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Brown BRP, Williams AE, Sabey KA, Onserio A, Ewoi J, Song SJ, Knight R, Ezenwa VO. Social behaviour mediates the microbiome response to antibiotic treatment in a wild mammal. Proc Biol Sci 2024; 291:20241756. [PMID: 39353556 PMCID: PMC11444789 DOI: 10.1098/rspb.2024.1756] [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: 08/21/2023] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 10/04/2024] Open
Abstract
High levels of social connectivity among group-living animals have been hypothesized to benefit individuals by creating opportunities to rapidly reseed the microbiome and maintain stability against disruption. We tested this hypothesis by perturbing the microbiome of a wild population of Grant's gazelles with an antibiotic and asking whether microbiome recovery differs between individuals with high versus low levels of social connectivity. We found that after treatment, individuals with high social connectivity experienced a faster increase in microbiome richness than less socially connected individuals. Unexpectedly, the rapid increase in microbiome richness of highly connected individuals that received treatment led to their microbiomes becoming more distinct relative to the background population. Our results suggest that the microbiome of individuals with high social connectivity can be rapidly recolonized after a perturbation event, but this leads to a microbiome that is more distinct from, rather than more similar to the unperturbed state. This work provides new insight into the role of social interactions in shaping the microbiome.
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Affiliation(s)
- Bianca R. P. Brown
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Kate A. Sabey
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | | | - John Ewoi
- Mpala Research Centre, Nanyuki, Kenya
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Vanessa O. Ezenwa
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Odum School of Ecology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
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2
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Trueba G, Cardenas P, Romo G, Gutierrez B. Reevaluating human-microbiota symbiosis: Strain-level insights and evolutionary perspectives across animal species. Biosystems 2024; 244:105283. [PMID: 39103138 DOI: 10.1016/j.biosystems.2024.105283] [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: 06/18/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
The prevailing consensus in scientific literature underscores the mutualistic bond between the microbiota and the human host, suggesting a finely tuned coevolutionary partnership that enhances the fitness of both parties. This symbiotic relationship has been extensively studied, with certain bacterial attributes being construed as hallmarks of natural selection favoring the benefit of the human host. Some scholars go as far as equating the intricate interplay between humans and their intestinal microbiota to that of endosymbiotic relationships, even conceptualizing microbiota as an integral human organ. However, amidst the prevailing narrative of bacterial species being categorized as beneficial or detrimental to human health, a critical oversight often emerges - the inherent functional diversity within bacterial strains. Such reductionist perspectives risk oversimplifying the complex dynamics at play within the microbiome. Recent genomic analysis at the strain level is highly limited, which is surprising given that strain information provides critical data about selective pressures in the intestine. These pressures appear to focus more on the well-being of bacteria rather than human health. Connected to this is the extent to which animals depend on metabolic activity from intestinal bacteria, which varies widely across species. While omnivores like humans exhibit lower dependency, certain herbivores rely entirely on bacterial activity and have developed specialized compartments to house these bacteria.
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Affiliation(s)
- Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Paul Cardenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - German Romo
- Escuela de Medicina Veterinaria, Universidad San Francisco de Quito, Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador; Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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3
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Bronstein JL, Sridhar H. Connecting and integrating cooperation within and between species. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230203. [PMID: 39034697 PMCID: PMC11293865 DOI: 10.1098/rstb.2023.0203] [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: 10/02/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 07/23/2024] Open
Abstract
There has long been a fundamental divide in the study of cooperation: researchers focus either on cooperation within species, including but not limited to sociality, or else on cooperation between species, commonly termed mutualism. Here, we explore the ecologically and evolutionarily significant ways in which within- and between-species cooperation interact. We highlight two primary cross-linkages. First, cooperation of one type can change the context in which cooperation of the other type functions, and thus potentially its outcome. We delineate three possibilities: (i) within-species cooperation modulates benefits for a heterospecific partner; (ii) between-species cooperation affects the dynamics of within-species cooperation; and (iii) both processes take place interactively. The second type of cross-linkage emerges when resources or services that cooperation makes available are obtainable either from members of the same species or from different species. This brings cooperation at the two levels into direct interaction, to some extent obscuring the distinction between them. We expand on these intersections between within- and between-species cooperation in a diversity of taxa and interaction types. These interactions have the potential to weave together social networks and trophic dynamics, contributing to the structure and functioning of ecological communities in ways that are just beginning to be explored. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.
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Affiliation(s)
- Judith L. Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ85721, USA
| | - Hari Sridhar
- Konrad Lorenz Institute for Evolution and Cognition Research, KlosterneuburgA-3400, Austria
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4
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Whitney TL, Mallott EK, Diakiw LO, Christie DM, Ting N, Amato KR, Tecot SR, Baden AL. Ecological and genetic variables co-vary with social group identity to shape the gut microbiome of a pair-living primate. Am J Primatol 2024; 86:e23657. [PMID: 38967215 DOI: 10.1002/ajp.23657] [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: 07/19/2023] [Revised: 05/17/2024] [Accepted: 06/08/2024] [Indexed: 07/06/2024]
Abstract
Primates exhibit diverse social systems that are intricately linked to their biology, behavior, and evolution, all of which influence the acquisition and maintenance of their gut microbiomes (GMs). However, most studies of wild primate populations focus on taxa with relatively large group sizes, and few consider pair-living species. To address this gap, we investigate how a primate's social system interacts with key environmental, social, and genetic variables to shape the GM in pair-living, red-bellied lemurs (Eulemur rubriventer). Previous research on this species suggests that social interactions within groups influence interindividual microbiome similarity; however, the impacts of other nonsocial variables and their relative contributions to gut microbial variation remain unclear. We sequenced the 16S ribosomal RNA hypervariable V4-V5 region to characterize the GM from 26 genotyped individuals across 11 social groups residing in Ranomafana National Park, Madagascar. We estimated the degree to which sex, social group identity, genetic relatedness, dietary diversity, and home range proximity were associated with variation in the gut microbial communities residing in red-bellied lemurs. All variables except sex played a significant role in predicting GM composition. Our model had high levels of variance inflation, inhibiting our ability to determine which variables were most predictive of gut microbial composition. This inflation is likely due to red-bellied lemurs' pair-living, pair-bonded social system that leads to covariation among environmental, social, and genetic variables. Our findings highlight some of the factors that predict GM composition in a tightly bonded, pair-living species and identify variables that require further study. We propose that future primate microbiome studies should simultaneously consider environmental, social, and genetic factors to improve our understanding of the relationships among sociality, the microbiome, and primate ecology and evolution.
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Affiliation(s)
- Tabor L Whitney
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Laura O Diakiw
- Department of Ecology, University of Wyoming, Laramie, Wyoming, USA
| | - Diana M Christie
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Stacey R Tecot
- School of Anthropology, University of Arizona, Tucson, Arizona, USA
| | - Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, New York City, New York, USA
- Department of Anthropology, The Graduate Center of the City University of New York, New York City, New York, USA
- The New York Consortium in Evolutionary Primatology, New York City, New York, USA
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5
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Martínez-Renau E, Martín-Platero AM, Bodawatta KH, Martín-Vivaldi M, Martínez-Bueno M, Poulsen M, Soler JJ. Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds. Anim Microbiome 2024; 6:47. [PMID: 39148142 PMCID: PMC11325624 DOI: 10.1186/s42523-024-00327-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 06/28/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Animal bacterial symbionts are established early in life, either through vertical transmission and/or by horizontal transmission from both the physical and the social environment, such as direct contact with con- or heterospecifics. The social environment particularly can influence the acquisition of both mutualistic and pathogenic bacteria, with consequences for the stability of symbiotic communities. However, segregating the effects of the shared physical environment from those of the social interactions is challenging, limiting our current knowledge on the role of the social environment in structuring bacterial communities in wild animals. Here, we take advantage of the avian brood-parasite system of Eurasian magpies (Pica pica) and great spotted cuckoos (Clamator glandarius) to explore how the interspecific social environment (magpie nestlings developing with or without heterospecifics) affects bacterial communities on uropygial gland skin. RESULTS We demonstrated interspecific differences in bacterial community compositions in members of the two species when growing up in monospecific nests. However, the bacterial community of magpies in heterospecific nests was richer, more diverse, and more similar to their cuckoo nest-mates than when growing up in monospecific nests. These patterns were alike for the subset of microbes that could be considered core, but when looking at the subset of potentially pathogenic bacterial genera, cuckoo presence reduced the relative abundance of potentially pathogenic bacterial genera on magpies. CONCLUSIONS Our findings highlight the role of social interactions in shaping the assembly of the avian skin bacterial communities during the nestling period, as exemplified in a brood parasite-host system.
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Affiliation(s)
- Ester Martínez-Renau
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), 04120, Almería, Spain.
| | - Antonio M Martín-Platero
- Departamento de Microbiología, Universidad de Granada, 18071, Granada, Spain
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain
| | - Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Martín-Vivaldi
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain
- Departamento de Zoología, Universidad de Granada, 18071, Granada, Spain
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, 18071, Granada, Spain
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Juan José Soler
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), 04120, Almería, Spain.
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain.
