometimes countervailing factors are illustrated with several scenarios of wastewater treatment technology and population growth in the Phoenix area. Management of N eventually must be coupled to management of other elements, notably carbon, phosphorus, and salts. We postulate that an ecosystem framework for pollution management will result in strategies that are more effective, fairer, and less expensive than current approaches.

  9. Coevolution of yeast mannan digestion: Convergence of the civilized human diet, distal gut microbiome, and host immunity.

    Science.gov (United States)

    Abbott, D Wade; Martens, Eric C; Gilbert, Harry J; Cuskin, Fiona; Lowe, Elisabeth C

    2015-01-01

    The complex carbohydrates accessible to the distal gut microbiota (DGM) are key drivers in determining the structure of this ecosystem. Typically, plant cell wall polysaccharides and recalcitrant starch (i.e. dietary fiber), in addition to host glycans are considered the primary nutrients for the DGM; however, we recently demonstrated that α-mannans, highly branched polysaccharides that decorate the surface of yeast, are also nutrients for several members of Bacteroides spp. This relationship suggests that the advent of yeast in contemporary food technologies and the colonization of the intestine by endogenous fungi have roles in microbiome structure and function. Here we discuss the process of yeast mannan metabolism, and the intersection between various sources of intestinal fungi and their roles in recognition by the host innate immune system.

  10. Indium-labelled human gut-derived T cells from healthy subjects with strong in vitro adhesion to MAdCAM-1 show no detectable homing to the gut in vivo

    DEFF Research Database (Denmark)

    Rømer, Johanne Lade

    2004-01-01

    cultivation. Whole colonic biopsies from healthy subjects were cultured in the presence of interleukin-2 (IL-2) and IL-4. The integrin expression of the cultured T cells was determined by flow cytometry and in vitro adhesion was assessed in a mucosal addressin cell adhesion molecule 1 (MAdCAM-1) adhesion...... to accomplish local delivery of intravenously injected regulatory T cells in inflamed gut mucosa. The present study aimed to investigate whether in vitro expanded human T cells from the colonic mucosa maintain integrin expression, show in vitro adhesion and retain in vivo gut-homing properties during...... assay. We studied the homing pattern after autologous infusion of 3 x 10(8 111)Indium ((111)In)-labelled T cells in five healthy subjects using scintigraphic imaging. The cultured CD4(+)CD45RO(+) gut-derived T cells express higher levels of integrin alpha4beta 7 than peripheral blood lymphocytes (PBLs...

  11. The Gut Microbiota: Ecology and Function

    Energy Technology Data Exchange (ETDEWEB)

    Willing, B.P.; Jansson, J.K.

    2010-06-01

    The gastrointestinal (GI) tract is teeming with an extremely abundant and diverse microbial community. The members of this community have coevolved along with their hosts over millennia. Until recently, the gut ecosystem was viewed as black box with little knowledge of who or what was there or their specific functions. Over the past decade, however, this ecosystem has become one of fastest growing research areas of focus in microbial ecology and human and animal physiology. This increased interest is largely in response to studies tying microbes in the gut to important diseases afflicting modern society, including obesity, allergies, inflammatory bowel diseases, and diabetes. Although the importance of a resident community of microorganisms in health was first hypothesized by Pasteur over a century ago (Sears, 2005), the multiplicity of physiological changes induced by commensal bacteria has only recently been recognized (Hooper et al., 2001). The term 'ecological development' was recently coined to support the idea that development of the GI tract is a product of the genetics of the host and the host's interactions with resident microbes (Hooper, 2004). The search for new therapeutic targets and disease biomarkers has escalated the need to understand the identities and functions of the microorganisms inhabiting the gut. Recent studies have revealed new insights into the membership of the gut microbial community, interactions within that community, as well as mechanisms of interaction with the host. This chapter focuses on the microbial ecology of the gut, with an emphasis on information gleaned from recent molecular studies.

  12. Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.

    Science.gov (United States)

    Ravcheev, Dmitry A; Godzik, Adam; Osterman, Andrei L; Rodionov, Dmitry A

    2013-12-12

    Bacteroides thetaiotaomicron, a predominant member of the human gut microbiota, is characterized by its ability to utilize a wide variety of polysaccharides using the extensive saccharolytic machinery that is controlled by an expanded repertoire of transcription factors (TFs). The availability of genomic sequences for multiple Bacteroides species opens an opportunity for their comparative analysis to enable characterization of their metabolic and regulatory networks. A comparative genomics approach was applied for the reconstruction and functional annotation of the carbohydrate utilization regulatory networks in 11 Bacteroides genomes. Bioinformatics analysis of promoter regions revealed putative DNA-binding motifs and regulons for 31 orthologous TFs in the Bacteroides. Among the analyzed TFs there are 4 SusR-like regulators, 16 AraC-like hybrid two-component systems (HTCSs), and 11 regulators from other families. Novel DNA motifs of HTCSs and SusR-like regulators in the Bacteroides have the common structure of direct repeats with a long spacer between two conserved sites. The inferred regulatory network in B. thetaiotaomicron contains 308 genes encoding polysaccharide and sugar catabolic enzymes, carbohydrate-binding and transport systems, and TFs. The analyzed TFs control pathways for utilization of host and dietary glycans to monosaccharides and their further interconversions to intermediates of the central metabolism. The reconstructed regulatory network allowed us to suggest and refine specific functional assignments for sugar catabolic enzymes and transporters, providing a substantial improvement to the existing metabolic models for B. thetaiotaomicron. The obtained collection of reconstructed TF regulons is available in the RegPrecise database (http://regprecise.lbl.gov).

  13. Human, donkey and cow milk differently affects energy efficiency and inflammatory state by modulating mitochondrial function and gut microbiota.

    Science.gov (United States)

    Trinchese, Giovanna; Cavaliere, Gina; Canani, Roberto Berni; Matamoros, Sebastien; Bergamo, Paolo; De Filippo, Chiara; Aceto, Serena; Gaita, Marcello; Cerino, Pellegrino; Negri, Rossella; Greco, Luigi; Cani, Patrice D; Mollica, Maria Pina

    2015-11-01

    Different nutritional components are able, by modulating mitochondrial function and gut microbiota composition, to influence body composition, metabolic homeostasis and inflammatory state. In this study, we aimed to evaluate the effects produced by the supplementation of different milks on energy balance, inflammatory state, oxidative stress and antioxidant/detoxifying enzyme activities and to investigate the role of the mitochondrial efficiency and the gut microbiota in the regulation of metabolic functions in an animal model. We compared the intake of human milk, gold standard for infant nutrition, with equicaloric supplementation of donkey milk, the best substitute for newborns due to its nutritional properties, and cow milk, the primary marketed product. The results showed a hypolipidemic effect produced by donkey and human milk intake in parallel with enhanced mitochondrial activity/proton leakage. Reduced mitochondrial energy efficiency and proinflammatory signals (tumor necrosis factor α, interleukin-1 and lipopolysaccharide levels) were associated with a significant increase of antioxidants (total thiols) and detoxifying enzyme activities (glutathione-S-transferase, NADH quinone oxidoreductase) in donkey- and human milk-treated animals. The beneficial effects were attributable, at least in part, to the activation of the nuclear factor erythroid-2-related factor-2 pathway. Moreover, the metabolic benefits induced by human and donkey milk may be related to the modulation of gut microbiota. In fact, milk treatments uniquely affected the proportions of bacterial phyla and genera, and we hypothesized that the increased concentration of fecal butyrate in human and donkey milk-treated rats was related to the improved lipid and glucose metabolism and detoxifying activities.

  14. GUTs without guts

    Science.gov (United States)

    Gato-Rivera, B.; Schellekens, A. N.

    2014-06-01

    The structure of a Standard Model family is derived in a class of brane models with a U(M)×U(N) factor, from two mildly anthropic requirements: a massless photon and a universe that does not turn into a plasma of massless charged particles. If we choose M=3 and N=2, the only option is shown to be the Standard Model with an undetermined number of families. We do not assume the U(1) embedding, charge quantization, family repetition, nor the fermion representations; all of these features are derived, assuming a doublet Higgs. With a slightly stronger assumption even the Higgs representation is determined. We also consider a more general class, requiring an asymptotically free strong SU(M) (with M⩾3) interaction from the first factor and an electromagnetic U(1) embedded in both factors. We allow Higgs symmetry breaking of the U(N)×U(1) flavor group by at most one Higgs boson in any representation, combined with any allowed chiral symmetry breaking by SU(M). For M=3 there is a large number of solutions with an unbroken U(1). In all of these, “quarks” have third-integral charges and color singlets have integer charges in comparison to leptons. Hence Standard Model charge quantization holds for any N. Only for N=2 these models allow an SU(5) GUT extension, but this extension offers no advantages whatsoever for understanding the Standard Model; it only causes complications, such as the doublet-triplet splitting problem. Although all these models have a massless photon, all except the Standard Model are ruled out by the second anthropic requirement. In this class of brane models the Standard Model is realized as a GUT with its intestines removed, to keep only the good parts: a GUT without guts.

  15. Structural basis for nutrient acquisition by dominant members of the human gut microbiota.

    Science.gov (United States)

    Glenwright, Amy J; Pothula, Karunakar R; Bhamidimarri, Satya P; Chorev, Dror S; Baslé, Arnaud; Firbank, Susan J; Zheng, Hongjun; Robinson, Carol V; Winterhalter, Mathias; Kleinekathöfer, Ulrich; Bolam, David N; van den Berg, Bert

    2017-01-19

    The human large intestine is populated by a high density of microorganisms, collectively termed the colonic microbiota, which has an important role in human health and nutrition. The survival of microbiota members from the dominant Gram-negative phylum Bacteroidetes depends on their ability to degrade dietary glycans that cannot be metabolized by the host. The genes encoding proteins involved in the degradation of specific glycans are organized into co-regulated polysaccharide utilization loci, with the archetypal locus sus (for starch utilisation system) encoding seven proteins, SusA-SusG. Glycan degradation mainly occurs intracellularly and depends on the import of oligosaccharides by an outer membrane protein complex composed of an extracellular SusD-like lipoprotein and an integral membrane SusC-like TonB-dependent transporter. The presence of the partner SusD-like lipoprotein is the major feature that distinguishes SusC-like proteins from previously characterized TonB-dependent transporters. Many sequenced gut Bacteroides spp. encode over 100 SusCD pairs, of which the majority have unknown functions and substrate specificities. The mechanism by which extracellular substrate binding by SusD proteins is coupled to outer membrane passage through their cognate SusC transporter is unknown. Here we present X-ray crystal structures of two functionally distinct SusCD complexes purified from Bacteroides thetaiotaomicron and derive a general model for substrate translocation. The SusC transporters form homodimers, with each β-barrel protomer tightly capped by SusD. Ligands are bound at the SusC-SusD interface in a large solvent-excluded cavity. Molecular dynamics simulations and single-channel electrophysiology reveal a 'pedal bin' mechanism, in which SusD moves away from SusC in a hinge-like fashion in the absence of ligand to expose the substrate-binding site to the extracellular milieu. These data provide mechanistic insights into outer membrane nutrient import by

  16. Human impact on lake ecosystems: the case of Lake Naivasha, Kenya

    African Journals Online (AJOL)

    Human impact on lake ecosystems: the case of Lake Naivasha, Kenya. ... of aquatic and terrestrial flora and fauna, including vegetation, birds, fish and mammals. ... Keywords: agriculture, alien species, bioindicator species, environmental ...

  17. Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

    Directory of Open Access Journals (Sweden)

    Brett eWagner Mackenzie

    2015-02-01

    Full Text Available The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation, with a smaller proportion of variation associated with DNA extraction method (technical variation and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

  18. Effect of prebiotics on the human gut microbiota of elderly persons.

    Science.gov (United States)

    Toward, Ruth; Montandon, Samantha; Walton, Gemma; Gibson, Glenn R

    2012-01-01

    The colonic microbiota undergoes certain age related changes that may affect health. For example, above the age of 55-65 y, populations of bifidobacteria are known to decrease markedly. Bifidobacteria are known inhibitors of pathogenic microbes and a decrease in their activities may increase susceptibility to infections. There is therefore interest in trying to reverse their decline in aged persons. As the gut microbiota responds to dietary intervention, both probiotics and prebiotics have been tested in this regard. Probiotics are live microbes in the diet, whereas prebiotics are fermentable ingredients that specifically target components of the indigenous microbiota seen to be beneficial. We have published a recent paper demonstrating that prebiotic galactooligosaccharides can exert power effects upon bifidobacteria in the gut flora of elderly persons (both in vivo and in vitro). This addendum summarizes research that led up to this study and discusses the possible impact of prebiotics in impacting upon the gut health of aged persons.

  19. Ecosystem Services and Human Well-Being: a Participatory Study in a Mountain Community in Portugal

    Directory of Open Access Journals (Sweden)

    Henrique Miguel Pereira

    2005-12-01

    Full Text Available Ecosystem services are essential for human well-being, but the links between ecosystem services and human well-being are complex, diverse, context-dependent, and complicated by the need to consider different spatial and temporal scales to assess them properly. We present the results of a study in the rural community of Sistelo in northern Portugal that formed part of the Portugal Millennium Ecosystem Assessment. The main purpose of our study was to assess the linkages between human well-being and ecosystem services at the local level, as perceived by the community. We used a range of tools that included participatory rural appraisal and rapid rural appraisal as well as other field methods such as direct observation, familiarization and participation in activities, semistructured interviews, trend lines, well-being ranking, and other ranking and scoring exercises. Sistelo has a unique landscape of agricultural terraces that are now being abandoned because of the depopulation of the region, a common trend in mountainous rural areas of Europe. From the community perspective, some components of well-being such as material well-being have been improving, whereas some ecosystem services, e.g., food production, have been declining. Although a few of the local criteria for well-being are closely related to local ecosystem services, most of them are not. People recognize many of the services provided by ecosystems, in particular, provisioning, cultural, and regulating services, although they feel that provisioning services are the most important for well-being. It is apparent that, for the Sistelo community, there is an increasing disconnect between local well-being and at least some local ecosystem services. This disconnect is associated with greater freedom of choice at the local level, which gives the local inhabitants the power to find substitutes for ecosystem services. The consequences of land abandonment for human well-being and ecosystem services

  20. A Subset of Polysaccharide Capsules in the Human Symbiont Bacteroides thetaiotaomicron Promote Increased Competitive Fitness in the Mouse Gut.

    Science.gov (United States)

    Porter, Nathan T; Canales, Pablo; Peterson, Daniel A; Martens, Eric C

    2017-09-27

    Capsular polysaccharides (CPSs) play multiple roles in protecting bacteria from host and environmental factors, and many commensal bacteria can produce multiple capsule types. To better understand the roles of different CPSs in competitive intestinal colonization, we individually expressed the eight different capsules of the human gut symbiont Bacteroides thetaiotaomicron. Certain CPSs were most advantageous in vivo, and increased anti-CPS immunoglobulin A correlated with increased fitness of a strain expressing one particular capsule, CPS5, suggesting that it promotes avoidance of adaptive immunity. A strain with the ability to switch between multiple capsules was more competitive than those expressing any single capsule except CPS5. After antibiotic perturbation, only the wild-type, capsule-switching strain remained in the gut, shifting to prominent expression of CPS5 only in mice with intact adaptive immunity. These data suggest that different capsules equip mutualistic gut bacteria with the ability to thrive in various niches, including those influenced by immune responses and antibiotic perturbations. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM.

    Science.gov (United States)

    Carvalho, Frédéric A; Barnich, Nicolas; Sivignon, Adeline; Darcha, Claude; Chan, Carlos H F; Stanners, Clifford P; Darfeuille-Michaud, Arlette

    2009-09-28

    Abnormal expression of CEACAM6 is observed at the apical surface of the ileal epithelium in Crohn's disease (CD) patients, and CD ileal lesions are colonized by pathogenic adherent-invasive Escherichia coli (AIEC). We investigated the ability of AIEC reference strain LF82 to colonize the intestinal mucosa and to induce inflammation in CEABAC10 transgenic mice expressing human CEACAMs. AIEC LF82 virulent bacteria, but not nonpathogenic E. coli K-12, were able to persist in the gut of CEABAC10 transgenic mice and to induce severe colitis with reduced survival rate, marked weight loss, increased rectal bleeding, presence of erosive lesions, mucosal inflammation, and increased proinflammatory cytokine expression. The colitis depended on type 1 pili expression by AIEC bacteria and on intestinal CEACAM expression because no sign of colitis was observed in transgenic mice infected with type 1 pili-negative LF82-Delta fimH isogenic mutant or in wild-type mice infected with AIEC LF82 bacteria. These findings strongly support the hypothesis that in CD patients having an abnormal intestinal expression of CEACAM6, AIEC bacteria via type 1 pili expression can colonize the intestinal mucosa and induce gut inflammation. Thus, targeting AIEC adhesion to gut mucosa represents a new strategy for clinicians to prevent and/or to treat ileal CD.

  2. Recombinant Human Leptin Does Not Alter Gut Hormone Levels after Gastric Bypass but May Attenuate Sweet Cravings

    Directory of Open Access Journals (Sweden)

    Rushika Conroy

    2014-01-01

    Full Text Available Bariatric surgery improves glucose homeostasis and alters gut hormones partly independent of weight loss. Leptin plays a role in these processes; levels are decreased following bariatric surgery, creating a relative leptin insufficiency. We previously showed that leptin administration in a weight-reduced state after Roux-en-Y gastric bypass (RYGB caused no further weight loss. Here, we discuss the impact of leptin administration on gut hormones, glucostasis, and appetite. Weight stable women after RYGB were randomized to receive placebo or recombinant human metreleptin (0.05 mg/kg twice daily. At weeks 0 and 16, a liquid meal challenge was performed. Glucose, insulin, C-peptide, GLP-1, PYY, glucagon, and ghrelin (total, acyl, and desacyl were measured fasting and postprandially. Appetite was assessed using a visual analog scale. Mean post-op period was 53±2.3 months; mean BMI was 34.6±0.2 kg/m2. At 16 weeks, there was no significant change in weight within or between groups. Fasting PYY was significantly different between groups and the leptin group had lower sweets craving at week 16 than the placebo group (P<0.05. No other differences were observed. Leptin replacement does not alter gut hormones or glucostasis but may diminish sweet cravings compared to placebo in this population of post-RYGB women.

  3. Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease.

    Science.gov (United States)

    Jiang, Weiwei; Wu, Na; Wang, Xuemei; Chi, Yujing; Zhang, Yuanyuan; Qiu, Xinyun; Hu, Ying; Li, Jing; Liu, Yulan

    2015-02-03

    Non-alcoholic fatty liver disease (NAFLD) has recently been considered to be under the influence of the gut microbiota, which might exert toxic effects on the human host after intestinal absorption and delivery to the liver via the portal vein. In this study, the composition of the gut microbiota in NAFLD patients and healthy subjects was determined via 16S ribosomal RNA Illumina next-generation sequencing. Among those taxa displaying greater than 0.1% average abundance in all samples, five genera, including Alistipes and Prevotella, were significantly more abundant in the gut microbiota of healthy subjects compared to NAFLD patients. Alternatively, Escherichia, Anaerobacter, Lactobacillus and Streptococcus were increased in the gut microbiota of NAFLD patients compared to healthy subjects. In addition, decreased numbers of CD4+ and CD8+ T lymphocytes and increased levels of TNF-α, IL-6 and IFN-γ were detected in the NAFLD group compared to the healthy group. Furthermore, irregularly arranged microvilli and widened tight junctions were observed in the gut mucosa of the NAFLD patients via transmission electron microscopy. We postulate that aside from dysbiosis of the gut microbiota, gut microbiota-mediated inflammation of the intestinal mucosa and the related impairment in mucosal immune function play an important role in the pathogenesis of NAFLD.

