151
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Stefano GB, Fine R, Kream RM. Microbiome and Health: Ramifications of Intelligent Deception. Med Sci Monit 2018; 24:2060-2062. [PMID: 29626394 PMCID: PMC5905352 DOI: 10.12659/msm.910248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ten thousand years ago, the foundation for agricultural development and animal domestication was laid. Neolithic founder crops were carbohydrate-laden cereal grasses that facilitated transformation of hunter-gather societies into ancient civilizations with realistic capabilities for population expansion. In the last 3–4 decades, however, debilitating medical consequences of a progressively narrowed high caloric diet incorporating processed carbohydrates, animal protein, saturated fat and cholesterol, are translated into a global epidemic of obesity linked to metabolic and endocrine disorders, which, in part, emerged from the enhancement of our longevity. The initiation and progression of pathophysiological processes associated with this restrictive diet may well reside in the gastrointestinal tract. The critical role of human gut microbiome in facilitating normal gut physiology and linkages to other physiological systems points to its significance in comorbid pathologies when its diversity is compromised. Cortical desensitization to the potentially damaging effects of intentionally restricted high carbohydrate diets is progressively enhanced by compromised metabolic activities and widespread pro-inflammatory processes within all organ systems. Our cognitive ability must overcome the desire for comfort foods. The solution is simple: minimize “processed” foods and those of similar commercial origin in our diet, restoring a more diverse gut microbiome. Initially the solution may be costly, however, within the scope of sustained healthy longevity it will “payoff”.
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Affiliation(s)
- George B Stefano
- Department of Psychiatry, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Center for Cognitive and Molecular Neuroscience, General University Hospital in Prague, Prague, Czech Republic
| | - Rachel Fine
- St. Anthony's High School, Melville, NY, USA
| | - Richard M Kream
- Senior Advisor, International Scientific Information, Inc., Melville, NY, USA
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152
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Nishida AH, Ochman H. Rates of gut microbiome divergence in mammals. Mol Ecol 2018; 27:1884-1897. [PMID: 29290090 PMCID: PMC5935551 DOI: 10.1111/mec.14473] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/14/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
The variation and taxonomic diversity among mammalian gut microbiomes raises several questions about the factors that contribute to the rates and patterns of change in these microbial communities. By comparing the microbiome compositions of 112 species representing 14 mammalian orders, we assessed how host and ecological factors contribute to microbiome diversification. Except in rare cases, the same bacterial phyla predominate in mammalian gut microbiomes, and there has been some convergence of microbiome compositions according to dietary category across all mammalians lineages except Chiropterans (bats), which possess high proportions of Proteobacteria and tend to be most similar to one another regardless of diet. At lower taxonomic ranks (families, genera, 97% OTUs), bacteria are more likely to be associated with a particular mammalian lineage than with a particular dietary category, resulting in a strong phylogenetic signal in the degree to which microbiomes diverge. Despite different physiologies, the gut microbiomes of several mammalian lineages have diverged at roughly the same rate over the past 75 million years; however, the gut microbiomes of Cetartiodactyla (ruminants, whales, hippopotami) have evolved much faster and those of Chiropterans much slower. Contrary to expectations, the number of dietary transitions within a lineage does not influence rates of microbiome divergence, but instead, some of the most dramatic changes are associated with the loss of bacterial taxa, such as those accompanying the transition from terrestrial to marine lifestyles and the evolution of hominids.
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Affiliation(s)
- Alex H Nishida
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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153
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Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. mSphere 2018; 3:mSphere00092-18. [PMID: 29600282 PMCID: PMC5874442 DOI: 10.1128/msphere.00092-18] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/05/2018] [Indexed: 02/07/2023] Open
Abstract
A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon's second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults. IMPORTANCE We sought to identify the fungi that colonize healthy GI tracts and that have a sustained influence on the diverse functions of the gut microbiome. Instead, we found that all fungi in the stool of healthy volunteers could be explained by their presence in oral and dietary sources and that our results, together with those from other analyses, support the model that there is little or no gastrointestinal colonization by fungi. This may be due to Westernization, primate evolution, fungal ecology, and/or the strong defenses of a healthy immune system. Importantly, fungal colonization of the GI tract may often be indicative of disease. As fungi can cause serious infections in immunocompromised individuals and are found at increased abundance in multiple disorders of the GI tract, understanding normal fungal colonization is essential for proper treatment and prevention of fungal pathogenesis.
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154
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The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition. Sci Rep 2018; 8:3214. [PMID: 29453448 PMCID: PMC5816653 DOI: 10.1038/s41598-018-21117-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
Nutrition and health of northern white-cheeked gibbons (Nomascus leucogenys) are considered to be primarily influenced by the diversity of their gastrointestinal tract (GIT) microbiota. However, the precise composition, structure, and role of the gibbon GIT microbiota remain unclear. Microbial communities from the GITs of gibbons from Nanning (NN, n = 36) and Beijing (BJ, n = 20) Zoos were examined through 16S rRNA sequencing. Gibbon’s GITs microbiomes contained bacteria from 30 phyla, dominated by human-associated microbial signatures: Firmicutes, Bacteroidetes, and Proteobacteria. Microbial species richness was markedly different between adult gibbons (>8 years) under distinct captive conditions. The relative abundance of 14 phyla varied significantly in samples of adults in BJ versus NN. Among the age groups examined in NN, microbiota of adult gibbons had greater species variation and richer community diversity than microbiota of nursing young (<6 months) and juveniles (2–5 years). Age-dependent increases in the relative abundances of Firmicutes and Fibrobacteres were detected, along with simultaneous increases in dietary fiber intake. A few differences were detected between sex cohorts in NN, suggesting a very weak correlation between sex and GIT microbiota. This study is the first to taxonomically identify gibbon’s GITs microbiota confirming that microbiota composition varies with age and captive condition.
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155
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Muraille E. Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis. Front Microbiol 2018; 9:223. [PMID: 29487592 PMCID: PMC5816788 DOI: 10.3389/fmicb.2018.00223] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 01/30/2018] [Indexed: 01/02/2023] Open
Abstract
Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG) mechanisms share common functional properties. They (i) contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii) favor robustness and collectivism among populations and (iii) operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size) has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the “White Queen” here. The existence of DGs leads to the view of evolution as a more “intelligent” and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and the intensity of selective pressure. The ubiquity of DGs also suggests that regulated auto-generation of diversity is a fundamental property of life.
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Affiliation(s)
- Eric Muraille
- Laboratoire de Parasitologie, Faculté de Médecine, Université Libre de Bruxelles, Brussels, Belgium
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156
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Voss JD, Goodson MS, Leon JC. Phenotype diffusion and one health: A proposed framework for investigating the plurality of obesity epidemics across many species. Zoonoses Public Health 2018; 65:279-290. [PMID: 29430857 DOI: 10.1111/zph.12445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Indexed: 01/07/2023]
Abstract
We propose the idea of "phenotype diffusion," which is a rapid convergence of an observed trait in some human and animal populations. The words phenotype and diffusion both imply observations independent of mechanism as phenotypes are observed traits with multiple possible genetic mechanisms and diffusion is an observed state of being widely distributed. Recognizing shared changes in phenotype in multiple species does not by itself reveal a particular mechanism such as a shared exposure, shared adaptive need, particular stochastic process or a transmission pathway. Instead, identifying phenotype diffusion suggests the mechanism should be explored to help illuminate the ways human and animal health are connected and new opportunities for optimizing these links. Using the plurality of obesity epidemics across multiple species as a prototype for shared changes in phenotype, the goal of this review was to explore eco-evolutionary theories that could inform further investigation. First, evolutionary changes described by hologenome evolution, pawnobe evolution, transposable element (TE) thrust and the drifty gene hypothesis will be discussed within the context of the selection asymmetries among human and animal populations. Secondly, the ecology of common source exposures (bovine milk, xenohormesis and "obesogens"), niche evolution and the hygiene hypothesis will be summarized. Finally, we synthesize these considerations. For example, many agricultural breeds have been aggressively selected for weight gain, microbiota (e.g., adenovirus 36, toxoplasmosis) associated with (or infecting) these breeds cause experimental weight gain in other animals, and these same microbes are associated with human obesity. We propose applications of phenotype diffusion could include zoonotic biosurveillance, biocontainment, antibiotic stewardship and environmental priorities. The One Health field is focused on the connections between the health of humans, animals and the environment, and so identification of phenotype diffusion is highly relevant for practitioners (public health officials, physicians and veterinarians) in this field.