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Finnegan PM, Garber PA, McKenney AC, Bicca-Marques JC, De la Fuente MF, Abreu F, Souto A, Schiel N, Amato KR, Mallott EK. Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate. mSphere 2024; 9:e0023324. [PMID: 38940510 PMCID: PMC11288025 DOI: 10.1128/msphere.00233-24] [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: 03/19/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
The gut microbiome has the potential to buffer temporal variations in resource availability and consumption, which may play a key role in the ability of animals to adapt to a broad range of habitats. We investigated the temporal composition and function of the gut microbiomes of wild common marmosets (Callithrix jacchus) exploiting a hot, dry environment-Caatinga-in northeastern Brazil. We collected fecal samples during two time periods (July-August and February-March) for 2 years from marmosets belonging to eight social groups. We used 16S rRNA gene amplicon sequencing, metagenomic sequencing, and butyrate RT-qPCR to assess changes in the composition and potential function of their gut microbiomes. Additionally, we identified the plant, invertebrate, and vertebrate components of the marmosets' diet via DNA metabarcoding. Invertebrate, but not plant or vertebrate, consumption varied across the year. However, gut microbiome composition and potential function did not markedly vary across study periods or as a function of diet composition. Instead, the gut microbiome differed markedly in both composition and potential function across marmosets residing in different social groups. We highlight the likely role of factors, such as behavior, residence, and environmental heterogeneity, in modulating the structure of the gut microbiome. IMPORTANCE In a highly socially cohesive and cooperative primate, group membership more strongly predicts gut microbiome composition and function than diet.
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Affiliation(s)
- Peter M. Finnegan
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Paul A. Garber
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, China
| | - Anna C. McKenney
- Department of Natural Sciences, Parkland College, Champaign, Illinois, USA
| | - Júlio César Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católicado Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Filipa Abreu
- Comparative BioCognition, Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
| | - Antonio Souto
- Department of Zoology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Nicola Schiel
- Laboratório de Etologia Teórica e Aplicada, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Katherine R. Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elizabeth K. Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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7
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Debray R, Dickson CC, Webb SE, Archie EA, Tung J. When is microbial strain sharing evidence for transmission? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604082. [PMID: 39071345 PMCID: PMC11275843 DOI: 10.1101/2024.07.18.604082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. However, social microbiome transmission can be difficult to identify if social partners also have other traits in common or live in a shared environment. Strain-resolved metagenomics has been proposed as a solution for tracking microbial transmission. Using a fecal microbiota transplant dataset, we show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous. However, gut metagenomes from a wild baboon population, where social networks predict compositional similarity, show that strain sharing is also driven by demographic and environmental factors that can override signals of social interactions. We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for conclusions about the underlying mechanisms.
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Affiliation(s)
- Reena Debray
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, Germany
| | - Carly C Dickson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Shasta E Webb
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jenny Tung
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, Germany
- Department of Biology, Duke University, Durham, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Duke Population Research Institute, Duke University, Durham, North Carolina, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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8
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Samartino S, Christie D, Penna A, Sicotte P, Ting N, Wikberg E. Social network dynamics, infant loss, and gut microbiota composition in female Colobus vellerosus during time periods with alpha male challenges. Primates 2024; 65:299-309. [PMID: 38735025 DOI: 10.1007/s10329-024-01132-w] [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: 09/08/2023] [Accepted: 04/11/2024] [Indexed: 05/13/2024]
Abstract
The gut microbiota of group-living animals is strongly influenced by their social interactions, but it is unclear how it responds to social instability. We investigated whether social instability associated with the arrival of new males and challenges to the alpha male position could explain differences in the gut microbiota in adult female Colobus vellerosus at Boabeng-Fiema, Ghana. First, we used a data set collected during May-August 2007 and May 2008-2009 that consisted of (i) 50 fecal samples from adult females in eight social groups for V4 16S rRNA sequencing to determine gut microbiota composition, and (ii) demographic and behavioral data ad libitum to determine male immigration, challenges to the alpha male position, and infant births and deaths. Sørensen and Bray-Curtis beta diversity indices (i.e., between-sample microbiota variation) were predicted by year, alpha male stability, group identity, and age. Next, we used a more detailed behavioral data set collected during focal observations of adult females in one group with a prolonged alpha male takeover and three cases of infant loss, to create 12-month versus 3-month 1-m proximity networks that preceded and overlapped the gut microbiome sampling period in that group. The long versus short-term networks were not correlated, suggesting temporal variation in proximity networks. In this group, beta diversity among the five adult females was predicted by similarity in infant loss status and short-term (rather than yearly) 1-m proximity ties. Although the mechanism driving this association needs to be further investigated in future studies, our findings indicate that alpha male takeovers are associated with gut microbiota variation and highlight the importance of taking demographic and social network dynamics into account.
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Affiliation(s)
- Shelby Samartino
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Diana Christie
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anna Penna
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Pascale Sicotte
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Nelson Ting
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Eva Wikberg
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
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9
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Marsh KJ, Bearhop S, Harrison XA. Linking microbiome temporal dynamics to host ecology in the wild. Trends Microbiol 2024:S0966-842X(24)00132-X. [PMID: 38797653 DOI: 10.1016/j.tim.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024]
Abstract
Ignoring the dynamic nature of microbial communities risks underestimating the power of microbes to impact the health of their hosts. Microbiomes are thought to be important for host fitness, yet the coarse temporal scale and population-level focus of many studies precludes the ability to investigate the importance of among-individual variation in stability and identify the ecological contexts in which this variation matters. Here we briefly summarise current knowledge of temporal dynamics in wild host-associated microbial communities. We then discuss the implications of among-individual variation in microbiota stability and suggest analytical approaches for understanding these patterns. One major requirement is for future studies to conduct individual-level longitudinal analyses, with some systems already well set up for answering these questions.
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Affiliation(s)
- Kirsty J Marsh
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK.
| | - Stuart Bearhop
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK
| | - Xavier A Harrison
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, UK.
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10
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Bendová B, Bímová BV, Čížková D, Daniszová K, Ďureje Ľ, Hiadlovská Z, Macholán M, Piálek J, Schmiedová L, Kreisinger J. The strength of gut microbiota transfer along social networks and genealogical lineages in the house mouse. FEMS Microbiol Ecol 2024; 100:fiae075. [PMID: 38730559 PMCID: PMC11134300 DOI: 10.1093/femsec/fiae075] [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: 10/17/2023] [Revised: 02/23/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The gut microbiota of vertebrates is acquired from the environment and other individuals, including parents and unrelated conspecifics. In the laboratory mouse, a key animal model, inter-individual interactions are severely limited and its gut microbiota is abnormal. Surprisingly, our understanding of how inter-individual transmission impacts house mouse gut microbiota is solely derived from laboratory experiments. We investigated the effects of inter-individual transmission on gut microbiota in two subspecies of house mice (Mus musculus musculus and M. m. domesticus) raised in a semi-natural environment without social or mating restrictions. We assessed the correlation between microbiota composition (16S rRNA profiles), social contact intensity (microtransponder-based social networks), and mouse relatedness (microsatellite-based pedigrees). Inter-individual transmission had a greater impact on the lower gut (colon and cecum) than on the small intestine (ileum). In the lower gut, relatedness and social contact independently influenced microbiota similarity. Despite female-biased parental care, both parents exerted a similar influence on their offspring's microbiota, diminishing with the offspring's age in adulthood. Inter-individual transmission was more pronounced in M. m. domesticus, a subspecies, with a social and reproductive network divided into more closed modules. This suggests that the transmission magnitude depends on the social and genetic structure of the studied population.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | | | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Ľudovít Ďureje
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Miloš Macholán
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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11
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Maritan E, Quagliariello A, Frago E, Patarnello T, Martino ME. The role of animal hosts in shaping gut microbiome variation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230071. [PMID: 38497257 PMCID: PMC10945410 DOI: 10.1098/rstb.2023.0071] [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: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Elisa Maritan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Enric Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, 34398 Montpellier, France
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
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12
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Hunter-Barnett S, Viney M. Gut protozoa of wild rodents - a meta-analysis. Parasitology 2024; 151:594-605. [PMID: 38714350 PMCID: PMC11427965 DOI: 10.1017/s0031182024000556] [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] [Indexed: 05/09/2024]
Abstract
Protozoa are well-known inhabitants of the mammalian gut and so of the gut microbiome. While there has been extensive study of a number of species of gut protozoa in laboratory animals, particularly rodents, the biology of the gut protozoa of wild rodents is much less well-known. Here we have systematically searched the published literature to describe the gut protozoa of wild rodents, in total finding records of 44 genera of protozoa infecting 228 rodent host species. We then undertook meta-analyses that estimated the overall prevalence of gut protozoa in wild rodents to be 24%, with significant variation in prevalence among some host species. We investigated how host traits may affect protozoa prevalence, finding that for some host lifestyles some protozoa differed in their prevalence. This synthesis of existing data on wild rodent gut protozoa provides a better understanding of the biology of these common gut inhabitants and suggests directions for their future study.
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Affiliation(s)
- Simon Hunter-Barnett
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
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13
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García-Cabrerizo R, Cryan JF. A gut (microbiome) feeling about addiction: Interactions with stress and social systems. Neurobiol Stress 2024; 30:100629. [PMID: 38584880 PMCID: PMC10995916 DOI: 10.1016/j.ynstr.2024.100629] [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: 11/23/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
In recent years, an increasing attention has given to the intricate and diverse connection of microorganisms residing in our gut and their impact on brain health and central nervous system disease. There has been a shift in mindset to understand that drug addiction is not merely a condition that affects the brain, it is now being recognized as a disorder that also involves external factors such as the intestinal microbiota, which could influence vulnerability and the development of addictive behaviors. Furthermore, stress and social interactions, which are closely linked to the intestinal microbiota, are powerful modulators of addiction. This review delves into the mechanisms through which the microbiota-stress-immune axis may shape drug addiction and social behaviors. This work integrates preclinical and clinical evidence that demonstrate the bidirectional communication between stress, social behaviors, substance use disorders and the gut microbiota, suggesting that gut microbes might modulate social stress having a significance in drug addiction.
