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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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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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3
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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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4
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Dasari MR, Roche KE, Jansen D, Anderson J, Alberts SC, Tung J, Gilbert JA, Blekhman R, Mukherjee S, Archie EA. Social and environmental predictors of gut microbiome age in wild baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.605707. [PMID: 39131274 PMCID: PMC11312535 DOI: 10.1101/2024.08.02.605707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Understanding why some individuals age faster than others is essential to evolutionary biology and geroscience, but measuring variation in biological age is difficult. One solution may lie in measuring gut microbiome composition because microbiota change with many age-related factors (e.g., immunity and behavior). Here we create a microbiome-based age predictor using 13,563 gut microbial profiles from 479 wild baboons collected over 14 years. The resulting "microbiome clock" predicts host chronological age. Deviations from the clock's predictions are linked to demographic and socio-environmental factors that predict baboon health and survival: animals who appear old-for-age tend to be male, sampled in the dry season (for females), and high social status (both sexes). However, an individual's "microbiome age" does not predict the attainment of developmental milestones or lifespan. Hence, the microbiome clock accurately reflects age and some social and environmental conditions, but not the pace of development or mortality risk.
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Affiliation(s)
- Mauna R. Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- California Academy of Sciences, San Francisco, CA, USA
| | - Kimberly E. Roche
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jordan Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Faculty of Life Sciences, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Jack A. Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sayan Mukherjee
- Departments of Statistical Science, Mathematics, Computer Science, and Bioinformatics & Biostatistics, Duke University, Durham, NC, USA
- Center for Scalable Data Analytics and Artificial Intelligence, University of Leipzig, Leipzig Germany
- Max Planck Institute for Mathematics in the Natural Sciences, Leipzig, Germany
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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5
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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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6
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Martignoni MM, Raulo A, Linkovski O, Kolodny O. SIR+ models: accounting for interaction-dependent disease susceptibility in the planning of public health interventions. Sci Rep 2024; 14:12908. [PMID: 38839831 PMCID: PMC11153654 DOI: 10.1038/s41598-024-63008-9] [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: 10/10/2023] [Accepted: 05/23/2024] [Indexed: 06/07/2024] Open
Abstract
Avoiding physical contact is regarded as one of the safest and most advisable strategies to follow to reduce pathogen spread. The flip side of this approach is that a lack of social interactions may negatively affect other dimensions of health, like induction of immunosuppressive anxiety and depression or preventing interactions of importance with a diversity of microbes, which may be necessary to train our immune system or to maintain its normal levels of activity. These may in turn negatively affect a population's susceptibility to infection and the incidence of severe disease. We suggest that future pandemic modelling may benefit from relying on 'SIR+ models': epidemiological models extended to account for the benefits of social interactions that affect immune resilience. We develop an SIR+ model and discuss which specific interventions may be more effective in balancing the trade-off between minimizing pathogen spread and maximizing other interaction-dependent health benefits. Our SIR+ model reflects the idea that health is not just the mere absence of disease, but rather a state of physical, mental and social well-being that can also be dependent on the same social connections that allow pathogen spread, and the modelling of public health interventions for future pandemics should account for this multidimensionality.
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Affiliation(s)
- Maria M Martignoni
- Department of Ecology, Evolution and Behavior, Faculty of Sciences, A. Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK
- Department of Computing, University of Turku, Turku, Finland
| | - Omer Linkovski
- Department of Psychology and The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, Faculty of Sciences, A. Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
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7
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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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8
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Bornbusch SL, Power ML, Schulkin J, Drea CM, Maslanka MT, Muletz-Wolz CR. Integrating microbiome science and evolutionary medicine into animal health and conservation. Biol Rev Camb Philos Soc 2024; 99:458-477. [PMID: 37956701 DOI: 10.1111/brv.13030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Michael L Power
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Jay Schulkin
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, 1959 NE Pacific St., Box 356460, Seattle, WA, 98195, USA
| | - Christine M Drea
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences, Campus Box 90383, Durham, NC, 27708, USA
| | - Michael T Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
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9
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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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10
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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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11
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Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML, Horvath JE. Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques. Microbiol Spectr 2023; 11:e0297423. [PMID: 37750731 PMCID: PMC10580906 DOI: 10.1128/spectrum.02974-23] [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: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
While skin microbes are known to mediate human health and disease, there has been minimal research on the interactions between skin microbiota, social behavior, and year-to-year effects in non-human primates-important animal models for translational biomedical research. To examine these relationships, we analyzed skin microbes from 78 rhesus macaques living on Cayo Santiago Island, Puerto Rico. We considered age, sex, and social group membership, and characterized social behavior by assessing dominance rank and patterns of grooming as compared to nonsocial behaviors. To measure the effects of a shifting environment, we sampled skin microbiota (based on sequence analysis of the 16S rRNA V4 region) and assessed weather across sampling periods between 2013 and 2015. We hypothesized that, first, monkeys with similar social behavior and/or in the same social group would possess similar skin microbial composition due, in part, to physical contact, and, second, microbial diversity would differ across sampling periods. We found significant phylum-level differences between social groups in the core microbiome as well as an association between total grooming rates and alpha diversity in the complete microbiome, but no association between microbial diversity and measures of rank or other nonsocial behaviors. We also identified alpha and beta diversity differences in microbiota and differential taxa abundance across two sampling periods. Our findings indicate that social dynamics interact with yearly environmental changes to shape the skin microbiota in rhesus macaques, with potential implications for understanding the factors affecting the microbiome in humans, which share many biological and social characteristics with these animals. IMPORTANCE Primate studies are valuable for translational and evolutionary insights into the human microbiome. The majority of primate microbiome studies focus on the gut, so less is known about the factors impacting the microbes on skin and how their links affect health and behavior. Here, we probe the impact of social interactions and the yearly environmental changes on food-provisioned, free-ranging monkeys living on a small island. We expected animals that lived together and groomed each other would have more similar microbes on their skin, but surprisingly found that the external environment was a stronger influence on skin microbiome composition. These findings have implications for our understanding of the human skin microbiome, including potential manipulations to improve health and treat disease.
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Affiliation(s)
| | - Michael J. Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - JiCi Wang
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Allison N. Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Angelina Ruiz-Lambides
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Lauren J. N. Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, United Kingdom
| | - Michael L. Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Marketing Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie E. Horvath
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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12
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Vaziri GJ, Jones MM, Carr HA, Nuñez CMV. Out of the stable: Social disruption and concurrent shifts in the feral mare ( Equus caballus) fecal microbiota. Ecol Evol 2023; 13:e10079. [PMID: 37187967 PMCID: PMC10175550 DOI: 10.1002/ece3.10079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
The disruption of animals' symbiotic bacterial communities (their microbiota) has been associated with myriad factors including changes to the diet, hormone levels, and various stressors. The maintenance of healthy bacterial communities may be especially challenging for social species as their microbiotas are also affected by group membership, social relationships, microbial transfer between individuals, and social stressors such as increased competition and rank maintenance. We investigated the effects of increased social instability, as determined by the number of group changes made by females, on the microbiota in free-living, feral horses (Equus caballus) on Shackleford Banks, a barrier island off the North Carolina coast. Females leaving their groups to join new ones had fecal microbial communities that were similarly diverse but compositionally different than those of females that did not change groups. Changing groups was also associated with the increased abundance of a several bacterial genera and families. These changes may be significant as horses are heavily dependent upon their microbial communities for nutrient absorption. Though we cannot identify the particular mechanism(s) driving these changes, to the best of our knowledge, ours is the first study to demonstrate an association between acute social perturbations and the microbiota in a free-ranging mammal.
