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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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2
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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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3
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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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4
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Grieneisen L, Hays A, Cook E, Blekhman R, Tecot S. Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type. Am J Primatol 2024:e23656. [PMID: 38873762 DOI: 10.1002/ajp.23656] [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: 06/01/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
The gut microbiome is a plastic phenotype; gut microbial composition is highly variable across an individual host's lifetime and between host social groups, and this variation has consequences for host health. However, we do not yet fully understand how longitudinal microbial dynamics and their social drivers may be influenced by ecological stressors, such as habitat degradation. Answering these questions is difficult in most wild animal systems, as it requires long-term collections of matched host, microbiome, and environmental trait data. To test if temporal and social influences on microbiome composition differ by the history of human disturbance, we leveraged banked, desiccated fecal samples collected over 5 months in 2004 from two ecologically distinct populations of wild, red-bellied lemurs (Eulemur rubriventer) that are part of a long-term study system. We found that social group explained more variation in microbiome composition than host population membership did, and that temporal variation in common microbial taxa was similar between populations, despite differences in history of human disturbance. Furthermore, we found that social group membership and collection month were both more important than individual lemur identity. Taken together, our results suggest that synchronized environments use can lead to synchronized microbial dynamics over time, even between habitats of varying quality, and that desiccated samples could become a viable approach for studying primate gut microbiota. Our work opens the door for other projects to utilize historic biological sample data sets to answer novel temporal microbiome questions in an ecological context.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, BC, Canada
| | - Allison Hays
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Erica Cook
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stacey Tecot
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
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5
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Raulo A, Bürkner PC, Finerty GE, Dale J, Hanski E, English HM, Lamberth C, Firth JA, Coulson T, Knowles SCL. Social and environmental transmission spread different sets of gut microbes in wild mice. Nat Ecol Evol 2024; 8:972-985. [PMID: 38689017 DOI: 10.1038/s41559-024-02381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/01/2024] [Indexed: 05/02/2024]
Abstract
Gut microbes shape many aspects of organismal biology, yet how these key bacteria transmit among hosts in natural populations remains poorly understood. Recent work in mammals has emphasized either transmission through social contacts or indirect transmission through environmental contact, but the relative importance of different routes has not been directly assessed. Here we used a novel radio-frequency identification-based tracking system to collect long-term high-resolution data on social relationships, space use and microhabitat in a wild population of mice (Apodemus sylvaticus), while regularly characterizing their gut microbiota with 16S ribosomal RNA profiling. Through probabilistic modelling of the resulting data, we identify positive and statistically distinct signals of social and environmental transmission, captured by social networks and overlap in home ranges, respectively. Strikingly, microorganisms with distinct biological attributes drove these different transmission signals. While the social network effect on microbiota was driven by anaerobic bacteria, the effect of shared space was most influenced by aerotolerant spore-forming bacteria. These findings support the prediction that social contact is important for the transfer of microorganisms with low oxygen tolerance, while those that can tolerate oxygen or form spores may be able to transmit indirectly through the environment. Overall, these results suggest social and environmental transmission routes can spread biologically distinct members of the mammalian gut microbiota.
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Affiliation(s)
- Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Computing, University of Turku, Turku, Finland.