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Affiliation(s)
- Rubén García-Cabrerizo
- IUNICS, University of the Balearic Islands, Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Medicine, University of the Balearic Islands, Palma, Spain
| | - John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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14
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Raulo A, Bürkner PC, Finerty GE, Dale J, Hanski E, English HM, Lamberth C, Firth JA, Coulson T, Knowles SCL. Social and environmental transmission spread different sets of gut microbes in wild mice. Nat Ecol Evol 2024; 8:972-985. [PMID: 38689017 DOI: 10.1038/s41559-024-02381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/01/2024] [Indexed: 05/02/2024]
Abstract
Gut microbes shape many aspects of organismal biology, yet how these key bacteria transmit among hosts in natural populations remains poorly understood. Recent work in mammals has emphasized either transmission through social contacts or indirect transmission through environmental contact, but the relative importance of different routes has not been directly assessed. Here we used a novel radio-frequency identification-based tracking system to collect long-term high-resolution data on social relationships, space use and microhabitat in a wild population of mice (Apodemus sylvaticus), while regularly characterizing their gut microbiota with 16S ribosomal RNA profiling. Through probabilistic modelling of the resulting data, we identify positive and statistically distinct signals of social and environmental transmission, captured by social networks and overlap in home ranges, respectively. Strikingly, microorganisms with distinct biological attributes drove these different transmission signals. While the social network effect on microbiota was driven by anaerobic bacteria, the effect of shared space was most influenced by aerotolerant spore-forming bacteria. These findings support the prediction that social contact is important for the transfer of microorganisms with low oxygen tolerance, while those that can tolerate oxygen or form spores may be able to transmit indirectly through the environment. Overall, these results suggest social and environmental transmission routes can spread biologically distinct members of the mammalian gut microbiota.
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Affiliation(s)
- Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Computing, University of Turku, Turku, Finland.
| | | | - Genevieve E Finerty
- Department of Biology, University of Oxford, Oxford, UK
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behaviour, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jarrah Dale
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Holly M English
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Curt Lamberth
- Department of Biology, University of Oxford, Oxford, UK
| | - Josh A Firth
- Department of Biology, University of Oxford, Oxford, UK
- School of Biology, University of Leeds, Leeds, UK
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, UK
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15
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Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J. Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Rep Med 2024; 5:101426. [PMID: 38366600 PMCID: PMC10982974 DOI: 10.1016/j.xcrm.2024.101426] [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: 04/12/2023] [Revised: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.
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Affiliation(s)
- Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Romulo de Oliveira
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; Department of Medicine and Life Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Isabel Ruf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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16
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Song P, Jiang F, Liu D, Cai Z, Gao H, Gu H, Zhang J, Li B, Xu B, Zhang T. Gut microbiota non-convergence and adaptations in sympatric Tibetan and Przewalski's gazelles. iScience 2024; 27:109117. [PMID: 38384851 PMCID: PMC10879710 DOI: 10.1016/j.isci.2024.109117] [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: 09/06/2023] [Revised: 11/17/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Unraveling the connection between gut microbiota and adaptability in wild species in natural habitats is imperative yet challenging. We studied the gut microbiota of sympatric and allopatric populations of two closely related species, the Procapra picticaudata and P. przewalskii, with the latter showing lower adaptability and adaptive potential than the former. Despite shared habitat, sympatric populations showed no convergence in gut microbiota, revealing distinct microbiota-environment relationships between the two gazelle species. Furthermore, the gut microbiota assembly process of the P. przewalskii was shifted toward homogeneous selection processes relative to that of the P. picticaudata. Those taxa which contributed to the shift were mainly from the phyla Firmicutes and Verrucomicrobiota, with functions highly related to micronutrient and macronutrient metabolism. Our study provides new insights into the complex dynamics between gut microbiota, host adaptability, and environment in wildlife adaptation and highlights the need to consider host adaptability when examining wildlife host-microbiome interplay.
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Affiliation(s)
- Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Daoxin Liu
- Qinghai University, Xining, Qinghai 810016, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Haifeng Gu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Bo Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai 810008, China
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17
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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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18
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Bornbusch SL, Bamford A, Thacher P, Crosier A, Marinari P, Bortner R, Garelle D, Livieri T, Santymire R, Comizzoli P, Maslanka M, Maldonado JE, Koepfli KP, Muletz-Wolz CR, DeCandia AL. Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes). Commun Biol 2024; 7:224. [PMID: 38396133 PMCID: PMC10891159 DOI: 10.1038/s42003-024-05908-0] [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: 09/26/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Reproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA.
- Department of Nutrition Science, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA.
| | | | - Piper Thacher
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Adrienne Crosier
- Center for Animal Care Services, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Paul Marinari
- Center for Animal Care Services, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Robyn Bortner
- National Black-Footed Ferret Conservation Center, US Fish and Wildlife Service, Carr, CO, USA
| | - Della Garelle
- National Black-Footed Ferret Conservation Center, US Fish and Wildlife Service, Carr, CO, USA
| | | | | | - Pierre Comizzoli
- Center for Species Survival, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Michael Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Center for Species Survival, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Alexandra L DeCandia
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
- Department of Biology, Georgetown University, Washington, DC, USA
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19
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Bogri A, Jensen EEB, Borchert AV, Brinch C, Otani S, Aarestrup FM. Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations. mSystems 2024; 9:e0101823. [PMID: 38095429 PMCID: PMC10805027 DOI: 10.1128/msystems.01018-23] [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: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance (AMR) is a major global health concern, further complicated by its spread via the microbiome bacterial members. While mathematical models discuss AMR transmission through the symbiotic microbiome, experimental studies are scarce. Herein, we used a gregarious cockroach, Pycnoscelus surinamensis, as an in vivo animal model for AMR transmission investigations. We explored whether the effect of antimicrobial treatment is detectable with metagenomic sequencing, and whether AMR genes can be spread and established in unchallenged (not treated with antibiotics) individuals following contact with treated donors, and under various frequencies of interaction. Gut and soil substrate microbiomes were investigated by metagenomic sequencing for bacterial community composition and resistome profiling. We found that tetracycline treatment altered the treated gut microbiome by decreasing bacterial diversity and increasing the abundance of tetracycline resistance genes. Untreated cockroaches that interacted with treated donors also had elevated tetracycline resistance. The levels of resistance differed depending on the magnitude and frequency of donor transfer. Additionally, treated donors showed signs of microbiome recovery due to their interaction with the untreated ones. Similar patterns were also recorded in the soil substrate microbiomes. Our results shed light on how interacting microbiomes facilitate AMR gene transmission to previously unchallenged hosts, a dynamic influenced by the interaction frequencies, using an in vivo model to validate theoretical AMR transmission models.IMPORTANCEAntimicrobial resistance is a rising threat to human and animal health. The spread of resistance through the transmission of the symbiotic gut microbiome is of concern and has been explored in theoretical modeling studies. In this study, we employ gregarious insect populations to examine the emergence and transmission of antimicrobial resistance in vivo and validate modeling hypotheses. We find that antimicrobial treatment increases the levels of resistance in treated populations. Most importantly, we show that resistance increased in untreated populations after interacting with the treated ones. The level of resistance transmission was affected by the magnitude and frequency of population mixing. Our results highlight the importance of microbial transmission in the spread of antimicrobial resistance.
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Affiliation(s)
- Amalia Bogri
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | | | - Asbjørn Vedel Borchert
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
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20
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Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Microbial transmission in the social microbiome and host health and disease. Cell 2024; 187:17-43. [PMID: 38181740 PMCID: PMC10958648 DOI: 10.1016/j.cell.2023.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Cameron J A McInroy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Siobhán Harty
- Independent, Tandy Court, Spitalfields, Dublin, Ireland
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK; Department of Computing, University of Turku, Turku, Finland
| | - Neil G O Ibata
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mireia Valles-Colomer
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Katerina V-A Johnson
- Institute of Psychology, Leiden University, Leiden, the Netherlands; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph Henrich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Francesca S Gazzaniga
- Molecular Pathology Unit, Cancer Center, Massachusetts General Hospital Research Institute, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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21
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Valles-Colomer M, Manghi P, Cumbo F, Masetti G, Armanini F, Asnicar F, Blanco-Miguez A, Pinto F, Punčochář M, Garaventa A, Amoroso L, Ponzoni M, Corrias MV, Segata N. Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding. EBioMedicine 2024; 99:104917. [PMID: 38104504 PMCID: PMC10731604 DOI: 10.1016/j.ebiom.2023.104917] [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: 07/12/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Neuroblastoma is the most frequent extracranial solid tumour in children, accounting for ∼15% of deaths due to cancer in childhood. The most common clinical presentation are abdominal tumours. An altered gut microbiome composition has been linked to multiple cancer types, and reported in murine models of neuroblastoma. Whether children with neuroblastoma display alterations in gut microbiome composition remains unexplored. METHODS We assessed gut microbiome composition by shotgun metagenomic profiling in an observational cross-sectional study on 288 individuals, consisting of patients with a diagnosis of neuroblastoma at disease onset (N = 63), healthy controls matching the patients on the main covariates of microbiome composition (N = 94), healthy siblings of the patients (N = 13), mothers of patients (N = 59), and mothers of the controls (N = 59). We examined taxonomic and functional microbiome composition and mother-infant strain transmission patterns. FINDINGS Patients with neuroblastoma displayed alterations in gut microbiome composition characterised by reduced microbiome richness, decreased relative abundances of 18 species (including Phocaeicola dorei and Bifidobacterium bifidum), enriched protein fermentation and reduced carbohydrate fermentation potential. Using machine learning, we could successfully discriminate patients from controls (AUC = 82%). Healthy siblings did not display such alterations but resembled the healthy control group. No significant differences in maternal microbiome composition nor mother-to-offspring transmission were detected. INTERPRETATION Patients with neuroblastoma display alterations in taxonomic and functional gut microbiome composition, which cannot be traced to differential maternal seeding. Follow-up research should include investigating potential causal links. FUNDING Italian Ministry of Health Ricerca Corrente and Ricerca Finalizzata 5 per mille (to MPonzoni); Fondazione Italiana Neuroblastoma (to MPonzoni); European Research Council (ERC-StG project MetaPG-716575 and ERC-CoG microTOUCH-101045015 to NS); the European H2020 program ONCOBIOME-825410 project (to NS); the National Cancer Institute of the National Institutes of Health 1U01CA230551 (to NS); the Premio Internazionale Lombardia e Ricerca 2019 (to NS); the MIUR Progetti di Ricerca di Rilevante Interesse Nazionale (PRIN) Bando 2017 Grant 2017J3E2W2 (to NS); EMBO ALTF 593-2020 and Knowledge Generation Project from the Spanish Ministry of Science and Innovation (PID2022-139328OA-I00) (to MV-C).