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Affiliation(s)
- Grace J. Vaziri
- Ecology and Evolutionary BiologyUniversity of ConnecticutMansfieldConnecticutUSA
| | - Maggie M. Jones
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmes, IowaUSA
- Present address:
School of Natural Resources and EnvironmentUniversity of FloridaGainesvilleFloridaUSA
| | - Haley A. Carr
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmes, IowaUSA
| | - Cassandra M. V. Nuñez
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmes, IowaUSA
- Department of Biological SciencesThe University of MemphisMemphisTennesseeUSA
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13
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Cheng Q, Krajmalnik-Brown R, DiBaise JK, Maldonado J, Guest MA, Todd M, Langer SL. Relationship Functioning and Gut Microbiota Composition among Older Adult Couples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085435. [PMID: 37107717 PMCID: PMC10138905 DOI: 10.3390/ijerph20085435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/11/2023] [Accepted: 03/23/2023] [Indexed: 05/11/2023]
Abstract
An emerging area of research extends work on couple functioning and physical health to gut health, a critical marker of general health and known to diminish with age. As a foray into this area, we conducted a pilot study to (1) determine the feasibility of remote data collection, including a fecal sample, from older adult couples, (2) examine within-couple concordance in gut microbiota composition, and (3) examine associations between relationship functioning and gut microbiota composition. Couples (N = 30) were recruited from the community. The participants' demographic characteristics were as follows: M (SD) age = 66.6 (4.8), 53% female, 92% White, and 2% Hispanic. Two of the couples were same-sex. All 60 participants completed self-report measures and supplied a fecal sample for microbiome analysis. Microbial DNA was extracted from the samples, and the 16S rRNA gene V4 region was amplified and sequenced. The results indicated that individuals shared more similar gut microbial composition with their partners than with others in the sample, p < 0.0001. In addition, individuals with better relationship quality (greater relationship satisfaction and intimacy and less avoidant communication) had greater microbial diversity, p < 0.05, a sign of healthier gut microbiota. Further research with a larger and more diverse sample is warranted to elucidate mechanisms.
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Affiliation(s)
- Qiwen Cheng
- Biodesign Center for Health through Microbiomes, Arizona State University, Tempe, AZ 85281, USA; (Q.C.); (R.K.-B.)
| | - Rosa Krajmalnik-Brown
- Biodesign Center for Health through Microbiomes, Arizona State University, Tempe, AZ 85281, USA; (Q.C.); (R.K.-B.)
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85281, USA
| | - John K. DiBaise
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic College of Medicine and Science, Scottsdale, AZ 85259, USA;
| | - Juan Maldonado
- Knowledge Enterprise Genomics Core, Arizona State University, Tempe, AZ 85281, USA;
| | - M. Aaron Guest
- Center for Innovation in Healthy and Resilient Aging, Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA;
| | - Michael Todd
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA
| | - Shelby L. Langer
- Center for Health Promotion and Disease Prevention, Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA
- Correspondence: ; Tel.: +1-602-496-0823
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14
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Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study. mSystems 2023; 8:e0096522. [PMID: 36533929 PMCID: PMC9948708 DOI: 10.1128/msystems.00965-22] [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] [Indexed: 12/23/2022] Open
Abstract
The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.
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15
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Bensch HM, Tolf C, Waldenström J, Lundin D, Zöttl M. Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent. Anim Microbiome 2023; 5:9. [PMID: 36765400 PMCID: PMC9912604 DOI: 10.1186/s42523-023-00231-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND In mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species. RESULTS We found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes. CONCLUSION We found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.
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Affiliation(s)
- Hanna M. Bensch
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden ,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| | - Conny Tolf
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Jonas Waldenström
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Daniel Lundin
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Markus Zöttl
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden ,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
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16
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Grieneisen L, Blekhman R, Archie E. How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome. Gut Microbes 2023; 15:2178797. [PMID: 36794811 PMCID: PMC9980606 DOI: 10.1080/19490976.2023.2178797] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
A key component of microbiome research is understanding the role of host genetic influence on gut microbial composition. However, it can be difficult to link host genetics with gut microbial composition because host genetic similarity and environmental similarity are often correlated. Longitudinal microbiome data can supplement our understanding of the relative role of genetic processes in the microbiome. These data can reveal environmentally contingent host genetic effects, both in terms of controlling for environmental differences and in comparing how genetic effects differ by environment. Here, we explore four research areas where longitudinal data could lend new insights into host genetic effects on the microbiome: microbial heritability, microbial plasticity, microbial stability, and host and microbiome population genetics. We conclude with a discussion of methodological considerations for future studies.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Elizabeth Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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17
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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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18
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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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19
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Yan B, Jia T, Wang Z, Zhu W. Comparative research of intestinal microbiota diversity and body mass regulation in Eothenomys miletus from different areas of Hengduan mountain regions. Front Microbiol 2022; 13:1026841. [PMID: 36325022 PMCID: PMC9619095 DOI: 10.3389/fmicb.2022.1026841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
In order to investigate the effects of different areas on intestinal bacterial diversity and body mass regulation in Eothenomys miletus from Hengduan mountain regions, and to explore the community structure and diversity of intestinal microflora and their role in body mass regulation. E. miletus was collected from five areas including Deqin (DQ), Xianggelila (XGLL), Lijiang (LJ), Jianchuan (JC), and Dali (DL), we used 16S rRNA sequencing technology combined with physiological and morphological methods to study the intestinal microbiota diversity, abundance and community structure of the intestinal bacteria in winter, and to explore the influence of geographical factors, physiological indicators including food intake, resting metabolic rate (RMR), non-shivering thermogenesis (NST), neuropeptide Y (NPY), Agouti-Related Protein (AgRP), proopiomelanocortin (POMC), cocaine and amphetamine regulated transcription peptide (CART), and morphological indicators including body mass, body length and other nine indicators on the intestinal microflora diversity in E. miletus. The results showed that there were significant differences in metabolic indexes such as RMR, NST, NPY, AgRP, and morphological indexes such as body length, tail length and ear length among the five regions. Bacterial community in intestinal tract of E. miletus mainly includes three phyla, of which Firmicutes is the dominant phyla, followed by Bacteroidetes and Tenericutes. At the genus level, the dominant bacterial genera were S24-7(UG), Clostridiales (UG), and Lachnospiraceae (UG), etc. α diversity of intestinal microorganisms in DL and JC were significantly different from that in the other three regions. Genera of intestinal microorganisms in DL and JC were also the most. Moreover, Bacteroides, Ruminococcus, and Treponema could affect energy metabolism in E. miletus, which were closely related to the environment in which they lived. All of these results indicated that different areas in Hengduan Mountain had certain effects on the structure of intestinal microbial community in E. miletus, which were responded positively to changes in food abundance and other environmental factors. Furthermore, Firmicutes and Bacteroidetes play an important role in the body mass regulation in E. miletus.