  4. Pacaella massiliensis gen. nov., sp. nov., a new bacterial species isolated from the human gut

    Directory of Open Access Journals (Sweden)

    S. Ndongo

    2017-03-01

    Full Text Available Herein, we report the main characteristics of a new species named Pacaella massiliensis gen. nov., sp. nov., strain Marseille-P2670T (CSUR P2670 that was isolated from the gut microbiota of a 45-year-old French patient.

  5. Christensenella timonensis, a new bacterial species isolated from the human gut

    Directory of Open Access Journals (Sweden)

    S. Ndongo

    2016-09-01

    Full Text Available We propose a new species, Christensenella timonensis, strain Marseille-P2437T (CSUR P2437T, which was isolated from gut microbiota of a 66-year-old patient as a part of culturomics study. C. timonensis represents the second species isolated within the Christensenella genus.

  6. The influence of a short-term gluten-free diet on the human gut microbiome

    NARCIS (Netherlands)

    Bonder, Marc Jan; Tigchelaar, Ettje F.; Cai, Xianghang; Trynka, Gosia; Cenit, Maria C; Hrdlickova, Barbara; Zhong, Huanzi; Vatanen, Tommi; Gevers, Dirk; Wijmenga, Cisca; Wang, Yang; Zhernakova, Alexandra

    2016-01-01

    Background: A gluten-free diet (GFD) is the most commonly adopted special diet worldwide. It is an effective treatment for coeliac disease and is also often followed by individuals to alleviate gastrointestinal complaints. It is known there is an important link between diet and the gut microbiome,

  7. Impact of the gut microbiota on rodent models of human disease.

    Science.gov (United States)

    Hansen, Axel Kornerup; Hansen, Camilla Hartmann Friis; Krych, Lukasz; Nielsen, Dennis Sandris

    2014-12-21

    Traditionally bacteria have been considered as either pathogens, commensals or symbionts. The mammal gut harbors 10(14) organisms dispersed on approximately 1000 different species. Today, diagnostics, in contrast to previous cultivation techniques, allow the identification of close to 100% of bacterial species. This has revealed that a range of animal models within different research areas, such as diabetes, obesity, cancer, allergy, behavior and colitis, are affected by their gut microbiota. Correlation studies may for some diseases show correlation between gut microbiota composition and disease parameters higher than 70%. Some disease phenotypes may be transferred when recolonizing germ free mice. The mechanistic aspects are not clear, but some examples on how gut bacteria stimulate receptors, metabolism, and immune responses are discussed. A more deeper understanding of the impact of microbiota has its origin in the overall composition of the microbiota and in some newly recognized species, such as Akkermansia muciniphila, Segmented filamentous bacteria and Faecalibacterium prausnitzii, which seem to have an impact on more or less severe disease in specific models. Thus, the impact of the microbiota on animal models is of a magnitude that cannot be ignored in future research. Therefore, either models with specific microbiota must be developed, or the microbiota must be characterized in individual studies and incorporated into data evaluation.

  8. The Gut Microbiota and Irritable Bowel Syndrome: Friend or Foe?

    Directory of Open Access Journals (Sweden)

    Uday C. Ghoshal

    2012-01-01

    Full Text Available Progress in the understanding of the pathophysiology of irritable bowel syndrome (IBS, once thought to be a purely psychosomatic disease, has advanced considerably and low-grade inflammation and changes in the gut microbiota now feature as potentially important. The human gut harbours a huge microbial ecosystem, which is equipped to perform a variety of functions such as digestion of food, metabolism of drugs, detoxification of toxic compounds, production of essential vitamins, prevention of attachment of pathogenic bacteria to the gut wall, and maintenance of homeostasis in the gastrointestinal tract. A subset of patients with IBS may have a quantitative increase in bacteria in the small bowel (small intestinal bacterial overgrowth. Qualitative changes in gut microbiota have also been associated with IBS. Targeting the gut microbiota using probiotics and antibiotics has emerged as a potentially effective approach to the treatment of this, hitherto enigmatic, functional bowel disorder. The gut microbiota in health, quantitative and qualitative microbiota changes, and therapeutic manipulations targeting the microbiota in patients with IBS are reviewed in this paper.

  9. Trajectories in human domination of ecosystems : Human appropriation of net primary production in the Philippines during the 20th century

    NARCIS (Netherlands)

    Kastner, Thomas

    2009-01-01

    The "human appropriation of net primary production" (HANPP) has been suggested as a comprehensive indicator to measure impacts of human land use on ecosystems. It accounts for (a) human-induced changes in biological productivity and (b) biomass harvest. This study presents an analysis of aboveground

  10. EnviroAtlas Connects Urban Ecosystem Services and Human ...

    Science.gov (United States)

    Ecosystem services in urban areas can improve public health and well-being by mitigating natural and anthropogenic pollution, and by promoting healthy lifestyles that include engagement with nature and enhanced opportunities for physical activity and social interaction. EPA’s EnviroAtlas online mapping tool identifies urban environmental features linked in the scientific and medical literature to specific aspects of public health and well-being. EnviroAtlas researchers have synthesized newly-generated one-meter resolution landcover data, downscaled census population data, and other existing datasets such as roads and parks. Resulting geospatial metrics represent health-related indicators of urban ecosystem services supply and demand by census block-group and finer scales. EnviroAtlas maps include percent of the population with limited window views of trees, tree cover along walkable roads, overall neighborhood green space, and proximity to parks. Demographic data can be overlaid to perform analyses of disproportionate distribution of urban ecosystem services across population groups. Together with the Eco-Health Relationship Browser, EnviroAtlas data can be linked to numerous aspects of public health and well-being including school performance, physical fitness, social capital, and longevity. EnviroAtlas maps have been developed using consistent methods to allow for comparisons between neighborhoods and across multiple U.S. communities. To feature eco-heal

  11. Trans locus inhibitors limit concomitant polysaccharide synthesis in the human gut symbiont Bacteroides fragilis.

    Science.gov (United States)

    Chatzidaki-Livanis, Maria; Weinacht, Katja G; Comstock, Laurie E

    2010-06-29

    Bacteroides is an abundant genus of bacteria of the human intestinal microbiota. Bacteroides species synthesize a large number of capsular polysaccharides (PS), a biological property not shared with closely related oral species, suggesting importance for intestinal survival. Bacteroides fragilis, for example, synthesizes eight capsular polysaccharides per strain, each of which phase varies via inversion of the promoters located upstream of seven of the eight polysaccharide biosynthesis operons. In a single cell, many of these polysaccharide loci promoters can be simultaneously oriented on for transcription of the downstream biosynthesis operons. Here, we demonstrate that despite the promoter orientations, concomitant transcription of multiple polysaccharide loci within a cell is inhibited. The proteins encoded by the second gene of each of these eight loci, collectively designated the UpxZ proteins, inhibit the synthesis of heterologous polysaccharides. These unique proteins interfere with the ability of UpxY proteins encoded by other polysaccharide loci to function in transcriptional antitermination of their respective operon. The eight UpxZs have different inhibitory spectra, thus establishing a hierarchical regulatory network for polysaccharide synthesis. Limitation of concurrent polysaccharide synthesis strongly suggests that these bacteria evolved this property as an evasion-type mechanism to avoid killing by polysaccharide-targeting factors in the ecosystem.

  12. A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut.

    Science.gov (United States)

    Karlsson, Fredrik H; Ussery, David W; Nielsen, Jens; Nookaew, Intawat

    2011-04-01

    The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number of extracytoplasmic function σ factors (ECF σ factors) and two component systems for extracellular signal transduction compared to other Bacteroidetes/Chlorobi species. A whole-genome phylogenetic analysis shows a very little difference between the Parabacteroides and Bacteroides genera. Further analysis shows that Bacteroides and Parabacteroides species share a large common core of 1,085 protein families. Genome atlases illustrate that there are few and only small unique areas on the chromosomes of four Bacteroides/Parabacteroides genomes. Functional classification to clusters of othologus groups show that Bacteroides species are enriched in carbohydrate transport and metabolism proteins. Classification of proteins in KEGG metabolic pathways gives a detailed view of the genome's metabolic capabilities that can be linked to its habitat. Bacteroides pectinophilus and Bacteroides capillosus do not cluster together with other Bacteroides species, based on analysis of 16S rRNA sequence, whole-genome protein families and functional content, 16S rRNA sequences of the two species suggest that they belong to the Firmicutes phylum. We have presented a more detailed and precise description of the phylogenetic relationships of members of the Bacteroidetes/Chlorobi phylum by whole genome comparison. Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for

  13. Persistence of trophic hotspots and relation to human impacts within an upwelling marine ecosystem.

    Science.gov (United States)

    Santora, Jarrod A; Sydeman, William J; Schroeder, Isaac D; Field, John C; Miller, Rebecca R; Wells, Brian K

    2017-03-01

    Human impacts (e.g., fishing, pollution, and shipping) on pelagic ecosystems are increasing, causing concerns about stresses on marine food webs. Maintaining predator-prey relationships through protection of pelagic hotspots is crucial for conservation and management of living marine resources. Biotic components of pelagic, plankton-based, ecosystems exhibit high variability in abundance in time and space (i.e., extreme patchiness), requiring investigation of persistence of abundance across trophic levels to resolve trophic hotspots. Using a 26-yr record of indicators for primary production, secondary (zooplankton and larval fish), and tertiary (seabirds) consumers, we show distributions of trophic hotspots in the southern California Current Ecosystem result from interactions between a strong upwelling center and a productive retention zone with enhanced nutrients, which concentrate prey and predators across multiple trophic levels. Trophic hotspots also overlap with human impacts, including fisheries extraction of coastal pelagic and groundfish species, as well as intense commercial shipping traffic. Spatial overlap of trophic hotspots with fisheries and shipping increases vulnerability of the ecosystem to localized depletion of forage fish, ship strikes on marine mammals, and pollution. This study represents a critical step toward resolving pelagic areas of high conservation interest for planktonic ecosystems and may serve as a model for other ocean regions where ecosystem-based management and marine spatial planning of pelagic ecosystems is warranted. © 2016 by the Ecological Society of America.

  14. The relationship between gut microbiota and human disease%肠道细菌微生态与人类疾病关系研究进展

    Institute of Scientific and Technical Information of China (English)

    鲜凌瑾(综述); 唐勇(审校)

    2015-01-01

    寄居在人类肠道的数以亿计的肠道细菌,已被证实与人类多种疾病有关。就肠道细菌与内分泌系统疾病、消化系统疾病、心血管系统疾病、神经系统疾病、获得性免疫缺陷综合征以及特应性疾病等的关系研究进展进行综述。%Billions of gut microbes which colonize in the human gut, is concerned with many human diseases, such as en-docrine system disease, digestive system disease, cardiovascular disease, neurological disease, autoimmune disease, etc. By knowing the relationship between gut micro-ecology and human diseases, we can get a new direction for prevention and treatment these diseases.

  15. Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans

    DEFF Research Database (Denmark)

    Reijnders, Dorien; Goossens, Gijs H; Hermes, Gerben D A

    2016-01-01

    . Vancomycin, but not amoxicillin, decreased bacterial diversity and reduced Firmicutes involved in short-chain fatty acid and bile acid metabolism, concomitant with altered plasma and/or fecal metabolite concentrations. Adipose tissue gene expression of oxidative pathways was upregulated by antibiotics......, whereas immune-related pathways were downregulated by vancomycin. Antibiotics did not affect tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability, and adipocyte size. Importantly, energy harvest, adipocyte size...

  16. Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut.

    Science.gov (United States)

    Lim, Bentley; Zimmermann, Michael; Barry, Natasha A; Goodman, Andrew L

    2017-04-20

    The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer. In the absence of inducer, promoter activity is fully repressed; addition of inducer rapidly increases gene expression by four to five orders of magnitude. Because the inducer is absent in mice and their diets, Bacteroides gene expression inside the gut can be modulated by providing the inducer in drinking water. We use this system to measure the dynamic relationship between commensal sialidase activity and liberation of mucosal sialic acid, a receptor and nutrient for pathogens. VIDEO ABSTRACT. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. The migration and loss of human primordial germ stem cells from the hind gut epithelium towards the gonadal ridge

    DEFF Research Database (Denmark)

    Mamsen, Linn Salto; Brøchner, Christian Beltoft; Byskov, Anne Grete

    2012-01-01

    Human primordial germ cells (PGCs) can be recognized in the yolk sac wall, from 3-4 weeks post conception (wpc), in the hind gut epithelium from week 4 and in the gonadal area from early week 5. The objective of this study was to map the migration route of PGCs and elucidate the role of the nervous...... system in this process. Sixteen human specimens, 5-14 wpc obtained from legal abortions were included. On serial paraffin sections, PGCs were detected immunohistochemically by expression of OCT4 and c-Kit, nerve fibers by ß-III-tubulin and stem cell factor (SCF) as a possible chemoattractive cue for PGC...... migration, but after establishment of connections between the enteric and sympathetic nervous systems. PGCs follow sympathetic nerve fibers towards the gonads. PGCs failing to exit the nerve branches at the gonadal site, may continue along the sympathetic trunk ending up in other organs where they may form...

  18. AI techniques for optimizing multi-objective reservoir operation upon human and riverine ecosystem demands

    Science.gov (United States)

    Tsai, Wen-Ping; Chang, Fi-John; Chang, Li-Chiu; Herricks, Edwin E.

    2015-11-01

    Flow regime is the key driver of the riverine ecology. This study proposes a novel hybrid methodology based on artificial intelligence (AI) techniques for quantifying riverine ecosystems requirements and delivering suitable flow regimes that sustain river and floodplain ecology through optimizing reservoir operation. This approach addresses issues to better fit riverine ecosystem requirements with existing human demands. We first explored and characterized the relationship between flow regimes and fish communities through a hybrid artificial neural network (ANN). Then the non-dominated sorting genetic algorithm II (NSGA-II) was established for river flow management over the Shihmen Reservoir in northern Taiwan. The ecosystem requirement took the form of maximizing fish diversity, which could be estimated by the hybrid ANN. The human requirement was to provide a higher satisfaction degree of water supply. The results demonstrated that the proposed methodology could offer a number of diversified alternative strategies for reservoir operation and improve reservoir operational strategies producing downstream flows that could meet both human and ecosystem needs. Applications that make this methodology attractive to water resources managers benefit from the wide spread of Pareto-front (optimal) solutions allowing decision makers to easily determine the best compromise through the trade-off between reservoir operational strategies for human and ecosystem needs.

  19. Metagenomic Surveys of Gut Microbiota

    Institute of Scientific and Technical Information of China (English)

    Rahul Shubhra Mandal; Sudipto Saha; Santasabuj Das

    2015-01-01

    Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational tax-onomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ulti-mately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interac-tion among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe inter-action networks.

  20. Metagenomic Surveys of Gut Microbiota

    Directory of Open Access Journals (Sweden)

    Rahul Shubhra Mandal

    2015-06-01

    Full Text Available Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational taxonomic unit (OTU levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interaction among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe interaction networks.

  1. Earth Observation Data for Mapping and Evaluation of Ecosystem Services to Improve Human Livelihoods and Conserve Species

    Science.gov (United States)

    Shapiro, Aurelie C.; Bhagabati, Nirmal

    2010-12-01

    Mapping and evaluating ecosystem services is of increasing concern and urgency for conservation organizations such as WWF. Coupling biodiversity assessments with ecosystem services e.g., carbon sequestration, water regulation, sediment reduction, is an effective way to visualize additional financial and human benefits of conservation for decision makers. WWF is eager to apply various Earth Observation data to conservation applications for consistent mapping and monitoring of natural ecosystems and the potential impacts of their loss on humans and wildlife alike. Such examples include forest carbon mapping, integrated evaluation of ecosystem services (via the InVEST tool) and bundling endangered Tiger habitat with various ecosystem services for bundled benefits.

  2. Hypertrophy, hyperplasia, and infectious virus in gut-associated lymphoid tissue of mice after oral inoculation with simian-human or bovine-human reassortant rotaviruses.

    Science.gov (United States)

    Moser, C A; Dolfi, D V; Di Vietro, M L; Heaton, P A; Offit, P A; Clark, H F

    2001-04-01

    Oral inoculation of infants with a vaccine that contains simian-human reassortant rotaviruses has been found to be a rare cause of intussusception. Because intussusception can be associated with enlargement of gut-associated lymphoid tissue, we studied the capacity of simian-human and bovine-human reassortant rotaviruses to cause lymphoid hypertrophy and hyperplasia of Peyer's patches (PP) of adult BALB/c mice. Neither hypertrophy nor hyperplasia was detected in PP after oral inoculation with simian-human or bovine-human reassortant rotaviruses. However, infectious virus was detected in PP and mesenteric lymph nodes after oral inoculation with simian, but not bovine, reassortant rotaviruses. Implications of these findings on the pathogenesis of intussusception are discussed.

  3. Human immune compartment comparisons: Optimization of proliferative assays for blood and gut T lymphocytes.

    Science.gov (United States)

    Dock, Jeffrey; Hultin, Lance; Hultin, Patricia; Elliot, Julie; Yang, Otto O; Anton, Peter A; Jamieson, Beth D; Effros, Rita B

    2017-03-21

    The accumulation of peripheral blood late-differentiated memory CD8 T cells with features of replicative (cellular) senescence, including inability to proliferate in vitro, has been extensively studied. Importantly, the abundance of these cells is directly correlated with increased morbidity and mortality in older persons. Of note, peripheral blood contains only 2% of the total body lymphocyte population. By contrast, the gut-associated lymphoid tissue (GALT) is the most extensive lymphoid organ, housing up to 60% of total body lymphocytes, but has never been assessed with respect to senescence profiles. We report here the development of a method for measuring and comparing proliferative capacity of peripheral blood and gut colorectal mucosa-derived CD8 T cells. The protocol involves a 5-day culture of mononuclear leukocyte populations, from blood and gut colorectal mucosa respectively, labeled with 5-(and 6)-carboxyfluorescein diacetate succinimidyl ester (CFSE) and 5-bromo-2'-deoxyuridine (BrdU) and stimulated with anti-CD2/3/28-linked microbeads. Variables tested and optimized as part of the protocol development include: mode of T cell stimulation, CFSE concentration, inclusion of a second proliferation marker, BrdU, culture duration, initial culture concentration, and inclusion of autologous irradiated feeder cells. Moving forward, this protocol demonstrates a significant advance in the ability of researchers to study compartment-specific differences of in vitro proliferative dynamics of CD8 T cells, as an indicator of replicative senescence and immunological aging. The study's two main novel contributions are (1) Optimization and adaptation of standard proliferative dynamics blood T cell protocols for T cells within the mucosal immune system. (2) Introduction of the novel technique of combining CFSE and BrdU staining to do so.

  4. Modelling of spatially complex human-ecosystem, rural-urban and rich-poor interactions

    CSIR Research Space (South Africa)

    Naude, AH

    2008-06-01

    Full Text Available ., Forsyth, G., Mans, G. and Hugo, W. (2008) Modeling of spatially complex human-ecosystem, rural-urban snd rich-poor interactions. Paper submitted to International Conference: “Studying, Modelling and Sense Making of Planet Earth”; 1 – 6 June, 2008... human-ecosystem, rural-urban snd rich-poor interactions. Paper submitted to International Conference: “Studying, Modelling and Sense Making of Planet Earth”; 1 – 6 June, 2008, Department of Geography, University of the Aegean. 2 Initially, most...