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Affiliation(s)
- Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; MELIS Department, Pompeu Fabra University, Barcelona, Spain.
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | | | | | | | | | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
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22
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Downie AE, Oyesola O, Barre RS, Caudron Q, Chen YH, Dennis EJ, Garnier R, Kiwanuka K, Menezes A, Navarrete DJ, Mondragón-Palomino O, Saunders JB, Tokita CK, Zaldana K, Cadwell K, Loke P, Graham AL. Spatiotemporal-social association predicts immunological similarity in rewilded mice. SCIENCE ADVANCES 2023; 9:eadh8310. [PMID: 38134275 PMCID: PMC10745690 DOI: 10.1126/sciadv.adh8310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual's interaction with its environment. We therefore tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including associations measured from spatiotemporal co-occurrences, to immune phenotypes. We found extensive variation in individual and social behavior among and within mouse strains upon rewilding. In addition, we found that the more associated two individuals were, the more similar their immune phenotypes were. Spatiotemporal association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or shared infection status. These results highlight the importance of shared spatiotemporal activity patterns and/or social networks for immune phenotype and suggest potential immunological correlates of social life.
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Affiliation(s)
- Alexander E. Downie
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Oyebola Oyesola
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramya S. Barre
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Sciences Center at San Antonio, San Antonio, TX 78229, USA
| | - Quentin Caudron
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Emily J. Dennis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Romain Garnier
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kasalina Kiwanuka
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arthur Menezes
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Daniel J. Navarrete
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jesse B. Saunders
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Christopher K. Tokita
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kimberly Zaldana
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - P’ng Loke
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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23
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Rose C, Lund MB, Schramm A, Bilde T, Bechsgaard J. Does ecological drift explain variation in microbiome composition among groups in a social host species? J Evol Biol 2023; 36:1684-1694. [PMID: 37776090 DOI: 10.1111/jeb.14228] [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: 12/30/2022] [Revised: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 10/01/2023]
Abstract
Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless divergence in microbiome composition among related groups arise. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider Stegodyphus dumicola. We simulated the initiation of new groups by splitting field-collected nests into groups of 1, 3, and 10 individuals respectively, and compared variation in microbiome composition among and within groups after 6 weeks using 16S rRNA gene sequencing. Theory predicts that ecological drift increases with decreasing group size. We found that microbiome composition among single founders was more dissimilar than among individuals kept in groups, supporting this prediction. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Individual founders appear to harbour higher relative abundances of non-core symbionts compared with founders in small groups, some of which are possible pathogens. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.
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Affiliation(s)
- Clémence Rose
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Marie Braad Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jesper Bechsgaard
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
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24
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Bensch HM, Lundin D, Tolf C, Waldenström J, Zöttl M. Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal. J Evol Biol 2023; 36:1753-1760. [PMID: 37584218 DOI: 10.1111/jeb.14208] [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: 12/09/2022] [Revised: 04/27/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
In social species, group members commonly show substantial similarity in gut microbiome composition. Such similarities have been hypothesized to arise either by shared environmental effects or by host relatedness. However, disentangling these factors is difficult, because group members are often related, and social groups typically share similar environmental conditions. In this study, we conducted a cross-foster experiment under controlled laboratory conditions in group-living Damaraland mole-rats (Fukomys damarensis) and used 16S amplicon sequencing to disentangle the effects of the environment and relatedness on gut microbiome similarity and diversity. Our results show that a shared environment is the main factor explaining gut microbiome similarity, overshadowing any effect of host relatedness. Together with studies in wild animal populations, our results suggest that among conspecifics environmental factors are more powerful drivers of gut microbiome composition similarity than host genetics.
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Affiliation(s)
- Hanna M Bensch
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
- Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| | - Daniel Lundin
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Conny Tolf
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Jonas Waldenström
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Markus Zöttl
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
- Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
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25
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Valdivia C, Newton JA, von Beeren C, O'Donnell S, Kronauer DJC, Russell JA, Łukasik P. Microbial symbionts are shared between ants and their associated beetles. Environ Microbiol 2023; 25:3466-3483. [PMID: 37968789 DOI: 10.1111/1462-2920.16544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
The transmission of microbial symbionts across animal species could strongly affect their biology and evolution, but our understanding of transmission patterns and dynamics is limited. Army ants (Formicidae: Dorylinae) and their hundreds of closely associated insect guest species (myrmecophiles) can provide unique insights into interspecific microbial symbiont sharing. Here, we compared the microbiota of workers and larvae of the army ant Eciton burchellii with those of 13 myrmecophile beetle species using 16S rRNA amplicon sequencing. We found that the previously characterized specialized bacterial symbionts of army ant workers were largely absent from ant larvae and myrmecophiles, whose microbial communities were usually dominated by Rickettsia, Wolbachia, Rickettsiella and/or Weissella. Strikingly, different species of myrmecophiles and ant larvae often shared identical 16S rRNA genotypes of these common bacteria. Protein-coding gene sequences confirmed the close relationship of Weissella strains colonizing army ant larvae, some workers and several myrmecophile species. Unexpectedly, these strains were also similar to strains infecting dissimilar animals inhabiting very different habitats: trout and whales. Together, our data show that closely interacting species can share much of their microbiota, and some versatile microbial species can inhabit and possibly transmit across a diverse range of hosts and environments.
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Affiliation(s)
- Catalina Valdivia
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Justin A Newton
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Christoph von Beeren
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
| | - Sean O'Donnell
- Department of Biodiversity, Earth & Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
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26
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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27
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Murphy KM, Le SM, Wilson AE, Warner DA. The Microbiome as a Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota. Integr Comp Biol 2023; 63:597-609. [PMID: 37218690 DOI: 10.1093/icb/icad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
The microbiome is an interactive and fluctuating community of microbes that colonize and develop across surfaces, including those associated with organismal hosts. A growing number of studies exploring how microbiomes vary in ecologically relevant contexts have recognized the importance of microbiomes in affecting organismal evolution. Thus, identifying the source and mechanism for microbial colonization in a host will provide insight into adaptation and other evolutionary processes. Vertical transmission of microbiota is hypothesized to be a source of variation in offspring phenotypes with important ecological and evolutionary implications. However, the life-history traits that govern vertical transmission are largely unexplored in the ecological literature. To increase research attention to this knowledge gap, we conducted a systematic review to address the following questions: (1) How often is vertical transmission assessed as a contributor to offspring microbiome colonization and development? (2) Do studies have the capacity to address how maternal transmission of microbes affects the offspring phenotype? (3) How do studies vary based on taxonomy and life history of the study organism, as well as the experimental, molecular, and statistical methods employed? Extensive literature searches reveal that many studies examining vertical transmission of microbiomes fail to collect whole microbiome samples from both maternal and offspring sources, particularly for oviparous vertebrates. Additionally, studies should sample functional diversity of microbes to provide a better understanding of mechanisms that influence host phenotypes rather than solely taxonomic variation. An ideal microbiome study incorporates host factors, microbe-microbe interactions, and environmental factors. As evolutionary biologists continue to merge microbiome science and ecology, examining vertical transmission of microbes across taxa can provide inferences on causal links between microbiome variation and phenotypic evolution.
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Affiliation(s)
- Kaitlyn M Murphy
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Samantha M Le
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Alan E Wilson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Daniel A Warner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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28
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Huaiquipán R, Quiñones J, Díaz R, Velásquez C, Sepúlveda G, Velázquez L, Paz EA, Tapia D, Cancino D, Sepúlveda N. Review: Effect of Experimental Diets on the Microbiome of Productive Animals. Microorganisms 2023; 11:2219. [PMID: 37764062 PMCID: PMC10536378 DOI: 10.3390/microorganisms11092219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 09/29/2023] Open
Abstract
The microorganisms that inhabit the gastrointestinal tract are responsible for multiple chains of reactions that affect their environment and modify the internal metabolism, their study receives the name of microbiome, which has become more relevant in recent years. In the near future, the challenges related to feeding are anticipated to escalate, encompassing the nutritional needs to sustain an overpopulated world. Therefore, it is expected that a better understanding of the interactions between microorganisms within the digestive tract will allow their modulation in order to provide an improvement in the immune system, feed efficiency or the promotion of nutritional characteristics in production animals, among others. In the present study, the main effects of experimental diets in production animals were described, emphasizing the diversity of the bacterial populations found in response to the diets, ordering them between polygastric and monogastric animals, and then describing the experimental diets used and their effect on the microorganisms. It is hoped that this study will help as a first general approach to the study of the role of the microbiome in production animals under different diets.