| | | | - Genevieve E Finerty
- Department of Biology, University of Oxford, Oxford, UK
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behaviour, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jarrah Dale
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Holly M English
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Curt Lamberth
- Department of Biology, University of Oxford, Oxford, UK
| | - Josh A Firth
- Department of Biology, University of Oxford, Oxford, UK
- School of Biology, University of Leeds, Leeds, UK
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, UK
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6
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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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7
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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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8
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Lin Z, He M, Zhong C, Li Y, Tang S, Kang X, Wu Z. Responses of gut microbiota in crocodile lizards ( Shinisaurus crocodilurus) to changes in temperature. Front Microbiol 2023; 14:1263917. [PMID: 38033565 PMCID: PMC10684959 DOI: 10.3389/fmicb.2023.1263917] [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: 07/20/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
The gut microbiota plays an essential role in maintaining the health and fitness of the host organism. As a critical environmental variable, temperature exerts significant effects on animal survival and reproduction. Elevated temperatures can influence the composition and function of the animal gut microbiota, which may have potentially detrimental effects on the host. The crocodile lizard (Shinisaurus crocodilurus) is an ancient and currently endangered reptile species due to human hunting and habitat destruction. Given the predicted shifts in global temperatures in the next century, it is important to understand how warming affects the gut microbiota of these vulnerable lizards, which remains unclear. To determine how the microbial communities change in crocodile lizards in response to warming, we analyzed the gut microbiota under five temperature conditions (22°C, 24°C, 26°C, 28°C, and 30°C) using 16S rRNA high-throughput sequencing. Results showed that the dominant phyla, Proteobacteria and Bacteroidetes, in gut microbiota were not significantly affected by temperature variations, but increasing temperature altered the structure and increased the community richness of the gut microbiota. In addition, warming changed the abundance of Pseudomonas aeruginosa and Actinobacteria, which may have negative effects on the physiological health of the crocodile lizards. Functional prediction analysis demonstrated that the functional pathways enriched in crocodile lizards were mainly related to metabolism, with no significant differences observed in these pathways at KEGG pathway level 1 after warming. These results provide valuable insights into the ecological adaptations and regulatory mechanisms employed by crocodile lizards in response to warming, which may be of benefit for their conservation.
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Affiliation(s)
- Zhengzhong Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Mingxian He
- College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi, China
| | - Chunying Zhong
- College of Vocational and Technical Education, Guangxi Science and Technology Normal University, Guangxi, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Sanqi Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Xindan Kang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
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9
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Tang K, Tao L, Wang Y, Wang Q, Fu C, Chen B, Zhang Z, Fu Y. Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation. Appl Environ Microbiol 2023; 89:e0074723. [PMID: 37272815 PMCID: PMC10305732 DOI: 10.1128/aem.00747-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.
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Affiliation(s)
- Keyi Tang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Ling Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yufeng Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Qiong Wang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Changkun Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Benping Chen
- Laojunshan National Nature Reserve Administration, Pingshan, Sichuan, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yiqiang Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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10
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Suenami S, Koto A, Miyazaki R. Basic Structures of Gut Bacterial Communities in Eusocial Insects. INSECTS 2023; 14:insects14050444. [PMID: 37233072 DOI: 10.3390/insects14050444] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
Gut bacterial communities assist host animals with numerous functions such as food digestion, nutritional provision, or immunity. Some social mammals and insects are unique in that their gut microbial communities are stable among individuals. In this review, we focus on the gut bacterial communities of eusocial insects, including bees, ants, and termites, to provide an overview of their community structures and to gain insights into any general aspects of their structural basis. Pseudomonadota and Bacillota are prevalent bacterial phyla commonly detected in those three insect groups, but their compositions are distinct at lower taxonomic levels. Eusocial insects harbor unique gut bacterial communities that are shared within host species, while their stability varies depending on host physiology and ecology. Species with narrow dietary habits, such as eusocial bees, harbor highly stable and intraspecific microbial communities, while generalists, such as most ant species, exhibit relatively diverse community structures. Caste differences could influence the relative abundance of community members without significantly altering the taxonomic composition.
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Affiliation(s)
- Shota Suenami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Akiko Koto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
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11
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Zhao J, Yao Y, Dong M, Xiao H, Xiong Y, Yang S, Li D, Xie M, Ni Q, Zhang M, Xu H. Diet and high altitude strongly drive convergent adaptation of gut microbiota in wild macaques, humans, and dogs to high altitude environments. Front Microbiol 2023; 14:1067240. [PMID: 36910187 PMCID: PMC9995840 DOI: 10.3389/fmicb.2023.1067240] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Animal gut microbiota plays an indispensable role in host adaptation to different altitude environments. At present, little is known about the mechanism of animal gut microbiota in host adaptation to high altitude environments. Here, we selected wild macaques, humans, and dogs with different levels of kinship and intimate relationships in high altitude and low altitude environments, and analyzed the response of their gut microbiota to the host diet and altitude environments. Alpha diversity analysis found that at high altitude, the gut microbiota diversity of wild macaques with more complex diet in the wild environments is much higher than that of humans and dogs with simpler diet (p < 0.05), and beta diversity analysis found that the UniFrac distance between humans and dogs was significantly lower than between humans and macaques (p < 0.05), indicating that diet strongly drive the convergence of gut microbiota among species. Meanwhile, alpha diversity analysis found that among three subjects, the gut microbiota diversity of high altitude population is higher than that of low altitude population (ACE index in three species, Shannon index in dog and macaque and Simpson index in dog, p < 0.05), and beta diversity analysis found that the UniFrac distances among the three subjects in the high altitude environments were significantly lower than in the low altitude environments (p < 0.05). Additionally, core shared ASVs analysis found that among three subjects, the number of core microbiota in high altitude environments is higher than in low altitude environments, up to 5.34 times (1,105/207), and the proportion and relative abundance of the core bacteria types in each species were significantly higher in high altitude environments than in low altitude environments (p < 0.05). The results showed that high altitude environments played an important role in driving the convergence of gut microbiota among species. Furthermore, the neutral community model trial found that the gut microbiota of the three subjects was dispersed much more at high altitude than at low altitude, implying that the gut microbiota convergence of animals at high altitudes may be partly due to the microbial transmission between hosts mediated by human activities.