  5. Interaction between Pirenzepine and Ninjinto, a Traditional Japanese Herbal Medicine, on the Plasma Gut-Regulated Peptide Levels in Humans.

    Science.gov (United States)

    Sato, Yuhki; Hiroki, Itoh; Suzuki, Yosuke; Tatsuta, Ryosuke; Takeyama, Masaharu

    2013-01-01

    The Japanese herbal medicine (Kampo) Ninjinto has been used for the treatment of gastroenteritis, esogastritis, gastric atony, gastrectasis, vomiting, and anorexia. The pharmacological effects of Ninjinto on the gastrointestine are due to changes in the levels of gut-regulated peptide, such as motilin, somatostatin, calcitonin gene-related peptide (CGRP), substance P, and vasoactive intestinal polypeptide (VIP). The release of these peptides is controlled by acetylcholine (ACh) from the preganglionic fibers of the parasympathetic nerve. Thus, we examined the effects of the selective M1 muscarinic receptor antagonist pirenzepine on the elevation of Ninjinto-induced plasma the area under the plasma gut-regulated peptide concentration-time curve from 0 to 240 min (AUC0→240 min) in humans. Oral pretreatment with pirenzepine significantly reduced the Ninjinto-induced elevation of plasma motilin and substance P release (AUC0→240 min). Combined treatment with Ninjinto and pirenzepine significantly increased the release of plasma somatostatin (AUC0→240 min) compared with administration of Ninjinto alone or placebo. Ninjinto appeared to induce the release of substance P and motilin into plasma mainly through the activation of M1 muscarinic receptors, and pirenzepine may affect the pharmacologic action of Ninjinto by the elevation of plasma substance P, motilin, and somatostatin.

  6. Interaction between Pirenzepine and Ninjinto, a Traditional Japanese Herbal Medicine, on the Plasma Gut-Regulated Peptide Levels in Humans

    Directory of Open Access Journals (Sweden)

    Yuhki Sato

    2013-01-01

    Full Text Available The Japanese herbal medicine (Kampo Ninjinto has been used for the treatment of gastroenteritis, esogastritis, gastric atony, gastrectasis, vomiting, and anorexia. The pharmacological effects of Ninjinto on the gastrointestine are due to changes in the levels of gut-regulated peptide, such as motilin, somatostatin, calcitonin gene-related peptide (CGRP, substance P, and vasoactive intestinal polypeptide (VIP. The release of these peptides is controlled by acetylcholine (ACh from the preganglionic fibers of the parasympathetic nerve. Thus, we examined the effects of the selective M1 muscarinic receptor antagonist pirenzepine on the elevation of Ninjinto-induced plasma the area under the plasma gut-regulated peptide concentration-time curve from 0 to 240 min ( in humans. Oral pretreatment with pirenzepine significantly reduced the Ninjinto-induced elevation of plasma motilin and substance P release (. Combined treatment with Ninjinto and pirenzepine significantly increased the release of plasma somatostatin ( compared with administration of Ninjinto alone or placebo. Ninjinto appeared to induce the release of substance P and motilin into plasma mainly through the activation of M1 muscarinic receptors, and pirenzepine may affect the pharmacologic action of Ninjinto by the elevation of plasma substance P, motilin, and somatostatin.

  7. High protective efficacy of rice bran against human rotavirus diarrhea via enhancing probiotic growth, gut barrier function, and innate immunity.

    Science.gov (United States)

    Yang, Xingdong; Twitchell, Erica; Li, Guohua; Wen, Ke; Weiss, Mariah; Kocher, Jacob; Lei, Shaohua; Ramesh, Ashwin; Ryan, Elizabeth P; Yuan, Lijuan

    2015-10-13

    Previously, we showed that rice bran (RB) was able to reduce human rotavirus (HRV) diarrhea in gnotobiotic pigs. Here, we investigated its effect on the growth of diarrhea-reducing probiotic Lactobacillus rhamnosus GG (LGG) and Escherichia coli Nissle (EcN), and the resulting effects on HRV diarrhea, gut epithelial health, permeability and innate immune responses during virulent HRV challenge. On 3, 5, and 7 days of age pigs were inoculated with 2 × 10(4) colony-forming-units LGG+EcN to initiate colonization. Daily RB supplementation (replacing 10% calorie intake) was started at 5 days of age and continued until euthanasia. A subset of pigs in each group was challenged orally with 10(5) focus-forming-units of virulent HRV at 33 days of age. RB completely prevented HRV diarrhea in LGG+EcN colonized pigs. RB significantly promoted the growth of both probiotic strains in the gut (~5 logs) and increased the body-weight-gain at 4-5 weeks of age compared to non-RB group. After HRV challenge, RB-fed pigs had significantly lower ileal mitotic index and villus width, and significantly increased intestinal IFN-γ and total IgA levels compared to non-RB group. Therefore, RB plus LGG+EcN colonization may represent a highly effective therapeutic approach against HRV and potentially a variety of other diarrhea-inducing enteric pathogens.

  8. Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes

    KAUST Repository

    Zhang, Meiling

    2014-08-18

    Enzymes that degrade dietary and host-derived glycans represent the most abundant functional activities encoded by genes unique to the human gut microbiome. However, the biochemical activities of a vast majority of the glycan-degrading enzymes are poorly understood. Here, we use transcriptome sequencing to understand the diversity of genes expressed by the human gut bacteria Bacteroides intestinalis and Bacteroides ovatus grown in monoculture with the abundant dietary polysaccharide xylan. The most highly induced carbohydrate active genes encode a unique glycoside hydrolase (GH) family 10 endoxylanase (BiXyn10A or BACINT-04215 and BACOVA-04390) that is highly conserved in the Bacteroidetes xylan utilization system. The BiXyn10A modular architecture consists of a GH10 catalytic module disrupted by a 250 amino acid sequence of unknown function. Biochemical analysis of BiXyn10A demonstrated that such insertion sequences encode a new family of carbohydrate-binding modules (CBMs) that binds to xy-lose- configured oligosaccharide/polysaccharide ligands, the substrate of the BiXyn10A enzymatic activity. The crystal structures of CBM1 from BiXyn10A (1.8 Å), a cocomplex of BiXyn10A CBM1 with xylohexaose (1.14 Å), and the CBM fromits homolog in the Prevotella bryantii B 14 Xyn10C (1.68 Å) reveal an unanticipated mode for ligand binding. Aminimal enzyme mix, composed of the gene products of four of the most highly up-regulated genes during growth on wheat arabinoxylan, depolymerizes the polysaccharide into its component sugars. The combined biochemical and biophysical studies presented here provide a framework for understanding fiber metabolism by an important group within the commensal bacterial population known to influence human health.

  9. Potential role of the gut microbiota in synthetic torpor and therapeutic hypothermia.

    Science.gov (United States)

    Sisa, Claudia; Turroni, Silvia; Amici, Roberto; Brigidi, Patrizia; Candela, Marco; Cerri, Matteo

    2017-01-21

    Therapeutic hypothermia is today used in several clinical settings, among them the gut related diseases that are influenced by ischemia/reperfusion injury. This perspective paved the way to the study of hibernation physiology, in natural hibernators, highlighting an unexpected importance of the gut microbial ecosystem in hibernation and torpor. In natural hibernators, intestinal microbes adaptively reorganize their structural configuration during torpor, and maintain a mutualistic configuration regardless of long periods of fasting and cold temperatures. This allows the gut microbiome to provide the host with metabolites, which are essential to keep the host immunological and metabolic homeostasis during hibernation. The emerging role of the gut microbiota in the hibernation process suggests the importance of maintaining a mutualistic gut microbiota configuration in the application of therapeutic hypothermia as well as in the development of new strategy such as the use of synthetic torpor in humans. The possible utilization of tailored probiotics to mold the gut ecosystem during therapeutic hypothermia can also be taken into consideration as new therapeutic strategy.

  10. Potential role of the gut microbiota in synthetic torpor and therapeutic hypothermia

    Science.gov (United States)

    Sisa, Claudia; Turroni, Silvia; Amici, Roberto; Brigidi, Patrizia; Candela, Marco; Cerri, Matteo

    2017-01-01

    Therapeutic hypothermia is today used in several clinical settings, among them the gut related diseases that are influenced by ischemia/reperfusion injury. This perspective paved the way to the study of hibernation physiology, in natural hibernators, highlighting an unexpected importance of the gut microbial ecosystem in hibernation and torpor. In natural hibernators, intestinal microbes adaptively reorganize their structural configuration during torpor, and maintain a mutualistic configuration regardless of long periods of fasting and cold temperatures. This allows the gut microbiome to provide the host with metabolites, which are essential to keep the host immunological and metabolic homeostasis during hibernation. The emerging role of the gut microbiota in the hibernation process suggests the importance of maintaining a mutualistic gut microbiota configuration in the application of therapeutic hypothermia as well as in the development of new strategy such as the use of synthetic torpor in humans. The possible utilization of tailored probiotics to mold the gut ecosystem during therapeutic hypothermia can also be taken into consideration as new therapeutic strategy. PMID:28210076

  11. Early life dynamics of the human gut virome and bacterial microbiome in infants.

    Science.gov (United States)

    Lim, Efrem S; Zhou, Yanjiao; Zhao, Guoyan; Bauer, Irma K; Droit, Lindsay; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Wang, David; Holtz, Lori R

    2015-10-01

    The early years of life are important for immune development and influence health in adulthood. Although it has been established that the gut bacterial microbiome is rapidly acquired after birth, less is known about the viral microbiome (or 'virome'), consisting of bacteriophages and eukaryotic RNA and DNA viruses, during the first years of life. Here, we characterized the gut virome and bacterial microbiome in a longitudinal cohort of healthy infant twins. The virome and bacterial microbiome were more similar between co-twins than between unrelated infants. From birth to 2 years of age, the eukaryotic virome and the bacterial microbiome expanded, but this was accompanied by a contraction of and shift in the bacteriophage virome composition. The bacteriophage-bacteria relationship begins from birth with a high predator-low prey dynamic, consistent with the Lotka-Volterra prey model. Thus, in contrast to the stable microbiome observed in adults, the infant microbiome is highly dynamic and associated with early life changes in the composition of bacteria, viruses and bacteriophages with age.

  12. Environmental and Human Controls of Ecosystem Functional Diversity in Temperate South America

    Directory of Open Access Journals (Sweden)

    Domingo Alcaraz-Segura

    2013-01-01

    Full Text Available The regional controls of biodiversity patterns have been traditionally evaluated using structural and compositional components at the species level, but evaluation of the functional component at the ecosystem level is still scarce. During the last decades, the role of ecosystem functioning in management and conservation has increased. Our aim was to use satellite-derived Ecosystem Functional Types (EFTs, patches of the land-surface with similar carbon gain dynamics to characterize the regional patterns of ecosystem functional diversity and to evaluate the environmental and human controls that determine EFT richness across natural and human-modified systems in temperate South America. The EFT identification was based on three descriptors of carbon gain dynamics derived from seasonal curves of the MODIS Enhanced Vegetation Index (EVI: annual mean (surrogate of primary production, seasonal coefficient of variation (indicator of seasonality and date of maximum EVI (descriptor of phenology. As observed for species richness in the southern hemisphere, water availability, not energy, emerged as the main climatic driver of EFT richness in natural areas of temperate South America. In anthropogenic areas, the role of both water and energy decreased and increasing human intervention increased richness at low levels of human influence, but decreased richness at high levels of human influence.

  13. Gut microbiota and liver diseases.

    Science.gov (United States)

    Minemura, Masami; Shimizu, Yukihiro

    2015-02-14

    Several studies revealed that gut microbiota are associated with various human diseases, e.g., metabolic diseases, allergies, gastroenterological diseases, and liver diseases. The liver can be greatly affected by changes in gut microbiota due to the entry of gut bacteria or their metabolites into the liver through the portal vein, and the liver-gut axis is important to understand the pathophysiology of several liver diseases, especially non-alcoholic fatty liver disease and hepatic encephalopathy. Moreover, gut microbiota play a significant role in the development of alcoholic liver disease and hepatocarcinogenesis. Based on these previous findings, trials using probiotics have been performed for the prevention or treatment of liver diseases. In this review, we summarize the current understanding of the changes in gut microbiota associated with various liver diseases, and we describe the therapeutic trials of probiotics for those diseases.

  14. The gut microbiota in type 2 diabetes

    DEFF Research Database (Denmark)

    Nielsen, Trine; Allin, Kristine Højgaard; Pedersen, Oluf

    2016-01-01

    The exploration of the gut microbiota has intensified within the past decade with the introduction of cultivation-independent methods. By investigation of the gut bacterial genes, our understanding of the compositional and functional capability of the gut microbiome has increased. It is now widel...... strategies to prevent or treat type 2 diabetes....... recognized that the gut microbiota has profound effect on host metabolism and recently changes in the gut microbiota have been associated with type 2 diabetes. Animal models and human studies have linked changes in the gut microbiota to the induction of low-grade inflammation, altered immune response...

  15. The Yellowstone hotspot, Greater Yellowstone ecosystem, and human geography

    Science.gov (United States)

    Pierce, Kenneth L.; Despain, D.G.; Morgan, Lisa A.; Good, John M.; Morgan Morzel, Lisa Ann.

    2007-01-01

    Active geologic processes associated with the Yellowstone hotspot are fundamental in shaping the landscapes of the greater Yellowstone ecosystem (GYE), a high volcanic plateau flanked by a crescent of still higher mountainous terrain. The processes associated with the Yellowstone hotspot are volcanism, faulting, and uplift and are observed in the geology at the surface. We attribute the driving forces responsible for the northeastward progression of these processes to a thermal plume rising through the Earth’s mantle into the base of the southwest-moving North American plate. This progression began 16 million years ago (Ma) near the Nevada-Oregon border and arrived at Yellowstone about 2 Ma. Before arrival of the hotspot, an older landscape existed, particularly mountains created during the Laramide orogeny about 70–50 Ma and volcanic terrain formed by Absaroka andesitic volcanism mostly between 50–45 Ma. These landscapes were more muted than the present, hotspot-modified landscape because the Laramide-age mountains had worn down and an erosion surface of low relief had developed on the Absaroka volcanic terrain.

  16. Human activity selectively impacts the ecosystem roles of parrotfishes on coral reefs

    KAUST Repository

    Bellwood, David R.

    2011-11-16

    Around the globe, coral reefs and other marine ecosystems are increasingly overfished. Conventionally, studies of fishing impacts have focused on the population size and dynamics of targeted stocks rather than the broader ecosystem-wide effects of harvesting. Using parrotfishes as an example, we show how coral reef fish populations respond to escalating fishing pressure across the Indian and Pacific Oceans. Based on these fish abundance data, we infer the potential impact on four key functional roles performed by parrotfishes. Rates of bioerosion and coral predation are highly sensitive to human activity, whereas grazing and sediment removal are resilient to fishing. Our results offer new insights into the vulnerability and resilience of coral reefs to the ever-growing human footprint. The depletion of fishes causes differential decline of key ecosystem functions, radically changing the dynamics of coral reefs and setting the stage for future ecological surprises. © 2011 The Royal Society.

  17. Emerging aspects of food and nutrition on gut microbiota.

    Science.gov (United States)

    He, Xuan; Marco, Maria L; Slupsky, Carolyn M

    2013-10-09

    The human gastrointestinal tract contains a highly complex ecosystem that harbors various microorganisms, which together create a unique environment within each individual. There is growing awareness that dietary habits are one of the essential factors contributing to the microbial diversity and community configuration that ultimately affects human health. From an evolutionary perspective, human dietary history can be viewed as a central factor in the selection of the gut microbial community and stabilization of the mutualistic host-microbial interaction, that together drive host phenotype. Herein, current knowledge concerning the influence of major dietary macrostructure and individual food ingredients is presented. This knowledge will provide perspectives for personalized gut microbiota management and, ultimately, movement toward an era of personalized nutrition and medicine.

  18. In vitro activity on human gut bacteria of murta leaf extracts (Ugni molinae Turcz. ), a native plant from southern chile

    DEFF Research Database (Denmark)

    Shene, C.; Canquil, N.; Jorquera, M.

    2012-01-01

    Despite the fact that murta infusions have been used to treat gut/urinary infections by native Chileans for centuries, the mechanisms promoting such effects still remain unclear. As a first attempt to unravel these mechanisms, human fecal samples were incubated in a medium containing water extrac...

  19. The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases

    NARCIS (Netherlands)

    Khan, M. Tanweer; Duncan, Sylvia H.; Stams, Alfons J. M.; van Dijl, Jan Maarten; Flint, Harry J.; Harmsen, Hermie J. M.

    2012-01-01

    Faecalibacterium prausnitzii is one of the most abundant bacteria in the human gut ecosystem and it is an important supplier of butyrate to the colonic epithelium. Low numbers of faecalibacteria have been associated with inflammatory bowel disease. Despite being extremely oxygen sensitive, F. prausn

  20. Colonization Resistance of the Gut Microbiota against Clostridium difficile

    Directory of Open Access Journals (Sweden)

    Ana Elena Pérez-Cobas

    2015-08-01

    Full Text Available Antibiotics strongly disrupt the human gut microbiota, which in consequence loses its colonization resistance capacity, allowing infection by opportunistic pathogens such as Clostridium difficile. This bacterium is the main cause of antibiotic-associated diarrhea and a current problem in developed countries, since its incidence and severity have increased during the last years. Furthermore, the emergence of antibiotic resistance strains has reduced the efficiency of the standard treatment with antibiotics, leading to a higher rate of relapses. Here, we review recent efforts focused on the impact of antibiotics in the gut microbiome and their relationship with C. difficile colonization, as well as, in the identification of bacteria and mechanisms involved in the protection against C. difficile infection. Since a healthy gut microbiota is able to avoid pathogen colonization, restoration of the gut microbiota seems to be the most promising approach to face C. difficile infection, especially for recurrent cases. Therefore, it would be possible to design probiotics for patients undergoing antimicrobial therapies in order to prevent or fight the expansion of the pathogen in the gut ecosystem.

  1. Acid sulfate soils and human health--a Millennium Ecosystem Assessment.

    Science.gov (United States)

    Ljung, Karin; Maley, Fiona; Cook, Angus; Weinstein, Philip

    2009-11-01

    Acid sulfate soils have been described as the "nastiest soils on earth" because of their strong acidity, increased mobility of potentially toxic elements and limited bioavailability of nutrients. They only cover a small area of the world's total problem soils, but often have significant adverse effects on agriculture, aquaculture and the environment on a local scale. Their location often coincides with high population density areas along the coasts of many developing countries. As a result, their negative impacts on ecosystems can have serious implications to those least equipped for coping with the low crop yields and reduced water quality that can result from acid sulfate soil disturbance. The Millennium Ecosystem Assessment called on by the United Nations in 2000 emphasised the importance of ecosystems for human health and well-being. These include the service they provide as sources of food and water, through the control of pollution and disease, as well as for the cultural services ecosystems provide. While the problems related to agriculture, aquaculture and the environment have been the focus of many acid sulfate soil management efforts, the connection to human health has largely been ignored. This paper presents the potential health issues of acid sulfate soils, in relation to the ecosystem services identified in the Millennium Ecosystem Assessment. It is recognised that significant implications on food security and livelihood can result, as well as on community cohesiveness and the spread of vector-borne disease. However, the connection between these outcomes and acid sulfate soils is often not obvious and it is therefore argued that the impact of such soils on human well-being needs to be recognised in order to raise awareness among the public and decision makers, to in turn facilitate proper management and avoid potential human ill-health.