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Affiliation(s)
- Rodrigo Huaiquipán
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - John Quiñones
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Rommy Díaz
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Carla Velásquez
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Gastón Sepúlveda
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Lidiana Velázquez
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Erwin A. Paz
- UWA Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - Daniela Tapia
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - David Cancino
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Néstor Sepúlveda
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
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29
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Florkowski MR, Hamer SA, Yorzinski JL. Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome. FEMS Microbiol Ecol 2023; 99:fiad096. [PMID: 37586886 DOI: 10.1093/femsec/fiad096] [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: 10/14/2022] [Revised: 06/07/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.
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Affiliation(s)
- Melanie R Florkowski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
| | - Sarah A Hamer
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Schubot Center for Avian Health, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 701 Farm to Market Service Road, College Station, TX 77840, United States
| | - Jessica L Yorzinski
- Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
- Department of Ecology and Conservation Biology, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77845, United States
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Zhu L. Editorial: Animal social behaviour and gut microbiome. Front Microbiol 2023; 14:1210717. [PMID: 37614609 PMCID: PMC10443586 DOI: 10.3389/fmicb.2023.1210717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023] Open
Affiliation(s)
- Lifeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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Rose C, Lund MB, Søgård AM, Busck MM, Bechsgaard JS, Schramm A, Bilde T. Social transmission of bacterial symbionts homogenizes the microbiome within and across generations of group-living spiders. ISME COMMUNICATIONS 2023; 3:60. [PMID: 37330540 PMCID: PMC10276852 DOI: 10.1038/s43705-023-00256-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 05/12/2023] [Indexed: 06/19/2023]
Abstract
Disentangling modes and fidelity of symbiont transmission are key for understanding host-symbiont associations in wild populations. In group-living animals, social transmission may evolve to ensure high-fidelity transmission of symbionts, since non-reproducing helpers constitute a dead-end for vertical transmission. We investigated symbiont transmission in the social spider Stegodyphus dumicola, which lives in family groups where the majority of females are non-reproducing helpers, females feed offspring by regurgitation, and individuals feed communally on insect prey. Group members share temporally stable microbiomes across generations, while distinct variation in microbiome composition exists between groups. We hypothesized that horizontal transmission of symbionts is enhanced by social interactions, and investigated transmission routes within (horizontal) and across (vertical) generations using bacterial 16S rRNA gene amplicon sequencing in three experiments: (i) individuals were sampled at all life stages to assess at which life stage the microbiome is acquired. (ii) a cross-fostering design was employed to test whether offspring carry the microbiome from their natal nest, or acquire the microbiome of the foster nest via social transmission. (iii) adult spiders with different microbiome compositions were mixed to assess whether social transmission homogenizes microbiome composition among group members. We demonstrate that offspring hatch symbiont-free, and bacterial symbionts are transmitted vertically across generations by social interactions with the onset of regurgitation feeding by (foster)mothers in an early life stage. Social transmission governs horizontal inter-individual mixing and homogenization of microbiome composition among nest mates. We conclude that temporally stable host-symbiont associations in social species can be facilitated and maintained by high-fidelity social transmission.
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Affiliation(s)
- Clémence Rose
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - Marie B Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andrea M Søgård
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Mette M Busck
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jesper S Bechsgaard
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
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32
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Wanelik KM, Raulo A, Troitsky T, Husby A, Knowles SCL. Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice. Anim Microbiome 2023; 5:29. [PMID: 37259168 DOI: 10.1186/s42523-023-00247-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/17/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND The mammalian gut microbiota influences a wide array of phenotypes which are relevant to fitness, yet knowledge about the transmission routes by which gut microbes colonise hosts in natural populations remains limited. Here, we use an intensively studied wild population of wood mice (Apodemus sylvaticus) to examine how vertical (maternal) and horizontal (social) transmission routes influence gut microbiota composition throughout life. RESULTS We identify independent signals of maternal transmission (sharing of taxa between a mother and her offspring) and social transmission (sharing of taxa predicted by the social network), whose relative magnitudes shift as hosts age. In early life, gut microbiota composition is predicted by both maternal and social relationships, but by adulthood the impact of maternal transmission becomes undetectable, leaving only a signal of social transmission. By exploring which taxa drive the maternal transmission signal, we identify a candidate maternally-transmitted bacterial family in wood mice, the Muribaculaceae. CONCLUSION Overall, our findings point to an ontogenetically shifting transmission landscape in wild mice, with a mother's influence on microbiota composition waning as offspring age, while the relative impact of social contacts grows.
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Affiliation(s)
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK
- Department of Computing, University of Turku, Turku, Finland
| | | | - Arild Husby
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Sprockett DD, Price JD, Juritsch AF, Schmaltz RJ, Real MV, Goldman SL, Sheehan M, Ramer-Tait AE, Moeller AH. Home-site advantage for host species-specific gut microbiota. SCIENCE ADVANCES 2023; 9:eadf5499. [PMID: 37184968 PMCID: PMC10184861 DOI: 10.1126/sciadv.adf5499] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here, we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wild-type (WT) and Rag1-knockout (Rag1-/-) house mice revealed widespread fitness advantages for native gut bacteria. Native bacterial lineages significantly outcompeted non-native lineages in both WT and Rag1-/- mice, indicating home-site advantage for native microbiota independent of host adaptive immunity. However, a minority of native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1-/- hosts, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates home-site advantage for native gut bacteria, consistent with local adaptation of gut microbiota to their mammalian species.
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Affiliation(s)
- Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeffrey D. Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anthony F. Juritsch
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Robert J. Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Madalena V. F. Real
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Michael Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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Bogri A, Otani S, Aarestrup FM, Brinch C. Interplay between strain fitness and transmission frequency determines prevalence of antimicrobial resistance. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.981377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The steep rise of infections caused by bacteria that are resistant to antimicrobial agents threatens global health. However, the association between antimicrobial use and the prevalence of resistance is not straightforward. Therefore, it is necessary to quantify the importance of additional factors that affect this relationship. We theoretically explore how the prevalence of resistance is affected by the combination of three factors: antimicrobial use, bacterial transmission, and fitness cost of resistance. We present a model that combines within-host, between-hosts and between-populations dynamics, built upon the competitive Lotka-Volterra equations. We developed the model in a manner that allows future experimental validation of the findings with single isolates in the laboratory. Each host may carry two strains (susceptible and resistant) that represent the host’s commensal microbiome and are not the target of the antimicrobial treatment. The model simulates a population of hosts who are treated periodically with antibiotics and transmit bacteria to each other. We show that bacterial transmission results in strain co-existence. Transmission disseminates resistant bacteria in the population, increasing the levels of resistance. Counterintuitively, when the cost of resistance is low, high transmission frequencies reduce resistance prevalence. Transmission between host populations leads to more similar resistance levels, increasing the susceptibility of the population with higher antimicrobial use. Overall, our results indicate that the interplay between bacterial transmission and strain fitness affects the prevalence of resistance in a non-linear way. We then place our results within the context of ecological theory, particularly on temporal niche partitioning and metapopulation rescue, and we formulate testable experimental predictions for future research.
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Shanahan F, Ghosh TS, O'Toole PW. Human microbiome variance is underestimated. Curr Opin Microbiol 2023; 73:102288. [PMID: 36889023 DOI: 10.1016/j.mib.2023.102288] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 03/08/2023]
Abstract
Most of the variance in the human microbiome remains unexplained. Although an extensive list of individual lifestyles shaping the microbiome has been identified, important gaps in knowledge persist. Most human microbiome data are from individuals living in socioeconomically developed countries. This may have skewed the interpretation of microbiome variance and its relationship to health and disease. Moreover, striking under-representation of minority groups in microbiome studies is a missed opportunity to assess context, history and the changing nature of the microbiome in relation to the risk of disease. Therefore, we focus here on areas of recent progress - ageing and ethnicity - both of which contribute to microbiome variance with particular lessons for the promise of microbiome-based diagnostics and therapeutics.
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Affiliation(s)
- Fergus Shanahan
- Department of Medicine, University College Cork, National University of Ireland, Ireland; APC Microbiome Ireland, University College Cork, National University of Ireland, Ireland.
| | - Tarini S Ghosh
- APC Microbiome Ireland, University College Cork, National University of Ireland, Ireland; Department of Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), New Delhi, India
| | - Paul W O'Toole
- School of Microbiology, University College Cork, National University of Ireland, Ireland; APC Microbiome Ireland, University College Cork, National University of Ireland, Ireland
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Host Hybridization Dominates over Cohabitation in Affecting Gut Microbiota of Intrageneric Hybrid Takifugu Pufferfish. mSystems 2023; 8:e0118122. [PMID: 36815841 PMCID: PMC10134855 DOI: 10.1128/msystems.01181-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Microbial symbionts are of great importance for macroscopic life, including fish, and both collectively comprise an integrated biological entity known as the holobiont. Yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to biotic and/or abiotic influences. Here, through amplicon profiling, the genealogical relationship between artificial F1 hybrid pufferfish with growth heterosis, produced from crossing female Takifugu obscurus with male Takifugu rubripes and its maternal halfsibling purebred, was well recapitulated by their gut microbial community similarities, indicating an evident parallelism between host phylogeny (hybridity) and microbiota relationships therein. Interestingly, modest yet significant fish growth promotion and gut microbiota alteration mediated by hybrid-purebred cohabitation were observed, in comparison with their respective monoculture cohorts that share common genetic makeups, implying a certain degree of environmental influences. Moreover, the underlying assemblage patterns of gut microbial communities were found associated with a trade-off between variable selection and dispersal limitation, which are plausibly driven by the augmented social interactions between hybrid and purebred cohabitants differing in behaviors. Results from this study not only can enrich, from a microbial perspective, the sophisticated understanding of complex and dynamic assemblage of the fish holobiont, but will also provide deeper insights into the ecophysiological factors imposed on the diversity-function relationships thereof. Our findings emphasize the intimate associations of gut microbiota in host genetics-environmental interactions and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve the production of farmed fishes. IMPORTANCE Microbial symbionts are of great importance for macroscopic life, including fish, and yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to the biotic and/or abiotic influences. Through gut microbiota profiling, we show that host intrageneric hybridization and cohabitation can impose a strong disturbance upon pufferfish gut microbiota. Moreover, marked alterations in the composition and function of gut microbiota in both hybrid and purebred pufferfish cohabitants were observed, which are potentially correlated with different metabolic priorities and behaviors between host genealogy. These results can enrich, from a microbial perspective, the sophisticated understanding of the complex and dynamic assemblage of the fish holobiont and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve farmed fish production.