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Affiliation(s)
- Junsong Zhao
- College of Life Science, Sichuan Agricultural University, Ya’an, China
- College of Agronomy and Life Sciences, Zhaotong University, Zhaotong, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Mengmeng Dong
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Hongtao Xiao
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Ying Xiong
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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12
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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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13
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Bunker ME, Arnold AE, Weiss SL. Wild microbiomes of striped plateau lizards vary with reproductive season, sex, and body size. Sci Rep 2022; 12:20643. [PMID: 36450782 PMCID: PMC9712514 DOI: 10.1038/s41598-022-24518-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
Long-term studies of animal microbiomes under natural conditions are valuable for understanding the effects of host demographics and environmental factors on host-associated microbial communities, and how those effects interact and shift over time. We examined how the cloacal microbiome of wild Sceloporus virgatus (the striped plateau lizard) varies under natural conditions in a multi-year study. Cloacal swabs were collected from wild-caught lizards across their entire active season and over three years in southeastern Arizona, USA. Analyses of 16S rRNA data generated on the Illumina platform revealed that cloacal microbiomes of S. virgatus vary as a function of season, sex, body size, and reproductive state, and do so independently of one another. Briefly, microbial diversity was lowest in both sexes during the reproductive season, was higher in females than in males, and was lowest in females when they were vitellogenic, and microbiome composition varied across seasons, sexes, and sizes. The pattern of decreased diversity during reproductive periods with increased sociality is surprising, as studies in other systems often suggest that microbial diversity generally increases with sociality. The cloacal microbiome was not affected significantly by hibernation and was relatively stable from year to year. This study highlights the importance of long term, wide-scale microbiome studies for capturing accurate perspectives on microbiome diversity and composition in animals. It also serves as a warning for comparisons of microbiomes across species, as each may be under a different suite of selective pressures or exhibit short-term variation from external or innate factors, which may differ in a species-specific manner.
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Affiliation(s)
- Marie E. Bunker
- grid.267047.00000 0001 2105 7936Department of Biology, University of Puget Sound, Tacoma, WA USA
| | - A. Elizabeth Arnold
- grid.134563.60000 0001 2168 186XSchool of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ USA
| | - Stacey L. Weiss
- grid.267047.00000 0001 2105 7936Department of Biology, University of Puget Sound, Tacoma, WA USA
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14
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Engel K, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota. MICROBIOME 2022; 10:202. [PMID: 36434663 PMCID: PMC9700942 DOI: 10.1186/s40168-022-01401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The establishment of the gut microbiota in early life is a critical process that influences the development and fitness of vertebrates. However, the relative influence of transmission from the early social environment and host selection throughout host ontogeny remains understudied, particularly in avian species. We conducted conspecific and heterospecific cross-fostering experiments in zebra finches (Taeniopygia guttata) and Bengalese finches (Lonchura striata domestica) under controlled conditions and repeatedly sampled the faecal microbiota of these birds over the first 3 months of life. We thus documented the development of the gut microbiota and characterised the relative impacts of the early social environment and host selection due to species-specific characteristics and individual genetic backgrounds across ontogeny by using 16S ribosomal RNA gene sequencing. RESULTS The taxonomic composition and community structure of the gut microbiota changed across ontogenetic stages; juvenile zebra finches exhibited higher alpha diversity than adults at the post-breeding stage. Furthermore, in early development, the microbial communities of juveniles raised by conspecific and heterospecific foster parents resembled those of their foster family, emphasising the importance of the social environment. In later stages, the social environment continued to influence the gut microbiota, but host selection increased in importance. CONCLUSIONS We provided a baseline description of the developmental succession of gut microbiota in zebra finches and Bengalese finches, which is a necessary first step for understanding the impact of the early gut microbiota on host fitness. Furthermore, for the first time in avian species, we showed that the relative strengths of the two forces that shape the establishment and maintenance of the gut microbiota (i.e. host selection and dispersal from the social environment) change during development, with host selection increasing in importance. This finding should be considered when experimentally manipulating the early-life gut microbiota. Our findings also provide new insights into the mechanisms of host selection. Video Abstract.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany.