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Affiliation(s)
- Bowen Yan
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Ting Jia
- Yunnan College of Business Management, Kunming, China
| | - Zhengkun Wang
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Wanlong Zhu
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Sciences, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan Province for Biomass Energy and Environment Biotechnology, Kunming, China
- *Correspondence: Wanlong Zhu,
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20
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Zhang T, Li M, Shi T, Yan Y, Niyazbekova Z, Wang X, Li Z, Jiang Y. Transmission of the gut microbiome in cohousing goats and pigs. Front Microbiol 2022; 13:948617. [PMID: 36160207 PMCID: PMC9490217 DOI: 10.3389/fmicb.2022.948617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Social interaction facilitates the horizontal transmission of the microbiota between different individuals. However, little is known about the level of microbiota transmission in different livestock animals and different digestive tracts. The Hainan black goat and Wuzhishan pig are typical tropical local breeds on Hainan Island in China. Thus, we sampled and analyzed the gut microbiome in Hainan black goats (cecum and rumen) and Wuzhishan pigs (cecum) to study horizontal transmission by rearing them in the same pen (six goats and six pigs) or separate pens (nine goats and nine pigs). De novo assembly and binning recovered 3,262 strain-level and 2,488 species-level metagenome-assembled genomes (MAGs) using ∼1.3 Tb sequencing data. Of these MAGs, 1,856 MAGs were identified as novel strain. Compared with goats living in separate pens, social interaction in the same pen promotes community homogeneity in the rumen microbiome (P < 0.05) and the cecum microbiome (P < 0.05), respectively. Notably, approximately 7.08% (231/3262) of the gut microbial population could transmit during cohousing, 12 strains only in inter-species transmission, versus 190 strains only in intra-species transmission, and 10 strains only in foregut and hindgut transmission. In addition, the social contact group has high transmitted strain abundance, which is correlated with community composition. This study provided a new insight into the influence of social interaction on the animal gut microbiota.
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Affiliation(s)
- Tingting Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mao Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Tao Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yueyang Yan
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhannur Niyazbekova
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Zongjun Li,
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- *Correspondence: Yu Jiang,
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21
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Pinacho-Guendulain B, Montiel-Castro AJ, Ramos-Fernández G, Pacheco-López G. Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates. Front Integr Neurosci 2022; 16:876849. [PMID: 36110388 PMCID: PMC9468716 DOI: 10.3389/fnint.2022.876849] [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: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.
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Affiliation(s)
- Braulio Pinacho-Guendulain
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Ciudad de México, Mexico
| | - Augusto Jacobo Montiel-Castro
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- *Correspondence: Augusto Jacobo Montiel-Castro,
| | - Gabriel Ramos-Fernández
- Institute for Research on Applied Mathematics and Systems (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Gustavo Pacheco-López
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- Gustavo Pacheco-López,
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22
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Fitzpatrick CR, Toor I, Holmes MM. Colony but not social phenotype or status structures the gut bacteria of a eusocial mammal. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03230-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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23
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Hernández M, Ancona S, Díaz De La Vega-Pérez AH, Muñoz-Arenas LC, Hereira-Pacheco SE, Navarro-Noya YE. Is Habitat More Important than Phylogenetic Relatedness for Elucidating the Gut Bacterial Composition in Sister Lizard Species? Microbes Environ 2022; 37. [PMID: 35768277 PMCID: PMC9530725 DOI: 10.1264/jsme2.me21087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The gut microbiota influences the phenotype and fitness of a host; however, limited information is currently available on the diversity and functions of the gut microbiota in wild animals. Therefore, we herein examined the diversity, composition, and potential functions of the gut microbiota in three Sceloporus lizards: Sceloporus aeneus, S. bicanthalis, and S. grammicus, inhabiting different habitats in a mountainous ecosystem. The gut bacterial community of S. bicanthalis from alpine grasslands at 4,150 m a.s.l. exhibited greater taxonomic, phylogenetic, and functional alpha diversities than its sister species S. aeneus from cornfields and human-induced grasslands at 2,600 m a.s.l. Bacteria of the genus Blautia and metabolic functions related to the degradation of aromatic compounds were more abundant in S. bicanthalis than in S. aeneus, whereas Oscillibacter and predicted functions related to amino acid metabolism and fermentation were more abundant in S. aeneus. The structure of the dominant and most prevalent bacteria, i.e., the core microbiota, was similar between the sister species from different habitats, but differed between S. grammicus and S. aeneus cohabiting at 2,600 m a.s.l. and between S. grammicus and S. bicanthalis cohabiting at 4,150 m a.s.l. These results suggest that phylogenetic relatedness defines the core microbiota, while the transient, i.e., non-core, microbiota is influenced by environmental differences in the habitats. Our comparisons between phylogenetically close species provide further evidence for the specialized and complex associations between hosts and the gut microbiota as well as insights into the roles of phylogeny and ecological factors as drivers of the gut microbiota in wild vertebrates.
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Affiliation(s)
- Mauricio Hernández
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala
| | - Sergio Ancona
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México
| | | | | | - Stephanie E Hereira-Pacheco
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala
| | - Yendi E Navarro-Noya
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala
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24
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Lajoie G, Parfrey LW. Beyond specialization: re-examining routes of host influence on symbiont evolution. Trends Ecol Evol 2022; 37:590-598. [PMID: 35466020 DOI: 10.1016/j.tree.2022.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 11/17/2022]
Abstract
Our understanding of host influence on microbial evolution has focused on symbiont specialization and the genomic streamlining that often accompanies it. However, a vast diversity of symbiotic lineages facultatively interact with hosts or associate with multiple hosts. Yet, there are no clear expectations for how host association influences the niche of these symbionts or their evolution. Here, we discuss how weak or variable selection on microbial symbiotic associations, horizontal transmission, and low costs of adaptation to novel host habitats are predicted to promote the expansion or maintenance of microbial niches. This broad perspective will aid in developing better and more general predictions for evolution in microbial symbioses.