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Musciotto F, Dobon B, Greenacre M, Mira A, Chaudhary N, Salali GD, Gerbault P, Schlaepfer R, Astete LH, Ngales M, Gomez-Gardenes J, Latora V, Battiston F, Bertranpetit J, Vinicius L, Migliano AB. Agta hunter-gatherer oral microbiomes are shaped by contact network structure. EVOLUTIONARY HUMAN SCIENCES 2023; 5:e9. [PMID: 37587930 PMCID: PMC10426009 DOI: 10.1017/ehs.2023.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 12/24/2022] [Accepted: 01/08/2023] [Indexed: 02/25/2023] Open
Abstract
Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African BaYaka hunter-gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses and even unrelated friends can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.
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Affiliation(s)
- Federico Musciotto
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy
- Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Begoña Dobon
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Michael Greenacre
- Department of Economics and Business, Universitat Pompeu Fabra & Barcelona Graduate School of Economics, Barcelona, Spain
- Faculty of Biosciences, Fisheries and Economics, University of Tromsø, Norway
| | - Alex Mira
- Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO Foundation, Valencia, Spain
- CIBER Center for Epidemiology and Public Health, Madrid, Spain
| | - Nikhil Chaudhary
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Gul Deniz Salali
- Department of Anthropology, University College London, London, UK
| | - Pascale Gerbault
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Leonora H. Astete
- Lyceum of the Philippines University, Intramuros, Manila, Philippines
| | - Marilyn Ngales
- Lyceum of the Philippines University, Intramuros, Manila, Philippines
| | - Jesus Gomez-Gardenes
- GOTHAM Lab, Institute for Biocomputation and Physics of Complex Systems, and Department of Condensed Matter Physics, University of Zaragoza, Zaragoza, Spain
- Center for Computational Social Science, Kobe University, Kobe, Japan
| | - Vito Latora
- School of Mathematical Sciences, Queen Mary University of London, London, UK
- Dipartimento di Fisica ed Astronomia, Università di Catania and INFN, Catania, Italy
- Complexity Science Hub Vienna, Vienna, Austria
| | - Federico Battiston
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Department of Network and Data Science, Central European University, Vienna, Austria
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Lucio Vinicius
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Department of Anthropology, University College London, London, UK
| | - Andrea Bamberg Migliano
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Department of Anthropology, University College London, London, UK
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Lai Y, Chen Y, Zheng J, Liu Z, Nong D, Liang J, Li Y, Huang Z. Gut microbiota of white-headed black langurs ( Trachypithecus leucocephalus) in responses to habitat fragmentation. Front Microbiol 2023; 14:1126257. [PMID: 36860490 PMCID: PMC9968942 DOI: 10.3389/fmicb.2023.1126257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
The white-headed black langur (Trachypithecus leucocephalus) is exclusively distributed in the karst forests and is critically endangered owing to habitat fragmentation. Gut microbiota can provide physiological data for a comprehensive study of the langur's response to human disturbance in the limestone forest; to date, data on spatial variations in the langurs' gut microbiota are limited. In this study, we examined intersite variations in the gut microbiota of white-headed black langurs in the Guangxi Chongzuo White-headed Langur National Nature Reserve, China. Our results showed that langurs in the Bapen area with a better habitat had higher gut microbiota diversity. In the Bapen group, the Bacteroidetes (13.65% ± 9.73% vs. 4.75% ± 4.70%) and its representative family, Prevotellaceae, were significantly enriched. In the Banli group, higher relative abundance of Firmicutes (86.30% ± 8.60% vs. 78.85% ± 10.35%) than the Bapen group was observed. Oscillospiraceae (16.93% ± 5.39% vs. 16.13% ± 3.16%), Christensenellaceae (15.80% ± 4.59% vs. 11.61% ± 3.60%), and norank_o__Clostridia_UCG-014 (17.43% ± 6.64% vs. 9.78% ± 3.83%) were increased in comparison with the Bapen group. These intersite variations in microbiota diversity and composition could be accounted for by differences in food resources caused by fragmentation. Furthermore, compared with the Banli group, the community assembly of gut microbiota in the Bapen group was influenced by more deterministic factors and had a higher migration rate, but the difference between the two groups was not significant. This might be attributed to the serious fragmentation of the habitats for both groups. Our findings highlight the importance of gut microbiota response for the integrity of wildlife habitats and the need in using physiological indicators to study the mechanisms by which wildlife responds to human disturbances or ecological variations.
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Affiliation(s)
- Ying Lai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Yanqiong Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Jingjin Zheng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zheng Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Dengpan Nong
- Administration Center of Guangxi Chongzuo White-headed Langur National Nature Reserve, Chongzuo, China
| | - Jipeng Liang
- Administration Center of Guangxi Chongzuo White-headed Langur National Nature Reserve, Chongzuo, China
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
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Cloacal microbiota are biogeographically structured in larks from desert, tropical and temperate areas. BMC Microbiol 2023; 23:40. [PMID: 36765278 PMCID: PMC9921332 DOI: 10.1186/s12866-023-02768-2] [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: 03/07/2022] [Accepted: 01/11/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND In contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks. RESULTS Geographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (< 0.5%) and 43 genera (5%) were shared by larks from all locations. Desert larks held fewer unique ASVs (25%) than temperate zone (31%) and tropical larks (34%). Five out of 33 detected bacterial phyla dominated lark cloacal gut microbiomes. In tropical larks three bacterial classes were overrepresented. Highlighting the distinctiveness of desert lark microbiota, the relative abundances of 52 ASVs differed among locations, which classified within three dominant and 11 low-abundance phyla. Clear and significant phylogenetic clustering in cloacal microbiota community composition (unweighted UniFrac) showed segregation with geography and host species, where microbiota of desert larks were distinct from those of tropical and temperate regions. Geographic distance was nonlinearly associated with pairwise unweighted UniFrac distances. CONCLUSIONS We conclude that host-associated microbiota are geographically structured in a group of widespread but closely-related bird species, following large-scale macro-ecological patterns and contrasting with previous findings for free-living microbes. Future work should further explore if and to what extent geographic variation in host-associated microbiota can be explained as result of co-evolution between gut microbes and host adaptive traits, and if and how acquisition from the environmental pool of bacteria contributes to explaining host-associated communities.
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40
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Florkowski MR, Yorzinski JL. Gut microbiome diversity and composition is associated with exploratory behavior in a wild-caught songbird. Anim Microbiome 2023; 5:8. [PMID: 36739424 PMCID: PMC9899379 DOI: 10.1186/s42523-023-00227-x] [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: 05/23/2022] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The gut microbiome influences its host in a myriad of ways, from immune system development to nutrient utilization. However, our understanding of the relationship between the gut microbiome and behavior, especially in wild species, is still poor. One behavior that potentially interacts with the gut microbiome is exploratory behavior, which animals use to acquire new information from the environment. We hypothesized that diversity of the gut microbiome will be correlated with exploratory behavior in a wild-caught bird species. To test this hypothesis, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure the diversity of their gut microbiomes. We then introduced individuals to a novel environment and measured their exploratory behavior. RESULTS We found that birds with higher alpha diversity of the gut microbiome exhibited higher exploratory behavior. These results suggest that high exploratory birds encounter more types of environmental microbes that contribute to their diverse gut microbiome compared with less exploratory birds. Alternatively, increased gut microbiome diversity may contribute to increased exploratory behavior. We also found differences in beta diversity when comparing high and low exploring birds, indicating differences in microbiome community structure. When comparing predicted functional pathways of the birds' microbiomes, we found that the microbiomes of high explorers contained more pathways involved in biofilm formation and xenobiotic degradation than those of low explorers. CONCLUSIONS Overall, we found that the alpha and beta diversity of the gut microbiome is correlated with exploratory behavior of house sparrows. The predicted functions of the gut microbiome from high explorers differs from that of low explorers. Our study highlights the importance of considering the gut microbiome when investigating animal behavior.
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Affiliation(s)
- Melanie R. Florkowski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA
| | - Jessica L. Yorzinski
- grid.264756.40000 0004 4687 2082Ecology and Evolutionary Biology Program, Texas A&M University, 534 John Kimbrough Blvd, College Station, TX 77843 USA ,grid.264756.40000 0004 4687 2082Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX USA
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41
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Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D, Armanini F, Cumbo F, Huang KD, Manara S, Masetti G, Pinto F, Piperni E, Punčochář M, Ricci L, Zolfo M, Farrant O, Goncalves A, Selma-Royo M, Binetti AG, Becerra JE, Han B, Lusingu J, Amuasi J, Amoroso L, Visconti A, Steves CM, Falchi M, Filosi M, Tett A, Last A, Xu Q, Qin N, Qin H, May J, Eibach D, Corrias MV, Ponzoni M, Pasolli E, Spector TD, Domenici E, Collado MC, Segata N. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 2023; 614:125-135. [PMID: 36653448 PMCID: PMC9892008 DOI: 10.1038/s41586-022-05620-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 118.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/02/2022] [Indexed: 01/19/2023]
Abstract
The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.