  2. The gut-brain peptide cyclo(His-Pro) is secreted in a pulsatile fashion in fasting humans.

    Science.gov (United States)

    Herminghuysen, D; Cook, C; Thompson, H; Bostick, D; Lee, F; Stokes, L; Hilton, C; Prasad, C

    1994-04-01

    Histidyl-proline diketopiperazine (CHP) is a cyclic dipeptide that is found in many animal tissues, most notably brain and gut. It has been found to have a variety of biologic actions and has been postulated to play a role in appetitive behavior and energy metabolism. This study was conducted in order to characterize the secretory pattern of CHP during a 24 h fast. Four subjects (2 obese and 2 lean) were studied during the latter 24 h of a 36 h fast. Blood was sampled every 10-15 min and assayed for CHP concentration using a specific radioimmunoassay. Analysis revealed that circulating CHP oscillates in humans and that diurnal variation occurred but only in the obese subjects.

  3. An extracellular cell-attached pullulanase confers branched α-glucan utilization in human gut Lactobacillus acidophilus

    DEFF Research Database (Denmark)

    Møller, Marie Sofie; Goh, Yong Jun; Rasmussen, Kasper Bøwig

    2017-01-01

    Of the few predicted extracellular glycan-active enzymes, glycoside hydrolase family 13 subfamily 14 (GH13_14) pullulanases are the most common in human gut lactobacilli. These enzymes share a unique modular organization, not observed in other bacteria, featuring a catalytic module, two starch...... binding modules, a domain of unknown function, and a C-terminal surface layer association protein (SLAP) domain. Here we explore the specificity of a representative of this group of pullulanases, LaPul13_14 and its role in branched α-glucans metabolism in the well characterized Lactobacillus acidophilus...... NCFM that is widely used as a probiotic. Growth experiments of L. acidophilus NCFM on starch-derived branched substrates revealed preference for α-glucans with short branches of about two to three glucosyl moieties over amylopectin with longer branches. Cell-attached debranching activity was measurable...

  4. Defensins, lectins, mucins, and secretory immunoglobulin A: microbe-binding biomolecules that contribute to mucosal immunity in the human gut.

    Science.gov (United States)

    Chairatana, Phoom; Nolan, Elizabeth M

    2017-02-01

    In the intestine, the mucosal immune system plays essential roles in maintaining homeostasis between the host and microorganisms, and protecting the host from pathogenic invaders. Epithelial cells produce and release a variety of biomolecules into the mucosa and lumen that contribute to immunity. In this review, we focus on a subset of these remarkable host-defense factors - enteric α-defensins, select lectins, mucins, and secretory immunoglobulin A - that have the capacity to bind microbes and thereby contribute to barrier function in the human gut. We provide an overview of the intestinal epithelium, describe specialized secretory cells named Paneth cells, and summarize our current understanding of the biophysical and functional properties of these select microbe-binding biomolecules. We intend for this compilation to complement prior reviews on intestinal host-defense factors, highlight recent advances in the field, and motivate investigations that further illuminate molecular mechanisms as well as the interplay between these molecules and microbes.

  5. Arabinoxylans and inulin differentially modulate the mucosal and luminal gut microbiota and mucin-degradation in humanized rats.

    Science.gov (United States)

    Van den Abbeele, Pieter; Gérard, Philippe; Rabot, Sylvie; Bruneau, Aurélia; El Aidy, Sahar; Derrien, Muriel; Kleerebezem, Michiel; Zoetendal, Erwin G; Smidt, Hauke; Verstraete, Willy; Van de Wiele, Tom; Possemiers, Sam

    2011-10-01

    The endogenous gut microbiota affects the host in many ways. Prebiotics should favour beneficial intestinal microbes and thus improve host health. In this study, we investigated how a novel class of potential prebiotic long-chain arabinoxylans (LC-AX) and the well-established prebiotic inulin (IN) modulate the gut microbiota of humanized rats. Six weeks after axenic rats were inoculated with a human faecal microbiota, their colonic microbiota was similar to this inoculum (∼ 70%), whereas their caecal microbiota was enriched with Verrucomicrobia and Firmicutes concomitant with lower abundance of Bacteroidetes. Moreover, different Bifidobacterium species colonized the lumen (B. adolescentis) and mucus (B. longum and B. bifidum). Both LC-AX and IN increased SCFA levels and induced a shift from acetate towards health-promoting propionate and butyrate respectively. By applying a high-resolution phylogenetic micro-array (HITChip) at the site of fermentation (caecum), IN and LC-AX were shown to stimulate bacterial groups with known butyrate-producers (Roseburia intestinalis, Eubacterium rectale, Anaerostipes caccae) and bifidobacteria (B. longum) respectively. Prebiotic administration also resulted in lower caecal abundances of the mucin-degrading Akkermansia muciniphila and potentially more mucin production by the host. Both factors might explain the increased caecal mucin levels for LC-AX (threefold) and IN (sixfold). These mucins were degraded along the colon, resulting in high faecal abundances of Akkermansia muciniphila for LC-AX and especially IN-treated rats. Finally, the microbial changes caused an adaptation period for the host with less weight gain, after which the host fine-tuned the interaction with this altered microbiota. Our results demonstrate that next to IN, LC-AX are promising prebiotic compounds by stimulating production of health-promoting metabolites by specific microbes in the proximal regions. Further, prebiotic supplementation shifted mucin

  6. Natural hazards, disasters and human kind: Whither ecosystem management?

    Digital Repository Service at National Institute of Oceanography (India)

    Mascarenhas, A.; Mudholkar, A.V.

    in the himalayas. Monetary loss due to the tsunami touched 3,242 crore rupees Encroachment of sensitive landforms such as coastal sand dunes and hill slopes is a major concern. As such, the relentless natural hazards culminate in disasters when humans come...

  7. The Gut Microbiota and Human Health%肠道微生物与人体健康研究进展

    Institute of Scientific and Technical Information of China (English)

    童雨心; 梁迎春

    2014-01-01

    人类肠道中定居着许多对宿主有益的微生物,包括细菌、病毒、真核生物等,它们在肠道内能与其他微生物及免疫系统相互作用,对人体健康具有重要影响,被称为“被遗忘的器官”,它们的基因组也被誉为人类的“第二基因组”,与人体的能量代谢及物质代谢有关。本文总结了人体肠道中病毒、真核生物、细菌和宿主免疫系统的相互作用,微生物群的失衡可能导致的疾病如肥胖和克罗恩病等,以及微生物环境在人体内的成熟过程,期望有助于诊断和治疗与肠道微生物失衡相关的疾病。%The human gut harbors diverse microbes that play a fundamental role in the well-being of their host. The constituents of the microbiota including bacteria, viruses, and eukaryotes have been shown to interact with one another and with the host immune system in ways that influence the development of disease. Gut microbi⁃ome is honoured as human's second genome. These interactions are reviewed and suggest that a holistic approach to studying the microbiota that goes beyond characterization of community composition and encompasses dynamic in⁃teractions between all components of the microbiota and host tissue over time will be crucial for building predic⁃tive models for diagnosis and treatment of diseases linked to imbalances in our microbiota.

  8. Cumulative human impacts on Mediterranean and Black Sea marine ecosystems: assessing current pressures and opportunities.

    Directory of Open Access Journals (Sweden)

    Fiorenza Micheli

    Full Text Available Management of marine ecosystems requires spatial information on current impacts. In several marine regions, including the Mediterranean and Black Sea, legal mandates and agreements to implement ecosystem-based management and spatial plans provide new opportunities to balance uses and protection of marine ecosystems. Analyses of the intensity and distribution of cumulative impacts of human activities directly connected to the ecological goals of these policy efforts are critically needed. Quantification and mapping of the cumulative impact of 22 drivers to 17 marine ecosystems reveals that 20% of the entire basin and 60-99% of the territorial waters of EU member states are heavily impacted, with high human impact occurring in all ecoregions and territorial waters. Less than 1% of these regions are relatively unaffected. This high impact results from multiple drivers, rather than one individual use or stressor, with climatic drivers (increasing temperature and UV, and acidification, demersal fishing, ship traffic, and, in coastal areas, pollution from land accounting for a majority of cumulative impacts. These results show that coordinated management of key areas and activities could significantly improve the condition of these marine ecosystems.

  9. Cumulative human impacts on Mediterranean and Black Sea marine ecosystems: assessing current pressures and opportunities.

    Science.gov (United States)

    Micheli, Fiorenza; Halpern, Benjamin S; Walbridge, Shaun; Ciriaco, Saul; Ferretti, Francesco; Fraschetti, Simonetta; Lewison, Rebecca; Nykjaer, Leo; Rosenberg, Andrew A

    2013-01-01

    Management of marine ecosystems requires spatial information on current impacts. In several marine regions, including the Mediterranean and Black Sea, legal mandates and agreements to implement ecosystem-based management and spatial plans provide new opportunities to balance uses and protection of marine ecosystems. Analyses of the intensity and distribution of cumulative impacts of human activities directly connected to the ecological goals of these policy efforts are critically needed. Quantification and mapping of the cumulative impact of 22 drivers to 17 marine ecosystems reveals that 20% of the entire basin and 60-99% of the territorial waters of EU member states are heavily impacted, with high human impact occurring in all ecoregions and territorial waters. Less than 1% of these regions are relatively unaffected. This high impact results from multiple drivers, rather than one individual use or stressor, with climatic drivers (increasing temperature and UV, and acidification), demersal fishing, ship traffic, and, in coastal areas, pollution from land accounting for a majority of cumulative impacts. These results show that coordinated management of key areas and activities could significantly improve the condition of these marine ecosystems.

  10. Persistent colonization of Helicobacter pylori in human gut induces gastroduodenal diseases

    Directory of Open Access Journals (Sweden)

    Animesh Sarker

    2014-12-01

    Full Text Available Helicobacter pylori are gut bacteria colonize in the epithelial cell lining of the stomach and persist there for long du­ration. Around two-thirds of the world’s populations are infected with H. pylori and cause more than 90 percent of ulcers. The development of persistent inflammation is the main cause of chronic gastritis that finally results in a severe consequence known as stomach cancer. Two major virulence factors cytotoxin-associated gene product (cagA and the vacuolating toxin (vacA are mostly investigated as their close association with gastric carcinoma. In this review, host im­munity against H. pylori infection and their evasion mechanism are intensely explored. It is the fact, that understanding pin point molecular mechanisms of any infection is critical to develop novel strategies to prevent pertinent diseases. .J Microbiol Infect Dis 2014; 4(4: 170-176

  11. The gut microbiota, obesity and insulin resistance

    Science.gov (United States)

    The human gut is densely populated by commensal and symbiotic microbes (the "gut microbiota"), with the majority of the constituent microorganisms being bacteria. Accumulating evidence indicates that the gut microbiota plays a significant role in the development of obesity, obesity-associated inflam...

  12. The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism.

    Science.gov (United States)

    Selma, María V; Romo-Vaquero, María; García-Villalba, Rocío; González-Sarrías, Antonio; Tomás-Barberán, Francisco A; Espín, Juan C

    2016-04-01

    We recently identified three metabotypes (0, A and B) that depend on the metabolic profile of urolithins produced from polyphenol ellagic acid (EA). The gut microbiota and Gordonibacter spp. recently were identified as species able to produce urolithins. A higher percentage of metabotype B was found in patients with metabolic syndrome or colorectal cancer in comparison with healthy individuals. The aim of the present study was to analyse differences in EA metabolism between healthy overweight-obese and normoweight individuals and evaluate the role of gut microbial composition including Gordonibacter. Although the three metabotypes were confirmed in both groups, metabotype B prevailed in overweight-obese (31%) versus normoweight (20%) individuals while metabotype A was higher in normoweight (70%) than the overweight-obese group (57%). This suggests that weight gain favours the growth of bacteria capable of producing urolithin B and/or isourolithin A with respect to urolithin A-producing bacteria. Gordonibacter spp. levels were not significantly different between normoweight and overweight-obese groups but higher Gordonibacter levels were found in metabotype A individuals than in those with metabotype B. Other bacterial species have been reported to show a much closer relationship to obesity and dysbiosis than Gordonibacter. However, Gordonibacter levels are negatively correlated with metabotype B, which prevails in metabolic syndrome and colorectal cancer. This is the first report that links overweight and obesity with an alteration in the catabolism of EA, and where the correlation of Gordonibacter to this alteration is shown. Future investigation of Gordonibacter and urolithin metabotypes as potential biomarkers or therapeutic targets of obesity-related diseases is warranted.

  13. Introduction to the special focus issue on the impact of diet on gut microbiota composition and function and future opportunities for nutritional modulation of the gut microbiome to improve human health.

    Science.gov (United States)

    Donovan, Sharon M

    2017-03-04

    Over the past decade, application of culture-independent, next generation DNA sequencing has dramatically enhanced our understanding of the composition of the gut microbiome and its association with human states of health and disease. Host genetics, age, and environmental factors such as where and who you live with, use of pre-, pro- and antibiotics, exercise and diet influence the short- and long-term composition of the microbiome. Dietary intake is a key determinant of microbiome composition and diversity and studies to date have linked long-term dietary patterns as well as short-term dietary interventions to the composition and diversity of the gut microbiome. The goal of this special focus issue was to review the role of diet in regulating the composition and function of the gut microbiota across the lifespan, from pregnancy to old age. Overall dietary patterns, as well as perturbations such as undernutrition and obesity, as well as the effects of dietary fiber/prebiotics and fat composition are explored.

  14. Bottlenecks in the Transferability of Antibiotic Resistance from Natural Ecosystems to Human Bacterial Pathogens

    OpenAIRE

    Martínez, José L.

    2012-01-01

    It is generally accepted that resistance genes acquired by human pathogens through horizontal gene transfer originated in environmental, non-pathogenic bacteria. As a consequence, there is increasing concern on the roles that natural, non-clinical ecosystems, may play in the evolution of resistance. Recent studies have shown that the variability of determinants that can provide antibiotic resistance on their expression in a heterologous host is much larger than what is actually found in human...

  15. The Three Genetics (Nuclear DNA, Mitochondrial DNA, and Gut Microbiome) of Longevity in Humans Considered as Metaorganisms

    Science.gov (United States)

    Candela, Marco; Brigidi, Patrizia; Luiselli, Donata; Bacalini, Maria Giulia; Salvioli, Stefano; Capri, Miriam; Collino, Sebastiano; Franceschi, Claudio

    2014-01-01

    Usually the genetics of human longevity is restricted to the nuclear genome (nDNA). However it is well known that the nDNA interacts with a physically and functionally separated genome, the mitochondrial DNA (mtDNA) that, even if limited in length and number of genes encoded, plays a major role in the ageing process. The complex interplay between nDNA/mtDNA and the environment is most likely involved in phenomena such as ageing and longevity. To this scenario we have to add another level of complexity represented by the microbiota, that is, the whole set of bacteria present in the different part of our body with their whole set of genes. In particular, several studies investigated the role of gut microbiota (GM) modifications in ageing and longevity and an age-related GM signature was found. In this view, human being must be considered as “metaorganism” and a more holistic approach is necessary to grasp the complex dynamics of the interaction between the environment and nDNA-mtDNA-GM of the host during ageing. In this review, the relationship between the three genetics and human longevity is addressed to point out that a comprehensive view will allow the researchers to properly address the complex interactions that occur during human lifespan. PMID:24868529

  16. Human gut endogenous proteins as a potential source of angiotensin-I-converting enzyme (ACE-I)-, renin inhibitory and antioxidant peptides.

    Science.gov (United States)

    Dave, Lakshmi A; Hayes, Maria; Montoya, Carlos A; Rutherfurd, Shane M; Moughan, Paul J

    2016-02-01

    It is well known that endogenous bioactive proteins and peptides play a substantial role in the body's first line of immunological defence, immune-regulation and normal body functioning. Further, the peptides derived from the luminal digestion of proteins are also important for body function. For example, within the peptide database BIOPEP (http://www.uwm.edu.pl/biochemia/index.php/en/biopep) 12 endogenous antimicrobial and 64 angiotensin-I-converting enzyme (ACE-I) inhibitory peptides derived from human milk and plasma proteins are listed. The antimicrobial peptide database (http://aps.unmc.edu/AP/main.php) lists over 111 human host-defence peptides. Several endogenous proteins are secreted in the gut and are subject to the same gastrointestinal digestion processes as food proteins derived from the diet. The human gut endogenous proteins (GEP) include mucins, serum albumin, digestive enzymes, hormones, and proteins from sloughed off epithelial cells and gut microbiota, and numerous other secreted proteins. To date, much work has been carried out regarding the health altering effects of food-derived bioactive peptides but little attention has been paid to the possibility that GEP may also be a source of bioactive peptides. In this review, we discuss the potential of GEP to constitute a gut cryptome from which bioactive peptides such as ACE-I inhibitory, renin inhibitory and antioxidant peptides may be derived.

  17. HUMAN-INDUCED CHANGES IN ECOSYSTEM SERVICES IN THE PETROŞANI DEPRESSION (SOUTHERN CARPATHIANS, ROMANIA

    Directory of Open Access Journals (Sweden)

    ANDRA COSTACHE

    2013-04-01

    Full Text Available The paper focuses on the changes in ecosystem services in the most important coal field from the Southern Carpathians (Romania. The time horizon considered is the interval 1950-2010, characterized by two major processes: intensive development of the mining industry (1950-1989 and subsequent restructuring of mining, with significant consequences since 1996. Socio-economic phenomena associated with these two stages in the evolution of the region have generated major changes in ecosystem services, leading to increased human vulnerability, both to extreme events (natural hazards and pressure from economic factors.

  18. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut.

    Science.gov (United States)

    Rivière, Audrey; Selak, Marija; Lantin, David; Leroy, Frédéric; De Vuyst, Luc

    2016-01-01

    With the increasing amount of evidence linking certain disorders of the human body to a disturbed gut microbiota, there is a growing interest for compounds that positively influence its composition and activity through diet. Besides the consumption of probiotics to stimulate favorable bacterial communities in the human gastrointestinal tract, prebiotics such as inulin-type fructans (ITF) and arabinoxylan-oligosaccharides (AXOS) can be consumed to increase the number of bifidobacteria in the colon. Several functions have been attributed to bifidobacteria, encompassing degradation of non-digestible carbohydrates, protection against pathogens, production of vitamin B, antioxidants, and conjugated linoleic acids, and stimulation of the immune system. During life, the numbers of bifidobacteria decrease from up to 90% of the total colon microbiota in vaginally delivered breast-fed infants to <5% in the colon of adults and they decrease even more in that of elderly as well as in patients with certain disorders such as antibiotic-associated diarrhea, inflammatory bowel disease, irritable bowel syndrome, obesity, allergies, and regressive autism. It has been suggested that the bifidogenic effects of ITF and AXOS are the result of strain-specific yet complementary carbohydrate degradation mechanisms within cooperating bifidobacterial consortia. Except for a bifidogenic effect, ITF and AXOS also have shown to cause a butyrogenic effect in the human colon, i.e., an enhancement of colon butyrate production. Butyrate is an essential metabolite in the human colon, as it is the preferred energy source for the colon epithelial cells, contributes to the maintenance of the gut barrier functions, and has immunomodulatory and anti-inflammatory properties. It has been shown that the butyrogenic effects of ITF and AXOS are the result of cross-feeding interactions between bifidobacteria and butyrate-producing colon bacteria, such as Faecalibacterium prausnitzii (clostridial cluster IV

  19. Lactobacillus rhamnosus GG and its SpaC pilus adhesin modulate inflammatory responsiveness and TLR-related gene expression in the fetal human gut

    Science.gov (United States)

    Ganguli, Kriston; Collado, Maria Carmen; Rautava, Jaana; Lu, Lei; Satokari, Reetta; von Ossowski, Ingemar; Reunanen, Justus; de Vos, Willem M.; Palva, Airi; Isolauri, Erika; Salminen, Seppo; Walker, W. Allan; Rautava, Samuli

    2015-01-01

    Background Bacterial contact in utero modulates fetal and neonatal immune responses. Maternal probiotic supplementation reduces the risk of immune-mediated disease in the infant. We investigated the immunomodulatory properties of live Lactobacillus rhamnosus GG and its SpaC pilus adhesin in human fetal intestinal models. Methods TNF-α mRNA expression was measured by qPCR in a human fetal intestinal organ culture model exposed to live L. rhamnosus GG and proinflammatory stimuli. Binding of recombinant SpaC pilus protein to intestinal epithelial cells was assessed in human fetal intestinal organ culture and the human fetal intestinal epithelial cell line H4 by immunohistochemistry and immunofluorescence, respectively. TLR-related gene expression in fetal ileal organ culture after exposure to recombinant SpaC was assessed by qPCR. Results Live L. rhamnosus GG significantly attenuates pathogen-induced TNF-α mRNA expression in the human fetal gut. Recombinant SpaC protein was found to adhere to the fetal gut and to modulate varying levels of TLR-related gene expression. Conclusion The human fetal gut is responsive to luminal microbes. L. rhamnosus GG significantly attenuates fetal intestinal inflammatory responses to pathogenic bacteria. The L. rhamnosus GG pilus adhesin SpaC binds to immature human intestinal epithelial cells and directly modulates intestinal epithelial cell innate immune gene expression. PMID:25580735

  20. Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut.

