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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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2
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Guerra A. Human associated Archaea: a neglected microbiome worth investigating. World J Microbiol Biotechnol 2024; 40:60. [PMID: 38172371 DOI: 10.1007/s11274-023-03842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.
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3
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Daybog I, Kolodny O. A computational framework for resolving the microbiome diversity conundrum. Nat Commun 2023; 14:7977. [PMID: 38042865 PMCID: PMC10693575 DOI: 10.1038/s41467-023-42768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 10/20/2023] [Indexed: 12/04/2023] Open
Abstract
Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
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Affiliation(s)
- Itay Daybog
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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4
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Handsley-Davis M, Anderson MZ, Bader AC, Ehau-Taumaunu H, Fox K, Kowal E, Weyrich LS. Microbiome ownership for Indigenous peoples. Nat Microbiol 2023; 8:1777-1786. [PMID: 37770744 DOI: 10.1038/s41564-023-01470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.
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Affiliation(s)
- Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada
| | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, PA, USA
| | - Keolu Fox
- Department of Anthropology, Global Health Program, and Indigenous Futures Institute, University of California, San Diego, CA, USA
| | - Emma Kowal
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Melbourne, Victoria, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
- Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, USA.
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5
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Vaill M, Kawanishi K, Varki N, Gagneux P, Varki A. Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes. Physiol Rev 2023; 103:2171-2229. [PMID: 36603157 PMCID: PMC10151058 DOI: 10.1152/physrev.00040.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.
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Affiliation(s)
- Michael Vaill
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Kunio Kawanishi
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nissi Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Pascal Gagneux
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Ajit Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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6
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Quan Y, Zhang KX, Zhang HY. The gut microbiota links disease to human genome evolution. Trends Genet 2023; 39:451-461. [PMID: 36872184 DOI: 10.1016/j.tig.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 03/06/2023]
Abstract
A large number of studies have established a causal relationship between the gut microbiota and human disease. In addition, the composition of the microbiota is substantially influenced by the human genome. Modern medical research has confirmed that the pathogenesis of various diseases is closely related to evolutionary events in the human genome. Specific regions of the human genome known as human accelerated regions (HARs) have evolved rapidly over several million years since humans diverged from a common ancestor with chimpanzees, and HARs have been found to be involved in some human-specific diseases. Furthermore, the HAR-regulated gut microbiota has undergone rapid changes during human evolution. We propose that the gut microbiota may serve as an important mediator linking diseases to human genome evolution.
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Affiliation(s)
- Yuan Quan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ke-Xin Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hong-Yu Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
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7
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Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar. Sci Rep 2022; 12:22388. [PMID: 36575246 PMCID: PMC9794702 DOI: 10.1038/s41598-022-26861-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Microbial rewilding, whereby exposure to naturalistic environments can modulate or augment gut microbiomes and improve host-microbe symbiosis, is being harnessed as an innovative approach to human health, one that may also have significant value to animal care and conservation. To test for microbial rewilding in animal microbiomes, we used a unique population of wild-born ring-tailed lemurs (Lemur catta) that were initially held as illegal pets in unnatural settings and, subsequently, relocated to a rescue center in Madagascar where they live in naturalistic environments. Using amplicon and shotgun metagenomic sequencing of lemur and environmental microbiomes, we found multiple lines of evidence for microbial rewilding in lemurs that were transitioned from unnatural to naturalistic environments: A lemur's duration of exposure to naturalistic settings significantly correlated with (a) increased compositional similarly to the gut communities of wild lemurs, (b) decreased proportions of antibiotic resistance genes that were likely acquired via human contact during pethood, and (c) greater covariation with soil microbiomes from natural habitats. Beyond the inherent psychosocial value of naturalistic environments, we find that actions, such as providing appropriate diets, minimizing contact with humans, and increasing exposure to natural environmental consortia, may assist in maximizing host-microbe symbiosis in animals under human care.
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8
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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9
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Moraitou M, Forsythe A, Fellows Yates JA, Brealey JC, Warinner C, Guschanski K. Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species. Mol Biol Evol 2022; 39:6874787. [PMID: 36472532 PMCID: PMC9778846 DOI: 10.1093/molbev/msac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.
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Affiliation(s)
| | | | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany,Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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10
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Qi W, Liu J, Yu T, Huang S, Song R, Qiao Z. Ae1/Sbe1 maize-derived high amylose improves gut barrier function and ameliorates type II diabetes in high-fat diet-fed mice by increasing Akkermansia. Front Nutr 2022; 9:999020. [PMID: 36245499 PMCID: PMC9556726 DOI: 10.3389/fnut.2022.999020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2022] [Indexed: 01/10/2023] Open
Abstract
Type II diabetes mellitus (T2DM) has its origins in chronic inflammation due to immune dysregulation. Improving chronic inflammation can significantly reduce the probability of T2DM and the rate of disease progression. Resistance to starch 2 (RSII) high-amylose maize starch (HAMS) has been widely implicated in the improvement and regulation of T2DM. However, its exact molecular mechanisms have not been fully discovered. Here, we used CRISPR/Cas9 technology to knock out two starch-branching enzyme genes, Ae1 and Sbe1, in maize to obtain mutants containing higher levels of HAMS. In experiments in which HAMS was fed to mice on a high-fat diet (HFD), we confirmed the function of HAMS in ameliorating hyperglycemia. Mechanistically, we found that HAMS improves the gut barrier function by increasing the Akkermansia abundance in the gut. This increase led to the alleviation of chronic inflammation in mice on a HFD, resulting in improved insulin sensitivity and a decrease in blood glucose.