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Affiliation(s)
- J D Voss
- Epidemiology Consult Service Division, United States Air Force School of Aerospace Medicine, Wright-Patterson AFB, OH, USA
| | - M S Goodson
- 711th Human Performance Wing, Human Effectiveness Directorate, Wright-Patterson AFB, OH, USA.,UES Inc., Dayton, OH, USA
| | - J C Leon
- Epidemiology Consult Service Division, United States Air Force School of Aerospace Medicine, Wright-Patterson AFB, OH, USA
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157
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Umanets A, de Winter I, IJdema F, Ramiro-Garcia J, van Hooft P, Heitkönig IMA, Prins HHT, Smidt H. Occupancy strongly influences faecal microbial composition of wild lemurs. FEMS Microbiol Ecol 2018; 94:4838981. [DOI: 10.1093/femsec/fiy017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/02/2018] [Indexed: 12/23/2022] Open
Affiliation(s)
- Alexander Umanets
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Iris de Winter
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
| | - Freek IJdema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Pim van Hooft
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
| | - Ignas M A Heitkönig
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
| | - Herbert H T Prins
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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158
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Abstract
The gastrointestinal (GI) tract is the residence of trillions of microorganisms that include bacteria, archaea, fungi and viruses. The collective genomes of whole microbial communities (microbiota) integrate the gut microbiome. Up to 100 genera and 1000 distinct bacterial species were identified in digestive tube niches. Gut microbiomes exert permanent pivotal functions by promoting food digestion, xenobiotic metabolism and regulation of innate and adaptive immunological processes. Proteins, peptides and metabolites released locally and at distant sites trigger many cell signalling and pathways. This intense crosstalk maintains the host-microbial homeostasis. Diet, age, diet, stress and diseases cause increases or decreases in relative abundance and diversity bacterial specie of GI and other body sites. Studies in animal models and humans have shown that a persistent imbalance of gut's microbial community, named dysbiosis, relates to inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), diabetes, obesity, cancer, cardiovascular and central nervous system disorders. Notably specific bacterial communities are promising clinical target to treat inflammatory and infectious diseases. In this context, intestinal microbiota transplantation (IMT) is one optional treatment for IBD, in particular to patients with recurrent Clostridium difficile-induced pseudo-membrane colitis. Here we discuss on recent discoveries linking whole gut microbiome dysbiosis to metabolic and inflammatory diseases and potential prophylactic and therapeutic applications of faecal and phage therapy, probiotic and prebiotic diets.
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Affiliation(s)
- José E Belizário
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Joel Faintuch
- Department of Gastroenterology of Medical School, University of Sao Paulo, São Paulo, Brazil
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159
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Abstract
The trillions of microbes living in the gut-the gut microbiota-play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity's near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations. Finally, we propose that this broader phylogenetic perspective is useful for understanding the mechanisms underlying human-microbiome interactions.
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Affiliation(s)
- Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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160
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Moeller AH, Suzuki TA, Lin D, Lacey EA, Wasser SK, Nachman MW. Dispersal limitation promotes the diversification of the mammalian gut microbiota. Proc Natl Acad Sci U S A 2017; 114:13768-13773. [PMID: 29229828 PMCID: PMC5748161 DOI: 10.1073/pnas.1700122114] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The gut bacterial communities of mammals have profound effects on host fitness, but the processes that generate and maintain gut bacterial diversity remain poorly understood. We mapped compositional variation (i.e., β-diversity) in the gut microbiotas of 136 pairs of wild mammalian species living throughout the Americas to assess how the distribution of mammals across geographic space influences the diversification of their gut bacteria. Comparing the gut microbiotas of sympatric and allopatric mammalian populations provided insights into the flow of gut bacteria within and between mammalian communities, revealing that spatial limits on bacterial dispersal promote β-diversity between the gut microbiotas of mammalian species. Each geographic locale displayed a unique gut-microbiota composition that could not be fully explained by the diets and phylogenetic histories of the resident mammalian hosts, indicating that some gut bacteria are geographically restricted. Across the western hemisphere, the compositional overlap between the gut microbiotas of allopatric mammalian populations decayed exponentially with the geographic distance separating the hosts. The relationship between geographic distances among hosts and compositional differences among their gut microbiotas was independent of dietary and phylogenetic divergence among hosts. Within mammalian communities, we observed widespread sharing of gut bacteria between predator-prey host-species pairs, indicating horizontal transfer of gut bacteria through mammalian food chains. Collectively, these results indicate that compositional differences between the gut microbiotas of mammalian taxa are generated and maintained by limits to bacterial dispersal imposed by physical distance between hosts.
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Affiliation(s)
- Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720;
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Dana Lin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Eileen A Lacey
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Samuel K Wasser
- Center for Conservation Biology, University of Washington, Seattle, WA 98195
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
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161
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Enterotypes in the landscape of gut microbial community composition. Nat Microbiol 2017; 3:8-16. [PMID: 29255284 DOI: 10.1038/s41564-017-0072-8] [Citation(s) in RCA: 597] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022]
Abstract
Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
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162
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Šket R, Treichel N, Kublik S, Debevec T, Eiken O, Mekjavić I, Schloter M, Vital M, Chandler J, Tiedje JM, Murovec B, Prevoršek Z, Likar M, Stres B. Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study. PLoS One 2017; 12:e0188556. [PMID: 29211803 PMCID: PMC5718606 DOI: 10.1371/journal.pone.0188556] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/07/2017] [Indexed: 12/27/2022] Open
Abstract
We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal environment such as defecation frequency, intestinal electrical conductivity (IEC), sterol and polyphenol content and diversity, indole, aromaticity and spectral characteristics of dissolved organic matter (DOM) were measured (64 variables). The structure and diversity of bacterial microbial community was assessed using 16S rRNA amplicon sequencing. Inactivity negatively affected frequency of defecation and in combination with hypoxia increased IEC (p < 0.05). In contrast, sterol and polyphenol diversity and content, various characteristics of DOM and aromatic compounds, the structure and diversity of bacterial microbial community were not significantly affected over time. A new in-house PlanHab database was established to integrate all measured variables on host physiology, diet, experiment, immune and metabolic markers (n = 231). The observed progressive decrease in defecation frequency and concomitant increase in IEC suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was dose dependent on the extent of time spent in inactivity and preceded or took place in absence of significant rearrangements in bacterial microbial community. Species B. thetaiotamicron, B. fragilis, B. dorei and other Bacteroides with reported relevance for dysbiotic medical conditions were significantly enriched in HBR, characterized with most severe inflammation symptoms, indicating a shift towards host mucin degradation and proinflammatory immune crosstalk.
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Affiliation(s)
- Robert Šket
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nicole Treichel
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Tadej Debevec
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Sport, Ljubljana, Slovenia
| | - Ola Eiken
- Department of Environmental Physiology, Swedish Aerospace Physiology Centre, Royal Institute of Technology, Stockholm, Sweden
| | - Igor Mekjavić
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Marius Vital
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jenna Chandler
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Boštjan Murovec
- Laboratory for Artificial Sight and Automation, Faculty of Electrical Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Zala Prevoršek
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Matevž Likar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Center for Clinical Neurophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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163
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Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA. Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka. Proc Biol Sci 2017; 284:20172274. [PMID: 29212730 PMCID: PMC5740288 DOI: 10.1098/rspb.2017.2274] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/09/2017] [Indexed: 12/15/2022] Open
Abstract
In wild primates, social behaviour influences exposure to environmentally acquired and directly transmitted microorganisms. Prior studies indicate that gut microbiota reflect pairwise social interactions among chimpanzee and baboon hosts. Here, we demonstrate that higher-order social network structure-beyond just pairwise interactions-drives gut bacterial composition in wild lemurs, which live in smaller and more cohesive groups than previously studied anthropoid species. Using 16S rRNA gene sequencing and social network analysis of grooming contacts, we estimate the relative impacts of hierarchical (i.e. multilevel) social structure, individual demographic traits, diet, scent-marking, and habitat overlap on bacteria acquisition in a wild population of Verreaux's sifaka (Propithecus verreauxi) consisting of seven social groups. We show that social group membership is clearly reflected in the microbiomes of individual sifaka, and that social groups with denser grooming networks have more homogeneous gut microbial compositions. Within social groups, adults, more gregarious individuals, and individuals that scent-mark frequently harbour the greatest microbial diversity. Thus, the community structure of wild lemurs governs symbiotic relationships by constraining transmission between hosts and partitioning environmental exposure to microorganisms. This social cultivation of mutualistic gut flora may be an evolutionary benefit of tight-knit group living.