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Institute for Bio- and Geosciences, Research Center Jülich, Jülich, Germany
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Kathrin Engel
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
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15
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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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16
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Kuthyar S, Watson K, Huang S, Brent LJN, Platt M, Horvath J, Gonzalez-Martinez J, Martínez M, Godoy-Vitorino F, Knight R, Dominguez-Bello MG, Amato KR. Limited microbiome differences in captive and semi-wild primate populations consuming similar diets. FEMS Microbiol Ecol 2022; 98:fiac098. [PMID: 36047944 PMCID: PMC9528791 DOI: 10.1093/femsec/fiac098] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Gut microbial communities are shaped by a myriad of extrinsic factors, including diet and the environment. Although distinct human populations consistently exhibit different gut microbiome compositions, variation in diet and environmental factors are almost always coupled, making it difficult to disentangle their relative contributions to shaping the gut microbiota. Data from discrete animal populations with similar diets can help reduce confounds. Here, we assessed the gut microbiota of free-ranging and captive rhesus macaques with at least 80% diet similarity to test the hypothesis that hosts in difference environments will have different gut microbiomes despite a shared diet. Although we found that location was a significant predictor of gut microbial composition, the magnitude of observed differences was relatively small. These patterns suggest that a shared diet may limit the typical influence of environmental microbial exposure on the gut microbiota.
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Affiliation(s)
- Sahana Kuthyar
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
- Division of Biological Sciences, University of California San Diego 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Karli Watson
- Institute of Cognitive Science, University of Colorado Boulder 1777 Exposition Drive Boulder, CO, 80309, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter Stocker Rd, Exeter EX4 4PY, United Kingdom
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd Philadelphia, PA, 19104, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, 425 S. University Ave Philadelphia, PA, 19104-6018, USA
- Department of Marketing, Wharton School of Business, University of Pennsylvania, 3620 Locust Walk, Philadelphia, PA, USA 19104, PA, USA
| | - Julie Horvath
- Research and Collections, North Carolina Museum of Natural Sciences, 11 W Jones St, Raleigh, NC, 27601, USA
- Biological and Biomedical Sciences Department, North Carolina Central University, 1801 Fayetteville St, Durham, NC, 27707, USA
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Campus Box 90383 Durham, NC, 27708, USA
- Department of Biological Sciences, North Carolina State University, 3510 Thomas Hall Campus Box 7614 Raleigh, NC, USA 27695, USA
| | - Janis Gonzalez-Martinez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Melween Martínez
- Caribbean Primate Research Center, Medical Sciences Campus, University of Puerto Rico Cayo Santiago, Punta Santiago, Puerto Rico, Humacao 00741, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, Medical Sciences Campus, PO BOX 365067 San Juan, PR 00936-5067, Puerto Rico
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego 9500 Gilman Dr, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego 9500 Gilman Drive La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
- Department of Computer Sciences and Engineering, University of California San Diego, 9500 Gilman Dr La Jolla, CA, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, USA 08901, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA 1810, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University 1810 Hinman Avenue Evanston, IL 60208, USA
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17
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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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18
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Age as a primary driver of the gut microbial composition and function in wild harbor seals. Sci Rep 2022; 12:14641. [PMID: 36030345 PMCID: PMC9420123 DOI: 10.1038/s41598-022-18565-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/16/2022] [Indexed: 11/08/2022] Open
Abstract
Dietary changes are the major variation cause in the composition of the gut microbiota. The short lactation phase in phocids provides an exceptional opportunity to explore the microbiota's response to a quick transition from a milk-based to a solid diet. We investigated the effects of age and sex on the gut microbiota of harbor seals in Mexico using rectal and fecal samples from pups and adults. 16S gene sequencing revealed age explains most of the observed variations in microbial composition. Individuals with frequent contact (pups-female adults) have major microbial similarities than those with little or no contact (pups-male adults). Overall, adults and females (regardless of sex and age, respectively) have a greater microbial richness; as seals grow, the core microbiome shrinks, and microbial diversity increases. We found pathways related to milk and chitin digestion in pups' microbiomes, indicating pups were transitioning to a solid diet. An enrichment of routes related to dramatic weight loss and body mass indicated higher metabolic stress in pups in late breeding season, when they are weaned and start intermittent fasting. Our findings highlight the host-microbiome interaction in harbor seals during late breeding season in response to food shifts and metabolic stress.