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Affiliation(s)
- Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jingchao Liu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Tante Yu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shengchan Huang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhenyi Qiao
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, China
- *Correspondence: Zhenyi Qiao
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11
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Comparison of Changes in Gut Microbiota in Wild Boars and Domestic Pigs Using 16S rRNA Gene and Metagenomics Sequencing Technologies. Animals (Basel) 2022; 12:ani12172270. [PMID: 36077990 PMCID: PMC9454828 DOI: 10.3390/ani12172270] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The microbiota co-evolves with the host and plays an important role in the host's health, immunity, and nutrient absorption. Wild boars are the ancestors of domestic pigs. During the long evolutionary process, the physiological structure and living habits of modern pigs have undergone tremendous changes. However, there are few studies on the evolution of gut microbiota of wild boars and domestic pigs. In this study, by comparing the changes in the composition and function of the gut microbiota of wild boars and domestic pigs, it was found that there were significant differences between the two groups, which indicated that the gut microbiota had changed during the evolution process. This study provides some data references for the evolution of gut microbiota. Abstract Gut microbiota diversity is a result of co-evolution between microorganisms and their hosts. However, there are few studies on the evolution of the gut microbiota of wild boars and domestic pigs. Therefore, this study aimed to analyze the composition and function of the gut microbiota of wild boars and domestic pigs using 16S rRNA gene V3-V4 region sequencing, 16S rRNA gene full-length sequencing, and metagenomic sequencing. This study showed that after a long evolution, as compared to wild boars, the domestic pigs exhibited significantly increased relative abundances of Lactobacillus, Lactobacillus reuteri, Lactobacillus johnsonii, Lactobacillus sp.DJF_WC5, and Lactobacillus; s_uncultured bacterium, while the relative abundances of Bifidobacterium and Methanococcaceae decreased significantly. In addition, the relative abundances of “carbohydrate metabolism”, “starch and sucrose metabolism”, “valine, leucine, and isoleucine biosynthesis”, “lysine biosynthesis”, and starch-degrading CAZymes were significantly increased in the domestic pigs, while the relative abundances of “environmental adaptation”, “immune system”, “fatty acid degradation and synthesis”, and cellulose-hemicellulose-degrading CAZymes were significantly increased in the wild boars. Finally, the diversity of ARGs and the “antimicrobial resistance genes” in domestic pigs also increased significantly. This study illustrates that the gut microbiota composition and function of wild boars and domestic pigs changed during the long evolution process. These findings provide a basic research theory for the evolution of gut microbiota and the treatment of health and disease.
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Yang L, Wang W, Wronski T, Sun P, Jin K, Tang W. Community structure and environmental determinants of the bacterial and fungal gut microflora in Hainan gibbons (Nomascus hainanus). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Abstract
Given the worldwide epidemic of diet-related chronic diseases, evidence-based dietary recommendations are fundamentally important for health promotion. Despite the importance of the human gut microbiota for the physiological effects of diet and chronic disease etiology, national dietary guidelines around the world are just beginning to capitalize on scientific breakthroughs in the microbiome field. In this review, we discuss contemporary nutritional recommendations from a microbiome science perspective, focusing on mechanistic evidence that established host-microbe interactions as mediators of the physiological effects of diet. We apply this knowledge to inform discussions of nutrition controversies, advance innovative dietary strategies, and propose an experimental framework that integrates the microbiome into nutrition research. The congruence of key paradigms in the nutrition and microbiome disciplines validates current recommendations in dietary guidelines, and the systematic incorporation of microbiome science into nutrition research has the potential to further improve and innovate healthy eating.