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Affiliation(s)
- Amanda C Perofsky
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rebecca J Lewis
- Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laura A Abondano
- Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
- Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anthony Di Fiore
- Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
- Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, TX 78712, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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164
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Kumar Mondal A, Kumar J, Pandey R, Gupta S, Kumar M, Bansal G, Mukerji M, Dash D, Singh Chauhan N. Comparative Genomics of Host-Symbiont and Free-Living Oceanobacillus Species. Genome Biol Evol 2017; 9:1175-1182. [PMID: 28460092 PMCID: PMC5425236 DOI: 10.1093/gbe/evx076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 12/12/2022] Open
Abstract
Survival in a given environment requires specific functions, so genomic variation is anticipated within in individual taxonomic groups that exhibit a large diversity in lifestyles. In this study, we sequence and assemble the genome of Oceanobacillus faecalis strain HM6, a resident of the human gut. Using the genus Oceanobacillus and the HM6 draft genome sequence, we explore the functional requirements for survival in a symbiotic arrangement within the human gut, in contrast to free living in the environment. Comparative genomics of seven available Oceanobacillus complete genomes highlight a genomically heterogeneous group. Our analysis did not find strict phylogenetic separation between free-living and host–symbiont Oceanobacillus members. By comparing functional gene content between host-associated and free-living species, we identified candidate genes that are potentially involved in symbiotic lifestyles, including phosphotransferase genes, transporters and two component response regulators. This study summarizes genomic and phylogenetic differences in the Oceanobacillus genus. Additionally, we highlight functions that may be key for survival in the human gut community.
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Affiliation(s)
- Anupam Kumar Mondal
- G.N.Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific & Innovative Research, New Delhi, India
| | - Jitendra Kumar
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shashank Gupta
- CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Manoj Kumar
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Gourja Bansal
- G.N.Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mitali Mukerji
- Academy of Scientific & Innovative Research, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine & CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Debasis Dash
- G.N.Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific & Innovative Research, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
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165
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Koskella B, Hall LJ, Metcalf CJE. The microbiome beyond the horizon of ecological and evolutionary theory. Nat Ecol Evol 2017; 1:1606-1615. [DOI: 10.1038/s41559-017-0340-2] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/07/2017] [Indexed: 01/16/2023]
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166
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Sharp KH, Pratte ZA, Kerwin AH, Rotjan RD, Stewart FJ. Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. MICROBIOME 2017; 5:120. [PMID: 28915923 PMCID: PMC5603060 DOI: 10.1186/s40168-017-0329-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/20/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome community composition. RESULTS Change in season had a strong effect on A. poculata microbiome composition. The seasonal shift was greatest upon the winter to spring transition, during which time A. poculata microbiome composition became more similar among host individuals. Within each of the four seasons, microbiome composition differed significantly from that of surrounding seawater but was surprisingly uniform between symbiotic and aposymbiotic corals, even in summer, when differences in Symbiodinium density between brown and white colonies are the highest, indicating that the observed seasonal shifts are not likely due to fluctuations in Symbiodinium density. CONCLUSIONS Our results suggest that symbiotic state may not be a primary driver of coral microbial community organization in A. poculata, which is a surprise given the long-held assumption that excess photosynthate is of importance to coral-associated microbes. Rather, other environmental or host factors, in this case, seasonal changes in host physiology associated with winter quiescence, may drive microbiome diversity. Additional studies of A. poculata and other facultatively symbiotic corals will provide important comparisons to studies of reef-building tropical corals and therefore help to identify basic principles of coral microbiome assembly, as well as functional relationships among holobiont members.
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Affiliation(s)
- Koty H. Sharp
- Department of Biology, Marine Biology and Environmental Science, Roger Williams University, 1 Old Ferry Road, Bristol, RI 02809 USA
| | | | | | - Randi D. Rotjan
- Boston University, Boston, USA
- New England Aquarium, Boston, USA
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167
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Muletz Wolz CR, Yarwood SA, Campbell Grant EH, Fleischer RC, Lips KR. Effects of host species and environment on the skin microbiome of Plethodontid salamanders. J Anim Ecol 2017; 87:341-353. [DOI: 10.1111/1365-2656.12726] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/08/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Carly R. Muletz Wolz
- Department of Biology; University of Maryland; College Park MD USA
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Stephanie A. Yarwood
- Department of Environmental Science & Technology; University of Maryland; College Park MD USA
| | - Evan H. Campbell Grant
- S.O. Conte Anadromous Fish Research Laboratory; United States Geological Survey Patuxent Wildlife Research Center; Turners Falls MA USA
| | - Robert C. Fleischer
- Center for Conservation Genomics; Smithsonian Conservation Biology Institute; National Zoological Park; Washington DC USA
| | - Karen R. Lips
- Department of Biology; University of Maryland; College Park MD USA
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168
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Kohl KD, Varner J, Wilkening JL, Dearing MD. Gut microbial communities of American pikas (
O
chotona princeps
): Evidence for phylosymbiosis and adaptations to novel diets. J Anim Ecol 2017; 87:323-330. [DOI: 10.1111/1365-2656.12692] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/21/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences Vanderbilt University Nashville TN USA
- Department of Biology University of Utah Salt Lake City UT USA
| | - Johanna Varner
- Department of Biology Colorado Mesa University Grand Junction CO USA
| | - Jennifer L. Wilkening
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
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169
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Moeller AH. The shrinking human gut microbiome. Curr Opin Microbiol 2017; 38:30-35. [PMID: 28458095 DOI: 10.1016/j.mib.2017.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 12/13/2022]
Abstract
Mammals harbor complex assemblages of gut bacteria that are deeply integrated with their hosts' digestive, immune, and neuroendocrine systems. Recent work has revealed that there has been a substantial loss of gut bacterial diversity from humans since the divergence of humans and chimpanzees. This bacterial depauperation began in humanity's ancient evolutionary past and has accelerated in recent years with the advent of modern lifestyles. Today, humans living in industrialized societies harbor the lowest levels of gut bacterial diversity of any primate for which metagenomic data are available, a condition that may increase risk of infections, autoimmune disorders, and metabolic syndrome. Some missing gut bacteria may remain within under-sampled human populations, whereas others may be globally extinct and unrecoverable.
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Affiliation(s)
- Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, 2538 Channing Way, Berkley, CA 94720, United States.
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170
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Martinson VG, Douglas AE, Jaenike J. Community structure of the gut microbiota in sympatric species of wild Drosophila. Ecol Lett 2017; 20:629-639. [PMID: 28371064 DOI: 10.1111/ele.12761] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/10/2017] [Accepted: 02/18/2017] [Indexed: 12/21/2022]
Abstract
Many aspects of animal ecology and physiology are influenced by the microbial communities within them. The underlying forces contributing to the assembly and diversity of gut microbiotas include chance events, host-based selection and interactions among microorganisms within these communities. We surveyed 215 wild individuals from four sympatric species of Drosophila that share a common diet of decaying mushrooms. Their microbiotas consistently contained abundant bacteria that were undetectable or at low abundance in their diet. Despite their deep phylogenetic divergence, all species had similar microbiotas, thus failing to support predictions of the phylosymbiosis hypothesis. Communities within flies were not random assemblages drawn from a common pool; instead, many bacterial operational taxonomic units (OTUs) were overrepresented or underrepresented relative to the neutral expectations, and OTUs exhibited checkerboard distributions among flies. These results suggest that selective factors play an important role in shaping the gut community structure of these flies.