    Science.gov (United States)

    Castro-Mejía, Josué L; Muhammed, Musemma K; Kot, Witold; Neve, Horst; Franz, Charles M A P; Hansen, Lars H; Vogensen, Finn K; Nielsen, Dennis S

    2015-11-17

    The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset. We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery, samples were spiked with low numbers of c2, ϕ29, and T4 phages (representatives of the Siphoviridae, Podoviridae, and Myoviridae families, respectively) and their concentration (plaque-forming units) followed at every step during the extraction procedure. Compared with LIT, TFF and PEG had higher recovery of all spiked phages, yielding up to 16 times more phage particles (PPs) and up to 68 times more phage DNA per volume, increasing thus the chances of extracting low abundant phages. TFF- and PEG-derived metaviromes showed 10% increase in relative abundance of Caudovirales and unclassified phages infecting gut-associated bacteria (>92% for TFF and PEG, 82.4% for LIT). Our methods obtained lower relative abundance of the Myoviridae family (32.5%, LIT 22.6%), which was achieved with the enhanced conditions of our procedures (e.g., reduced filter clogging). A high degree of phage diversity in samples extracted using TFF and PEG was documented by transmission electron microscopy. Two procedures (TFF and PEG) for extraction of bacteriophages from fecal samples were optimized using a set of spiked bacteriophages as process control. These protocols are highly efficient tools for extraction and purification of PPs prior

  1. Global Human Footprint on the Linkage between Biodiversity and Ecosystem Functioning in Reef Fishes

    Science.gov (United States)

    Mora, Camilo; Aburto-Oropeza, Octavio; Ayala Bocos, Arturo; Ayotte, Paula M.; Banks, Stuart; Bauman, Andrew G.; Beger, Maria; Bessudo, Sandra; Booth, David J.; Brokovich, Eran; Brooks, Andrew; Chabanet, Pascale; Cinner, Joshua E.; Cortés, Jorge; Cruz-Motta, Juan J.; Cupul Magaña, Amilcar; DeMartini, Edward E.; Edgar, Graham J.; Feary, David A.; Ferse, Sebastian C. A.; Friedlander, Alan M.; Gaston, Kevin J.; Gough, Charlotte; Graham, Nicholas A. J.; Green, Alison; Guzman, Hector; Hardt, Marah; Kulbicki, Michel; Letourneur, Yves; López Pérez, Andres; Loreau, Michel; Loya, Yossi; Martinez, Camilo; Mascareñas-Osorio, Ismael; Morove, Tau; Nadon, Marc-Olivier; Nakamura, Yohei; Paredes, Gustavo; Polunin, Nicholas V. C.; Pratchett, Morgan S.; Reyes Bonilla, Héctor; Rivera, Fernando; Sala, Enric; Sandin, Stuart A.; Soler, German; Stuart-Smith, Rick; Tessier, Emmanuel; Tittensor, Derek P.; Tupper, Mark; Usseglio, Paolo; Vigliola, Laurent; Wantiez, Laurent; Williams, Ivor; Wilson, Shaun K.; Zapata, Fernando A.

    2011-01-01

    Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass) scales in a non-saturating manner with biodiversity (as measured by species and functional richness) in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs). Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the world's coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas. PMID:21483714

  2. Global human footprint on the linkage between biodiversity and ecosystem functioning in reef fishes.

    Directory of Open Access Journals (Sweden)

    Camilo Mora

    2011-04-01

    Full Text Available Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass scales in a non-saturating manner with biodiversity (as measured by species and functional richness in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs. Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the world's coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas.

  3. Impact of human interventions on mangrove ecosystem in spatial perspective

    Science.gov (United States)

    Rasyid, Abd.; Akbar AS, M.; Nurdin, Nurjannah; Jaya, Ilham; Ibrahim

    2016-11-01

    Climate change components that affect mangroves include changes in sea level, high water events, storms, precipitation, temperature, and oceanic circulation. Cumulative impacts of these factors have a distinct synergy with respect to an accelerated rate of mangrove degradation. development of coastal agricultural land and shrimp farming ponds in intertidal areas are considered as the major factors behind mangrove delineation. There is no agreement for the extensive of mangrove forest in Indonesia, but invarious forums it is usually used the number of 4.25 million ha for that. At approximately 9 years ago, the extensive vast of mangrove forest in Indonesia was about 4.13 million ha but now it is only 2.49 million ha (60%). The methodology of this study consisted of two main steps: (1) image analysis, and (2) post classification. The aim of this study is to analysis the human intervention base on spatial dynamic of mangrove. The study site was selected Sagara island in Spermonde Archipelago. The results of analyze shows that decreasing of mangrove is caused human intervention.

  4. ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts.

    Science.gov (United States)

    Wei, Guifang; Pan, Li; Du, Huimin; Chen, Junyi; Zhao, Liping

    2004-10-01

    Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.

  5. A galectin-specific signature in the gut delineates Crohn's disease and ulcerative colitis from other human inflammatory intestinal disorders.

    Science.gov (United States)

    Papa Gobbi, Rodrigo; De Francesco, Nicolás; Bondar, Constanza; Muglia, Cecilia; Chirdo, Fernando; Rumbo, Martín; Rocca, Andrés; Toscano, Marta A; Sambuelli, Alicia; Rabinovich, Gabriel A; Docena, Guillermo H

    2016-01-01

    Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory conditions of the gastrointestinal tract including Crohn's disease (CD) and ulcerative colitis (UC). Galectins, defined by shared consensus amino acid sequence and affinity for β-galactosides, are critical modulators of the inflammatory response. However, the relevance of the galectin network in the pathogenesis of human IBD has not yet been explored. Here, we analyzed the expression of relevant members of the galectin family in intestinal biopsies, and identified their contribution as novel mucosal markers in IBD. Colonic biopsies were obtained from 59 IBD patients (22 CD and 37 UC), 9 patients with gut rejection after transplantation, 8 adult celiac patients, and 32 non-IBD donors. Galectin mRNA expression was analyzed by RT-PCR and qPCR using specific primers for individual galectins. A linear discriminant analysis (LDA) was used to analyze galectin expression in individual intestinal samples. Expression of common mucosal-associated galectins (Gal-1, -3, -4, -9) is dysregulated in inflamed tissues of IBD patients compared with non-inflamed IBD or control samples. LDA discriminated between different inflammation grades in active IBD and showed that remission IBD samples were clusterized with control samples. Galectin profiling could not distinguish CD and UC. Furthermore, inflamed IBD was discriminated from inflamed tissue of rejected gut in transplanted patients and duodenum of celiac patients, which could not be distinguished from control duodenum samples. The integrative analysis of galectins discriminated IBD from other intestinal inflammatory conditions and could be used as potential mucosal biomarker.

  6. Study of the aminoglycoside subsistence phenotype of bacteria residing in the gut of humans and zoo animals

    Directory of Open Access Journals (Sweden)

    Teresita De Jesus eBello Gonzalez

    2016-01-01

    Full Text Available Recent studies indicate that next to antibiotic resistance, bacteria are able to subsist on antibiotics as a carbon source. Here we evaluated the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics. Nine gut isolates of Escherichia coli and Cellulosimicrobium spp. displayed increases in colony forming units during incubations in minimal medium with only antibiotics added, i.e. the antibiotic subsistence phenotype. Furthermore, laboratory strains of E. coli and Pseudomonas putida equipped with the aminoglycoside 3’phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides. In order to address which endogenous genes could be involved in these subsistence phenotypes, the broad-range glycosyl-hydrolase inhibiting iminosugar deoxynojirimycin (DNJ was used. Addition of DNJ to minimal medium containing glucose showed initial growth retardation of resistant E. coli, which was rapidly recovered to normal growth. In contrast, addition of DNJ to minimal medium containing kanamycin arrested resistant E. coli growth, suggesting that glycosyl-hydrolases were involved in the subsistence phenotype. However, antibiotic degradation experiments showed no reduction in kanamycin, even though the number of colony forming units increased. Although antibiotic subsistence phenotypes are readily observed in bacterial species, and are even found in susceptible laboratory strains carrying standard resistance genes, we conclude there is a discrepancy between the observed antibiotic subsistence phenotype and actual antibiotic degradation. Based on these results we can hypothesise that aminoglycoside modifying enzymes might first inactivate the antibiotic (i.e. by acetylation of amino groups, modification of hydroxyl groups by adenylation and phosphorylation respectively, before the subsequent action of catabolic enzymes. Even though we do not dispute that antibiotics could be used as a single carbon

  7. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol.

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    Bédis Dridi

    Full Text Available BACKGROUND: The low and variable prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae DNA in human stool contrasts with the paramount role of these methanogenic Archaea in digestion processes. We hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon DNA extraction. We developed a new protocol for the extraction and PCR-based detection of M. smithii and M. stadtmanae DNA in human stool. METHODOLOGY/PRINCIPAL FINDINGS: Stool specimens collected from 700 individuals were filtered, mechanically lysed twice, and incubated overnight with proteinase K prior to DNA extraction using a commercial DNA extraction kit. Total DNA was used as a template for quantitative real-time PCR targeting M. smithii and M. stadtmanae 16S rRNA and rpoB genes. Amplification of 16S rRNA and rpoB yielded positive detection of M. smithii in 95.7% and M. stadtmanae in 29.4% of specimens. Sequencing of 16S rRNA gene PCR products from 30 randomly selected specimens (15 for M. smithii and 15 for M. stadtmanae yielded a sequence similarity of 99-100% using the reference M. smithii ATCC 35061 and M. stadtmanae DSM 3091 sequences. CONCLUSIONS/SIGNIFICANCE: In contrast to previous reports, these data indicate a high prevalence of the methanogens M. smithii and M. stadtmanae in the human gut, with the former being an almost ubiquitous inhabitant of the intestinal microbiome.

  8. Recent advances in the role of probiotics in human inflammation and gut health.

    Science.gov (United States)

    Rupa, Prithy; Mine, Yoshinori

    2012-08-29

    The gastrointestinal (GI) tract provides residence to an astounding number of bacterial species, which have profound effects on host biology, function, physiology, and immune response. Discovery of "symbiosis factors" from symbionts that facilitate the peaceful coexistence of microbiota and the host immune system are of interest. Symbionts synthesize immunomodulatory molecules that guide maturation of the immune system and have pivotal roles in many biological processes; however, individuals differ in the makeup of their GI microbiota, which is influenced by many external and internal factors such as diet, antibiotic use, and host genetics, which in turn influences health and disease outcomes. Various endogenous, genetic, and environmental factors influence GI development including species composition and health status of neonates, resulting in interactions that occur between the bacteria and the host. Mechanisms of probiotics involved in homeostasis of a balanced immune system have been inconclusive. The probable mechanism of action may be postulated as direct competition between pathogenic bacteria in the gut and/or immune modulation. This review focuses on probiotics in health and disease prevention, especially the biological importance of intestinal regulation of inflammatory processes that may be beneficial in a multitude of disorders both inside and outside the GI tract.

  9. Influence of H7N9 virus infection and associated treatment on human gut microbiota

    Science.gov (United States)

    Qin, Nan; Zheng, Beiwen; Yao, Jian; Guo, Lihua; Zuo, Jian; Wu, Lingjiao; Zhou, Jiawei; Liu, Lin; Guo, Jing; Ni, Shujun; Li, Ang; Zhu, Yixin; Liang, Weifeng; Xiao, Yonghong; Ehrlich, S. Dusko; Li, Lanjuan

    2015-01-01

    Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp. 7 2 43FAA and Enterococcus faecium. It was concluded that H7N9 viral infection and antibiotic administration have a significant effect on the microbiota community with decreased diversity and overgrowth of the bacteria such as Escherichia coli and Enterococcus faecium. Enterotype analysis showed that the communities were unstable. Treatment including antivirals, probiotics and antibiotics helps to improve the microbiota diversity and the abundance of beneficial bacteria in the gut. PMID:26490635

  10. Vulnerability assessment of urban ecosystems driven by water resources, human health and atmospheric environment

    Science.gov (United States)

    Shen, Jing; Lu, Hongwei; Zhang, Yang; Song, Xinshuang; He, Li

    2016-05-01

    As ecosystem management is a hotspot and urgent topic with increasing population growth and resource depletion. This paper develops an urban ecosystem vulnerability assessment method representing a new vulnerability paradigm for decision makers and environmental managers, as it's an early warning system to identify and prioritize the undesirable environmental changes in terms of natural, human, economic and social elements. The whole idea is to decompose a complex problem into sub-problem, and analyze each sub-problem, and then aggregate all sub-problems to solve this problem. This method integrates spatial context of Geographic Information System (GIS) tool, multi-criteria decision analysis (MCDA) method, ordered weighted averaging (OWA) operators, and socio-economic elements. Decision makers can find out relevant urban ecosystem vulnerability assessment results with different vulnerable attitude. To test the potential of the vulnerability methodology, it has been applied to a case study area in Beijing, China, where it proved to be reliable and consistent with the Beijing City Master Plan. The results of urban ecosystem vulnerability assessment can support decision makers in evaluating the necessary of taking specific measures to preserve the quality of human health and environmental stressors for a city or multiple cities, with identifying the implications and consequences of their decisions.

  11. Ecological service assessment of human-dominated freshwater ecosystem with a case study in Yangzhou Prefecture,China

    Institute of Scientific and Technical Information of China (English)

    YE Ya-ping; WANG Ru-song; REN Jing-ming; HU Dan; YUAN Shao-jun; WANG Min

    2004-01-01

    Freshwater ecosystems provide a host of services to humanity. These services are now rapidly being lost, not least because of the inability of making the impacts measurable. To overcome this obstacle, assessment frameworks for freshwater ecosystem services are needed. A simple water equivalent framework to assess the ecological services provided by freshwater ecosystems was developed in this study. It translated the occupation of freshwater ecosystem services into biologically freshwater volumes and then compares this consumption to the freshwater throughput, that is, the ecological capacity available in this region. In this way, we use the example of Yangzhou Prefecture, to account the main categories of human occupation of water ecosystem services. The result showed that there is a huge gap between the consumption and the supply of freshwater ecosystem services. This must encourage local government to make land-use and water management decisions both economically rational and environmentally sound.

  12. Micromorphometrical analysis of rodent related (SPF) and unrelated (human) gut microbial flora in germfree mice by digital image processing

    NARCIS (Netherlands)

    Veenendaal, D.; Boer, J. de; Waaij, D. van der; Wilkinson, M.H.F.; Meijer, B.C

    Digital image processing (DIP) of bacterial smears is a new method of analysing the composition of the gut microbial flora. This method provides the opportunity to compare and evaluate differences in the complex highly concentrated anaerobic fraction of gut microbial flora, based on

  13. Do nutrient-gut-microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes?

    Science.gov (United States)

    Diamant, M; Blaak, E E; de Vos, W M

    2011-04-01

    The current obesity and type 2 diabetes pandemics have causes beyond changes in eating and exercise habits against a susceptible genetic background. Gut bacteria seem to additionally contribute to the differences in body weight, fat distribution, insulin sensitivity and glucose- and lipid-metabolism. Data, mostly derived from preclinical studies, suggest that gut microbiota play an important role in conditions such as obesity, diabetes, metabolic syndrome and non-alcoholic fatty liver disease. Regulation of energy uptake from the gut, by digesting otherwise indigestible common polysaccharides in our diet, production or activation of signalling molecules involved in host metabolism, modification of gut permeability, the release of gut hormones and inflammation, are among the mechanisms by which gut microbiota may influence the host cardiometabolic phenotype. Recent evidence suggests that quantitative and qualitative differences in gut microbiota exist between lean and obese, and between diabetic and non-diabetic individuals. Modification of the gut microbiota composition and/or its biochemical capacity by specific dietary or pharmacological interventions may favourably affect host metabolism. Large-scale intervention trials, investigating the potential benefit of prebiotics and probiotics in improving cardiometabolic health in high-risk populations, are eagerly awaited.

  14. Micromorphometrical analysis of rodent related (SPF) and unrelated (human) gut microbial flora in germfree mice by digital image processing

    NARCIS (Netherlands)

    Veenendaal, D.; Boer, J. de; Waaij, D. van der; Wilkinson, M.H.F.; Meijer, B.C

    1996-01-01

    Digital image processing (DIP) of bacterial smears is a new method of analysing the composition of the gut microbial flora. This method provides the opportunity to compare and evaluate differences in the complex highly concentrated anaerobic fraction of gut microbial flora, based on micromorphologic

  15. The Dynamics of the Human Infant Gut Microbiome in Development and in Progression Toward Type1 Diabetes

    Science.gov (United States)

    2016-09-09

    SECURITY CLASSIFICATION OF: Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease...core gut microbiome in obese and lean twins. Nature 457, 480–484. Vaarala, O., Atkinson, M.A., and Neu , J. (2008). The ‘‘perfect storm’’ for type 1

  16. Gut microbiota and allogeneic transplantation.

    Science.gov (United States)

    Wang, Weilin; Xu, Shaoyan; Ren, Zhigang; Jiang, Jianwen; Zheng, Shusen

    2015-08-23

    The latest high-throughput sequencing technologies show that there are more than 1000 types of microbiota in the human gut. These microbes are not only important to maintain human health, but also closely related to the occurrence and development of various diseases. With the development of transplantation technologies, allogeneic transplantation has become an effective therapy for a variety of end-stage diseases. However, complications after transplantation still restrict its further development. Post-transplantation complications are closely associated with a host's immune system. There is also an interaction between a person's gut microbiota and immune system. Recently, animal and human studies have shown that gut microbial populations and diversity are altered after allogeneic transplantations, such as liver transplantation (LT), small bowel transplantation (SBT), kidney transplantation (KT) and hematopoietic stem cell transplantation (HTCT). Moreover, when complications, such as infection, rejection and graft versus host disease (GVHD) occur, gut microbial populations and diversity present a significant dysbiosis. Several animal and clinical studies have demonstrated that taking probiotics and prebiotics can effectively regulate gut microbiota and reduce the incidence of complications after transplantation. However, the role of intestinal decontamination in allogeneic transplantation is controversial. This paper reviews gut microbial status after transplantation and its relationship with complications. The role of intervention methods, including antibiotics, probiotics and prebiotics, in complications after transplantation are also discussed. Further research in this new field needs to determine the definite relationship between gut microbial dysbiosis and complications after transplantation. Additionally, further research examining gut microbial intervention methods to ameliorate complications after transplantation is warranted. A better understanding of the

  17. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.