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14
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Aximujiang K, Kaheman K, Wushouer X, Wu G, Ahemaiti A, Yunusi K. Lactobacillus acidophilus and HKL Suspension Alleviates Ulcerative Colitis in Rats by Regulating Gut Microbiota, Suppressing TLR9, and Promoting Metabolism. Front Pharmacol 2022; 13:859628. [PMID: 35600873 PMCID: PMC9118348 DOI: 10.3389/fphar.2022.859628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic non-specific inflammatory bowel disease with complex pathogenesis. The intestinal flora disturbance affects the homeostasis of the intestinal environment, leading to metabolic imbalance and immune abnormalities of the host, contributing to the perpetuation of intestinal inflammation. We suggest that the combination of anti-inflammatory therapy and the regulation of intestinal flora balance may help in the treatment process. Previously, we used a combination treatment consisting of Lactobacillus acidophilus (Lac) and Chinese medicine Huan Kui Le (HKL) suspension in a UC rat model, where the combined intervention was more effective than either treatment alone. Herein, the mechanism of action of this combined treatment has been investigated using 16S rRNA sequencing, immunohistochemistry, and ELISA methods in the colon, and untargeted metabolomics profiling in serum. Colon protein expression levels of IL-13 and TGF-β were upregulated, whereas those of TLR9 and TLR4 were downregulated, consistent with an anti-inflammatory effect. In addition, gut microbiota structure changed, shown by a decrease in opportunistic pathogens correlated with intestinal inflammation, such as Klebsiella and Escherichia-Shigella, and an increase in beneficial bacteria such as Bifidobacterium. The latter correlated positively with IL-13 and TGF-β and negatively with IFN-γ. Finally, this treatment alleviated the disruption of the metabolic profile observed in UC rats by increasing short-chain fatty acid (SCFA)–producing bacteria in the colonic epithelium. This combination treatment also affected the metabolism of lactic acid, creatine, and glycine and inhibited the growth of Klebsiella. Overall, we suggest that treatment combining probiotics and traditional Chinese medicine is a novel strategy beneficial in UC that acts by modulating gut microbiota and its metabolites, TLR9, and cytokines in different pathways.
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Affiliation(s)
- Kasimujiang Aximujiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- College of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Kuerbannaimu Kaheman
- Department of Rehabilitation Medicine, First Affiliated Hospital in Xinjiang Medical University, Urumqi, China
| | - Xilinguli Wushouer
- Department of Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Guixia Wu
- Department of Physiology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Abulaiti Ahemaiti
- The Functional Center, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Kurexi Yunusi
- Uygur Medical College, Xinjiang Medical University, Urumqi, China
- *Correspondence: Kurexi Yunusi,
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15
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Bornbusch SL, Greene LK, Rahobilalaina S, Calkins S, Rothman RS, Clarke TA, LaFleur M, Drea CM. Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota. Anim Microbiome 2022; 4:29. [PMID: 35484581 PMCID: PMC9052671 DOI: 10.1186/s42523-022-00176-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 03/29/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Inter-population variation in host-associated microbiota reflects differences in the hosts' environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured in these comparisons. Moreover, intraspecific variation in gut microbiota, generally attributed to diet, may also stem from differential acquisition of environmental microbes-an understudied mechanism by which host microbiomes are directly shaped by environmental microbes. To more comprehensively characterize gut microbiota in an ecologically flexible host, the ring-tailed lemur (Lemur catta; n = 209), while also investigating the role of environmental acquisition, we used 16S rRNA sequencing of lemur gut and soil microbiota sampled from up to 13 settings, eight in the wilderness of Madagascar and five in captivity in Madagascar or the U.S. Based on matched fecal and soil samples, we used microbial source tracking to examine covariation between the two types of consortia. RESULTS The diversity of lemur gut microbes varied markedly within and between settings. Microbial diversity was not consistently greater in wild than in captive lemurs, indicating that this metric is not necessarily an indicator of host habitat or environmental condition. Variation in microbial composition was inconsistent both with a single, representative gut community for wild conspecifics and with a universal 'signal of captivity' that homogenizes the gut consortia of captive animals. Despite the similar, commercial diets of captive lemurs on both continents, lemur gut microbiomes within Madagascar were compositionally most similar, suggesting that non-dietary factors govern some of the variability. In particular, soil microbial communities varied across geographic locations, with the few samples from different continents being the most distinct, and there was significant and context-specific covariation between gut and soil microbiota. CONCLUSIONS As one of the broadest, single-species investigations of primate microbiota, our study highlights that gut consortia are sensitive to multiple scales of environmental differences. This finding begs a reevaluation of the simple 'captive vs. wild' dichotomy. Beyond the important implications for animal care, health, and conservation, our finding that environmental acquisition may mediate aspects of host-associated consortia further expands the framework for how host-associated and environmental microbes interact across different microbial landscapes.