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Affiliation(s)
| | - Angela E Douglas
- Department of Entomology and Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14627, USA
| | - John Jaenike
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
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171
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Li T, Long M, Li H, Gatesoupe FJ, Zhang X, Zhang Q, Feng D, Li A. Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes. Front Microbiol 2017; 8:454. [PMID: 28367147 PMCID: PMC5355437 DOI: 10.3389/fmicb.2017.00454] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/03/2017] [Indexed: 12/21/2022] Open
Abstract
Gut microbiota play key roles in host nutrition and metabolism. However, little is known about the relationship between host genetics, gut microbiota and metabolic profiles. Here, we used high-throughput sequencing and gas chromatography/mass spectrometry approaches to characterize the microbiota composition and the metabolite profiles in the gut of five cyprinid fish species with three different feeding habits raised under identical husbandry conditions. Our results showed that host species and feeding habits significantly affect not only gut microbiota composition but also metabolite profiles (ANOSIM, p ≤ 0.05). Mantel test demonstrated that host phylogeny, gut microbiota, and metabolite profiles were significantly related to each other (p ≤ 0.05). Additionally, the carps with the same feeding habits had more similarity in gut microbiota composition and metabolite profiles. Various metabolites were correlated positively with bacterial taxa involved in food degradation. Our results shed new light on the microbiome and metabolite profiles in the gut content of cyprinid fishes, and highlighted the correlations between host genotype, fish gut microbiome and putative functions, and gut metabolite profiles.
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Affiliation(s)
- Tongtong Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesWuhan, China; Key Laboratory of Environmental and Applied Microbiology, and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of SciencesChengdu, China
| | - Meng Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan, China
| | - Huan Li
- Key Laboratory of Environmental and Applied Microbiology, and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu, China
| | - François-Joël Gatesoupe
- Nutrition, Métabolisme et Aquaculture, Institut National de la Recherche Agronomique, University of Pau and Pays de l'Adour Saint-Pée-sur-Nivelle, France
| | - Xujie Zhang
- College of Fisheries and Life Science, Shanghai Ocean University Shanghai, China
| | - Qianqian Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesWuhan, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural UniversityWuhan, China
| | - Dongyue Feng
- National Fisheries Technical Extension Center, Ministry of Agriculture Beijing, China
| | - Aihua Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesWuhan, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural UniversityWuhan, China
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172
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Kwong WK, Medina LA, Koch H, Sing KW, Soh EJY, Ascher JS, Jaffé R, Moran NA. Dynamic microbiome evolution in social bees. SCIENCE ADVANCES 2017; 3:e1600513. [PMID: 28435856 PMCID: PMC5371421 DOI: 10.1126/sciadv.1600513] [Citation(s) in RCA: 268] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 02/10/2017] [Indexed: 05/18/2023]
Abstract
The highly social (eusocial) corbiculate bees, comprising the honey bees, bumble bees, and stingless bees, are ubiquitous insect pollinators that fulfill critical roles in ecosystem services and human agriculture. Here, we conduct wide sampling across the phylogeny of these corbiculate bees and reveal a dynamic evolutionary history behind their microbiota, marked by multiple gains and losses of gut associates, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size). Across four continents, we found that different host species have distinct gut communities, largely independent of geography or sympatry. Nonetheless, their microbiota has a shared heritage: The emergence of the eusocial corbiculate bees from solitary ancestors appears to coincide with the acquisition of five core gut bacterial lineages, supporting the hypothesis that host sociality facilitates the development and maintenance of specialized microbiomes.
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Affiliation(s)
- Waldan K. Kwong
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
- Corresponding author. (W.K.K.); (N.A.M.)
| | - Luis A. Medina
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
| | - Hauke Koch
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
| | - Kong-Wah Sing
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Eunice Jia Yu Soh
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - John S. Ascher
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Rodolfo Jaffé
- Vale Institute of Technology, Sustainable Development, 66055-090 Belém PA, Brazil
- Department of Ecology, Universidade de São Paulo, Rua do Matão 321, 05508-090 São Paulo SP, Brazil
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
- Corresponding author. (W.K.K.); (N.A.M.)
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173
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Raymann K, Moeller AH, Goodman AL, Ochman H. Unexplored Archaeal Diversity in the Great Ape Gut Microbiome. mSphere 2017; 2:e00026-17. [PMID: 28251182 PMCID: PMC5322346 DOI: 10.1128/msphere.00026-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 02/03/2017] [Indexed: 12/14/2022] Open
Abstract
Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.
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Affiliation(s)
- Kasie Raymann
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Andrew H. Moeller
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Andrew L. Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
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174
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Ryan PM, Stanton C, Caplice NM. Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Diabetol Metab Syndr 2017; 9:102. [PMID: 29299069 PMCID: PMC5745752 DOI: 10.1186/s13098-017-0299-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/07/2017] [Indexed: 02/07/2023] Open
Abstract
While basic and clinical research over the last several decades has recognized a number of modifiable risk factors associated with cardiometabolic disease progression, additional and alternative biological perspectives may offer novel targets for prevention and treatment of this disease set. There is mounting preclinical and emerging clinical evidence indicating that the mass of metabolically diverse microorganisms which inhabit the human gastrointestinal tract may be implicated in initiation and modulation of cardiovascular and metabolic disease outcomes. The following review will discuss this gut microbiome-host metabolism axis and address newly proposed bile-mediated signaling pathways through which dysregulation of this homeostatic axis may influence host cardiovascular risk. With a central focus on the major nuclear and membrane-bound bile acid receptor ligands, we aim to review the putative impact of microbial bile acid modification on several major phenotypes of metabolic syndrome, from obesity to heart failure. Finally, attempting to synthesize several separate but complementary hypotheses, we will review current directions in preclinical and clinical investigation in this evolving field.
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Affiliation(s)
- Paul M. Ryan
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork, Ireland
- Centre for Research in Vascular Biology, University College Cork, Co. Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Noel M. Caplice
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork, Ireland
- Centre for Research in Vascular Biology, University College Cork, Co. Cork, Ireland
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175
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Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, Caviedes-Vidal E, Bordenstein SR. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Mol Ecol 2016; 26:1175-1189. [PMID: 27862531 DOI: 10.1111/mec.13921] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/24/2016] [Accepted: 11/01/2016] [Indexed: 12/13/2022]
Abstract
Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Antonio Brun
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Melisa Magallanes
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Joshua Brinkerhoff
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Alejandro Laspiur
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Juan Carlos Acosta
- Centro de Investigaciones de la Geósfera y la Biósfera (CIGEOBIO-CONICET) - Departamento de Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de San Juan, Av. José I. de la Roza 590 Oeste, J5402DCS, San Juan, Argentina
| | - Enrique Caviedes-Vidal
- Laboratorio de Biología Integrativa, Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, San Luis, 5700, Argentina.,Departamento de Bioquímica y Ciencias Biológicas, Universidad Nacional de San Luis, Chacabuco 917, San Luis, 5700, Argentina
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, 465 21st Ave South, Nashville, TN, 37235, USA
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176
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Brooks AW, Kohl KD, Brucker RM, van Opstal EJ, Bordenstein SR. Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History. PLoS Biol 2016; 14:e2000225. [PMID: 27861590 PMCID: PMC5115861 DOI: 10.1371/journal.pbio.2000225] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/20/2016] [Indexed: 02/07/2023] Open
Abstract
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we test the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, and Nasonia wasps), and we reevaluate the phylosymbiotic relationships of seven species of wild hominids. We demonstrate three key findings. First, intraspecific microbiota variation is consistently less than interspecific microbiota variation, and microbiota-based models predict host species origin with high accuracy across the dataset. Interestingly, the age of host clade divergence positively associates with the degree of microbial community distinguishability between species within the host clades, spanning recent host speciation events (~1 million y ago) to more distantly related host genera (~108 million y ago). Second, topological congruence analyses of each group's complete phylogeny and microbiota dendrogram reveal significant degrees of phylosymbiosis, irrespective of host clade age or taxonomy. Third, consistent with selection on host–microbiota interactions driving phylosymbiosis, there are survival and performance reductions when interspecific microbiota transplants are conducted between closely related and divergent host species pairs. Overall, these findings indicate that the composition and functional effects of an animal's microbial community can be closely allied with host evolution, even across wide-ranging timescales and diverse animal systems reared under controlled conditions. Studies on the assembly and function of host-microbiota symbioses are inherently complicated by the diverse effects of diet, age, sex, host genetics, and endosymbionts. Central to unraveling one effect from the other is an experimental framework that reduces confounders. Using common rearing conditions across four animal groups (deer mice, flies, mosquitoes, and wasps) that span recent host speciation events to more distantly related host genera, this study tests whether microbial community assembly is generally random with respect to host relatedness or "phylosymbiotic," in which the phylogeny of the host group is congruent with ecological relationships of their microbial communities. Across all four animal groups and one external dataset of great apes, we apply several statistics for analyzing congruencies and demonstrate phylosymbiosis to varying degrees in each group. Moreover, consistent with selection on host–microbiota interactions driving phylosymbiosis, transplanting interspecific microbial communities in mice significantly decreased their ability to digest food. Similarly, wasps that received transplants of microbial communities from different wasp species had lower survival than those given their own microbiota. Overall, this experimental and statistical framework shows how microbial community assembly and functionality across related species can be linked to animal evolution, health, and survival.