    Science.gov (United States)

    Greenblum, Sharon; Turnbaugh, Peter J; Borenstein, Elhanan

    2012-01-10

    The human microbiome plays a key role in a wide range of host-related processes and has a profound effect on human health. Comparative analyses of the human microbiome have revealed substantial variation in species and gene composition associated with a variety of disease states but may fall short of providing a comprehensive understanding of the impact of this variation on the community and on the host. Here, we introduce a metagenomic systems biology computational framework, integrating metagenomic data with an in silico systems-level analysis of metabolic networks. Focusing on the gut microbiome, we analyze fecal metagenomic data from 124 unrelated individuals, as well as six monozygotic twin pairs and their mothers, and generate community-level metabolic networks of the microbiome. Placing variations in gene abundance in the context of these networks, we identify both gene-level and network-level topological differences associated with obesity and inflammatory bowel disease (IBD). We show that genes associated with either of these host states tend to be located at the periphery of the metabolic network and are enriched for topologically derived metabolic "inputs." These findings may indicate that lean and obese microbiomes differ primarily in their interface with the host and in the way they interact with host metabolism. We further demonstrate that obese microbiomes are less modular, a hallmark of adaptation to low-diversity environments. We additionally link these topological variations to community species composition. The system-level approach presented here lays the foundation for a unique framework for studying the human microbiome, its organization, and its impact on human health.

  18. Human gut dendritic cells drive aberrant gut-specific t-cell responses in ulcerative colitis, characterized by increased IL-4 production and loss of IL-22 and IFNγ.

    Science.gov (United States)

    Mann, Elizabeth R; Bernardo, David; Ng, Siew C; Rigby, Rachael J; Al-Hassi, Hafid O; Landy, Jon; Peake, Simon T C; Spranger, Henning; English, Nicholas R; Thomas, Linda V; Stagg, Andrew J; Knight, Stella C; Hart, Ailsa L

    2014-12-01

    : The pathogenesis of inflammatory bowel disease is incompletely understood but results from a dysregulated intestinal immune response to the luminal microbiota. CD4 T cells mediate tissue injury in the inflammatory bowel disease-associated immune response. Dendritic cells (DC) generate primary T-cell responses and mediate intestinal immune tolerance to prevent overt inflammation in response to the gut microbiota. However, most information regarding function of intestinal DC has come from mouse models, and information in humans is scarce. We show here that intestinal DC subsets are skewed in ulcerative colitis (UC) in humans, with a loss of CD103 lymph-node homing DC; this intestinal DC subset preferentially generates regulatory T cells in mice. We show infiltrates of DC negative for myeloid marker CD11c, with enhanced expression of Toll-like receptors for bacterial recognition. After mixed leukocyte reaction, DC from the inflamed UC colon had an enhanced ability to generate gut-specific CD4 T cells with enhanced production of interleukin-4 but a loss of interferon γ and interleukin-22 production. Conditioning intestinal DC with probiotic strain Lactobacillus casei Shirota in UC partially restored their normal function indicated by reduced Toll-like receptor 2/4 expression and restoration of their ability to imprint homing molecules on T cells and to generate interleukin-22 production by stimulated T cells. This study suggests that T-cell dysfunction in UC is driven by DC. T-cell responses can be manipulated indirectly through effects of bacterial conditioning on gut DC with implications for immunomodulatory effects of the commensal microbiota in vivo. Manipulation of DC to allow generation of DC-specific therapy may be beneficial in inflammatory bowel disease.

  19. The Enigmatic Universe of the Herbivore Gut.

    Science.gov (United States)

    Glass, N Louise

    2016-07-01

    The herbivore gut is a fascinating ecosystem exquisitely adapted to plant biomass degradation. Within this ecosystem, anaerobic fungi invade biomass and secrete hydrolytic enzymes. In a recent study, Solomon et al. characterized three anaerobic fungi by transcriptomics, proteomics, and functional analyses to identify novel components essential for plant biomass deconstruction.

  20. Monitoring host responses to the gut microbiota.

    Science.gov (United States)

    Lichtman, Joshua S; Sonnenburg, Justin L; Elias, Joshua E

    2015-09-01

    The gastrointestinal (GI) ecosystem is increasingly understood to be a fundamental component of health, and has been identified as a new focal point for diagnosing, correcting and preventing countless disorders. Shotgun DNA sequencing has emerged as the dominant technology for determining the genetic and microbial composition of the gut microbiota. This technology has linked microbiota dysbioses to numerous GI diseases including inflammatory bowel disease, obesity and allergy, and to non-GI diseases like autism and depression. The importance of establishing causality in the deterioration of the host-microbiota relationship is well appreciated; however, discovery of candidate molecules and pathways that underlie mechanisms remains a major challenge. Targeted approaches, transcriptional assays, cytokine panels and imaging analyses, applied to animals, have yielded important insight into host responses to the microbiota. However, non-invasive, hypothesis-independent means of measuring host responses in humans are necessary to keep pace with similarly unbiased sequencing efforts that monitor microbes. Mass spectrometry-based proteomics has served this purpose in many other fields, but stool proteins exist in such diversity and dynamic range as to overwhelm conventional proteomics technologies. Focused analysis of host protein secretion into the gut lumen and monitoring proteome-level dynamics in stool provides a tractable route toward non-invasively evaluating dietary, microbial, surgical or pharmacological intervention efficacies. This review is intended to guide GI biologists and clinicians through the methods currently used to elucidate host responses in the gut, with a specific focus on mass spectrometry-based shotgun proteomics applied to the study of host protein dynamics within the GI ecosystem.

  1. Nonlinearly combined impacts of initial perturbation from human activities and parameter perturbation from climate change on the grassland ecosystem

    Directory of Open Access Journals (Sweden)

    G. Sun

    2011-11-01

    Full Text Available Human activities and climate change are important factors that affect grassland ecosystems. A new optimization approach, the approach of conditional nonlinear optimal perturbation (CNOP related to initial and parameter perturbations, is employed to explore the nonlinearly combined impacts of human activities and climate change on a grassland ecosystem using a theoretical grassland model. In our study, it is assumed that the initial perturbations and parameter perturbations are regarded as human activities and climate change, respectively. Numerical results indicate that the climate changes causing the maximum effect in the grassland ecosystem are different under disparate intensities of human activities. This implies the pattern of climate change is very critical to the maintenance or degradation of grassland ecosystem in light of high intensity of human activities and that the grassland ecosystem should be rationally managed when the moisture index decreases. The grassland ecosystem influenced by the nonlinear combination of human activities and climate change undergoes abrupt change, while the grassland ecosystem affected by other types of human activities and climate change fails to show the abrupt change under a certain range of perturbations with the theoretical model. The further numerical analyses also indicate that the growth of living biomass and the evaporation from soil surface shaded by the wilted biomass may be crucial factors contributing to the abrupt change of the grassland equilibrium state within the theoretical model.

  2. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Xu, Qingping; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L; Bakolitsa, Constantina; Cai, Xiaohui; Carlton, Dennis; Chen, Connie; Chiu, Hsiu Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C; Duan, Lian; Ellrott, Kyle; Farr, Carol L; Feuerhelm, Julie; Grant, Joanna C; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K; Klock, Heath E; Knuth, Mark W; Kozbial, Piotr; Krishna, S Sri; Kumar, Abhinav; Lam, Winnie W; Marciano, David; Miller, Mitchell D; Morse, Andrew T; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Tien, Henry J; Trame, Christine B; van den Bedem, Henry; Weekes, Dana; Wooten, Tiffany; Yeh, Andrew; Zhou, Jiadong; Hodgson, Keith O; Wooley, John; Elsliger, Marc André; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A

    2010-10-01

    Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.

  3. Characterization of Xyn10A, a highly active xylanase from the human gut bacterium Bacteroides xylanisolvens XB1A.

    Science.gov (United States)

    Mirande, Caroline; Mosoni, Pascale; Béra-Maillet, Christel; Bernalier-Donadille, Annick; Forano, Evelyne

    2010-08-01

    A xylanase gene xyn10A was isolated from the human gut bacterium Bacteroides xylanisolvens XB1A and the gene product was characterized. Xyn10A is a 40-kDa xylanase composed of a glycoside hydrolase family 10 catalytic domain with a signal peptide. A recombinant His-tagged Xyn10A was produced in Escherichia coli and purified. It was active on oat spelt and birchwood xylans and on wheat arabinoxylans. It cleaved xylotetraose, xylopentaose, and xylohexaose but not xylobiose, clearly indicating that Xyn10A is a xylanase. Surprisingly, it showed a low activity against carboxymethylcellulose but no activity at all against aryl-cellobioside and cellooligosaccharides. The enzyme exhibited K (m) and V (max) of 1.6 mg ml(-1) and 118 micromol min(-1) mg(-1) on oat spelt xylan, and its optimal temperature and pH for activity were 37 degrees C and pH 6.0, respectively. Its catalytic properties (k (cat)/K (m) = 3,300 ml mg(-1) min(-1)) suggested that Xyn10A is one of the most active GH10 xylanase described to date. Phylogenetic analyses showed that Xyn10A was closely related to other GH10 xylanases from human Bacteroides. The xyn10A gene was expressed in B. xylanisolvens XB1A cultured with glucose, xylose or xylans, and the protein was associated with the cells. Xyn10A is the first family 10 xylanase characterized from B. xylanisolvens XB1A.

  4. The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner.

    Science.gov (United States)

    Ó Cuív, Páraic; de Wouters, Tomas; Giri, Rabina; Mondot, Stanislas; Smith, Wendy J; Blottière, Hervé M; Begun, Jakob; Morrison, Mark

    2017-10-01

    The gut microbiota is increasingly implicated in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC) although the identity of the bacteria that underpin these diseases has remained elusive. The pathobiont Bacteroides vulgatus has been associated with both diseases although relatively little is known about how its growth and functional activity might drive the host inflammatory response. We identified an ATP Binding Cassette (ABC) export system and lipoprotein in B. vulgatus ATCC 8482 and B. vulgatus PC510 that displayed significant sequence similarity to an NF-κB immunomodulatory regulon previously identified on a CD-derived metagenomic fosmid clone. Interestingly, the ABC export system was specifically enriched in CD subjects suggesting that it may be important for colonization and persistence in the CD gut environment. Both B. vulgatus ATCC 8482 and PC510 activated NF-κB in a strain and growth phase specific manner in a HT-29/kb-seap-25 enterocyte like cell line. B. vulgatus ATCC 8482 also activated NF-κB in a Caco-2-NF-κBluc enterocyte like and an LS174T-NF-κBluc goblet cell like cell lines, and induced NF-κB-p65 subunit nuclear translocation and IL-6, IL-8, CXCL-10 and MCP-1 gene expression. Despite this, NF-κB activation was not coincident with maximal expression of the ABC exporter or lipoprotein in B. vulgatus PC510 suggesting that the regulon may be necessary but not sufficient for the immunomodulatory effects. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  5. In vitro growth of four individual human gut bacteria on oligosaccharides produced by chemoenzymatic synthesis.

    Science.gov (United States)

    Vigsnaes, Louise K; Nakai, Hiroyuki; Hemmingsen, Lene; Andersen, Joakim M; Lahtinen, Sampo J; Rasmussen, Louise E; Hachem, Maher Abou; Petersen, Bent O; Duus, Jens Ø; Meyer, Anne S; Licht, Tine R; Svensson, Birte

    2013-04-30

    The present study aimed at examining oligosaccharides (OS) for potential stimulation of probiotic bacteria. Nineteen structurally well-defined candidate OS covering groups of β-glucosides, α-glucosides and α-galactosides with degree of polymerization 2-4 were prepared in >100 mg amounts by chemoenzymatic synthesis (i.e. reverse phosphorolysis or transglycosylation). Fourteen of the OS are not naturally occurring and five (β-D-glucosyl-fructose, β-D-glucosyl-xylitol, α-glucosyl-(1,4)-D-mannose, α-glucosyl-(1,4)-D-xylose; α-glucosyl-(1,4)-L-fucose) have recently been synthesized for the first time. These OS have not been previously tested for effects of bacterial growth and here the ability of all 19 OS to support growth of four gastrointestinal bacteria: three probiotic bacteria Bifidobacterium lactis, Bifidobacterium longum, and Lactobacillus acidophilus, and one commensal bacterium, Bacteroides vulgatus has been evaluated in monocultures. The disaccharides β-D-glucosyl-xylitol and β-D-glucosyl-(1,4)-xylose noticeably stimulated growth yields of L. acidophilus NCFM, and additionally, β-D-glucosyl-(1,4)-xylose stimulated B. longum Bl-05. α-Glucosyl-(1,4)-glucosamine and α-glucosyl-(1,4)-N-acetyl-glucosamine enhanced the growth rate of B. animalis subsp. lactis and B. longum Bl-05, whereas L. acidophilus NCFM and Bac. vulgatus did not grow on these OS. α-Galactosyl-(1,6)-α-galactosyl-(1,6)-glucose advanced the growth rate of B. animalis subsp. lactis and L. acidophilus NCFM. Thus several of the structurally well-defined OS supported growth of beneficial gut bacteria. This reflects a broad specificity of their sugar transporters for OS, including specificity for non-naturally occurring OS, hence showing promise for design of novel prebiotics.

  6. l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota.

    Science.gov (United States)

    Hobbs, Merlin Eric; Williams, Howard J; Hillerich, Brandan; Almo, Steven C; Raushel, Frank M

    2014-07-22

    A previously unknown metabolic pathway for the utilization of l-galactose was discovered in a prevalent gut bacterium, Bacteroides vulgatus. The new pathway consists of three previously uncharacterized enzymes that were found to be responsible for the conversion of l-galactose to d-tagaturonate. Bvu0219 (l-galactose dehydrogenase) was determined to oxidize l-galactose to l-galactono-1,5-lactone with kcat and kcat/Km values of 21 s(-1) and 2.0 × 10(5) M(-1) s(-1), respectively. The kinetic product of Bvu0219 is rapidly converted nonenzymatically to the thermodynamically more stable l-galactono-1,4-lactone. Bvu0220 (l-galactono-1,5-lactonase) hydrolyzes both the kinetic and thermodynamic products of Bvu0219 to l-galactonate. However, l-galactono-1,5-lactone is estimated to be hydrolyzed 300-fold faster than its thermodynamically more stable counterpart, l-galactono-1,4-lactone. In the final step of this pathway, Bvu0222 (l-galactonate dehydrogenase) oxidizes l-galactonate to d-tagaturonate with kcat and kcat/Km values of 0.6 s(-1) and 1.7 × 10(4) M(-1) s(-1), respectively. In the reverse direction, d-tagaturonate is reduced to l-galactonate with values of kcat and kcat/Km of 90 s(-1) and 1.6 × 10(5) M(-1) s(-1), respectively. d-Tagaturonate is subsequently converted to d-glyceraldehyde and pyruvate through enzymes encoded within the degradation pathway for d-glucuronate and d-galacturonate.

  7. Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

    Directory of Open Access Journals (Sweden)

    Emily Vogtmann

    Full Text Available Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. This demonstrated that within the same sample set, most, but not all taxonomic associations were seen with both methods. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in a recently published French metagenomics dataset, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In total, colorectal cancer status in the Washington, DC study was associated with 39% of the metagenome-predicted genes, modules, and pathways identified in the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies should have larger sample sizes or pool data across studies to have sufficient

  8. Integrated modelling for assessing the risk of TCE groundwater contamination to human and surface water ecosystems

    DEFF Research Database (Denmark)

    McKnight, Ursula S.; Funder, Simon Goltermann; Finkel, Michael;

    2009-01-01

    management tools designed to work with sparse data sets from preliminary site assessments are needed which can explicitly link contaminant point sources with groundwater, surface water and ecological impacts. Here, a novel integrated modelling approach was employed for evaluating the impact of a TCE...... groundwater plume, located in an area with protected drinking water interests, to human health and surface water ecosystems. This is accomplished by coupling the system dynamics-based decision support system CARO-Plus to the aquatic ecosystem model AQUATOX via an analytical volatilisation model for the stream...... of “effective” parameters in groundwater transport modelling. The initial modelling results indicate that TCE contaminant plumes with μgL-1 concentrations entering surface water systems do not pose a significant risk to either human or ecological receptors. The current work will be extended to additional...

  9. Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates.

    Science.gov (United States)

    Lamb, Joleah B; van de Water, Jeroen A J M; Bourne, David G; Altier, Craig; Hein, Margaux Y; Fiorenza, Evan A; Abu, Nur; Jompa, Jamaluddin; Harvell, C Drew

    2017-02-17

    Plants are important in urban environments for removing pathogens and improving water quality. Seagrass meadows are the most widespread coastal ecosystem on the planet. Although these plants are known to be associated with natural biocide production, they have not been evaluated for their ability to remove microbiological contamination. Using amplicon sequencing of the 16S ribosomal RNA gene, we found that when seagrass meadows are present, there was a 50% reduction in the relative abundance of potential bacterial pathogens capable of causing disease in humans and marine organisms. Moreover, field surveys of more than 8000 reef-building corals located adjacent to seagrass meadows showed twofold reductions in disease levels compared to corals at paired sites without adjacent seagrass meadows. These results highlight the importance of seagrass ecosystems to the health of humans and other organisms.

  10. Ecosystem approaches to human health Abordagens ecossistêmicas à saúde humana

    Directory of Open Access Journals (Sweden)

    N. Ole Nielsen

    2001-01-01

    Full Text Available The promotion of human health must be embedded in the wider pursuit of ecosystem health. Interventions will be impaired if ecosystem-linked determinants of health are not taken into account. In the extreme case, if ecosystems lose their capacity for renewal, society will lose life support services. Essential features of ecosystem health are the capacity to maintain integrity and to achieve reasonable and sustainable human goals. An ecosystem approach to research and management must be transdisciplinary and assure participation of stakeholders. These requisites provide a means for science to better deal with the complexity of ecosystems, and for policy-makers and managers to establish and achieve reasonable societal goals. The ecosystem approach can determine links between human health and activities or events which disturb ecosystem state and function. Examples are: landscape disturbance in agriculture, mining, forestry, urbanization, and natural disasters. An understanding of these links can provide guidance for management interventions and policy options that promote human health. An ecosystem approach to management must be adaptive because of irreducible uncertainty in ecosystem function.A promoção da saúde humana deve estar embutida na busca maior pela saúde do ecossistema. As intervenções estarão prejudicadas se os determinantes ecossistêmicos da saúde não forem levados em conta. Em caso extremo, se os ecossistemas perderem a capacidade de se renovarem, a sociedade ficará privada de serviços essenciais à sustentação da vida. As características essenciais da saúde ecossistêmica são a capacidade de manter a integridade e a de atingir metas humanas razoáveis e sustentáveis. Uma abordagem ecossistêmica para a pesquisa e gestão deve ser transdisciplinar e assegurar a participação dos diferentes atores. Tais características fornecem um meio à ciência para lidar melhor com a complexidade dos ecossistemas, bem como aos

  11. Enrichment of Bifidobacterium longum subsp. infantis ATCC 15697 within the human gut microbiota using alginate-poly-L-lysine-alginate microencapsulation oral delivery system: an in vitro analysis using a computer-controlled dynamic human gastrointestinal model.