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Affiliation(s)
- Sally L. Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, NC USA
| | | | | | - Samantha Calkins
- Department of Psychology, Program in Animal Behavior and Conservation, Hunter College, New York, NY USA
| | - Ryan S. Rothman
- Institute for the Conservation of Tropical Environments, Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY USA
| | - Tara A. Clarke
- Department of Sociology and Anthropology, North Carolina State University, Raleigh, NC USA
| | - Marni LaFleur
- Department of Anthropology, University of San Diego, 5998 Alcala Park, San Diego, CA USA
| | - Christine M. Drea
- Department of Evolutionary Anthropology, Duke University, Durham, NC USA
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16
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Yuan L, Zhang X, Luo B, Li X, Tian F, Yan W, Ni Y. Ethnic Specificity of Species and Strain Composition of Lactobacillus Populations From Mother–Infant Pairs, Uncovered by Multilocus Sequence Typing. Front Microbiol 2022; 13:814284. [PMID: 35387090 PMCID: PMC8979337 DOI: 10.3389/fmicb.2022.814284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
The maternal gut is thought to be the principal source of potential probiotic bacteria in the infant gut during the lactation stage. It is not clear whether facultative symbiont lactobacilli strictly follow vertical transmission from mother to infant and display the ethnic specificity in terms of species and strain composition in mother–infant cohorts. In the present study, a total of 16 former Lactobacillus species (365 strains) and 11 species (280 strains) were retrieved from 31 healthy mother–infant pairs of two ethnic groups, which have never intermarried, respectively. The result showed that the composition and number of Lactobacillus species between the two ethnic groups varied. Among 106 Lacticaseibacillus paracasei strains isolated, 64 representative strains were classified into 27 sequence types (ST) by means of multilocus sequence typing (MLST), of which 20 STs derived from 33 Uighur strains and 7 STs from 31 Li strains, and no homologous recombination event of genes was detected between strains of different ethnic groups. A go-EBURST analysis revealed that except for a few mother–infant pairs in which more than one STs were detected, L. paracasei isolates from the same mother–infant pair were found to be monophyletic in most cases, confirming vertical transfer of Lactobacillus at the strain level. More notably, L. paracasei isolates from the same ethnic group were more likely than strains from another to be incorporated into a specific phylogenetic clade or clonal complex (CC) with similar metabolic profile of glycan, supporting the hypothesis of ethnic specificity to a large degree. Our study provides evidence for the development of personalized probiotic tailored to very homogenous localized populations from the perspective of maternal and child health.
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Affiliation(s)
- Lixia Yuan
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Xueling Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Baolong Luo
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Xu Li
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Fengwei Tian
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Yan
- School of Food Science and Technology, Shihezi University, Shihezi, China
- *Correspondence: Wenli Yan,
| | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi, China
- Yongqing Ni,
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17
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Rosenberg E, Zilber-Rosenberg I. Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations. Microorganisms 2021; 10:microorganisms10010070. [PMID: 35056519 PMCID: PMC8780831 DOI: 10.3390/microorganisms10010070] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.
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18
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Muehlbauer AL, Richards AL, Alazizi A, Burns MB, Gomez A, Clayton JB, Petrzelkova K, Cascardo C, Resztak J, Wen X, Pique-Regi R, Luca F, Blekhman R. Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Rep 2021; 37:110057. [PMID: 34818542 PMCID: PMC8647622 DOI: 10.1016/j.celrep.2021.110057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/22/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology across species and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterize the transcriptional response of human colonic epithelial cells in vitro to live microbial communities extracted from humans, chimpanzees, gorillas, and orangutans. We find that most host genes exhibit a conserved response, whereby they respond similarly to the four hominid microbiomes. However, hundreds of host genes exhibit a divergent response, whereby they respond only to microbiomes from specific host species. Such genes are associated with intestinal diseases in humans, including inflammatory bowel disease and Crohn’s disease. Last, we find that inflammation-associated microbial species regulate the expression of host genes previously associated with inflammatory bowel disease, suggesting health-related consequences for species-specific host-microbiome interactions across hominids. Muehlbauer et al. investigate how variation between different hominid microbiomes drives host gene expression in colonic epithelial cell cultures. They find that host genes that respond only to microbiomes from a specific hominid species are linked to gastrointestinal diseases, suggesting implications for understanding how the microbiome can impact human health.
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Affiliation(s)
- Amanda L Muehlbauer
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Michael B Burns
- Department of Biology, Loyola University, Chicago, IL 60660, USA
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, Saint Paul, MN, USA
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NB, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NB, USA
| | - Klara Petrzelkova
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic; Liberec Zoo, Liberec, Czech Republic; The Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic
| | - Camilla Cascardo
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Justyna Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA.
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19
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Sawaswong V, Praianantathavorn K, Chanchaem P, Khamwut A, Kemthong T, Hamada Y, Malaivijitnond S, Payungporn S. Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand. Sci Rep 2021; 11:14280. [PMID: 34253790 PMCID: PMC8275770 DOI: 10.1038/s41598-021-93779-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Long-tailed macaques (Macaca fascicularis), distributed in Southeast Asia, are generally used in biomedical research. At present, the expansion of human communities overlapping of macaques’ natural habitat causes human-macaque conflicts. To mitigate this problem in Thailand, the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), was granted the permit to catch the surplus wild-born macaques and transfer them to the center. Based on the fact that the diets provided and the captive environments were different, their oral-gut microbiota should be altered. Thus, we investigated and compared the oral and fecal microbiome between wild-born macaques that lived in the natural habitats and those transferred to and reared in the NPRCT-CU for 1 year. The results from 16S rRNA high-throughput sequencing showed that the captive macaques had distinct oral-gut microbiota profiles and lower bacterial richness compared to those in wild macaques. The gut of wild macaques was dominated by Firmicutes which is probably associated with lipid absorption and storage. These results implicated the effects of captivity conditions on the microbiome that might contribute to crucial metabolic functions. Our study should be applied to the animal health care program, with respect to microbial functions, for non-human primates.