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19
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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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20
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Forsythe A, Fontaine N, Bissonnette J, Hayashi B, Insuk C, Ghosh S, Kam G, Wong A, Lausen C, Xu J, Cheeptham N. Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings. Sci Rep 2022; 12:9895. [PMID: 35701553 PMCID: PMC9198084 DOI: 10.1038/s41598-022-14223-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudogymnoascus destructans (Pd) is the causative agent of white-nose syndrome, which has resulted in the death of millions of bats in North America (NA) since 2006. Based on mortalities in eastern NA, the westward spread of infections likely poses a significant threat to western NA bats. To help prevent/reduce Pd infections in bats in western NA, we isolated bacteria from the wings of wild bats and screened for inhibitory activity against Pd. In total, we obtained 1,362 bacterial isolates from 265 wild bats of 13 species in western Canada. Among the 1,362 isolates, 96 showed inhibitory activity against Pd based on a coculture assay. The inhibitory activities varied widely among these isolates, ranging from slowing fungal growth to complete inhibition. Interestingly, host bats containing isolates with anti-Pd activities were widely distributed, with no apparent geographic or species-specific pattern. However, characteristics of roosting sites and host demography showed significant associations with the isolation of anti-Pd bacteria. Specifically, anthropogenic roosts and swabs from young males had higher frequencies of anti-Pd bacteria than those from natural roosts and those from other sex and age-groups, respectively. These anti-Pd bacteria could be potentially used to help mitigate the impact of WNS. Field trials using these as well as additional microbes from future screenings are needed in order to determine their effectiveness for the prevention and treatment against WNS.
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Affiliation(s)
- Adrian Forsythe
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nick Fontaine
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Julianna Bissonnette
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Brandon Hayashi
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Chadabhorn Insuk
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.,Department of Genetics, Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Gabrielle Kam
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Aaron Wong
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Cori Lausen
- Wildlife Conservation Society Canada, P.O. Box 606, Kaslo, BC, V0G 1M0, Canada.
| | - Jianping Xu
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.
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21
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Donohue ME, Rowe AK, Kowalewski E, Hert ZL, Karrick CE, Randriamanandaza LJ, Zakamanana F, Nomenjanahary S, Andriamalala RY, Everson KM, Law AD, Moe L, Wright PC, Weisrock DW. Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes. ISME COMMUNICATIONS 2022; 2:33. [PMID: 37938265 PMCID: PMC9723590 DOI: 10.1038/s43705-022-00115-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 04/27/2023]
Abstract
Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.