    Science.gov (United States)

    Rodes, Laetitia; Tomaro-Duchesneau, Catherine; Saha, Shyamali; Paul, Arghya; Malhotra, Meenakshi; Marinescu, Daniel; Shao, Wei; Kahouli, Imen; Prakash, Satya

    2014-01-01

    This study evaluates alginate-poly-L-lysine-alginate Bifidobacterium longum subsp. infantis ATCC 15697-loaded microcapsules to enrich the human gut microbiota. The cell survival of alginate-poly-L-lysine-alginate microencapsulated B. infantis ATCC 15697 in gastric acid, bile, and through human gastrointestinal transit was investigated, as well as the formulation's effect on the gut microbiota. Results show that microencapsulation increases B. infantis ATCC 15697 cell survival at pH1.0 (33.54 ± 2.80% versus  0.05) colonic microbiota.

  12. MALDI-TOF identification of the human Gut microbiome in people with and without diarrhea in Senegal.

    Directory of Open Access Journals (Sweden)

    Bissoume Samb-Ba

    Full Text Available BACKGROUND: In Africa, there are several problems with the specific identification of bacteria. Recently, MALDI-TOF mass spectrometry has become a powerful tool for the routine microbial identification in many clinical laboratories. METHODOLOGY/PRINCIPAL FINDINGS: This study was conducted using feces from 347 individuals (162 with diarrhea and 185 without diarrhea sampled in health centers in Dakar, Senegal. Feces were transported from Dakar to Marseille, France, where they were cultured using different culture conditions. The isolated colonies were identified using MALDI-TOF. If a colony was unidentified, 16S rRNA sequencing was performed. Overall, 2,753 isolates were tested, allowing for the identification of 189 bacteria from 5 phyla, including 2 previously unknown species, 11 species not previously reported in the human gut, 10 species not previously reported in humans, and 3 fungi. 2,718 bacterial isolates (98.8% out of 2,750 yielded an accurate identification using mass spectrometry, as did the 3 Candida albicans isolates. Thirty-two bacterial isolates not identified by MALDI-TOF (1.2% were identified by sequencing, allowing for the identification of 2 new species. The number of bacterial species per fecal sample was significantly higher among patients without diarrhea (8.6±3 than in those with diarrhea (7.3±3.4; P = 0.0003. A modification of the gut microbiota was observed between the two groups. In individuals with diarrhea, major commensal bacterial species such as E. coli were significantly decreased (85% versus 64%, as were several Enterococcus spp. (E. faecium and E. casseliflavus and anaerobes, such as Bacteroides spp. (B. uniformis and B. vulgatus and Clostridium spp. (C. bifermentans, C. orbiscindens, C. perfringens, and C. symbosium. Conversely, several Bacillus spp. (B. licheniformis, B. mojavensis, and B. pumilus were significantly more frequent among patients with diarrhea. CONCLUSIONS/SIGNIFICANCE: MALDI-TOF is a

  13. Effect of a synbiotic food consumption on human gut metabolic profiles evaluated by (1)H Nuclear Magnetic Resonance spectroscopy.

    Science.gov (United States)

    Ndagijimana, Maurice; Laghi, Luca; Vitali, Beatrice; Placucci, Giuseppe; Brigidi, Patrizia; Guerzoni, M Elisabetta

    2009-08-31

    The capacity of human lactobacilli and bifidobacteria to produce metabolites under conditions that may prevail in the human intestine has been studied "in vitro". However, the effect of systematic probiotic consumption on human metabolic phenotype has not been investigated in faeces. This paper shows the potential for the use of (1)H Nuclear Magnetic Resonance ((1)H NMR) spectroscopy for studying the changes of the metabolic profiles of human faecal slurries. Faeces of 16 subjects, characterized by different natural levels of lactobacilli and bifidobacteria were recovered before and after 1 month of supplementation with a synbiotic food based on Lactobacillus acidophilus, Bifidobacterium longum and fructooligosaccharides, and analyzed by (1)H NMR. Multivariate statistical approach has been applied to the data obtained and particularly Canonical Discriminant Analysis of Principal Coordinates (CAP). More than 150 molecules belonging to short chain fatty acids, organic acids, esters, alcohols and amino acids were detected and quantified in the samples considered. The number and the extent of these molecules in faecal slurries were strongly affected by the synbiotic food consumption and gave rise to characteristic metabolic signature. In particular, the short chain fatty acid concentrations significantly increased while the amino acids contents decreased. The comparison of the data indicated that the intake of the synbiotic food alters the host metabolism in a measure dependent on the initial level of lactobacilli and bifidobacteria detected in the faecal specimens. The analysis of (1)H NMR profiles with CAP allowed a separation of faecal samples of the subjects on the basis of the synbiotic food intake. The multivariate statistical approach used demonstrated the potential of NMR metabolic profiles to provide biomarkers of the gut-microbial activity related to dietary supplementation of probiotics.

  14. In vitro study of soil arsenic release by human gut microbiota and its intestinal absorption by Caco-2 cells.

    Science.gov (United States)

    Yin, Naiyi; Cai, Xiaolin; Du, Huili; Zhang, Zhennan; Li, Zejiao; Chen, Xiaochen; Sun, Guoxin; Cui, Yanshan

    2017-02-01

    Arsenic (As) speciation is essential in assessing health risks from As-contaminated soil. Release of soil-bound arsenic, As transformation by human gut microbiota, and the subsequent intestinal absorption of soil As metabolites were evaluated. A colon microbial community in a dynamic human gut model and the intestinal epithelial cell line Caco-2 were cultured. Arsenic speciation analysis and absorption of different As species were undertaken. In this study, soil As release (3.7-581.2 mg kg(-1)) was observed in the colon. Arsenic in the colon digests was transformed more quickly than that in the soil solid phase. X-ray absorption near-edge spectroscopy (XANES) analysis showed that 44.2-97.6% of arsenite [As(III)] generated due to arsenate [As(V)] reduction was in the soil solid phase after the colon phase. We observed a high degree of cellular absorption of soil As metabolites, exhibiting that the intestinal absorption of monomethylarsonic acid and As(III) (33.6% and 30.2% resp.) was slightly higher than that of dimethylarsinic acid and As(V) (25.1% and 21.7% resp.). Our findings demonstrate that human gut microbiota can directly release soil-bound arsenic, particularly As-bearing amorphous Fe/Al-oxides. Determining As transformation and intestinal absorption simultaneously will result in an accurate risk assessment of human health with soil As exposures. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients

    Directory of Open Access Journals (Sweden)

    Arthur E. Frankel

    2017-10-01

    Full Text Available This is the first prospective study of the effects of human gut microbiota and metabolites on immune checkpoint inhibitor (ICT response in metastatic melanoma patients. Whereas many melanoma patients exhibit profound response to ICT, there are fewer options for patients failing ICT—particularly with BRAF-wild-type disease. In preclinical studies, specific gut microbiota promotes regression of melanoma in mice. We therefore conducted a study of the effects of pretreatment gut microbiota and metabolites on ICT Response Evaluation Criteria in Solid Tumors response in 39 metastatic melanoma patients treated with ipilimumab, nivolumab, ipilimumab plus nivolumab (IN, or pembrolizumab (P. IN yielded 67% responses and 8% stable disease; P achieved 23% responses and 23% stable disease. ICT responders for all types of therapies were enriched for Bacteroides caccae. Among IN responders, the gut microbiome was enriched for Faecalibacterium prausnitzii, Bacteroides thetaiotamicron, and Holdemania filiformis. Among P responders, the microbiome was enriched for Dorea formicogenerans. Unbiased shotgun metabolomics revealed high levels of anacardic acid in ICT responders. Based on these pilot studies, both additional confirmatory clinical studies and preclinical testing of these bacterial species and metabolites are warranted to confirm their ICT enhancing activity.

  16. From the Cover: Feature Article: Ecosystem variability and early human habitats in eastern Africa

    Science.gov (United States)

    Magill, Clayton R.; Ashley, Gail M.; Freeman, Katherine H.

    2013-01-01

    The role of savannas during the course of early human evolution has been debated for nearly a century, in part because of difficulties in characterizing local ecosystems from fossil and sediment records. Here, we present high-resolution lipid biomarker and isotopic signatures for organic matter preserved in lake sediments at Olduvai Gorge during a key juncture in human evolution about 2.0 Ma-the emergence and dispersal of Homo erectus (sensu lato). Using published data for modern plants and soils, we construct a framework for ecological interpretations of stable carbon-isotope compositions (expressed as δ13C values) of lipid biomarkers from ancient plants. Within this framework, δ13C values for sedimentary leaf lipids and total organic carbon from Olduvai Gorge indicate recurrent ecosystem variations, where open C4 grasslands abruptly transitioned to closed C3 forests within several hundreds to thousands of years. Carbon-isotopic signatures correlate most strongly with Earth's orbital geometry (precession), and tropical sea-surface temperatures are significant secondary predictors in partial regression analyses. The scale and pace of repeated ecosystem variations at Olduvai Gorge contrast with long-held views of directional or stepwise aridification and grassland expansion in eastern Africa during the early Pleistocene and provide a local perspective on environmental hypotheses of human evolution.

  17. Food and human gut as reservoirs of transferable antibiotic resistance encoding genes

    Directory of Open Access Journals (Sweden)

    Jean-Marc eRolain

    2013-06-01

    Full Text Available The increase and spread of antibiotic resistance (AR over the past decade in human pathogens has become a worldwide health concern. Recent genomic and metagenomic studies in humans, animals, in food and in the environment have led to the discovery of a huge reservoir of AR genes called the resistome that could be mobilized and transferred from these sources to human pathogens. AR is a natural phenomenon developed by bacteria to protect antibiotic-producing bacteria from their own products and also to increase their survival in highly competitive microbial environments. Although antibiotics are used extensively in humans and animals, there is also considerable usage of antibiotics in agriculture, especially in animal feeds and aquaculture. The aim of this review is to give an overview of the sources of AR and the use of antibiotics in these reservoirs as selectors for emergence of AR bacteria in humans via the food chain.

  18. Beyond the roots of human inaction: Fostering collective effort toward ecosystem conservation.

    Science.gov (United States)

    Amel, Elise; Manning, Christie; Scott, Britain; Koger, Susan

    2017-04-21

    The term "environmental problem" exposes a fundamental misconception: Disruptions of Earth's ecosystems are at their root a human behavior problem. Psychology is a potent tool for understanding the external and internal drivers of human behavior that lead to unsustainable living. Psychologists already contribute to individual-level behavior-change campaigns in the service of sustainability, but attention is turning toward understanding and facilitating the role of individuals in collective and collaborative actions that will modify the environmentally damaging systems in which humans are embedded. Especially crucial in moving toward long-term human and environmental well-being are transformational individuals who step outside of the norm, embrace ecological principles, and inspire collective action. Particularly in developed countries, fostering legions of sustainability leaders rests upon a fundamental renewal of humans' connection to the natural world. Copyright © 2017, American Association for the Advancement of Science.

  19. Development and validation of a chemostat gut model to study both planktonic and biofilm modes of growth of Clostridium difficile and human microbiota.

    Science.gov (United States)

    Crowther, Grace S; Chilton, Caroline H; Todhunter, Sharie L; Nicholson, Scott; Freeman, Jane; Baines, Simon D; Wilcox, Mark H

    2014-01-01

    The human gastrointestinal tract harbours a complex microbial community which exist in planktonic and sessile form. The degree to which composition and function of faecal and mucosal microbiota differ remains unclear. We describe the development and characterisation of an in vitro human gut model, which can be used to facilitate the formation and longitudinal analysis of mature mixed species biofilms. This enables the investigation of the role of biofilms in Clostridium difficile infection (CDI). A well established and validated human gut model of simulated CDI was adapted to incorporate glass rods that create a solid-gaseous-liquid interface for biofilm formation. The continuous chemostat model was inoculated with a pooled human faecal emulsion and controlled to mimic colonic conditions in vivo. Planktonic and sessile bacterial populations were enumerated for up to 46 days. Biofilm consistently formed macroscopic structures on all glass rods over extended periods of time, providing a framework to sample and analyse biofilm structures independently. Whilst variation in biofilm biomass is evident between rods, populations of sessile bacterial groups (log10 cfu/g of biofilm) remain relatively consistent between rods at each sampling point. All bacterial groups enumerated within the planktonic communities were also present within biofilm structures. The planktonic mode of growth of C. difficile and gut microbiota closely reflected observations within the original gut model. However, distinct differences were observed in the behaviour of sessile and planktonic C. difficile populations, with C. difficile spores preferentially persisting within biofilm structures. The redesigned biofilm chemostat model has been validated for reproducible and consistent formation of mixed species intestinal biofilms. This model can be utilised for the analysis of sessile mixed species communities longitudinally, potentially providing information of the role of biofilms in CDI.

  20. Taking the "waste" out of "wastewater" for human water security and ecosystem sustainability.

    Science.gov (United States)

    Grant, Stanley B; Saphores, Jean-Daniel; Feldman, David L; Hamilton, Andrew J; Fletcher, Tim D; Cook, Perran L M; Stewardson, Michael; Sanders, Brett F; Levin, Lisa A; Ambrose, Richard F; Deletic, Ana; Brown, Rebekah; Jiang, Sunny C; Rosso, Diego; Cooper, William J; Marusic, Ivan

    2012-08-10

    Humans create vast quantities of wastewater through inefficiencies and poor management of water systems. The wasting of water poses sustainability challenges, depletes energy reserves, and undermines human water security and ecosystem health. Here we review emerging approaches for reusing wastewater and minimizing its generation. These complementary options make the most of scarce freshwater resources, serve the varying water needs of both developed and developing countries, and confer a variety of environmental benefits. Their widespread adoption will require changing how freshwater is sourced, used, managed, and priced.

  1. The microbiota-gut-brain axis: neurobehavioral correlates, health and sociality.

    Science.gov (United States)

    Montiel-Castro, Augusto J; González-Cervantes, Rina M; Bravo-Ruiseco, Gabriela; Pacheco-López, Gustavo

    2013-10-07

    Recent data suggest that the human body is not such a neatly self-sufficient island after all. It is more like a super-complex ecosystem containing trillions of bacteria and other microorganisms that inhabit all our surfaces; skin, mouth, sexual organs, and specially intestines. It has recently become evident that such microbiota, specifically within the gut, can greatly influence many physiological parameters, including cognitive functions, such as learning, memory and decision making processes. Human microbiota is a diverse and dynamic ecosystem, which has evolved in a mutualistic relationship with its host. Ontogenetically, it is vertically inoculated from the mother during birth, established during the first year of life and during lifespan, horizontally transferred among relatives, mates or close community members. This micro-ecosystem serves the host by protecting it against pathogens, metabolizing complex lipids and polysaccharides that otherwise would be inaccessible nutrients, neutralizing drugs and carcinogens, modulating intestinal motility, and making visceral perception possible. It is now evident that the bidirectional signaling between the gastrointestinal tract and the brain, mainly through the vagus nerve, the so called "microbiota-gut-vagus-brain axis," is vital for maintaining homeostasis and it may be also involved in the etiology of several metabolic and mental dysfunctions/disorders. Here we review evidence on the ability of the gut microbiota to communicate with the brain and thus modulate behavior, and also elaborate on the ethological and cultural strategies of human and non-human primates to select, transfer and eliminate microorganisms for selecting the commensal profile.

  2. The Gut

    DEFF Research Database (Denmark)

    Holst, Jens Juul; Pedersen, Jens; Wewer Albrechtsen, Nicolai Jacob

    2017-01-01

    In this communication we discuss the role of the gut for the development of type 2 diabetes mellitus (T2DM). Gastric emptying rates importantly determine postprandial glucose excursions and regulate postprandial secretion of the incretin hormones, glucose-dependent insulinotropic polypeptide (GIP...

  3. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.

    Science.gov (United States)

    Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E

    2013-10-01

    Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation 'Melainabacteria'. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI:http://dx.doi.org/10.7554/eLife.01102.001.

  4. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

    Science.gov (United States)

    Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E

    2013-01-01

    Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation ‘Melainabacteria’. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI: http://dx.doi.org/10.7554/eLife.01102.001 PMID:24137540

  5. Dynamic In Vitro Models of the Human Gastrointestinal Tract as Relevant Tools to Assess the Survival of Probiotic Strains and Their Interactions with Gut Microbiota

    Directory of Open Access Journals (Sweden)

    Charlotte Cordonnier

    2015-10-01

    Full Text Available The beneficial effects of probiotics are conditioned by their survival during passage through the human gastrointestinal tract and their ability to favorably influence gut microbiota. The main objective of this study was to use dynamic in vitro models of the human digestive tract to investigate the effect of fasted or fed state on the survival kinetics of the new probiotic Saccharomyces cerevisiae strain CNCM I-3856 and to assess its influence on intestinal microbiota composition and activity. The probiotic yeast showed a high survival rate in the upper gastrointestinal tract whatever the route of admistration, i.e., within a glass of water or a Western-type meal. S. cerevisiae CNCM I-3856 was more sensitive to colonic conditions, as the strain was not able to colonize within the bioreactor despite a twice daily administration. The main bacterial populations of the gut microbiota, as well as the production of short chain fatty acids were not influenced by the probiotic treatment. However, the effect of the probiotic on the gut microbiota was found to be individual dependent. This study shows that dynamic in vitro models can be advantageously used to provide useful insight into the behavior of probiotic strains in the human digestive environment.

  6. The human gut microbiome in health: establishment and resilience of microbiota over a lifetime.

    Science.gov (United States)

    Greenhalgh, Kacy; Meyer, Kristen M; Aagaard, Kjersti M; Wilmes, Paul

    2016-07-01

    With technological advances in culture-independent molecular methods, we are uncovering a new facet of our natural history by accounting for the vast diversity of microbial life which colonizes the human body. The human microbiome contributes functional genes and metabolites which affect human physiology and are, therefore, considered an important factor for maintaining health. Much has been described in the past decade based primarily on 16S rRNA gene amplicon sequencing regarding the diversity, structure, stability and dynamics of human microbiota in their various body habitats, most notably within the gastrointestinal tract (GIT). Relatively high levels of variation have been described across different stages of life and geographical locations for the GIT microbiome. These observations may prove helpful for the future contextualization of patterns in other body habitats especially in relation to identifying generalizable trends over human lifetime. Given the large degree of complexity and variability, a key challenge will be how to define baseline healthy microbiomes and how to identify features which reflect deviations therefrom in the future. In this context, metagenomics and functional omics will likely play a central role as they will allow resolution of microbiome-conferred functionalities associated with health. Such information will be vital for formulating therapeutic interventions aimed at managing microbiota-mediated health particularly in the GIT over the course of a human lifetime.

  7. Correlation Between Gut Microbiota and Depression

    OpenAIRE

    Naseribafrouei, Ali

    2013-01-01

    Gut microbiota consist of a variety of microorganisms which inhabit the human gut. They play many well-known roles in human gut homeostasis and may be implicated in some pathologic processes especially immunological events. Depression is a chronic syndrome with a pathogenesis linked to various genetic, biological and environmental factors. In recent years inflammatory factors has been mentioned as contributing factors for development and exacerbation of depression. Most of these inflammatory ...