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Affiliation(s)
- Geneviève Lajoie
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4.
| | - Laura Wegener Parfrey
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4
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25
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Sadoughi B, Schneider D, Daniel R, Schülke O, Ostner J. Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized. MICROBIOME 2022; 10:95. [PMID: 35718778 PMCID: PMC9206754 DOI: 10.1186/s40168-022-01283-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pronounced heterogeneity of age trajectories has been identified as a hallmark of the gut microbiota in humans and has been explained by marked changes in lifestyle and health condition. Comparatively, age-related personalization of microbiota is understudied in natural systems limiting our comprehension of patterns observed in humans from ecological and evolutionary perspectives. RESULTS Here, we tested age-related changes in the diversity, stability, and composition of the gut bacterial community using 16S rRNA gene sequencing with dense repeated sampling over three seasons in a cross-sectional age sample of adult female Assamese macaques (Macaca assamensis) living in their natural forest habitat. Gut bacterial composition exhibited a personal signature which became less stable as individuals aged. This lack of stability was not explained by differences in microbiota diversity but rather linked to an increase in the relative abundance of rare bacterial taxa. The lack of age-related changes in core taxa or convergence with age to a common state of the community hampered predicting gut bacterial composition of aged individuals. On the contrary, we found increasing personalization of the gut bacterial composition with age, indicating that composition in older individuals was increasingly divergent from the rest of the population. Reduced direct transmission of bacteria resulting from decreasing social activity may contribute to, but not be sufficient to explain, increasing personalization with age. CONCLUSIONS Together, our results challenge the assumption of a constant microbiota through adult life in a wild primate. Within the limits of this study, the fact that increasing personalization of the aging microbiota is not restricted to humans suggests the underlying process to be evolved instead of provoked only by modern lifestyle of and health care for the elderly. Video abstract.
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Affiliation(s)
- Baptiste Sadoughi
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany.
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Oliver Schülke
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Julia Ostner
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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26
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Petrullo L, Ren T, Wu M, Boonstra R, Palme R, Boutin S, McAdam AG, Dantzer B. Glucocorticoids coordinate changes in gut microbiome composition in wild North American red squirrels. Sci Rep 2022; 12:2605. [PMID: 35173201 PMCID: PMC8850573 DOI: 10.1038/s41598-022-06359-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/24/2022] [Indexed: 12/31/2022] Open
Abstract
The gut microbiome impacts host health and fitness, in part through the diversification of gut metabolic function and pathogen protection. Elevations in glucocorticoids (GCs) appear to reduce gut microbiome diversity in experimental studies, suggesting that a loss of microbial diversity may be a negative consequence of increased GCs. However, given that ecological factors like food availability and population density may independently influence both GCs and microbial diversity, understanding how these factors structure the GC-microbiome relationship is crucial to interpreting its significance in wild populations. Here, we used an ecological framework to investigate the relationship between GCs and gut microbiome diversity in wild North American red squirrels (Tamiasciurus hudsonicus). As expected, higher GCs predicted lower gut microbiome diversity and an increase in metabolic taxa. Surprisingly, but in line with prior empirical studies on wild animals, gastrointestinal pathogens decreased as GCs increased. Both dietary heterogeneity and an upcoming food pulse exhibited direct effects on gut microbiome diversity, whereas conspecific density and reproductive activity impacted diversity indirectly via changes in host GCs. Our results provide evidence of a gut-brain axis in wild red squirrels and highlight the importance of situating the GC-gut microbiome relationship within an ecological framework.
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Affiliation(s)
- Lauren Petrullo
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48108, USA.
| | - Tiantian Ren
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Rudy Boonstra
- Department of Biological Sciences, Centre for the Neurobiology of Stress, University of Toronto Scarborough, Toronto, ON, M1C 1A6, Canada
| | - Rupert Palme
- Unit of Physiology, Pathophysiology and Experimental Endocrinology, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Veterina ̈rplatz 1, 1210, Vienna, Austria
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Andrew G McAdam
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ben Dantzer
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48108, USA.
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48108, USA.
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27
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Rudolph K, Schneider D, Fichtel C, Daniel R, Heistermann M, Kappeler PM. Drivers of gut microbiome variation within and between groups of a wild Malagasy primate. MICROBIOME 2022; 10:28. [PMID: 35139921 PMCID: PMC8827170 DOI: 10.1186/s40168-021-01223-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/20/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Various aspects of sociality can benefit individuals' health. The host social environment and its relative contributions to the host-microbiome relationship have emerged as key topics in microbial research. Yet, understanding the mechanisms that lead to structural variation in the social microbiome, the collective microbial metacommunity of an animal's social network, remains difficult since multiple processes operate simultaneously within and among animal social networks. Here, we examined the potential drivers of the convergence of the gut microbiome on multiple scales among and within seven neighbouring groups of wild Verreaux's sifakas (Propithecus verreauxi) - a folivorous primate of Madagascar. RESULTS Over four field seasons, we collected 519 faecal samples of 41 animals and determined gut communities via 16S and 18S rRNA gene amplicon analyses. First, we examined whether group members share more similar gut microbiota and if diet, home range overlap, or habitat similarity drive between-group variation in gut communities, accounting for seasonality. Next, we examined within-group variation in gut microbiota by examining the potential effects of social contact rates, male rank, and maternal relatedness. To explore the host intrinsic effects on the gut community structure, we investigated age, sex, faecal glucocorticoid metabolites, and female reproductive state. We found that group members share more similar gut microbiota and differ in alpha diversity, while none of the environmental predictors explained the patterns of between-group variation. Maternal relatedness played an important role in within-group microbial homogeneity and may also explain why adult group members shared the least similar gut microbiota. Also, dominant males differed in their bacterial composition from their group mates, which might be driven by rank-related differences in physiology and scent-marking behaviours. Links to sex, female reproductive state, or faecal glucocorticoid metabolites were not detected. CONCLUSIONS Environmental factors define the general set-up of population-specific gut microbiota, but intrinsic and social factors have a stronger impact on gut microbiome variation in this primate species. Video abstract.
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Affiliation(s)
- Katja Rudolph
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
- Department of Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August University Göttingen, Kellnerweg 6, 37077, Göttingen, Germany.
- Leibniz Science Campus "Primate Cognition", Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Claudia Fichtel
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
- Leibniz Science Campus "Primate Cognition", Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Michael Heistermann
- Endocrinology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
| | - Peter M Kappeler
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
- Department of Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg-August University Göttingen, Kellnerweg 6, 37077, Göttingen, Germany
- Leibniz Science Campus "Primate Cognition", Göttingen, Germany
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28
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Murillo T, Schneider D, Fichtel C, Daniel R. Dietary shifts and social interactions drive temporal fluctuations of the gut microbiome from wild redfronted lemurs. ISME COMMUNICATIONS 2022; 2:3. [PMID: 37938637 PMCID: PMC9723586 DOI: 10.1038/s43705-021-00086-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/12/2021] [Accepted: 12/21/2021] [Indexed: 05/06/2023]
Abstract
Animals living in highly seasonal environments adapt their diets accordingly to changes in food availability. The gut microbiome as an active participant in the metabolization of the host's diet should adapt and change with temporal diet fluctuations, but dietary shifts can be short-term and, hence, difficult to detect in cross-sectional studies. Therefore, we performed a longitudinal study combining repeated sampling of fecal samples with observations of feeding behavior in wild redfronted lemurs. We amplified taxonomical marker genes for assessing the bacteria, archaea, protozoa, helminths, and fungi, as well as the active bacterial community inhabiting their gut. We found that the most abundant protozoans were Trichostomatia and Trichomonadida, and the most abundant helminths were Chromadorea. We detected known members of the gut mycobiome from humans but in low abundances. The archaeal community is composed only of members of Methanomethylophilaceae. The predominant phyla in the entire bacterial community were Bacteroidota and Firmicutes while the most abundant genera harbor so far unknown bacteria. Temporal fluctuations at the entire community level were driven by consumption of fruits and flowers, and affiliative interactions. Changes in alpha diversity correlated only with the consumption of flowers and leaves. The composition of the entire and active bacterial community was not significantly different, but the most abundant taxa differed. Our study revealed that monthly changes in the bacterial community composition were linked to fruit and flower consumption and affiliative interactions. Thus, portraying the importance of longitudinal studies for understanding the adaptations and alterations of the gut microbiome to temporal fluctuations.