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Affiliation(s)
- Andrew W. Brooks
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin D. Kohl
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert M. Brucker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
| | - Edward J. van Opstal
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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177
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Vlčková K, Gomez A, Petrželková KJ, Whittier CA, Todd AF, Yeoman CJ, Nelson KE, Wilson BA, Stumpf RM, Modrý D, White BA, Leigh SR. Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla). MICROBIAL ECOLOGY 2016; 72:943-954. [PMID: 26984253 DOI: 10.1007/s00248-016-0745-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 02/21/2016] [Indexed: 05/20/2023]
Abstract
The mammalian gastrointestinal (GI) microbiome, which plays indispensable roles in host nutrition and health, is affected by numerous intrinsic and extrinsic factors. Among them, antibiotic (ATB) treatment is reported to have a significant effect on GI microbiome composition in humans and other animals. However, the impact of ATBs on the GI microbiome of free-ranging or even captive great apes remains poorly characterized. Here, we investigated the effect of cephalosporin treatment (delivered by intramuscular dart injection during a serious respiratory outbreak) on the GI microbiome of a wild habituated group of western lowland gorillas (Gorilla gorilla gorilla) in the Dzanga Sangha Protected Areas, Central African Republic. We examined 36 fecal samples from eight individuals, including samples before and after ATB treatment, and characterized the GI microbiome composition using Illumina-MiSeq sequencing of the bacterial 16S rRNA gene. The GI microbial profiles of samples from the same individuals before and after ATB administration indicate that the ATB treatment impacts GI microbiome stability and the relative abundance of particular bacterial taxa within the colonic ecosystem of wild gorillas. We observed a statistically significant increase in Firmicutes and a decrease in Bacteroidetes levels after ATB treatment. We found disruption of the fibrolytic community linked with a decrease of Ruminoccocus levels as a result of ATB treatment. Nevertheless, the nature of the changes observed after ATB treatment differs among gorillas and thus is dependent on the individual host. This study has important implications for ecology, management, and conservation of wild primates.
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Affiliation(s)
- Klára Vlčková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, Brno, 61242, Czech Republic.
| | - Andres Gomez
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, Brno, 60365, Czech Republic
- Liberec Zoo, Masarykova 1347/31, Liberec, 46001, Czech Republic
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, České Budějovice, 37005, Czech Republic
| | - Christopher A Whittier
- Cummings School of Veterinary Medicine at Tufts University, 200 Westboro Road, North Grafton, MA, 01536, USA
- Department of Wildlife Health Sciences, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue Northwest, Washington, DC, 20008, USA
| | - Angelique F Todd
- WWF, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, P.O. Box 172900, Bozeman, MT, 59717-2900, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Brenda A Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Rebecca M Stumpf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, Brno, 61242, Czech Republic
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, České Budějovice, 37005, Czech Republic
- CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1/3, Brno, 61242, Czech Republic
| | - Bryan A White
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Steven R Leigh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
- Department of Anthropology, University of Colorado at Boulder, 1350 Pleasant Street, Boulder, CO, 80309-0233, USA
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178
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Berg M, Zhou XY, Shapira M. Host-Specific Functional Significance of Caenorhabditis Gut Commensals. Front Microbiol 2016; 7:1622. [PMID: 27799924 PMCID: PMC5066524 DOI: 10.3389/fmicb.2016.01622] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/27/2022] Open
Abstract
The gut microbiota is an important contributor to host health and fitness. Given its importance, microbiota composition should not be left to chance. However, what determines this composition is far from clear, with results supporting contributions of both environmental factors and host genetics. To gauge the relative contributions of host genetics and environment, specifically the microbial diversity, we characterized the gut microbiotas of Caenorhabditis species spanning 200-300 million years of evolution, and raised on different composted soil environments. Comparisons were based on 16S rDNA deep sequencing data, as well as on functional evaluation of gut isolates. Worm microbiotas were distinct from those in their respective soil environment, and included bacteria previously identified as part of the C. elegans core microbiota. Microbiotas differed between experiments initiated with different soil communities, but within each experiment, worm microbiotas clustered according to host identity, demonstrating a dominant contribution of environmental diversity, but also a significant contribution of host genetics. The dominance of environmental contributions hindered identification of host-associated microbial taxa from 16S data. Characterization of gut isolates from C. elegans and C. briggsae, focusing on the core family Enterobacteriaceae, were also unable to expose phylogenetic distinctions between microbiotas of the two species. However, functional evaluation of the isolates revealed host-specific contributions, wherein gut commensals protected their own host from infection, but not a non-host. Identification of commensal host-specificity at the functional level, otherwise overlooked in standard sequence-based analyses, suggests that the contribution of host genetics to shaping of gut microbiotas may be greater than previously realized.
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Affiliation(s)
- Maureen Berg
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Xiao Ying Zhou
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, BerkeleyBerkeley, CA, USA; Graduate Group in Microbiology, University of California, BerkeleyBerkeley, CA, USA
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179
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Abdul-Aziz MA, Cooper A, Weyrich LS. Exploring Relationships between Host Genome and Microbiome: New Insights from Genome-Wide Association Studies. Front Microbiol 2016; 7:1611. [PMID: 27785127 PMCID: PMC5061000 DOI: 10.3389/fmicb.2016.01611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/26/2016] [Indexed: 12/20/2022] Open
Abstract
As our understanding of the human microbiome expands, impacts on health and disease continue to be revealed. Alterations in the microbiome can result in dysbiosis, which has now been linked to subsequent autoimmune and metabolic diseases, highlighting the need to identify factors that shape the microbiome. Research has identified that the composition and functions of the human microbiome can be influenced by diet, age, sex, and environment. More recently, studies have explored how human genetic variation may also influence the microbiome. Here, we review several recent analytical advances in this new research area, including those that use genome-wide association studies to examine host genome-microbiome interactions, while controlling for the influence of other factors. We find that current research is limited by small sample sizes, lack of cohort replication, and insufficient confirmatory mechanistic studies. In addition, we discuss the importance of understanding long-term interactions between the host genome and microbiome, as well as the potential impacts of disrupting this relationship, and explore new research avenues that may provide information about the co-evolutionary history of humans and their microorganisms.
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Affiliation(s)
| | | | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, AdelaideSA, Australia
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180
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Gut microbiome and dietary patterns in different Saudi populations and monkeys. Sci Rep 2016; 6:32191. [PMID: 27578328 PMCID: PMC5006041 DOI: 10.1038/srep32191] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/07/2016] [Indexed: 02/06/2023] Open
Abstract
Host genetics, environment, lifestyle and proximity between hosts strongly influence the composition of the gut microbiome. To investigate the association of dietary variables with the gut microbiota, we used 16S rDNA sequencing to test the fecal microbiome of Bedouins and urban Saudis and we compared it to the gut microbiome of baboons living in close contact with Bedouins and eating their leftovers. We also analyzed fermented dairy products commonly consumed by Bedouins in order to investigate their impact on the gut microbiome of this population. We found that the gut microbiomes of westernized urban Saudis had significantly lower richness and biodiversity than the traditional Bedouin population. The gut microbiomes of baboons were more similar to that of Bedouins compared to urban Saudis, probably due the dietary overlap between baboons and Bedouins. Moreover, we found clusters that were compositionally similar to clusters identified in humans and baboons, characterized by differences in Acinetobacter, Turicibacter and Collinsella. The fermented food presented significantly more bacteria genera common to the gut microbiome of Bedouins compared to urban Saudis. These results support the hypothesis that dietary habits influence the composition of the gut microbiome.
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181
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Abstract
The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.