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Affiliation(s)
- Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.,Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ariya Khamwut
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand. .,Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand. .,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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20
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Abstract
Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.
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21
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Zilber-Rosenberg I, Rosenberg E. Microbial driven genetic variation in holobionts. FEMS Microbiol Rev 2021; 45:6261188. [PMID: 33930136 DOI: 10.1093/femsre/fuab022] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.
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Affiliation(s)
- Ilana Zilber-Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
| | - Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
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22
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Zlatkov N, Nadeem A, Uhlin BE, Wai SN. Eco-evolutionary feedbacks mediated by bacterial membrane vesicles. FEMS Microbiol Rev 2021; 45:fuaa047. [PMID: 32926132 PMCID: PMC7968517 DOI: 10.1093/femsre/fuaa047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial membrane vesicles (BMVs) are spherical extracellular organelles whose cargo is enclosed by a biological membrane. The cargo can be delivered to distant parts of a given habitat in a protected and concentrated manner. This review presents current knowledge about BMVs in the context of bacterial eco-evolutionary dynamics among different environments and hosts. BMVs may play an important role in establishing and stabilizing bacterial communities in such environments; for example, bacterial populations may benefit from BMVs to delay the negative effect of certain evolutionary trade-offs that can result in deleterious phenotypes. BMVs can also perform ecosystem engineering by serving as detergents, mediators in biochemical cycles, components of different biofilms, substrates for cross-feeding, defense systems against different dangers and enzyme-delivery mechanisms that can change substrate availability. BMVs further contribute to bacteria as mediators in different interactions, with either other bacterial species or their hosts. In short, BMVs extend and deliver phenotypic traits that can have ecological and evolutionary value to both their producers and the ecosystem as a whole.
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Affiliation(s)
- Nikola Zlatkov
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Aftab Nadeem
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
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23
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Rampelli S, Turroni S, Mallol C, Hernandez C, Galván B, Sistiaga A, Biagi E, Astolfi A, Brigidi P, Benazzi S, Lewis CM, Warinner C, Hofman CA, Schnorr SL, Candela M. Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Commun Biol 2021; 4:169. [PMID: 33547403 PMCID: PMC7864912 DOI: 10.1038/s42003-021-01689-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Carolina Mallol
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain.,Archaeological Micromorphology and Biomarker Research Lab, University of La Laguna, Avenida Astrofísico Francisco Sánchez 2, La Laguna, Tenerife, Spain.,ICArEHB - Interdisciplinary Center for Archaeology and the Evolution of Human Behaviour, Universidade do Algarve, Campus de Gambelas, Edificio 1, Faro, Portugal
| | - Cristo Hernandez
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain
| | - Bertila Galván
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain
| | - Ainara Sistiaga
- Earth, Atmospheric and Planetary Sciences Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, USA.,GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Oester Voldgade 5-7, Copenhagen, Denmark
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Annalisa Astolfi
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Via Massarenti 11, Bologna, Italy.,Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Via Fossato di Mortara 70, Ferrara, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, Bologna, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, Ravenna, Italy.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, Jena, Germany
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Martinstraße 12, Klosterneuburg, Austria. .,Department of Anthropology, University of Nevada, 4505S. Maryland Pkwy, Las Vegas, NV, USA.
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy.
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24
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Non-oral Prevotella stepping into the spotlight. Anaerobe 2021; 68:102321. [PMID: 33482304 DOI: 10.1016/j.anaerobe.2021.102321] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023]
Abstract
Species now affiliated to genus Prevotella have been known for decades as an integral part of human oral cavity microbiota. They were frequently isolated from patients with periodontitis or from dental root canals but also from healthy subjects. With the exception of Prevotella intermedia, they were considered opportunistic pathogens, as they were isolated also from various bacterial abscesses from the head, neck, breast, skin and various other body sites. Consequently, Prevotella were not in the focus of research activities. On the other hand, the four species found in the rumen never caused any disease and seemed early on to be numerous and important part of the rumen ecosystem indicating this genus harbored bacteria with enormously diverse habitats and lifestyles. The purpose of this review is to illustrate the main research themes performed in Prevotella on a path from less noted oral bacteria and from hard to cultivate and study rumen organisms to important mutualistic bacteria in guts of various mammals warranting major research efforts.