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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
| | - Dominik Schneider
- 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
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany.
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29
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Yarlagadda K, Razik I, Malhi RS, Carter GG. Social convergence of gut microbiomes in vampire bats. Biol Lett 2021; 17:20210389. [PMID: 34727703 PMCID: PMC8563296 DOI: 10.1098/rsbl.2021.0389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
The 'social microbiome' can fundamentally shape the costs and benefits of group-living, but understanding social transmission of microbes in free-living animals is challenging due to confounding effects of kinship and shared environments (e.g. highly associated individuals often share the same spaces, food and water). Here, we report evidence for convergence towards a social microbiome among introduced common vampire bats, Desmodus rotundus, a highly social species in which adults feed only on blood, and engage in both mouth-to-body allogrooming and mouth-to-mouth regurgitated food sharing. Shotgun sequencing of samples from six zoos in the USA, 15 wild-caught bats from a colony in Belize and 31 bats from three colonies in Panama showed that faecal microbiomes were more similar within colonies than between colonies. To assess microbial transmission, we created an experimentally merged group of the Panama bats from the three distant sites by housing these bats together for four months. In this merged colony, we found evidence that dyadic gut microbiome similarity increased with both clustering and oral contact, leading to microbiome convergence among introduced bats. Our findings demonstrate that social interactions shape microbiome similarity even when controlling for past social history, kinship, environment and diet.
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Affiliation(s)
- Karthik Yarlagadda
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Imran Razik
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Ripan S. Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gerald G. Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
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30
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Perofsky AC, Ancel Meyers L, Abondano LA, Di Fiore A, Lewis RJ. Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes. Mol Ecol 2021; 30:6759-6775. [PMID: 34558751 DOI: 10.1111/mec.16193] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/25/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022]
Abstract
Primates acquire gut microbiota from conspecifics through direct social contact and shared environmental exposures. Host behaviour is a prominent force in structuring gut microbial communities, yet the extent to which group or individual-level forces shape the long-term dynamics of gut microbiota is poorly understood. We investigated the effects of three aspects of host sociality (social groupings, dyadic interactions, and individual dispersal between groups) on gut microbiome composition and plasticity in 58 wild Verreaux's sifaka (Propithecus verreauxi) from six social groups. Over the course of three dry seasons in a 5-year period, the six social groups maintained distinct gut microbial signatures, with the taxonomic composition of individual communities changing in tandem among coresiding group members. Samples collected from group members during each season were more similar than samples collected from single individuals across different years. In addition, new immigrants and individuals with less stable social ties exhibited elevated rates of microbiome turnover across seasons. Our results suggest that permanent social groupings shape the changing composition of commensal and mutualistic gut microbial communities and thus may be important drivers of health and resilience in wild primate populations.
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Affiliation(s)
- Amanda C Perofsky
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA.,Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Laura A Abondano
- Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA.,Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, Texas, USA
| | - Anthony Di Fiore
- Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA.,Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, Texas, USA
| | - Rebecca J Lewis
- Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA
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31
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Wang Y, Zhou R, Yu Q, Feng T, Li H. Gut microbiome adaptation to extreme cold winter in wild plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau. FEMS Microbiol Lett 2021; 367:5896949. [PMID: 32840567 DOI: 10.1093/femsle/fnaa134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
The Qinghai-Tibet Plateau is a harsh environment characterized by low temperature, high altitude and hypoxia, although some native mammals may adapt well to the extreme climate. However, how animal gut microbial community structure and function adapt to extreme cold climates is not well understood. Plateau pika (Ochotona curzoniae) is an ideal animal model with which to study the effects of climate change on host adaptation by studing intestinal microorganisms. Here, we used 16S rRNA sequencing technology combined with physiological methods to investigate plateau pika gut microbiota in summer and winter. Due to limited diet resources, the pikas in winter have a lower ability of degradation and fermentation for plant-based food (reduced cellulase activity and total short-chain fatty acids) by decreasing gut microbial diversity and some functional microbes, such as fiber-degrading bacteria Oscillospira and Treponema. Metagenomic prediction showed that most of those gene functions associated with metabolism (e.g. energy metabolism and lipid metabolism) were less abundant in winter, implying that the plateau pika slows diet fermentation and weakens energy requirements in the cold season. Our results have significance for explaining the mechanism of wild plateau mammals adapting to a high-altitude cold environment from the perspective of gut microbiome.
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Affiliation(s)
- Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China.,Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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32
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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 PMCID: PMC8377764 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
- The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
- Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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DeCandia AL, Cassidy KA, Stahler DR, Stahler EA, vonHoldt BM. Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves ( Canis lupus). Ecol Evol 2021; 11:9472-9488. [PMID: 34306636 PMCID: PMC8293786 DOI: 10.1002/ece3.7767] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
The host-associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site-specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site-specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long-term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.
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Affiliation(s)
- Alexandra L. DeCandia
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Kira A. Cassidy
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Daniel R. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Erin A. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
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Cusick JA, Wellman CL, Demas GE. The call of the wild: using non-model systems to investigate microbiome-behaviour relationships. J Exp Biol 2021; 224:jeb224485. [PMID: 33988717 PMCID: PMC8180253 DOI: 10.1242/jeb.224485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
On and within most sites across an animal's body live complex communities of microorganisms. These microorganisms perform a variety of important functions for their hosts, including communicating with the brain, immune system and endocrine axes to mediate physiological processes and affect individual behaviour. Microbiome research has primarily focused on the functions of the microbiome within the gastrointestinal tract (gut microbiome) using biomedically relevant laboratory species (i.e. model organisms). These studies have identified important connections between the gut microbiome and host immune, neuroendocrine and nervous systems, as well as how these connections, in turn, influence host behaviour and health. Recently, the field has expanded beyond traditional model systems as it has become apparent that the microbiome can drive differences in behaviour and diet, play a fundamental role in host fitness and influence community-scale dynamics in wild populations. In this Review, we highlight the value of conducting hypothesis-driven research in non-model organisms and the benefits of a comparative approach that assesses patterns across different species or taxa. Using social behaviour as an intellectual framework, we review the bidirectional relationship between the gut microbiome and host behaviour, and identify understudied mechanisms by which these effects may be mediated.