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182
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Hamajima H, Matsunaga H, Fujikawa A, Sato T, Mitsutake S, Yanagita T, Nagao K, Nakayama J, Kitagaki H. Japanese traditional dietary fungus koji Aspergillus oryzae functions as a prebiotic for Blautia coccoides through glycosylceramide: Japanese dietary fungus koji is a new prebiotic. SPRINGERPLUS 2016; 5:1321. [PMID: 27563516 PMCID: PMC4980852 DOI: 10.1186/s40064-016-2950-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/29/2016] [Indexed: 01/16/2023]
Abstract
Background
The Japanese traditional cuisine, Washoku, considered to be responsible for increased longevity among the Japanese, comprises various foods fermented with the non-pathogenic fungus Aspergillus oryzae (koji). We have recently revealed that koji contains an abundant amount of glycosylceramide. Intestinal microbes have significant effect on health. However, the effects of koji glycosylceramide on intestinal microbes have not been studied. Materials and methods Glycosylceramide was extracted and purified from koji. C57BL/6N mice were fed a diet containing 1 % purified koji glycosylceramide for 1 week. Nutritional parameters and faecal lipid constituents were analyzed. The intestinal microbial flora of mice on this diet was investigated. Results Ingested koji glycosylceramide was neither digested by intestinal enzymes nor was it detected in the faeces, suggesting that koji glycosylceramide was digested by the intestinal microbial flora. Intestinal microbial flora that digested koji glycosylceramide had an increased ratio of Blautia coccoides. Stimulation of B. coccoides growth by pure koji glycosylceramide was confirmed in vitro. Conclusions Koji functions as a prebiotic for B. coccoides through glycosylceramide. Since there are many reports of the effects of B. coccoides on health, an increase in intestinal B. coccoides by koji glycosylceramide might be the connection between Japanese cuisine, intestinal microbial flora, and longevity.
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Affiliation(s)
- Hiroshi Hamajima
- Department of Environmental Science, Faculty of Agriculture, Saga University, Honjo-cho, Saga City, Saga Japan
| | - Haruka Matsunaga
- Department of Environmental Science, Faculty of Agriculture, Saga University, Honjo-cho, Saga City, Saga Japan
| | - Ayami Fujikawa
- Department of Environmental Science, Faculty of Agriculture, Saga University, Honjo-cho, Saga City, Saga Japan
| | - Tomoya Sato
- Department of Environmental Science, Faculty of Agriculture, Saga University, Honjo-cho, Saga City, Saga Japan
| | - Susumu Mitsutake
- Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Honjo-cho, Saga City, Saga Japan
| | - Teruyoshi Yanagita
- Faculty of Health and Nutrition Science, Nishikyushu University, Ozaki, Kanzaki-cho, Kanzaki City, Saga Japan
| | - Koji Nagao
- Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Honjo-cho, Saga City, Saga Japan
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Hiroshi Kitagaki
- Department of Environmental Science, Faculty of Agriculture, Saga University, Honjo-cho, Saga City, Saga Japan
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183
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Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, Muller MN, Pusey AE, Peeters M, Hahn BH, Ochman H. Cospeciation of gut microbiota with hominids. Science 2016; 353:380-2. [PMID: 27463672 DOI: 10.1126/science.aaf3951] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/02/2016] [Indexed: 12/14/2022]
Abstract
The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations. Divergence times of these cospeciating gut bacteria are congruent with those of hominids, indicating that nuclear, mitochondrial, and gut bacterial genomes diversified in concert during hominid evolution. This study identifies human gut bacteria descended from ancient symbionts that speciated simultaneously with humans and the African apes.
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Affiliation(s)
- Andrew H Moeller
- Department of Integrative Biology, 2506 Speedway A5000, University of Texas at Austin, Austin, TX 78712, USA. Miller Institute for Basic Research in Science, 2536 Channing Way, University of California, Berkeley, CA 94720, USA
| | | | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Alexander V Georgiev
- Department of Anthropology, Northwestern University, 1810 Hinman Avenue, Evanston, IL 60208, USA. Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, LSP 261B, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, MSC01-1040, Albuquerque, NM 87131, USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology, 101 Biological Sciences Building, Duke University, Durham, NC 27708, USA
| | - Martine Peeters
- Institut de Recherche pour le Développement, University of Montpellier, 34394 Montpellier, France
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, 409 Johnson Pavilion, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Ochman
- Department of Integrative Biology, 2506 Speedway A5000, University of Texas at Austin, Austin, TX 78712, USA.
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184
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Schnorr SL, Sankaranarayanan K, Lewis CM, Warinner C. Insights into human evolution from ancient and contemporary microbiome studies. Curr Opin Genet Dev 2016; 41:14-26. [PMID: 27507098 DOI: 10.1016/j.gde.2016.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA.
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185
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Dominguez-Bello MG, Blaser MJ. Asthma: Undoing millions of years of coevolution in early life? Sci Transl Med 2016; 7:307fs39. [PMID: 26424565 DOI: 10.1126/scitranslmed.aad2741] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maria Gloria Dominguez-Bello
- Division of Translational Medicine, Department of Medicine, New York University Langone Medical Center, (NYULMC) New York, NY 10016, USA.
| | - Martin J Blaser
- Division of Translational Medicine, Department of Medicine, New York University Langone Medical Center, (NYULMC) New York, NY 10016, USA. Department of Microbiology, NYULMC, New York, NY 10016, USA. Department of Veterans Affairs New York Harbor Medical Center, New York, NY 10010, USA.
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186
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Martínez-García Á, Martín-Vivaldi M, Ruiz-Rodríguez M, Martínez-Bueno M, Arco L, Rodríguez-Ruano SM, Peralta-Sánchez JM, Soler JJ. The Microbiome of the Uropygial Secretion in Hoopoes Is Shaped Along the Nesting Phase. MICROBIAL ECOLOGY 2016; 72:252-261. [PMID: 27075655 DOI: 10.1007/s00248-016-0765-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/01/2016] [Indexed: 06/05/2023]
Abstract
Microbial symbiont acquisition by hosts may determine the effectiveness of the mutualistic relationships. A mix of vertical and horizontal transmission may be advantageous for hosts by allowing plastic changes of microbial communities depending on environmental conditions. Plasticity is well known for gut microbiota but is poorly understood for other symbionts of wild animals. We here explore the importance of environmental conditions experienced by nestling hoopoes (Upupa epops) during the late nesting phase determining microbiota in their uropygial gland. In cross-fostering experiments of 8 days old nestlings, "sibling-sibling" and "mother-offspring" comparisons were used to explore whether the bacterial community naturally established in the uropygial gland of nestlings could change depending on experimental environmental conditions (i.e., new nest environment). We found that the final microbiome of nestlings was mainly explained by nest of origin. Moreover, cross-fostered nestlings were more similar to their siblings and mothers than to their stepsiblings and stepmothers. We also detected a significant effect of nest of rearing, suggesting that nestling hoopoes acquire most bacterial symbionts during the first days of life but that the microbiome is dynamic and can be modified along the nestling period depending on environmental conditions. Estimated effects of nest of rearing, but also most of those of nest of origin are associated to environmental characteristics of nests, which are extended phenotypes of parents. Thus, natural selection may favor the acquisition of appropriated microbial symbionts for particular environmental conditions found in nests.
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Affiliation(s)
| | | | | | | | - Laura Arco
- Departamento de Zoología Universidad de Granada, E-18071, Granada, Spain
| | | | | | - Juan José Soler
- Estación Experimental de Zonas Áridas (CSIC), E-04120, Almería, Spain.
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187
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Bull JW, Maron M. How humans drive speciation as well as extinction. Proc Biol Sci 2016; 283:20160600. [PMID: 27358365 PMCID: PMC4936035 DOI: 10.1098/rspb.2016.0600] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022] Open
Abstract
A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation-and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon 'no net loss' conservation literature-considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.
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Affiliation(s)
- J W Bull
- Department of Food and Resource Economics and Center for Macroecology, Evolution and Climate, University of Copenhagen, Rolighedsvej 23, 1958 Copenhagen, Denmark
| | - M Maron
- School of Geography, Planning and Environmental Management, The University of Queensland, Brisbane, Queensland 4072, Australia
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188
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Wang H, Dai W, Qiu C, Li S, Wang W, Xu J, Li Z, Wang H, Li Y, Yang Z, Feng X, Zhou Q, Han L, Li Y, Zheng Y. Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota. J Thorac Dis 2016; 8:1316-22. [PMID: 27293852 DOI: 10.21037/jtd.2016.04.63] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pneumonia is one of the most serious diseases for children, with which lung microbiota are proved to be associated. We performed 16S rDNA analysis on broncho-alveolar lavage fluid (BALF) for 32 children with tracheomalacia (C group), pneumonia infected with Streptococcus pneumoniae (S. pneumoniae) (D1 group) or Mycoplasma pneumoniae (M. pneumoniae) (D2 group). Children with tracheomalacia held lower microbial diversity and accumulated Lactococcus (mean ± SD, 45.21%±5.07%, P value <0.05), Porphyromonas (0.12%±0.31%, P value <0.05). D1 and D2 group were enriched by Streptococcus (7.57%±11.61%, P value <0.01 when compared with D2 group) and Mycoplasma (0.67%±1.25%, P value <0.01) respectively. Bacterial correlation in C group was mainly intermediated by Pseudomonas and Arthrobacter. Whilst, D1 group harbored simplest microbial correlation in three groups, and D2 group held the most complicated network, involving enriched Staphylococcus (0.26%±0.71%), Massilia (0.81%±2.42%). This will be of significance for understanding pneumonia incidence and progression more comprehensively, and discerning between bacterial infection and carriage.