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Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, NY, USA
| | - Eric Kowalewski
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Zoe L Hert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | | | - Stela Nomenjanahary
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | - Rostant Y Andriamalala
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | | | - Audrey D Law
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Luke Moe
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Patricia C Wright
- Centre ValBio Research Station, Ranomafana, Madagascar
- Department of Anthropology, Stony Brook University, Stony Brook, New York, NY, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
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22
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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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23
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Xia W, Liu G, Wang D, Chen H, Zhu L, Li D. Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome. Comput Struct Biotechnol J 2022; 20:685-699. [PMID: 35140888 PMCID: PMC8814018 DOI: 10.1016/j.csbj.2022.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/15/2021] [Accepted: 01/13/2022] [Indexed: 12/28/2022] Open
Abstract
The gut microbiomes of non-human primates have received a great deal of attention due to their close relationship to humans. In recent years, these studies have mainly focused on the gut microbiome of wild primates, which will be helpful to understanding the evolution of primates and their gut microbiomes (e.g., gut microbiome plasticity and diet flexibility). However, there is still a lack of basic information on the gut microbiomes from wild populations. Here, we investigated the gut microbial composition (16S rRNA gene) and function (metagenome and metagenome-assembled genomes (MAGs)) of Yunnan snub-nosed monkey populations in Weixi County, Yunnan Province, China, that had diets either completely based on wild-foraging or were regularly supplemented with human provisioned food. We found a significant difference in the gut microbiome between these two populations: the gut microbiome of the wild-foraging (no food provision) population was enriched genes involved in the detoxification of bamboo cyanide (high proportion of bamboo shoot intake) and chitin (from insect diet) digestion, while the gut microbiome of the food provisioned (e.g., fruits) wild populations were enriched genes involved in carbohydrate metabolism. Moreover, the gut microbiome of the wild-foraging population shared a putatively functional convergence with the gut microbiome of wild bamboo-eating pandas: such as microbes and genes involved in the cyanide detoxification. Therefore, the gut microbiome of the Yunnan snub-nosed monkey displayed the potential plasticity in response to diet flexibility. Long-term food-provisioning of the wild population has led to dramatic changes in gut microbial composition, function, and even antibiotic resistance. The antibiotic resistance profile for the wild Yunnan snub-nosed monkey population could be considered the baseline and an important piece of information for conservation.
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Affiliation(s)
- Wancai Xia
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Institute of Rare Animals and Plants, China West Normal University, Nanchong, Sichuan, China
| | - Guoqi Liu
- Mingke Biotechnology, Hangzhou, China
| | - Dali Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Institute of Rare Animals and Plants, China West Normal University, Nanchong, Sichuan, China
| | - Hua Chen
- Mingke Biotechnology, Hangzhou, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Corresponding authors at: College of Life Science, Nanjing Normal University, Nanjing, China (L. Zhu); Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), Nanchong, China West Normal University, China (D. Li).
| | - Dayong Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Institute of Rare Animals and Plants, China West Normal University, Nanchong, Sichuan, China
- Corresponding authors at: College of Life Science, Nanjing Normal University, Nanjing, China (L. Zhu); Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), Nanchong, China West Normal University, China (D. Li).
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24
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Gartland LA, Firth JA, Laskowski KL, Jeanson R, Ioannou CC. Sociability as a personality trait in animals: methods, causes and consequences. Biol Rev Camb Philos Soc 2021; 97:802-816. [PMID: 34894041 DOI: 10.1111/brv.12823] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 02/06/2023]
Abstract
Within animal populations there is variation among individuals in their tendency to be social, where more sociable individuals associate more with other individuals. Consistent inter-individual variation in 'sociability' is considered one of the major axes of personality variation in animals along with aggressiveness, activity, exploration and boldness. Not only is variation in sociability important in terms of animal personalities, but it holds particular significance for, and can be informed by, two other topics of major interest: social networks and collective behaviour. Further, knowledge of what generates inter-individual variation in social behaviour also holds applied implications, such as understanding disorders of social behaviour in humans. In turn, research using non-human animals in the genetics, neuroscience and physiology of these disorders can inform our understanding of sociability. For the first time, this review brings together insights across these areas of research, across animal taxa from primates to invertebrates, and across studies from both the laboratory and field. We show there are mixed results in whether and how sociability correlates with other major behavioural traits. Whether and in what direction these correlations are observed may differ with individual traits such as sex and body condition, as well as ecological conditions. A large body of evidence provides the proximate mechanisms for why individuals vary in their social tendency. Evidence exists for the importance of genes and their expression, chemical messengers, social interactions and the environment in determining an individual's social tendency, although the specifics vary with species and other variables such as age, and interactions amongst these proximate factors. Less well understood is how evolution can maintain consistent variation in social tendencies within populations. Shifts in the benefits and costs of social tendencies over time, as well as the social niche hypothesis, are currently the best supported theories for how variation in sociability can evolve and be maintained in populations. Increased exposure to infectious diseases is the best documented cost of a greater social tendency, and benefits include greater access to socially transmitted information. We also highlight that direct evidence for more sociable individuals being safer from predators is lacking. Variation in sociability is likely to have broad ecological consequences, but beyond its importance in the spread of infectious diseases, direct evidence is limited to a few examples related to dispersal and invasive species biology. Overall, our knowledge of inter-individual variation in sociability is highly skewed towards the proximate mechanisms. Our review also demonstrates, however, that considering research from social networks and collective behaviour greatly enriches our understanding of sociability, highlighting the need for greater integration of these approaches into future animal personality research to address the imbalance in our understanding of sociability as a personality trait.