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Affiliation(s)
- Jessica A. Cusick
- Department of Biology, Indiana University, Biology Building 142, 1001 East Third Street, Bloomington, IN 47405, USA
- Animal Behavior Program, Indiana University, 409 N. Park Avenue, Bloomington, IN 47405, USA
| | - Cara L. Wellman
- Animal Behavior Program, Indiana University, 409 N. Park Avenue, Bloomington, IN 47405, USA
- Department of Psychological and Brain Sciences, Indiana University, 1101 E. 10th Street, Bloomington, IN 47405-7007, USA
- Program in Neuroscience, Indiana University, Psychology Building, 1101 E 10th Street Bloomington, IN 47405-2204, USA
| | - Gregory E. Demas
- Department of Biology, Indiana University, Biology Building 142, 1001 East Third Street, Bloomington, IN 47405, USA
- Animal Behavior Program, Indiana University, 409 N. Park Avenue, Bloomington, IN 47405, USA
- Program in Neuroscience, Indiana University, Psychology Building, 1101 E 10th Street Bloomington, IN 47405-2204, USA
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Risely A, Gillingham MAF, Béchet A, Brändel S, Heni AC, Heurich M, Menke S, Manser MB, Tschapka M, Wasimuddin, Sommer S. Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species. Front Microbiol 2021; 12:659918. [PMID: 34046023 PMCID: PMC8144293 DOI: 10.3389/fmicb.2021.659918] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
The filtering of gut microbial datasets to retain high prevalence taxa is often performed to identify a common core gut microbiome that may be important for host biological functions. However, prevalence thresholds used to identify a common core are highly variable, and it remains unclear how they affect diversity estimates and whether insights stemming from core microbiomes are comparable across studies. We hypothesized that if macroecological patterns in gut microbiome prevalence and abundance are similar across host species, then we would expect that increasing prevalence thresholds would yield similar changes to alpha diversity and beta dissimilarity scores across host species datasets. We analyzed eight gut microbiome datasets based on 16S rRNA gene amplicon sequencing and collected from different host species to (1) compare macroecological patterns across datasets, including amplicon sequence variant (ASV) detection rate with sequencing depth and sample size, occupancy-abundance curves, and rank-abundance curves; (2) test whether increasing prevalence thresholds generate universal or host-species specific effects on alpha and beta diversity scores; and (3) test whether diversity scores from prevalence-filtered core communities correlate with unfiltered data. We found that gut microbiomes collected from diverse hosts demonstrated similar ASV detection rates with sequencing depth, yet required different sample sizes to sufficiently capture rare ASVs across the host population. This suggests that sample size rather than sequencing depth tends to limit the ability of studies to detect rare ASVs across the host population. Despite differences in the distribution and detection of rare ASVs, microbiomes exhibited similar occupancy-abundance and rank-abundance curves. Consequently, increasing prevalence thresholds generated remarkably similar trends in standardized alpha diversity and beta dissimilarity across species datasets until high thresholds above 70%. At this point, diversity scores tended to become unpredictable for some diversity measures. Moreover, high prevalence thresholds tended to generate diversity scores that correlated poorly with the original unfiltered data. Overall, we recommend that high prevalence thresholds over 70% are avoided, and promote the use of diversity measures that account for phylogeny and abundance (Balance-weighted phylogenetic diversity and Weighted Unifrac for alpha and beta diversity, respectively), because we show that these measures are insensitive to prevalence filtering and therefore allow for the consistent comparison of core gut microbiomes across studies without the need for prevalence filtering.
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Affiliation(s)
- Alice Risely
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Mark A. F. Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Arnaud Béchet
- Institut de Recherche de la Tour du Valat, Le Sambuc, Arles, France
| | - Stefan Brändel
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Alexander C. Heni
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Marco Heurich
- Department of Visitor Management and National Park Monitoring, Bavarian Forest National Park, Grafenau, Germany
- Chair of Wildlife Ecology and Management, University of Freiburg, Freiburg, Germany
- Institute for Forest and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
| | - Sebastian Menke
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Marta B. Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Wasimuddin
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Bo TB, Kohl KD. Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry. Anim Microbiome 2021; 3:26. [PMID: 33785073 PMCID: PMC8011129 DOI: 10.1186/s42523-021-00087-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may underlie the evolution of natal philopatry, such as genetic optimization, suitable living conditions, and friendly neighbors, which can improve the survival rates of offspring. However, here we propose that a key factor that has been overlooked could be the colonization of gut microbiota during early life and the effects these microorganisms have on host performance and fitness. In addition to the bacteria transmitted from the mother to offspring, microbes from the surrounding environment also account for a large proportion of the developing gut microbiome. While it was long believed that microbial species all have global distributions, we now know that there are substantial geographic differences and dispersal limitations to environmental microbes. The establishment of gut microbiota during early life has enormous impacts on animal development, including energy metabolism, training of the immune system, and cognitive development. Moreover, these microbial effects scale to influence animal performance and fitness, raising the possibility for natural selection to act on the integrated combination of gut microbial communities and host genetics (i.e. the holobiont). Therefore, in this paper, we propose a hypothesis: that optimization of host-microbe-environment interactions represents a potentially important yet overlooked reason for natal philopatry. Microbiota obtained by natal philopatry could help animals adapt to the environment and improve the survival rates of their young. We propose future directions to test these ideas, and the implications that this hypothesis has for our understanding of host-microbe interactions.
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Affiliation(s)
- Ting-Bei Bo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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Raulo A, Allen BE, Troitsky T, Husby A, Firth JA, Coulson T, Knowles SCL. Social networks strongly predict the gut microbiota of wild mice. ISME JOURNAL 2021; 15:2601-2613. [PMID: 33731838 PMCID: PMC8397773 DOI: 10.1038/s41396-021-00949-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
Abstract
The mammalian gut teems with microbes, yet how hosts acquire these symbionts remains poorly understood. Research in primates suggests that microbes can be picked up via social contact, but the role of social interactions in non-group-living species remains underexplored. Here, we use a passive tracking system to collect high resolution spatiotemporal activity data from wild mice (Apodemus sylvaticus). Social network analysis revealed social association strength to be the strongest predictor of microbiota similarity among individuals, controlling for factors including spatial proximity and kinship, which had far smaller or nonsignificant effects. This social effect was limited to interactions involving males (male-male and male-female), implicating sex-dependent behaviours as driving processes. Social network position also predicted microbiota richness, with well-connected individuals having the most diverse microbiotas. Overall, these findings suggest social contact provides a key transmission pathway for gut symbionts even in relatively asocial mammals, that strongly shapes the adult gut microbiota. This work underlines the potential for individuals to pick up beneficial symbionts as well as pathogens from social interactions.
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Affiliation(s)
- Aura Raulo
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Bryony E Allen
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Tanya Troitsky
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Arild Husby
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Josh A Firth
- Department of Zoology, University of Oxford, Oxford, UK
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, UK
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38
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Funosas G, Triadó-Margarit X, Castro F, Villafuerte R, Delibes-Mateos M, Rouco C, Casamayor EO. Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus). Sci Rep 2021; 11:766. [PMID: 33436896 PMCID: PMC7804928 DOI: 10.1038/s41598-020-80782-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.
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Affiliation(s)
- Gerard Funosas
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Francisca Castro
- Departamento de Didácticas Específicas, Universidad de Córdoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14004, Córdoba, Spain
| | - Rafael Villafuerte
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Miguel Delibes-Mateos
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Carlos Rouco
- Ecology Area, Faculty of Science, University of Cordoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14071, Córdoba, Spain
| | - Emilio O Casamayor
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain.