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Affiliation(s)
- Heping Wang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Wenkui Dai
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Chuangzhao Qiu
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Shuaicheng Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Wenjian Wang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Jianqiang Xu
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Zhichuan Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Hongmei Wang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Yuzheng Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Zhenyu Yang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Xin Feng
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Qian Zhou
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Lijuan Han
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Yinhu Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Yuejie Zheng
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
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189
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Lyte M, Fodor AA, Chapman CD, Martin GG, Perez-Chanona E, Jobin C, Dess NK. Gut Microbiota and a Selectively Bred Taste Phenotype: A Novel Model of Microbiome-Behavior Relationships. Psychosom Med 2016; 78:610-9. [PMID: 27035357 DOI: 10.1097/psy.0000000000000318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVES The microbiota-gut-brain axis is increasingly implicated in obesity, anxiety, stress, and other health-related processes. Researchers have proposed that gut microbiota may influence dietary habits, and pathways through the microbiota-gut-brain axis make such a relationship feasible; however, few data bear on the hypothesis. As a first step in the development of a model system, the gut microbiome was examined in rat lines selectively outbred on a taste phenotype with biobehavioral profiles that have diverged with respect to energy regulation, anxiety, and stress. METHODS Occidental low and high-saccharin-consuming rats were assessed for body mass and chow, water, and saccharin intake; littermate controls had shared cages with rats in the experimental group but were not assessed. Cecum and colon microbial communities were profiled using Illumina 16S rRNA sequencing and multivariate analysis of microbial diversity and composition. RESULTS The saccharin phenotype was confirmed (low-saccharin-consuming rats, 0.7Δ% [0.9Δ%]; high-saccharin-consuming rats, 28.1Δ% [3.6Δ%]). Regardless of saccharin exposure, gut microbiota differed between lines in terms of overall community similarity and taxa at lower phylogenetic levels. Specifically, 16 genera in three phyla distinguished the lines at a 10% false discovery rate. DISCUSSION The study demonstrates for the first time that rodent lines created through selective pressure on taste and differing on functionally related correlates host different microbial communities. Whether the microbiota are causally related to the taste phenotype or its correlates remains to be determined. These findings encourage further inquiry on the relationship of the microbiome to taste, dietary habits, emotion, and health.
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Affiliation(s)
- Mark Lyte
- From the Department of Veterinary Microbiology and Preventive Medicine, School of Veterinary Medicine (Lyte), Iowa State University, Ames, Iowa; Department of Immunotherapeutics and Biotechnology (Lyte), Texas Tech University Health Sciences Center, Abilene, Texas; Department of Bioinformatics and Genomics (Fodor), University of North Carolina at Charlotte, North Carolina; School of Medicine (Perez-Chanona), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Division of Gastroenterology, Department of Medicine (Jobin), University of Florida College of Medicine, Gainesville, Florida; and Occidental College (Chapman, Martin, Dess), Los Angeles, California
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190
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Abstract
The gut microbiota can have profound effects on hosts, but the study of these relationships in humans is challenging. The specialized gut microbial community of honey bees is similar to the mammalian microbiota, as both are mostly composed of host-adapted, facultatively anaerobic and microaerophilic bacteria. However, the microbial community of the bee gut is far simpler than the mammalian microbiota, being dominated by only nine bacterial species clusters that are specific to bees and that are transmitted through social interactions between individuals. Recent developments, which include the discovery of extensive strain-level variation, evidence of protective and nutritional functions, and reports of eco-physiological or disease-associated perturbations to the microbial community, have drawn attention to the role of the microbiota in bee health and its potential as a model for studying the ecology and evolution of gut symbionts.
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Affiliation(s)
- Waldan K Kwong
- Department of Integrative Biology, University of Texas, Austin, Texas 78712, USA
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas, Austin, Texas 78712, USA
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191
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Li K, Dan Z, Gesang L, Wang H, Zhou Y, Du Y, Ren Y, Shi Y, Nie Y. Comparative Analysis of Gut Microbiota of Native Tibetan and Han Populations Living at Different Altitudes. PLoS One 2016; 11:e0155863. [PMID: 27232599 PMCID: PMC4883765 DOI: 10.1371/journal.pone.0155863] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 05/05/2016] [Indexed: 12/15/2022] Open
Abstract
The factors driving the composition of gut microbiota are still only partly understood but appear to include environmental, cultural, and genetic factors. In order to obtain more insight into the relative importance of these factors, we analyzed the microbiome composition in subjects of Tibetan or Han descent living at different altitudes. DNA was isolated from stool samples. Using polymerase chain reaction methodology, the 16S rRNA V1-V3 regions were amplified and the sequence information was analyzed by principal coordinates analysis and Lefse analyses. Contrasting the Tibetan and Han populations both living at the 3600 m altitude, we found that the Tibetan microbiome is characterized by a relative abundance of Prevotella whereas the Han stool was enriched in Bacteroides. Comparing the microbiome of Han stool obtained from populations living at different altitudes revealed a more energy efficient flora in samples from those living at higher altitude relative to their lower-altitude counterparts. Comparison of the stool microbiome of Tibetan herders living at 4800 m to rural Tibetans living at 3600 m altitude shows that the former have a flora enriched in butyrate-producing bacteria, possibly in response to the harsher environment that these herders face. Thus, the study shows that both altitude and genetic/cultural background have a significant influence on microbiome composition, and it represents the first attempt to compare stool microbiota of Tibetan and Han populations in relation to altitude.