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Affiliation(s)
- Lizzy A Gartland
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, U.K
| | - Josh A Firth
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, OX1 3SZ, U.K
| | - Kate L Laskowski
- Department of Evolution and Ecology, University of California Davis, Davis, CA, 95616, U.S.A
| | - Raphael Jeanson
- Centre de Recherches sur la Cognition Animale (UMR5169), Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, 31062, Toulouse, France
| | - Christos C Ioannou
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, U.K
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25
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Killen SS, Cortese D, Cotgrove L, Jolles JW, Munson A, Ioannou CC. The Potential for Physiological Performance Curves to Shape Environmental Effects on Social Behavior. Front Physiol 2021; 12:754719. [PMID: 34858209 PMCID: PMC8632012 DOI: 10.3389/fphys.2021.754719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/19/2021] [Indexed: 01/03/2023] Open
Abstract
As individual animals are exposed to varying environmental conditions, phenotypic plasticity will occur in a vast array of physiological traits. For example, shifts in factors such as temperature and oxygen availability can affect the energy demand, cardiovascular system, and neuromuscular function of animals that in turn impact individual behavior. Here, we argue that nonlinear changes in the physiological traits and performance of animals across environmental gradients—known as physiological performance curves—may have wide-ranging effects on the behavior of individual social group members and the functioning of animal social groups as a whole. Previous work has demonstrated how variation between individuals can have profound implications for socially living animals, as well as how environmental conditions affect social behavior. However, the importance of variation between individuals in how they respond to changing environmental conditions has so far been largely overlooked in the context of animal social behavior. First, we consider the broad effects that individual variation in performance curves may have on the behavior of socially living animals, including: (1) changes in the rank order of performance capacity among group mates across environments; (2) environment-dependent changes in the amount of among- and within-individual variation, and (3) differences among group members in terms of the environmental optima, the critical environmental limits, and the peak capacity and breadth of performance. We then consider the ecological implications of these effects for a range of socially mediated phenomena, including within-group conflict, within- and among group assortment, collective movement, social foraging, predator-prey interactions and disease and parasite transfer. We end by outlining the type of empirical work required to test the implications for physiological performance curves in social behavior.