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Giuffrè M, Moretti R, Campisciano G, da Silveira ABM, Monda VM, Comar M, Di Bella S, Antonello RM, Luzzati R, Crocè LS. You Talking to Me? Says the Enteric Nervous System (ENS) to the Microbe. How Intestinal Microbes Interact with the ENS. J Clin Med 2020; 9:E3705. [PMID: 33218203 PMCID: PMC7699249 DOI: 10.3390/jcm9113705] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Mammalian organisms form intimate interfaces with commensal and pathogenic gut microorganisms. Increasing evidence suggests a close interaction between gut microorganisms and the enteric nervous system (ENS), as the first interface to the central nervous system. Each microorganism can exert a different effect on the ENS, including phenotypical neuronal changes or the induction of chemical transmitters that interact with ENS neurons. Some pathogenic bacteria take advantage of the ENS to create a more suitable environment for their growth or to promote the effects of their toxins. In addition, some commensal bacteria can affect the central nervous system (CNS) by locally interacting with the ENS. From the current knowledge emerges an interesting field that may shape future concepts on the pathogen-host synergic interaction. The aim of this narrative review is to report the current findings regarding the inter-relationships between bacteria, viruses, and parasites and the ENS.
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Affiliation(s)
- Mauro Giuffrè
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
- Italian Liver Foundation, 34129 Trieste, Italy
| | - Rita Moretti
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Giuseppina Campisciano
- Department of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (G.C.); (M.C.)
| | | | | | - Manola Comar
- Department of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (G.C.); (M.C.)
| | - Stefano Di Bella
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Roberta Maria Antonello
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Roberto Luzzati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Lory Saveria Crocè
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
- Italian Liver Foundation, 34129 Trieste, Italy
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40
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Seitz BM, Aktipis A, Buss DM, Alcock J, Bloom P, Gelfand M, Harris S, Lieberman D, Horowitz BN, Pinker S, Wilson DS, Haselton MG. The pandemic exposes human nature: 10 evolutionary insights. Proc Natl Acad Sci U S A 2020; 117:27767-27776. [PMID: 33093198 PMCID: PMC7668083 DOI: 10.1073/pnas.2009787117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Humans and viruses have been coevolving for millennia. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus that causes COVID-19) has been particularly successful in evading our evolved defenses. The outcome has been tragic-across the globe, millions have been sickened and hundreds of thousands have died. Moreover, the quarantine has radically changed the structure of our lives, with devastating social and economic consequences that are likely to unfold for years. An evolutionary perspective can help us understand the progression and consequences of the pandemic. Here, a diverse group of scientists, with expertise from evolutionary medicine to cultural evolution, provide insights about the pandemic and its aftermath. At the most granular level, we consider how viruses might affect social behavior, and how quarantine, ironically, could make us susceptible to other maladies, due to a lack of microbial exposure. At the psychological level, we describe the ways in which the pandemic can affect mating behavior, cooperation (or the lack thereof), and gender norms, and how we can use disgust to better activate native "behavioral immunity" to combat disease spread. At the cultural level, we describe shifting cultural norms and how we might harness them to better combat disease and the negative social consequences of the pandemic. These insights can be used to craft solutions to problems produced by the pandemic and to lay the groundwork for a scientific agenda to capture and understand what has become, in effect, a worldwide social experiment.
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Affiliation(s)
- Benjamin M Seitz
- Department of Psychology, University of California, Los Angeles, CA 90095;
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ 85287
| | - David M Buss
- Department of Psychology, University of Texas at Austin, Austin, TX 78712
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM 87131
| | - Paul Bloom
- Department of Psychology, Yale University, New Haven, CT 06520
| | - Michele Gelfand
- Department of Psychology, University of Maryland, College Park, MD 20742
| | | | - Debra Lieberman
- Department of Psychology, University of Miami, Coral Gables, FL 33124
| | - Barbara N Horowitz
- Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Steven Pinker
- Department of Psychology, Harvard University, Cambridge, MA 02138
| | - David Sloan Wilson
- Department of Biological Sciences, Binghamton University, Binghamton, NY 13902
| | - Martie G Haselton
- Department of Psychology, University of California, Los Angeles, CA 90095;
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Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States. mSystems 2020; 5:5/6/e00834-20. [PMID: 33144313 PMCID: PMC7646528 DOI: 10.1128/msystems.00834-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis). Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes. IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).
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Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190598. [PMID: 32772669 PMCID: PMC7435160 DOI: 10.1098/rstb.2019.0598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2020] [Indexed: 12/23/2022] Open
Abstract
Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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43
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Noble AS, Noe S, Clearwater MJ, Lee CK. A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand. PLoS One 2020; 15:e0237079. [PMID: 32790769 PMCID: PMC7425925 DOI: 10.1371/journal.pone.0237079] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/19/2020] [Indexed: 12/30/2022] Open
Abstract
The phyllosphere microbiome is increasingly recognised as an influential component of plant physiology, yet it remains unclear whether stable host-microbe associations generally exist in the phyllosphere. Leptospermum scoparium (mānuka) is a tea tree indigenous to New Zealand, and honey derived from mānuka is widely known to possess unique antimicrobial properties. However, the host physiological traits associated with these antimicrobial properties vary widely, and the specific cause of such variation has eluded scientists despite decades of research. Notably, the mānuka phyllosphere microbiome remains uncharacterised, and its potential role in mediating host physiology has not been considered. Working within the prevailing core microbiome conceptual framework, we hypothesise that the phyllosphere microbiome of mānuka exhibits specific host association patterns congruent with those of a microbial community under host selective pressure (null hypothesis: the mānuka phyllosphere microbiome is recruited stochastically from the surrounding environment). To examine our hypothesis, we characterised the phyllosphere and associated soil microbiomes of five distinct and geographically distant mānuka populations across the North Island of New Zealand. We identified a habitat-specific and relatively abundant core microbiome in the mānuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. Our results demonstrate the existence of a dominant and ubiquitous core microbiome in the phyllosphere of mānuka, supporting our hypothesis that phyllosphere microorganisms of mānuka exhibit specific host association and potentially mediate physiological traits of this nationally and culturally treasured indigenous plant. In addition, our results illustrate biogeographical patterns in mānuka phyllosphere microbiomes and offer insight into factors contributing to phyllosphere microbiome assembly.