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25
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Conner WR, Delaney EK, Bronski MJ, Ginsberg PS, Wheeler TB, Richardson KM, Peckenpaugh B, Kim KJ, Watada M, Hoffmann AA, Eisen MB, Kopp A, Cooper BS, Turelli M. A phylogeny for the Drosophila montium species group: A model clade for comparative analyses. Mol Phylogenet Evol 2020; 158:107061. [PMID: 33387647 DOI: 10.1016/j.ympev.2020.107061] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/22/2022]
Abstract
The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution - even when complete genome sequences are available - as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.
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Affiliation(s)
- William R Conner
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA(1)
| | - Emily K Delaney
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Michael J Bronski
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Paul S Ginsberg
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA(1)
| | - Timothy B Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA(1)
| | - Kelly M Richardson
- Bio21 Institute, School of BioScience, University of Melbourne, Victoria 3010, Australia
| | - Brooke Peckenpaugh
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA; Department of Biology, Indiana University, Bloomington, IN 47405, USA(1)
| | - Kevin J Kim
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Ary A Hoffmann
- Bio21 Institute, School of BioScience, University of Melbourne, Victoria 3010, Australia
| | - Michael B Eisen
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA(1)
| | - Michael Turelli
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
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26
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A glance at the gut microbiota of five experimental animal species through fecal samples. Sci Rep 2020; 10:16628. [PMID: 33024229 PMCID: PMC7538948 DOI: 10.1038/s41598-020-73985-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Experimental animals including the ferret, marmoset, woodchuck, mini pig, and tree shrew have been used in biomedical research. However, their gut microbiota have not been fully investigated. In this study, the gut microbiota of these five experimental animals were analyzed with 16S rRNA sequencing. The phyla Firmicutes, Bacteroidetes, and Fusobacteria were present in the gut microbiota of all the species. Specific phyla were present in different animals: Proteobacteria in the ferret, Tenericutes in the marmoset, and Spirochaetes in the mini pig. Fusobacterium and unidentified Clostridiales were the dominant genera in the ferret, whereas Libanicoccus, Lactobacillus, Porphyromonas, and Peptoclostridium were specific to marmoset, mini pig, woodchuck, and tree shrew, respectively. A clustering analysis showed that the overall distribution of microbial species in the guts of these species mirrored their mammalian phylogeny, and the microbiota of the marmoset and tree shrew showed the closest bray_curtis distances to that of humans. PICRUSt functional prediction separated the woodchuck from the other species, which may reflect its herbivorous diet. In conclusion, both the evolutionary phylogeny and daily diet affect the gut microbiota of these experimental animals, which should not be neglected for their usage in biomedical research.
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27
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Sarkar A, Harty S, Johnson KVA, Moeller AH, Carmody RN, Lehto SM, Erdman SE, Dunbar RIM, Burnet PWJ. The role of the microbiome in the neurobiology of social behaviour. Biol Rev Camb Philos Soc 2020; 95:1131-1166. [PMID: 32383208 PMCID: PMC10040264 DOI: 10.1111/brv.12603] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
Microbes colonise all multicellular life, and the gut microbiome has been shown to influence a range of host physiological and behavioural phenotypes. One of the most intriguing and least understood of these influences lies in the domain of the microbiome's interactions with host social behaviour, with new evidence revealing that the gut microbiome makes important contributions to animal sociality. However, little is known about the biological processes through which the microbiome might influence host social behaviour. Here, we synthesise evidence of the gut microbiome's interactions with various aspects of host sociality, including sociability, social cognition, social stress, and autism. We discuss evidence of microbial associations with the most likely physiological mediators of animal social interaction. These include the structure and function of regions of the 'social' brain (the amygdala, the prefrontal cortex, and the hippocampus) and the regulation of 'social' signalling molecules (glucocorticoids including corticosterone and cortisol, sex hormones including testosterone, oestrogens, and progestogens, neuropeptide hormones such as oxytocin and arginine vasopressin, and monoamine neurotransmitters such as serotonin and dopamine). We also discuss microbiome-associated host genetic and epigenetic processes relevant to social behaviour. We then review research on microbial interactions with olfaction in insects and mammals, which contribute to social signalling and communication. Following these discussions, we examine evidence of microbial associations with emotion and social behaviour in humans, focussing on psychobiotic studies, microbe-depression correlations, early human development, autism, and issues of statistical power, replication, and causality. We analyse how the putative physiological mediators of the microbiome-sociality connection may be investigated, and discuss issues relating to the interpretation of results. We also suggest that other candidate molecules should be studied, insofar as they exert effects on social behaviour and are known to interact with the microbiome. Finally, we consider different models of the sequence of microbial effects on host physiological development, and how these may contribute to host social behaviour.