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Affiliation(s)
| | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Elisa Piperni
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | | | - Liviana Ricci
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Olivia Farrant
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Goncalves
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Marta Selma-Royo
- Department CIBIO, University of Trento, Trento, Italy
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Ana G Binetti
- Instituto de Lactología Industrial (CONICET-UNL), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jimmy E Becerra
- Grupo de Investigación Alimentación y Comportamiento Humano, Universidad Metropolitana, Barranquilla, Colombia
| | - Bei Han
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - John Lusingu
- National Institute for Medical Research, Tanga Medical Research Centre, Tanga, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire M Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna Last
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Qian Xu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Nan Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Huanlong Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples 'Federico II', Portici, Italy
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Enrico Domenici
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Computational and Systems Biology (COSBI), Microsoft Research Foundation, Rovereto, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
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Xu P, Stirling E, Xie H, Li W, Lv X, Matsumoto H, Cheng H, Xu A, Lai W, Wang Y, Zheng Z, Wang M, Liu X, Ma B, Xu J. Continental scale deciphering of microbiome networks untangles the phyllosphere homeostasis in tea plant. J Adv Res 2023; 44:13-22. [PMID: 36725184 PMCID: PMC9936419 DOI: 10.1016/j.jare.2022.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/21/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Assembly and co-occurrence of the host co-evolved microbiota are essential ecological and evolutionary processes, which is not only crucial for managing individual plant fitness but also ecological function. However, understanding of the microbiome assembly and co-occurrence in higher plants is not well understood. The tea plant was shown to contribute the forest fitness due to the microbiome assembled in the phyllosphere; the landscape of microbiome assembly in the tea plants and its potential implication on phyllosphere homestasis still remains untangled. OBJECTIVES This study aimed to deciphering of the microbiome networks of the tea plants at a continental scale. It would provide fundamental insights into the factors driving the microbiome assembly, with an extended focus on the resilience towards the potential pathogen in the phyllosphere. METHODS We collected 225 samples from 45 locations spanning approximately 2000-km tea growing regions across China. By integration of high-throughput sequencing data, physicochemical properties profiling and bioinformatics analyses, we investigated continental scale microbiome assembly and co-occurrence in the tea plants. Synthetic assemblages, interaction assay and RT-qPCR were further implemented to analyze the microbial interaction indexed in phyllosphere. RESULTS A trade-off between stochastic and deterministic processes in microbiomes community assembly was highlighted. Assembly processes were dominated by deterministic processes in bulk and rhizosphere soils, and followed by stochastic processes in roots and leaves with amino acids as critical drivers for environmental selection. Sphingobacteria and Proteobacteria ascended from soils to leaves to sustain a core leaf taxa. The core taxa formed a close association with a prevalent foliar pathogen in the co-occurrence network and significantly attenuated the expression of a set of essential virulence genes in pathogen. CONCLUSION Our study unveils the mechanism underpinning microbiome assembly in the tea plants, and a potential implication of the microbiome-mediated resilience framework on the phyllosphere homeostasis.
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Affiliation(s)
- Ping Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Erinne Stirling
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Hengtong Xie
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Wenbing Li
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou 310018, China
| | - Haruna Matsumoto
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Haiyan Cheng
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Anan Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Wanyi Lai
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Yuefei Wang
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Zuntao Zheng
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China.
| | - Xingmei Liu
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China.
| | - Jianming Xu
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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Murillo T, Schneider D, Heistermann M, Daniel R, Fichtel C. Assessing the drivers of gut microbiome composition in wild redfronted lemurs via longitudinal metacommunity analysis. Sci Rep 2022; 12:21462. [PMID: 36509795 PMCID: PMC9744850 DOI: 10.1038/s41598-022-25733-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiome influences host's immunity, development, and metabolism and participates in the gut-brain axis, thus impacting the health of the host. It is a dynamic community varying between individuals and within individuals at different time points. Hence, determining the factors causing this variability may elucidate their impact on host's health. However, understanding the drivers of variation has proven difficult particularly as multiple interactions occur simultaneously in the gut microbiome. We investigated the factors shaping the gut microbiome by applying the metacommunity concept where the gut microbiome is considered as a microbial community shaped by the interactions within the community, with the host and microbial communities outside the host, this through a longitudinal study in a wild primate. Focal behavioral data were collected for 1 year in four groups of redfronted lemurs to determine individual social and feeding behaviors. In addition, regular fecal samples were collected to assess bacteria, protozoa, and helminths through marker gene analysis and to measure fecal glucocorticoid metabolite (fGCM) concentrations to investigate the impact of physiological stress on the gut microbiome. Higher consumption of leaves and elevated fGCM concentrations correlated with higher alpha diversity, which also differed among groups. The major drivers of variation in beta diversity were group membership, precipitation and fGCM concentrations. We found positive and negative associations between bacterial genera and almost all studied factors. Correlations between bacterial indicator networks and social networks indicate transmission of bacteria between interacting individuals. We detected that processes occurring inside the gut environment are shaping the gut microbiome. Host associated factors such as, HPA axis, dietary changes, and fluctuations in water availability had a greater impact than interactions within the microbial community. The interplay with microbial communities outside the host also shape the gut microbiome through the exchange of bacteria through social relationships between individuals and the acquisition of microorganisms from environmental water sources.
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Affiliation(s)
- Tatiana Murillo
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany.
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | | | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Claudia Fichtel
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany
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44
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The nonindustrialised microbiome in a modern world. Clin Sci (Lond) 2022; 136:1683-1690. [DOI: 10.1042/cs20220203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022]
Abstract
Abstract
The microbiome contributes to human development and maturation, and is essential for maintenance of health and prevention of disease. While the human genome encodes one’s identity, the microbiome – also individually unique – provides a window on one’s lifestyle and exposure to environmental variables. The microbiome thus serves as a biomarker of host health and a driver of certain diseases. However, current understanding of the gut microbiome is largely based on studies of industrialised peoples of North America and Europe. Gaps in knowledge of the microbiomes of other groups, particularly those in developing or nonindustrialised societies, are important, particularly in view of contrasting epidemiological risks of acquiring chronic inflammatory and metabolic disorders. Here, we explore underlying mechanisms of microbiome differences and whether the potential benefits of nonindustrialised microbiome can be realised in a modern world.
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45
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Johnson KVA, Watson KK, Dunbar RIM, Burnet PWJ. Sociability in a non-captive macaque population is associated with beneficial gut bacteria. Front Microbiol 2022; 13:1032495. [PMID: 36439813 PMCID: PMC9691693 DOI: 10.3389/fmicb.2022.1032495] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022] Open
Abstract
The relationship between social behaviour and the microbiome is known to be reciprocal. Research in wild animal populations, particularly in primate social groups, has revealed the role that social interactions play in microbial transmission, whilst studies in laboratory animals have demonstrated that the gut microbiome can affect multiple aspects of behaviour, including social behaviour. Here we explore behavioural variation in a non-captive animal population with respect to the abundance of specific bacterial genera. Social behaviour based on grooming interactions is assessed in a population of rhesus macaques (Macaca mulatta), and combined with gut microbiome data. We focus our analyses on microbiome genera previously linked to sociability and autistic behaviours in rodents and humans. We show in this macaque population that some of these genera are also related to an individual's propensity to engage in social interactions. Interestingly, we find that several of the genera positively related to sociability, such as Faecalibacterium, are well known for their beneficial effects on health and their anti-inflammatory properties. In contrast, the genus Streptococcus, which includes pathogenic species, is more abundant in less sociable macaques. Our results indicate that microorganisms whose abundance varies with individual social behaviour also have functional links to host immune status. Overall, these findings highlight the connections between social behaviour, microbiome composition, and health in an animal population.
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Affiliation(s)
- Katerina V.-A. Johnson
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom,Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom,*Correspondence: Katerina V.-A. Johnson,
| | - Karli K. Watson
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, CO, United States
| | - Robin I. M. Dunbar
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
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Zhu D, Xie T, Du R, Guo L. Characterizing the Gut Microbiota of Eurasian Otter ( Lutra lutra chinensis) and Snub-Nosed Monkey ( Rhinopithecus roxellana) to Enhance Conservation Practices in the Foping National Nature Reserve of China. Animals (Basel) 2022; 12:ani12223097. [PMID: 36428325 PMCID: PMC9686598 DOI: 10.3390/ani12223097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Understanding the interaction between the microbial composition in the habitat and the gut of wildlife will contribute to conservation efforts since changes in the gut microbiome have been proven to influence the healthy and nutritional status of the host. This study analyzed the relationship between soil microbes and the microbial diversity and structure of the distal gut of the terrestrial golden snub-nosed monkey and Eurasian otter in the Foping National Nature Reserve (FNNR). A total of 15 otter fecal samples and 18 monkey fecal samples were collected from which 5 and 6 samples, respectively, were randomly selected for microbiome analysis. The remaining samples were used for fecal short-chain fatty acids (SCFAs) analysis. Soil samples from the otter and monkey habitats at each sampling point (eight in total) were also collected for microbiome analysis. The microbial phyla with the greatest relative abundance in soil or animal samples were Proteobacteria (41.2, 32.7, and 73.3% for soil, otters, and monkeys, respectively), Firmicutes (0.4% soil, 30.1% otters, and 14.4% monkeys), Bacteroidota (5.6% soil, 17.0% otters, and 8.3% monkeys), and Acidobacteriota (24.6% soil, 1.7% otters, and 0.1% monkeys). The estimation of alpha diversity indices revealed that the feature, Chao1, and Shannon indices of the soil microbiome were the greatest (p < 0.01) among the three groups, followed by those of the otter microbiome and those of the monkey microbiome (p < 0.01). Beta diversity analyses confirmed differences in the microbiota of the three types of samples. The determination of SCFA concentration in feces revealed that total volatile fatty acids, acetic acid, and isovaleric acid were greater (p < 0.05) in otters than in monkeys, while propionic acid followed the opposite pattern (p < 0.05). Correlation analysis of the microbiome and SCFA contents showed that propionic acid was positively correlated with significantly different bacterial groups, while acetic and butyric acid and total volatile acids were negatively correlated. This study confirmed that the fecal microbes of Eurasian otters and golden snub-nosed monkeys in the reserve are related to the soil microbial communities of their habitats, but they have different bacterial community structures and compositions, and there are different SCFA metabolic patterns in the gut of the two animals. The present study will help to improve wildlife protection in the FNNR.