  8. Interaction between Pirenzepine and Ninjinto, a Traditional Japanese Herbal Medicine, on the Plasma Gut-Regulated Peptide Levels in Humans

    National Research Council Canada - National Science Library

    Sato, Yuhki; Hiroki, Itoh; Suzuki, Yosuke; Tatsuta, Ryosuke; Takeyama, Masaharu

    2013-01-01

    ...) from the preganglionic fibers of the parasympathetic nerve. Thus, we examined the effects of the selective M1 muscarinic receptor antagonist pirenzepine on the elevation of Ninjinto-induced plasma the area under the plasma gut-regulated peptide concentration...

  9. Gut microbiota role in irritable bowel syndrome: New therapeutic strategies.

    Science.gov (United States)

    Distrutti, Eleonora; Monaldi, Lorenzo; Ricci, Patrizia; Fiorucci, Stefano

    2016-02-21

    In the last decade the impressive expansion of our knowledge of the vast microbial community that resides in the human intestine, the gut microbiota, has provided support to the concept that a disturbed intestinal ecology might promote development and maintenance of symptoms in irritable bowel syndrome (IBS). As a correlate, manipulation of gut microbiota represents a new strategy for the treatment of this multifactorial disease. A number of attempts have been made to modulate the gut bacterial composition, following the idea that expansion of bacterial species considered as beneficial (Lactobacilli and Bifidobacteria) associated with the reduction of those considered harmful (Clostridium, Escherichia coli, Salmonella, Shigella and Pseudomonas) should attenuate IBS symptoms. In this conceptual framework, probiotics appear an attractive option in terms of both efficacy and safety, while prebiotics, synbiotics and antibiotics still need confirmation. Fecal transplant is an old treatment translated from the cure of intestinal infective pathologies that has recently gained a new life as therapeutic option for those patients with a disturbed gut ecosystem, but data on IBS are scanty and randomized, placebo-controlled studies are required.

  10. Gut microbiota role in irritable bowel syndrome: New therapeutic strategies

    Science.gov (United States)

    Distrutti, Eleonora; Monaldi, Lorenzo; Ricci, Patrizia; Fiorucci, Stefano

    2016-01-01

    In the last decade the impressive expansion of our knowledge of the vast microbial community that resides in the human intestine, the gut microbiota, has provided support to the concept that a disturbed intestinal ecology might promote development and maintenance of symptoms in irritable bowel syndrome (IBS). As a correlate, manipulation of gut microbiota represents a new strategy for the treatment of this multifactorial disease. A number of attempts have been made to modulate the gut bacterial composition, following the idea that expansion of bacterial species considered as beneficial (Lactobacilli and Bifidobacteria) associated with the reduction of those considered harmful (Clostridium, Escherichia coli, Salmonella, Shigella and Pseudomonas) should attenuate IBS symptoms. In this conceptual framework, probiotics appear an attractive option in terms of both efficacy and safety, while prebiotics, synbiotics and antibiotics still need confirmation. Fecal transplant is an old treatment translated from the cure of intestinal infective pathologies that has recently gained a new life as therapeutic option for those patients with a disturbed gut ecosystem, but data on IBS are scanty and randomized, placebo-controlled studies are required. PMID:26900286

  11. Gut microorganisms as promising targets for the management of type 2 diabetes.

    Science.gov (United States)

    Delzenne, Nathalie M; Cani, Patrice D; Everard, Amandine; Neyrinck, Audrey M; Bindels, Laure B

    2015-10-01

    Each human intestine harbours not only hundreds of trillions of bacteria but also bacteriophage particles, viruses, fungi and archaea, which constitute a complex and dynamic ecosystem referred to as the gut microbiota. An increasing number of data obtained during the last 10 years have indicated changes in gut bacterial composition or function in type 2 diabetic patients. Analysis of this 'dysbiosis' enables the detection of alterations in specific bacteria, clusters of bacteria or bacterial functions associated with the occurrence or evolution of type 2 diabetes; these bacteria are predominantly involved in the control of inflammation and energy homeostasis. Our review focuses on two key questions: does gut dysbiosis truly play a role in the occurrence of type 2 diabetes, and will recent discoveries linking the gut microbiota to host health be helpful for the development of novel therapeutic approaches for type 2 diabetes? Here we review how pharmacological, surgical and nutritional interventions for type 2 diabetic patients may impact the gut microbiota. Experimental studies in animals are identifying which bacterial metabolites and components act on host immune homeostasis and glucose metabolism, primarily by targeting intestinal cells involved in endocrine and gut barrier functions. We discuss novel approaches (e.g. probiotics, prebiotics and faecal transfer) and the need for research and adequate intervention studies to evaluate the feasibility and relevance of these new therapies for the management of type 2 diabetes.

  12. Roles of CUP-5, the Caenorhabditis elegans orthologue of human TRPML1, in lysosome and gut granule biogenesis

    Directory of Open Access Journals (Sweden)

    Fares Hanna

    2010-06-01

    Full Text Available Abstract Background CUP-5 is a Transient Receptor Potential protein in C. elegans that is the orthologue of mammalian TRPML1. Loss of TRPML1 results in the lysosomal storage disorder Mucolipidosis type IV. Loss of CUP-5 results in embryonic lethality and the accumulation of enlarged yolk granules in developing intestinal cells. The embryonic lethality of cup-5 mutants is rescued by mutations in mrp-4, which is required for gut granule differentiation. Gut granules are intestine-specific lysosome-related organelles that accumulate birefringent material. This link between CUP-5 and gut granules led us to determine the roles of CUP-5 in lysosome and gut granule biogenesis in developing intestinal cells. Results We show that CUP-5 protein localizes to lysosomes, but not to gut granules, in developing intestinal cells. Loss of CUP-5 results in defects in endo-lysosomal transport in developing intestinal cells of C. elegans embryos. This ultimately leads to the appearance of enlarged terminal vacuoles that show defective lysosomal degradation and that have lysosomal and endosomal markers. In contrast, gut granule biogenesis is normal in the absence of CUP-5. Furthermore, loss of CUP-5 does not result in inappropriate fusion or mixing of content between lysosomes and gut granules. Conclusions Using an in vivo model of MLIV, we show that there is a defect in lysosomal transport/biogenesis that is earlier than the presumed function of TRPML1 in terminal lysosomes. Our results indicate that CUP-5 is required for the biogenesis of lysosomes but not of gut granules. Thus, cellular phenotypes in Mucolipidosis type IV are likely not due to defects in lysosome-related organelle biogenesis, but due to progressive defects in lysosomal transport that lead to severe lysosomal dysfunction.

  13. Emerging synbiotics and their effect on the composition and functionality of the human gut microbiota

    DEFF Research Database (Denmark)

    van Zanten, Gabriella Christina

    , may be used to change the composition and activity of the human GM and thereby potentially affect the host health beneficially. In this PhD study it was hypothesized that emerging synbiotics have the potential of modulating the human GM composition as well as the functionality. To gain the beneficial...... effects of both probiotics and prebiotics, they may be combined to synbiotics. The definition of synbiotics implies that the prebiotic should be specific to the probiotic in question. Therefore, a library of 37 emerging prebiotics, comprising carbohydrates with a large range of degrees of polymerization...... emerging prebiotics were selected for further investigation using a four-stage semi-continuous model system of the human colon. The selected combinations were NCFM with isomaltulose, cellobiose, raffinose and oat β-glucan hydrolyzed with endo-1,3-β-glucanase (OBGH), respectively and Bl-04 with melibiose...

  14. Integrated modelling for assessing the risk of groundwater contaminants to human health and surface water ecosystems

    DEFF Research Database (Denmark)

    McKnight, Ursula S.; Rasmussen, Jes; Funder, Simon G.

    2010-01-01

    for evaluating the impact of a TCE groundwater plume, located in an area with protected drinking water interests, to human health and surface water ecosystems. This is accomplished by coupling the system dynamicsbased decision support system CARO-Plus to the aquatic ecosystem model AQUATOX via an analytical......The practical implementation of the European Water Framework Directive has resulted in an increased focus on the groundwater-surface water interaction zone. A gap exists with respect to preliminary assessment methodologies that are capable of evaluating and prioritising point sources...... volatilisation model for the stream. The model is tested on a Danish case study involving a 750 m long TCE groundwater plume discharging into a stream. The initial modelling results indicate that TCE contaminant plumes with μgL-1 concentrations entering surface water systems do not pose a significant risk...

  15. Review of Human Study on Mountain Ecosystems%山地生态系统人文研究综述

    Institute of Scientific and Technical Information of China (English)

    方一平

    2001-01-01

    Author analysed the background of human study on mountain ecosystems, which cover MAB_6 project initia tive, focus on aspects, activities framwork.and the major fields of human study on mountain ecosystems since 1971. Of all fields, four mafor aspects studyed wer e set forth as follows:(1)The theory of model of human study on mountain ecosyst ems.(2)The mechanism and application between human and mountain ecosystem intera ction, Which include the study of impacts, relationships, pov erty relief, and sustainable development in mountain regions. (3)The study of pr oceeding between human and mountain ecosystems interaction. (4)The study of reso urces management in mountain regions, Which cover natural, social and economic r esources. (5)The study of role of women in mountain ecosystem protection.Finally , the differences between domestic and oversea in the aspects of human study of mountain ecosystem are discussed as a focal point, which cover the fiel ds of study,the levels of study the methods of study and schematic ideas of st udy.%回顾和评述了近二十多年来国外山地生态系统人文研 究的相关领域。同时对比分析了我国与国外在该领域的研究内容、层次、方法和观念方面的 差异。

  16. Antibiotic resistance reservoirs: the cases of sponge and human gut microbiota

    NARCIS (Netherlands)

    Versluis, Dennis

    2016-01-01

    One of the major threats to human health in the 21st century is the emergence of pathogenic bacteria that are resistant to multiple antibiotics, thereby limiting treatment options. An important route through which pathogens become resistant is via acquisition of resistance genes from environmental a

  17. Persistence of Bacillus thuringiensis bioinsecticides in the gut of human-flora-associated rats

    DEFF Research Database (Denmark)

    Wilcks, Andrea; Hansen, Bjarne Munk; Hendriksen, Niels Bohse;

    2006-01-01

    The capability of two bioinsecticide strains of Bacillus thuringiensis (ssp. israelensis and ssp. kurstaki) to germinate and persist in vivo in the gastrointestinal tract of human-flora-associated rats was studied. Rats were dosed either with vegetative cells or spores of the bacteria for 4 conse...

  18. Persistence of Bacillus thuringiensis bioinsecticides in the gut of human-flora-associated rats

    DEFF Research Database (Denmark)

    Wilcks, Andrea; Hansen, Bjarne Munk; Hendriksen, Niels Bohse

    2006-01-01

    The capability of two bioinsecticide strains of Bacillus thuringiensis (ssp. israelensis and ssp. kurstaki) to germinate and persist in vivo in the gastrointestinal tract of human-flora-associated rats was studied. Rats were dosed either with vegetative cells or spores of the bacteria for 4...

  19. The arable plant ecosystem as battleground for emergence of human pathogens

    Directory of Open Access Journals (Sweden)

    Leo eVan Overbeek

    2014-03-01

    Full Text Available Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh vegetables, sprouts and occasionally fruits made clear that these pathogens are not only transmitted to humans via the ‘classical’ routes of meat, eggs and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure, water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.

  20. A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface.

    Directory of Open Access Journals (Sweden)

    Xiaoxiao Li

    Full Text Available Aberrant interactions between the host and the intestinal bacteria are thought to contribute to the pathogenesis of many digestive diseases. However, studying the complex ecosystem at the human mucosal-luminal interface (MLI is challenging and requires an integrative systems biology approach. Therefore, we developed a novel method integrating lavage sampling of the human mucosal surface, high-throughput proteomics, and a unique suite of bioinformatic and statistical analyses. Shotgun proteomic analysis of secreted proteins recovered from the MLI confirmed the presence of both human and bacterial components. To profile the MLI metaproteome, we collected 205 mucosal lavage samples from 38 healthy subjects, and subjected them to high-throughput proteomics. The spectral data were subjected to a rigorous data processing pipeline to optimize suitability for quantitation and analysis, and then were evaluated using a set of biostatistical tools. Compared to the mucosal transcriptome, the MLI metaproteome was enriched for extracellular proteins involved in response to stimulus and immune system processes. Analysis of the metaproteome revealed significant individual-related as well as anatomic region-related (biogeographic features. Quantitative shotgun proteomics established the identity and confirmed the biogeographic association of 49 proteins (including 3 functional protein networks demarcating the proximal and distal colon. This robust and integrated proteomic approach is thus effective for identifying functional features of the human mucosal ecosystem, and a fresh understanding of the basic biology and disease processes at the MLI.

  1. Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance

    Directory of Open Access Journals (Sweden)

    Femke-Anouska Heinsen

    2016-11-01

    Full Text Available Objective: In the present study, we examined the effect of a very low-calorie diet(VLCD-based obesity program on human gut microbiome diversity and metabolism during weight loss and weight maintenance. Methods: Obese subjects underwent 3 months of VLCD followed by 3 months of weight maintenance. A lean and an obese control group were included. The microbiome was characterized by performing high-throughput dual-indexed 16S rDNA amplicon sequencing. Results: At baseline, a significant difference in the Firmicutes/Bacteroidetes ratio between the lean and obese individuals was observed (p = 0.047. The VLCD resulted in significant alterations in gut microbiome diversity from baseline to 3 months (p = 0.0053. Acinetobacter represented an indicator species for the observed effect (indicator value = 0.998, p = 0.006. Metabolic analyses revealed alterations of the bacterial riboflavin pathway from baseline to 3 months (pnom = 0.0078. These changes in diversity and bacterial metabolism induced by VLCD diminished during the weight maintenance phase, despite sustained reductions in body weight and sustained improvements of insulin sensitivity. Conclusion: The present data show that a VLCD is able to beneficially alter both gut microbiome diversity and metabolism in obese humans, but that these changes are not sustained during weight maintenance. This finding might suggest that the microbiome should be targeted during obesity programs.

  2. In vitro fermentation by human gut bacteria of proteolytically digested caseinomacropeptide nonenzymatically glycosylated with prebiotic carbohydrates.

    Science.gov (United States)

    Hernandez-Hernandez, Oswaldo; Sanz, M Luz; Kolida, Sofia; Rastall, Robert A; Moreno, F Javier

    2011-11-23

    The in vitro fermentation selectivity of hydrolyzed caseinomacropeptide (CMP) glycosylated, via Maillard reaction (MR), with lactulose, galacto-oligosaccharides from lactose (GOSLa), and galacto-oligosaccharides from lactulose (GOSLu) was evaluated, using pH-controlled small-scale batch cultures at 37 °C under anaerobic conditions with human feces. After 10 and 24 h of fermentation, neoglyconjugates exerted a bifidogenic activity, similar to those of the corresponding prebiotic carbohydrates. No significant differences were found in Bacteroides , Lactobacillus - Enterococcus , Clostridium histolyticum subgroup, Atopobium and Clostridium coccoides - Eubacterium rectale populations. Concentrations of lactic acid and short-chain fatty acids (SCFA) produced during the fermentation of prebiotic carbohydrates were similar to those produced for their respective neoglycoconjugates at both fermentation times. These findings, joined with the functional properties attributed to CMP, could open up new applications of MR products involving prebiotics as novel multiple-functional ingredients with potential beneficial effects on human health.

  3. Progress and Challenges in Developing Metabolic Footprints from Diet in Human Gut Microbial Cometabolism12

    OpenAIRE

    Duffy, Linda C; Raiten, Daniel J; Hubbard, S.; Starke-Reed, Pamela

    2015-01-01

    Homo sapiens harbor trillions of microbes, whose microbial metagenome (collective genome of a microbial community) using omic validation interrogation tools is estimated to be at least 100-fold that of human cells, which comprise 23,000 genes. This article highlights some of the current progress and open questions in nutrition-related areas of microbiome research. It also underscores the metabolic capabilities of microbial fermentation on nutritional substrates that require further mechanisti...

  4. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism.

    Science.gov (United States)

    Cuskin, Fiona; Lowe, Elisabeth C; Temple, Max J; Zhu, Yanping; Cameron, Elizabeth A; Pudlo, Nicholas A; Porter, Nathan T; Urs, Karthik; Thompson, Andrew J; Cartmell, Alan; Rogowski, Artur; Hamilton, Brian S; Chen, Rui; Tolbert, Thomas J; Piens, Kathleen; Bracke, Debby; Vervecken, Wouter; Hakki, Zalihe; Speciale, Gaetano; Munōz-Munōz, Jose L; Day, Andrew; Peña, Maria J; McLean, Richard; Suits, Michael D; Boraston, Alisdair B; Atherly, Todd; Ziemer, Cherie J; Williams, Spencer J; Davies, Gideon J; Abbott, D Wade; Martens, Eric C; Gilbert, Harry J

    2015-01-08

    Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a 'selfish' model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.

  5. Gut microbiota and metabolic syndrome.

    Science.gov (United States)

    Festi, Davide; Schiumerini, Ramona; Eusebi, Leonardo Henry; Marasco, Giovanni; Taddia, Martina; Colecchia, Antonio

    2014-11-21

    Gut microbiota exerts a significant role in the pathogenesis of the metabolic syndrome, as confirmed by studies conducted both on humans and animal models. Gut microbial composition and functions are strongly influenced by diet. This complex intestinal "superorganism" seems to affect host metabolic balance modulating energy absorption, gut motility, appetite, glucose and lipid metabolism, as well as hepatic fatty storage. An impairment of the fine balance between gut microbes and host's immune system could culminate in the intestinal translocation of bacterial fragments and the development of "metabolic endotoxemia", leading to systemic inflammation and insulin resistance. Diet induced weight-loss and bariatric surgery promote significant changes of gut microbial composition, that seem to affect the success, or the inefficacy, of treatment strategies. Manipulation of gut microbiota through the administration of prebiotics or probiotics could reduce intestinal low grade inflammation and improve gut barrier integrity, thus, ameliorating metabolic balance and promoting weight loss. However, further evidence is needed to better understand their clinical impact and therapeutic use.

  6. Role of gut microbiota in atherosclerosis

    DEFF Research Database (Denmark)

    Jonsson, Annika Lindskog; Bäckhed, Gert Fredrik

    2017-01-01

    Infections have been linked to the development of cardiovascular disease and atherosclerosis. Findings from the past decade have identified microbial ecosystems residing in different habitats of the human body that contribute to metabolic and cardiovascular-related disorders. In this Review, we...... of atherosclerotic plaques. Third, diet and specific components that are metabolized by gut microbiota can have various effects on atherosclerosis; for example, dietary fibre is beneficial, whereas the bacterial metabolite trimethylamine-N-oxide is considered harmful. Although specific bacterial taxa have been...... associated with atherosclerosis, which is supported by increasing mechanistic evidence, several questions remain to be answered to understand fully how the microbiota contributes to atherosclerosis and cardiovascular disease. Such knowledge might pave the way for novel diagnostics and therapeutics based...

  7. The importance of biodiversity and dominance for multiple ecosystem functions in a human-modified tropical landscape.

    Science.gov (United States)

    Lohbeck, Madelon; Bongers, Frans; Martinez-Ramos, Miguel; Poorter, Lourens

    2016-10-01

    Many studies suggest that biodiversity may be particularly important for ecosystem multifunctionality, because different species with different traits can contribute to different functions. Support, however, comes mostly from experimental studies conducted at small spatial scales in low-diversity systems. Here, we test whether different species contribute to different ecosystem functions that are important for carbon cycling in a high-diversity human-modified tropical forest landscape in Southern Mexico. We quantified aboveground standing b