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Affiliation(s)
- Amar Sarkar
- Trinity College, Trinity Street, University of Cambridge, Cambridge, CB2 1TQ, U.K.,Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, Fitzwilliam Street, University of Cambridge, Cambridge, CB2 1QH, U.K
| | - Siobhán Harty
- Institute of Neuroscience, Trinity College Dublin, Dublin 2, Dublin, Ireland.,School of Psychology, Trinity College Dublin, Dublin 2, Dublin, Ireland
| | - Katerina V-A Johnson
- Department of Experimental Psychology, Radcliffe Observatory Quarter, University of Oxford, Oxford, OX2 6GG, U.K.,Pembroke College, University of Oxford, Oxford, OX1 1DW, U.K.,Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, OX3 7JX, U.K
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Corson Hall, Tower Road, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Peabody Museum, 11 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Soili M Lehto
- Psychiatry, University of Helsinki and Helsinki University Hospital, PL 590, FI-00029, Helsinki, Finland.,Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, P.O. Box 6, FI-00014, Helsinki, Finland.,Institute of Clinical Medicine/Psychiatry, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Susan E Erdman
- Division of Comparative Medicine, Massachusetts Institute of Technology, Building 16-825, 77 Massachusetts Avenue, Cambridge, MA, 02139, U.S.A
| | - Robin I M Dunbar
- Department of Experimental Psychology, Radcliffe Observatory Quarter, University of Oxford, Oxford, OX2 6GG, U.K
| | - Philip W J Burnet
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, OX3 7JX, U.K
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28
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Abstract
Metagenomic sequencing of the gut microbial communities of two closely related bee species, the Western honey bee (Apis mellifera) and the Eastern honey bee (Apis cerana), show that organisms with similar characteristics can harbor unexpected differences in their microbiomes.
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Affiliation(s)
- Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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29
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Walter J, Armet AM, Finlay BB, Shanahan F. Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents. Cell 2020; 180:221-232. [PMID: 31978342 DOI: 10.1016/j.cell.2019.12.025] [Citation(s) in RCA: 278] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/31/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023]
Abstract
Human diseases are increasingly linked with an altered or "dysbiotic" gut microbiota, but whether such changes are causal, consequential, or bystanders to disease is, for the most part, unresolved. Human microbiota-associated (HMA) rodents have become a cornerstone of microbiome science for addressing causal relationships between altered microbiomes and host pathology. In a systematic review, we found that 95% of published studies (36/38) on HMA rodents reported a transfer of pathological phenotypes to recipient animals, and many extrapolated the findings to make causal inferences to human diseases. We posit that this exceedingly high rate of inter-species transferable pathologies is implausible and overstates the role of the gut microbiome in human disease. We advocate for a more rigorous and critical approach for inferring causality to avoid false concepts and prevent unrealistic expectations that may undermine the credibility of microbiome science and delay its translation.
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Affiliation(s)
- Jens Walter
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Medicine and APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland; School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
| | - Anissa M Armet
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Fergus Shanahan
- Department of Medicine and APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
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30
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Campbell TP, Sun X, Patel VH, Sanz C, Morgan D, Dantas G. The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography. ISME JOURNAL 2020; 14:1584-1599. [PMID: 32203121 DOI: 10.1038/s41396-020-0634-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/25/2022]
Abstract
The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.
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Affiliation(s)
- Tayte P Campbell
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Vishal H Patel
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Crickette Sanz
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Congo Program, Wildlife Conservation Society, Brazzaville, Republic of Congo
| | - David Morgan
- Lincoln Park Zoo, Lester E. Fisher Center, Chicago, IL, 60614, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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31
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Alam MT, Amos GCA, Murphy ARJ, Murch S, Wellington EMH, Arasaradnam RP. Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut Pathog 2020; 12:1. [PMID: 31911822 PMCID: PMC6942256 DOI: 10.1186/s13099-019-0341-6] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute > 98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of > 22,000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database (Mitchell et al. in Nucleic Acids Res 46:D726–D735, 2018). By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD.
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Affiliation(s)
| | - Gregory C A Amos
- 2School of Life Sciences, University of Warwick, Coventry, UK.,6Present Address: G.C.A.A National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK
| | | | - Simon Murch
- 1Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Ramesh P Arasaradnam
- 1Warwick Medical School, University of Warwick, Coventry, UK.,3Department of Gastroenterology, University Hospitals Coventry & Warwickshire NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX UK.,4School of Life Sciences, University of Coventry, Coventry, UK.,5Faculty of Life Science, University of Leicester, Leicester, UK
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32
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Manara S, Asnicar F, Beghini F, Bazzani D, Cumbo F, Zolfo M, Nigro E, Karcher N, Manghi P, Metzger MI, Pasolli E, Segata N. Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species. Genome Biol 2019; 20:299. [PMID: 31883524 PMCID: PMC6935492 DOI: 10.1186/s13059-019-1923-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches. RESULTS We reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories. CONCLUSIONS The newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.