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Affiliation(s)
- Dapeng Zhu
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- Foping National Nature Reserve, Hanzhong 723000, China
| | - Tongtong Xie
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ruifang Du
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Long Guo
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou 730020, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- Correspondence:
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Kuthyar S, Watson K, Huang S, Brent LJN, Platt M, Horvath J, Gonzalez-Martinez J, Martínez M, Godoy-Vitorino F, Knight R, Dominguez-Bello MG, Amato KR. Limited microbiome differences in captive and semi-wild primate populations consuming similar diets. FEMS Microbiol Ecol 2022; 98:fiac098. [PMID: 36047944 PMCID: PMC9528791 DOI: 10.1093/femsec/fiac098] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Gut microbial communities are shaped by a myriad of extrinsic factors, including diet and the environment. Although distinct human populations consistently exhibit different gut microbiome compositions, variation in diet and environmental factors are almost always coupled, making it difficult to disentangle their relative contributions to shaping the gut microbiota. Data from discrete animal populations with similar diets can help reduce confounds. Here, we assessed the gut microbiota of free-ranging and captive rhesus macaques with at least 80% diet similarity to test the hypothesis that hosts in difference environments will have different gut microbiomes despite a shared diet. Although we found that location was a significant predictor of gut microbial composition, the magnitude of observed differences was relatively small. These patterns suggest that a shared diet may limit the typical influence of environmental microbial exposure on the gut microbiota.
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Affiliation(s)
- Sahana Kuthyar
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
- Division of Biological Sciences, University of California San Diego 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Karli Watson
- Institute of Cognitive Science, University of Colorado Boulder 1777 Exposition Drive Boulder, CO, 80309, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter Stocker Rd, Exeter EX4 4PY, United Kingdom
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd Philadelphia, PA, 19104, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, 425 S. University Ave Philadelphia, PA, 19104-6018, USA
- Department of Marketing, Wharton School of Business, University of Pennsylvania, 3620 Locust Walk, Philadelphia, PA, USA 19104, PA, USA
| | - Julie Horvath
- Research and Collections, North Carolina Museum of Natural Sciences, 11 W Jones St, Raleigh, NC, 27601, USA
- Biological and Biomedical Sciences Department, North Carolina Central University, 1801 Fayetteville St, Durham, NC, 27707, USA
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Campus Box 90383 Durham, NC, 27708, USA
- Department of Biological Sciences, North Carolina State University, 3510 Thomas Hall Campus Box 7614 Raleigh, NC, USA 27695, USA
| | - Janis Gonzalez-Martinez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Melween Martínez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, Medical Sciences Campus, PO BOX 365067 San Juan, PR 00936-5067, Puerto Rico
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
- Department of Computer Sciences and Engineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, USA 08901, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA 1810, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
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48
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Liu H, Chen T, Li Y, Zheng J, Liu Z, Li Y, Huang Z. Seasonal variations in gut microbiota of semiprovisioned rhesus macaques (Macaca mulatta) living in a limestone forest of Guangxi, China. Front Microbiol 2022; 13:951507. [PMID: 36204603 PMCID: PMC9530203 DOI: 10.3389/fmicb.2022.951507] [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: 05/24/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022] Open
Abstract
Assessment of gut microbiota, used to explore ecological adaptation strategies and evolutionary potential of species, provides a new viewpoint to the conservation and management of endangered animals. In this research, the gut microbiota of a group of semiprovisioned rhesus macaques (Macaca mulatta) living in a limestone forest exhibiting seasonal changes in plant items were studied to investigate the adaptation strategies of these macaques to this specific habitat. The findings revealed significant seasonal changes in the diversity and composition of the rhesus macaques’ gut microbiota, which were higher in the rainy season than in the dry season. In the rainy season, Bacteroidetes (31.83 ± 16.14% vs. 19.91 ± 18.20%) were significantly increased and Prevotella (23.70 ± 15.33% vs. 15.40 ± 16.10%), UCG-002 (4.48 ± 3.16% vs. 2.18 ± 2.01%), and UCG-005 (4.22 ± 2.90% vs. 2.03 ± 1.82%) were more enriched at the genus level. In the dry season, Firmicutes significantly increased (71.84 ± 19.28% vs. 60.91 ± 16.77%), and Clostridium_sensu_stricto_1 (8.45 ± 9.72% vs. 4.76 ± 6.64%), Enterococcus (10.17 ± 13.47% vs. 0.69 ± 2.36%), and Sarcina (4.72 ± 7.66% vs. 2.45 ± 4.71%) were more enriched at the genus level. These differences in gut microbiota may be due to seasonal variations in plant items in these habitats alongside changes in the provisioned foods from tourists. Additionally, deterministic processes predominate the assembly of the macaque’s gut microbiota community. This indicates that the animal’s high reliance on natural plants and provisioned foods increased the impact of deterministic processes. This study concludes that a balance between provisioned foods and natural plants might be vital in shaping the gut microbiota in the macaques. Furthermore, the dynamic adjustment in gut microbiota might be a physiological mechanism for the macaques in response to the seasonal variations in the ecological factors and food provision.
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Affiliation(s)
- Hongying Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Ting Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Jingjin Zheng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zheng Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
- *Correspondence: Zhonghao Huang,
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Baniel A, Petrullo L, Mercer A, Reitsema L, Sams S, Beehner JC, Bergman TJ, Snyder-Mackler N, Lu A. Maternal effects on early-life gut microbiota maturation in a wild nonhuman primate. Curr Biol 2022; 32:4508-4520.e6. [PMID: 36099914 DOI: 10.1016/j.cub.2022.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
Early-life microbial colonization is an important process shaping host physiology,1-3 immunity,4-6 and long-term health outcomes7-10 in humans. However, our understanding of this dynamic process remains poorly investigated in wild animals,11-13 where developmental mechanisms can be better understood within ecological and evolutionarily relevant contexts.11,12 Using one of the largest developmental datasets on a wild primate-the gelada (Theropithecus gelada)-we used 16S rRNA amplicon sequencing to characterize gut microbiota maturation during the first 3 years of life and assessed the role of maternal effects in shaping offspring microbiota assembly. In contrast to recent data on chimpanzees, postnatal microbial colonization in geladas was highly similar to humans:14 microbial alpha diversity increased rapidly following birth, followed by gradual changes in composition until weaning. Dietary changes associated with weaning (from milk- to plant-based diet) were the main drivers of shifts in taxonomic composition and microbial predicted functional pathways. Maternal effects were also an important factor influencing the offspring gut microbiota. During nursing (<12 months), offspring of experienced (multi-time) mothers exhibited faster functional microbial maturation, likely reflecting the general faster developmental pace of infants born to these mothers. Following weaning (>18 months), the composition of the juvenile microbiota tended to be more similar to the maternal microbiota than to the microbiota of other adult females, highlighting that maternal effects may persist even after nursing cessation.15,16 Together, our findings highlight the dynamic nature of early-life gut colonization and the role of maternal effects in shaping this trajectory in a wild primate.
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Affiliation(s)
- Alice Baniel
- Center for Evolution and Medicine, Arizona State University, E Tyler Mall, Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, E Tyler Mall, Tempe, AZ 85287, USA.
| | - Lauren Petrullo
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA
| | - Arianne Mercer
- Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA
| | - Laurie Reitsema
- Department of Anthropology, University of Georgia, Jackson St., Athens, GA 30602, USA
| | - Sierra Sams
- Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA
| | - Jacinta C Beehner
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA; Department of Anthropology, University of Michigan, S University Ave., Ann Arbor, MI 48109, USA
| | - Thore J Bergman
- Department of Psychology, University of Michigan, Church St., Ann Arbor, MI 48109, USA; Department of Ecology and Evolutionary Biology, University of Michigan, N University Ave., Ann Arbor, MI 48109, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, E Tyler Mall, Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, E Tyler Mall, Tempe, AZ 85287, USA; Department of Psychology, University of Washington, Okanogan Ln., Seattle, WA 98195, USA; School for Human Evolution and Social Change, Arizona State University, Cady Mall, Tempe, AZ 85287, USA.
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Circle Rd., Stony Brook, NY 11794, USA.
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50
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Abstract
The gut microbiome is a contributory factor in ageing-related health loss and in several non-communicable diseases in all age groups. Some age-linked and disease-linked compositional and functional changes overlap, while others are distinct. In this Review, we explore targeted studies of the gut microbiome of older individuals and general cohort studies across geographically distinct populations. We also address the promise of the targeted restoration of microorganisms associated with healthier ageing.
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Affiliation(s)
- Tarini Shankar Ghosh
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
- Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland.
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
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