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Affiliation(s)
- Kang Li
- Department of Gastroenterology, Guangzhou First People’s Hospital of Guangzhou Medical University, Guangzhou, 510180, Guangdong Province, China
- High Altitude Medical Research Institute, People’s Hospital of Tibet Autonomous Region, Lhasa, 850000, China
| | - Zeng Dan
- High Altitude Medical Research Institute, People’s Hospital of Tibet Autonomous Region, Lhasa, 850000, China
| | - Luobu Gesang
- High Altitude Medical Research Institute, People’s Hospital of Tibet Autonomous Region, Lhasa, 850000, China
| | - Hong Wang
- Department of Gastroenterology, Guangzhou First People’s Hospital of Guangzhou Medical University, Guangzhou, 510180, Guangdong Province, China
| | - Yongjian Zhou
- Department of Gastroenterology, Guangzhou First People’s Hospital of Guangzhou Medical University, Guangzhou, 510180, Guangdong Province, China
| | - Yanlei Du
- Department of Gastroenterology, Guangzhou First People’s Hospital of Guangzhou Medical University, Guangzhou, 510180, Guangdong Province, China
| | - Yi Ren
- Shanghai Major Bio-pharm Technology Co., Ltd., Shanghai, 201203, China
| | - Yixiang Shi
- Shanghai Major Bio-pharm Technology Co., Ltd., Shanghai, 201203, China
| | - Yuqiang Nie
- Department of Gastroenterology, Guangzhou First People’s Hospital of Guangzhou Medical University, Guangzhou, 510180, Guangdong Province, China
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192
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Bennett G, Malone M, Sauther ML, Cuozzo FP, White B, Nelson KE, Stumpf RM, Knight R, Leigh SR, Amato KR. Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta). Am J Primatol 2016; 78:883-92. [PMID: 27177345 DOI: 10.1002/ajp.22555] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 04/09/2016] [Accepted: 04/12/2016] [Indexed: 02/06/2023]
Abstract
The gut microbiota contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of the immune system. The composition of the gut microbiota can change dramatically within and between individuals of a species as a result of diet, age, or habitat. Therefore, understanding the factors determining gut microbiota diversity and composition can contribute to our knowledge of host ecology as well as to conservation efforts. Here we use high-throughput sequencing to describe variation in the gut microbiota of the endangered ring-tailed lemur (Lemur catta) at the Bezà Mahafaly Special Reserve (BMSR) in southwestern Madagascar. Specifically, we measured the diversity and composition of the gut microbiota in relation to social group, age, sex, tooth wear and loss, and habitat disturbance. While we found no significant variation in the diversity of the ring-tailed lemur gut microbiota in response to any variable tested, the taxonomic composition of the gut microbiota was influenced by social group, age, and habitat disturbance. However, effect sizes were small and appear to be driven by the presence or absence of relatively low abundance taxa. These results suggest that habitat disturbance may not impact the lemur gut microbiota as strongly as it impacts the gut microbiota of other primate species, highlighting the importance of distinct host ecological and physiological factors on host-gut microbe relationships. Am. J. Primatol. 78:883-892, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Genevieve Bennett
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Matthew Malone
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado
| | - Michelle L Sauther
- Department of Anthropology, University of Colorado Boulder, Boulder, Colorado
| | - Frank P Cuozzo
- Department of Anthropology, University of North Dakota, Grand Forks, North Dakota
| | - Bryan White
- C.R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | | | - Rebecca M Stumpf
- C.R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, California
- Department of Computer Science and Engineering, University of California, San Diego, California
| | - Steven R Leigh
- Department of Anthropology, University of Colorado Boulder, Boulder, Colorado
| | - Katherine R Amato
- Department of Anthropology, University of Colorado Boulder, Boulder, Colorado
- Department of Anthropology, Northwestern University, Evanston, Illinois
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193
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Ren T, Grieneisen LE, Alberts SC, Archie EA, Wu M. Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons. Environ Microbiol 2016; 18:1312-25. [PMID: 25818066 PMCID: PMC5941927 DOI: 10.1111/1462-2920.12852] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 12/18/2022]
Abstract
Gut bacterial communities play essential roles in host biology, but to date we lack information on the forces that shape gut microbiota between hosts and over time in natural populations. Understanding these forces in wild primates provides a valuable comparative context that enriches scientific perspectives on human gut microbiota. To this end, we tested predictors of gut microbial composition in a well-studied population of wild baboons. Using cross-sectional and longitudinal samples collected over 13 years, we found that baboons harbour gut microbiota typical of other omnivorous primates, albeit with an especially high abundance of Bifidobacterium. Similar to previous work in humans and other primates, we found strong effects of both developmental transitions and diet on gut microbial composition. Strikingly, baboon gut microbiota appeared to be highly dynamic such that samples collected from the same individual only a few days apart were as different from each other as samples collected over 10 years apart. Despite the dynamic nature of baboon gut microbiota, we identified a set of core taxa that is common among primates, supporting the hypothesis that microbiota codiversify with their host species. Our analysis identified two tentative enterotypes in adult baboons that differ from those of humans and chimpanzees.
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Affiliation(s)
- Tiantian Ren
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Laura E. Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46617 USA
| | - Susan C. Alberts
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
- Department of Biology, Duke University, Durham, NC 27708 USA
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46617 USA
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
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194
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Willermet C. Biological Anthropology in 2015: Open Access, Biocultural Interactions, and Social Change. AMERICAN ANTHROPOLOGIST 2016. [DOI: 10.1111/aman.12529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cathy Willermet
- Department of Sociology, Anthropology, and Social Work; Central Michigan University; Mount Pleasant MI 48859
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195
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Shapira M. Gut Microbiotas and Host Evolution: Scaling Up Symbiosis. Trends Ecol Evol 2016; 31:539-549. [PMID: 27039196 DOI: 10.1016/j.tree.2016.03.006] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/18/2016] [Accepted: 03/05/2016] [Indexed: 02/07/2023]
Abstract
Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation.
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Affiliation(s)
- Michael Shapira
- University of California, Berkeley, department of Integrative Biology and Graduate Group in Microbiology. Valley Life Sciences Building, room 5155, Berkeley, CA 94720, USA.
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196
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Kohl KD, Yahn J. Effects of environmental temperature on the gut microbial communities of tadpoles. Environ Microbiol 2016; 18:1561-5. [DOI: 10.1111/1462-2920.13255] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/05/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Kevin D. Kohl
- Department of Biological SciencesVanderbilt UniversityNashville TN37232 USA
| | - Jeremiah Yahn
- Department of ZoologyUniversity of Wisconsin – MadisonMadison WI53706 USA
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197
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Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Rep 2016; 14:2142-2153. [PMID: 26923597 DOI: 10.1016/j.celrep.2016.02.013] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 12/07/2015] [Accepted: 01/28/2016] [Indexed: 12/20/2022] Open
Abstract
To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.
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Affiliation(s)
- Andres Gomez
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno 603 65, Czech Republic; Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Liberec Zoo, Liberec 460 01, Czech Republic
| | - Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Klara Vlckova
- Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - David Modry
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic; CEITEC, Central European Institute for Technology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - Angelique Todd
- Dzanga-Sangha Protected Areas, World Wildlife Fund, Bayanga, Central African Republic
| | | | - Melissa J Remis
- Department of Anthropology, Purdue University, West Lafayette, IN 47907, USA
| | | | - Elise Morton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Juan D Umaña
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AK 72704, USA
| | - H Rex Gaskins
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Brenda A Wilson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rebecca M Stumpf
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bryan A White
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steven R Leigh
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Colorado, Boulder, CO 80309, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
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198
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Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H. Social behavior shapes the chimpanzee pan-microbiome. SCIENCE ADVANCES 2016; 2:e1500997. [PMID: 26824072 PMCID: PMC4730854 DOI: 10.1126/sciadv.1500997] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/19/2015] [Indexed: 05/21/2023]
Abstract
Animal sociality facilitates the transmission of pathogenic microorganisms among hosts, but the extent to which sociality enables animals' beneficial microbial associations is poorly understood. The question is critical because microbial communities, particularly those in the gut, are key regulators of host health. We show evidence that chimpanzee social interactions propagate microbial diversity in the gut microbiome both within and between host generations. Frequent social interaction promotes species richness within individual microbiomes as well as homogeneity among the gut community memberships of different chimpanzees. Sampling successive generations across multiple chimpanzee families suggests that infants inherited gut microorganisms primarily through social transmission. These results indicate that social behavior generates a pan-microbiome, preserving microbial diversity across evolutionary time scales and contributing to the evolution of host species-specific gut microbial communities.
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Affiliation(s)
- Andrew H. Moeller
- Department of Integrative Biology, University of California, Berkeley, 1005 Valley Life Sciences Building #3101, Berkeley, CA 94720, USA
| | - Steffen Foerster
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Building, Durham, NC 27708, USA
| | - Michael L. Wilson
- Department of Anthropology, University of Minnesota, 301 19th Avenue South, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108 USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Building, Durham, NC 27708, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, Philadelphia, PA 19104, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, 2506 Speedway A5000, Austin, TX 78712, USA
- Corresponding author. E-mail:
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199
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Miller WB. The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life. Front Pediatr 2016; 4:96. [PMID: 27668211 PMCID: PMC5016513 DOI: 10.3389/fped.2016.00096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022] Open
Abstract
All eukaryotic organisms are holobionts representing complex collaborations between the entire microbiome of each eukaryote and its innate cells. These linked constituencies form complex localized and interlocking ecologies in which the specific microbial constituents and their relative abundance differ substantially according to age and environmental exposures. Rapid advances in microbiology and genetic research techniques have uncovered a significant previous underestimate of the extent of that microbial contribution and its metabolic and developmental impact on holobionts. Therefore, a re-calibration of the neonatal period is suggested as a transitional phase in development that includes the acquisition of consequential collaborative microbial life from extensive environmental influences. These co-dependent, symbiotic relationships formed in the fetal and neonatal stages extend into adulthood and even across generations.
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Affiliation(s)
- William B Miller
- Independent Researcher, Previously affiliated with Pinnacle Health , Harrisburg, PA , USA
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200
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Malhi RS, Bader AC. ENGAGING NATIVE AMERICANS IN GENOMICS RESEARCH. AMERICAN ANTHROPOLOGIST 2015; 117:743-744. [PMID: 27799658 DOI: 10.1111/aman.12369] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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