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Affiliation(s)
- Serena Manara
- CIBIO Department, University of Trento, Trento, Italy
| | | | | | | | - Fabio Cumbo
- CIBIO Department, University of Trento, Trento, Italy
| | - Moreno Zolfo
- CIBIO Department, University of Trento, Trento, Italy
| | | | | | - Paolo Manghi
- CIBIO Department, University of Trento, Trento, Italy
| | | | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy.
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33
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Jeyakumar T, Beauchemin N, Gros P. Impact of the Microbiome on the Human Genome. Trends Parasitol 2019; 35:809-821. [PMID: 31451407 DOI: 10.1016/j.pt.2019.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/30/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023]
Abstract
Humans live in a microbial world that includes pathogenic bacteria, viruses, and fungi that cause lethal infections. In addition, a large number of microbial communities inhabit mucosal surfaces where they provide key metabolic activities, facilitating adaptation to changing environments. New genome technologies enable both sequencing of the human genome and sequence-based cataloging of microbial communities inhabiting human mucosal surfaces. These have revealed intricate two-way relationships between the microbiome and the genome, including strong effects of human genotypes on the composition and activity of the microbiome. Likewise, the microbiome plays an important role in training and regulating the immune system, and acts to modify expression of human genetic risk for debilitating chronic inflammatory and immune conditions. These studies are suggesting a new role of the microbiome in human health and disease.
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Affiliation(s)
- Thiviya Jeyakumar
- Department of Biochemistry, McGill University, Montreal, Canada; McGill Center for the Study of Complex Traits, McGill University, Montreal, Canada
| | - Nicole Beauchemin
- Department of Biochemistry, McGill University, Montreal, Canada; Goodman Cancer Research Center, McGill University, Montreal, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, Canada; McGill Center for the Study of Complex Traits, McGill University, Montreal, Canada; Goodman Cancer Research Center, McGill University, Montreal, Canada.
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34
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Renelies-Hamilton J, Noguera-Julian M, Parera M, Paredes R, Pacheco L, Dacal E, Saugar JM, Rubio JM, Poulsen M, Köster PC, Carmena D. Exploring interactions between Blastocystis sp., Strongyloides spp. and the gut microbiomes of wild chimpanzees in Senegal. INFECTION GENETICS AND EVOLUTION 2019; 74:104010. [PMID: 31442596 DOI: 10.1016/j.meegid.2019.104010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/02/2019] [Accepted: 08/18/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Gut parasites exert an important influence on the gut microbiome, with many studies focusing on the human gut microbiome. It has, however, undergone severe richness depletion. Hygienic lifestyle, antimicrobial treatments and altered gut homeostasis (e.g., chronic inflammation) reduce gut microbiome richness and also parasite prevalence; which may confound results. Studying species closely related to humans could help overcome this problem by providing insights into the ancestral relationship between humans, their gut microbiome and their gut parasites. Chimpanzees are a particularly promising model as they have similar gut microbiomes to humans and many parasites infect both species. AIMS We study the interaction between gut microbiome and enteric parasites in chimpanzees. Investigating what novel insights a closely related species can reveal when compared to studies on humans. METHODS Using eighty-seven faecal samples from wild western chimpanzees (Pan troglodytes verus) in Senegal, we combine 16S rRNA gene amplicon sequencing for gut microbiome characterization with PCR detection of parasite taxa (Blastocystis sp., Strongyloides spp., Giardia duodenalis, Cryptosporidium spp., Plasmodium spp., Filariae and Trypanosomatidae). We test for differences in gut microbiota ecosystem traits and taxonomical composition between Blastocystis and Strongyloides bearing and non-bearing samples. RESULTS For Blastocystis, twelve differentially abundant taxa (e.g., Methanobrevibacter), including Prevotella and Ruminococcus-Methanobrevibacter enterotype markers, replicate findings in humans. However, several richness indices are lower in Blastocystis carriers, contradicting human studies. This indicates Blastocystis, unlike Strongyloides, is associated to a "poor health" gut microbiome, as does the fact that Faecalibacterium, a bacterium with gut protective traits, is absent in Blastocystis-positive samples. Strongyloides was associated to Alloprevotella and five other taxonomic groups. Each parasite had its unique impact on the gut microbiota indicating parasite-specific niches. Our results suggest that studying the gut microbiomes of wild chimpanzees could help disentangle biological from artefactual associations between gut microbiomes and parasites.
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Affiliation(s)
- Justinn Renelies-Hamilton
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Jane Goodall Institute Spain, Station Biologique Fouta Djallon, Dindéfélo, Kédougou, Senegal.
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain; Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic - Central University of Catalonia (UVic - UCC), Vic, Spain
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain; Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic - Central University of Catalonia (UVic - UCC), Vic, Spain
| | - Liliana Pacheco
- Jane Goodall Institute Spain, Station Biologique Fouta Djallon, Dindéfélo, Kédougou, Senegal
| | - Elena Dacal
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - José M Saugar
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - José M Rubio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
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