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Affiliation(s)
- Anya S. Noble
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Stevie Noe
- School of Science, University of Waikato, Hamilton, New Zealand
| | | | - Charles K. Lee
- School of Science, University of Waikato, Hamilton, New Zealand
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44
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Microbial transmission in animal social networks and the social microbiome. Nat Ecol Evol 2020; 4:1020-1035. [DOI: 10.1038/s41559-020-1220-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/11/2020] [Indexed: 12/15/2022]
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45
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Vendl C, Slavich E, Nelson T, Acevedo-Whitehouse K, Montgomery K, Ferrari B, Thomas T, Rogers T. Does sociality drive diversity and composition of airway microbiota in cetaceans? ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:324-333. [PMID: 32162479 DOI: 10.1111/1758-2229.12835] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/25/2020] [Accepted: 03/09/2020] [Indexed: 05/23/2023]
Abstract
The number of social contacts of mammals is positively correlated with the diversity of their gut microbes. There is some evidence that sociality also affects microbes in the respiratory tract. We tested whether the airway microbiota of cetacean species differ depending on the whales' level of sociality. We sampled the blow of blue (Balaenoptera musculus), grey (Eschrichtius robustus), humpback (Megaptera novaeangliae) and long-finned pilot whales (PWs) (Globicephala melas) and analysed the blow microbiota by barcode tag sequencing targeting the V4 region of the bacterial 16S rRNA gene. Humpback whales (HWs) show higher levels of sociality than blue (BW) and grey (GW), while PWs are the most gregarious among the four species. The blow samples of the HWs showed the highest richness and diversity. HWs were also the only species with a species-specific clustering of their microbial community composition and a relatively large number of core taxa. Therefore, we conclude that it cannot be sociality alone shaping the diversity and composition of airway microbiota. We suggest the whale species' lung volume and size of the plume of exhaled air as an additional factor impacting the transmission potential of blow microbiota from one individual whale to another.
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Affiliation(s)
- Catharina Vendl
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Eve Slavich
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, UNSW, 2052, Australia
| | - Tiffanie Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Building G40, Level 9, Gold Coast Campus, Griffith University, Southport, QLD, 4215, Australia
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Queretaro, 76230, Mexico
| | - Kate Montgomery
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Belinda Ferrari
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre of Marine Bio-Innovation (CMB), School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Tracey Rogers
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
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46
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Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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47
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Rojas CA, Holekamp KE, Winters AD, Theis KR. Body site-specific microbiota reflect sex and age-class among wild spotted hyenas. FEMS Microbiol Ecol 2020; 96:5700710. [PMID: 31926016 DOI: 10.1093/femsec/fiaa007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Host-associated microbial communities, henceforth 'microbiota', can affect the physiology and behavior of their hosts. In mammals, host ecological, social and environmental variables are associated with variation in microbial communities. Within individuals in a given mammalian species, the microbiota also partitions by body site. Here, we build on this work and sequence the bacterial 16S rRNA gene to profile the microbiota at six distinct body sites (ear, nasal and oral cavities, prepuce, rectum and anal scent gland) in a population of wild spotted hyenas (Crocuta crocuta), which are highly social, large African carnivores. We inquired whether microbiota at these body sites vary with host sex or social rank among juvenile hyenas, and whether they differ between juvenile females and adult females. We found that the scent gland microbiota differed between juvenile males and juvenile females, whereas the prepuce and rectal microbiota differed between adult females and juvenile females. Social rank, however, was not a significant predictor of microbiota profiles. Additionally, the microbiota varied considerably among the six sampled body sites and exhibited strong specificity among individual hyenas. Thus, our findings suggest that site-specific niche selection is a primary driver of microbiota structure in mammals, but endogenous host factors may also be influential.
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Affiliation(s)
- Connie A Rojas
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
| | - Kevin R Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
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48
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Risely A. Applying the core microbiome to understand host-microbe systems. J Anim Ecol 2020; 89:1549-1558. [PMID: 32248522 DOI: 10.1111/1365-2656.13229] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/13/2020] [Indexed: 12/16/2022]
Abstract
The host-associated core microbiome was originally coined to refer to common groups of microbes or genes that were likely to be particularly important for host biological function. However, the term has evolved to encompass variable definitions across studies, often identifying key microbes with respect to their spatial distribution, temporal stability or ecological influence, as well as their contribution to host function and fitness. A major barrier to reaching a consensus over how to define the core microbiome and its relevance to biological, ecological and evolutionary theory is a lack of precise terminology and associated definitions, as well the persistent association of the core microbiome with host function. Common, temporal and ecological core microbiomes can together generate insights into ecological processes that act independently of host function, while functional and host-adapted cores distinguish between facultative and near-obligate symbionts that differ in their effects on host fitness. This commentary summarizes five broad definitions of the core microbiome that have been applied across the literature, highlighting their strengths and limitations for advancing our understanding of host-microbe systems, noting where they are likely to overlap, and discussing their potential relevance to host function and fitness. No one definition of the core microbiome is likely to capture the range of key microbes across a host population. Applied together, they have the potential to reveal different layers of microbial organization from which we can begin to understand the ecological and evolutionary processes that govern host-microbe interactions.
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Affiliation(s)
- Alice Risely
- Institute for Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Demmelmair H, Jiménez E, Collado MC, Salminen S, McGuire MK. Maternal and Perinatal Factors Associated with the Human Milk Microbiome. Curr Dev Nutr 2020; 4:nzaa027. [PMID: 32270132 PMCID: PMC7127925 DOI: 10.1093/cdn/nzaa027] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/12/2020] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Microbes are present in human milk regardless of the mother's health. The origins of the milk microbiota likely include the mother's skin, infant's mouth, and transfer from the maternal gastrointestinal (GI) tract. Prominent bacterial taxa in human milk are Staphylococcus and Streptococcus, but many other genera are also found including anaerobic Lactobacillus, Bifidobacterium, and Bacteroides. The milk microbiome is highly variable and potentially influenced by geographic location, delivery mode, time postpartum, feeding mode, social networks, environment, maternal diet, and milk composition. Mastitis alters the milk microbiome, and the intake of Lactobacilli has shown potential for mastitis treatment and prevention. Although milk and infant fecal microbiomes are different, their variations appear to be related - suggesting that milk is an important contributor of early GI colonization. Nonetheless, nothing is known regarding whether the milk microbiome influences infant health. Further research and clinical interventions are needed to determine if changes in the microbiomes of human milk and infant formula/food impact health.
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Affiliation(s)
- Hans Demmelmair
- Dr. von Hauner Children´s Hospital, University of Munich Medical Center, Munich, Germany
| | - Esther Jiménez
- ProbiSearch SLU, Madrid, Spain
- Department of Nutrition, Food Science, and Technology, University Complutense, Madrid, Spain
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology, Spanish National Research Council, Valencia, Spain
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Michelle K McGuire
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, USA
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50
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Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis. Methods Protoc 2020; 3:mps3010022. [PMID: 32178466 PMCID: PMC7189665 DOI: 10.3390/mps3010022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 02/05/2023] Open
Abstract
The advent of next-generation sequencing has allowed for higher-throughput determination of which species live within a specific location. Here we establish that three analysis methods for estimating diversity within samples—namely, Operational Taxonomic Units; the newer Amplicon Sequence Variants; and a method commonly found in sequence analysis, minhash—are affected by various properties of these sequence data. Using simulations we show that the presence of Single Nucleotide Polymorphisms and the depth of coverage from each species affect the correlations between these approaches. Through this analysis, we provide insights which would affect the decisions on the application of each method. Specifically, the presence of sequence read errors and variability in sequence read coverage deferentially affects these processing methods.
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