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Affiliation(s)
- Shaun S Killen
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Daphne Cortese
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Lucy Cotgrove
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Jolle W Jolles
- Center for Ecological Research and Forestry Applications (CREAF), Campus de Bellaterra (UAB), Barcelona, Spain
| | - Amelia Munson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Christos C Ioannou
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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26
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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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27
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Correa F, Torti V, Spiezio C, Checcucci A, Modesto M, Borruso L, Cavani L, Mimmo T, Cesco S, Luise D, Randrianarison RM, Gamba M, Rarojoson NJ, Sanguinetti M, Di Vito M, Bugli F, Mattarelli P, Trevisi P, Giacoma C, Sandri C. Disentangling the Possible Drivers of Indri indri Microbiome: A Threatened Lemur Species of Madagascar. Front Microbiol 2021; 12:668274. [PMID: 34421838 PMCID: PMC8378179 DOI: 10.3389/fmicb.2021.668274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/08/2021] [Indexed: 01/04/2023] Open
Abstract
Research on the gut microbiome may help with increasing our understanding of primate health with species' ecology, evolution, and behavior. In particular, microbiome-related information has the potential to clarify ecology issues, providing knowledge in support of wild primates conservation and their associated habitats. Indri (Indri indri) is the largest extant living lemur of Madagascar. This species is classified as "critically endangered" by the IUCN Red List of Threatened Species, representing one of the world's 25 most endangered primates. Indris diet is mainly folivorous, but these primates frequently and voluntarily engage in geophagy. Indris have never been successfully bred under human care, suggesting that some behavioral and/or ecological factors are still not considered from the ex situ conservation protocols. Here, we explored gut microbiome composition of 18 indris belonging to 5 different family groups. The most represented phyla were Proteobacteria 40.1 ± 9.5%, Bacteroidetes 28.7 ± 2.8%, Synergistetes 16.7 ± 4.5%, and Firmicutes 11.1 ± 1.9%. Further, our results revealed that bacterial alpha and beta diversity were influenced by indri family group and sex. In addition, we investigated the chemical composition of geophagic soil to explore the possible ecological value of soil as a nutrient supply. The quite acidic pH and high levels of secondary oxide-hydroxides of the soils could play a role in the folivorous diet's gut detoxification activity. In addition, the high contents of iron and manganese found the soils could act as micronutrients in the indris' diet. Nevertheless, the concentration of a few elements (i.e., calcium, sulfur, boron, nickel, sodium, and chromium) was higher in non-geophagic than in geophagic soils. In conclusion, the data presented herein provide a baseline for outlining some possible drivers responsible for the gut microbiome diversity in indris, thus laying the foundations for developing further strategies involved in indris' conservation.
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Affiliation(s)
- Federico Correa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Valeria Torti
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
| | - Alice Checcucci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Luciano Cavani
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Rose M. Randrianarison
- Groupe d’Étude et de Recherche sur les Primates de Madagascar, Antananarivo, Madagascar
- Mention d’Anthropobiologie et de Deìveloppement Durable, Université de Antananarivo, Antananarivo, Madagascar
| | - Marco Gamba
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | | | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maura Di Vito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Bugli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giacoma
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Camillo Sandri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
- Department of Animal Health Care and Management, Parco Natura Viva – Garda Zoological Park, Verona, Italy
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28
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Rojas CA, Ramírez-Barahona S, Holekamp KE, Theis KR. Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales. Anim Microbiome 2021; 3:33. [PMID: 33892813 PMCID: PMC8063394 DOI: 10.1186/s42523-021-00094-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/04/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.
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Affiliation(s)
- Connie A. Rojas
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Santiago Ramírez-Barahona
- Departament of Botany, Institute of Biology, Universidad Nacional Autónoma de México, Mexico City, MX Mexico
| | - Kay E. Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
| | - Kevin R. Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 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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30
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Identifying Microbiome-Mediated Behaviour in Wild Vertebrates. Trends Ecol Evol 2020; 35:972-980. [DOI: 10.1016/j.tree.2020.06.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 02/07/2023]
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Lindsay EC, Metcalfe NB, Llewellyn MS. The potential role of the gut microbiota in shaping host energetics and metabolic rate. J Anim Ecol 2020; 89:2415-2426. [PMID: 32858775 DOI: 10.1111/1365-2656.13327] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
It is increasingly recognized that symbiotic microbiota (especially those present in the gut) have important influences on the functioning of their host. Here, we review the interplay between this microbial community and the growth, metabolic rate and nutritional energy harvest of the host. We show how recent developments in experimental and analytical methods have allowed much easier characterization of the nature, and increasingly the functioning, of the gut microbiota. Manipulation studies that remove or augment gut microorganisms or transfer them between hosts have allowed unprecedented insights into their impact. Whilst much of the information to date has come from studies of laboratory model organisms, recent studies have used a more diverse range of host species, including those living in natural conditions, revealing their ecological relevance. The gut microbiota can provide the host with dietary nutrients that would be otherwise unobtainable, as well as allow the host flexibility in its capacity to cope with changing environments. The composition of the gut microbial community of a species can vary seasonally or when the host moves between environments (e.g. fresh and sea water in the case of migratory fish). It can also change with host diet choice, metabolic rate (or demands) and life stage. These changes in gut microbial community composition enable the host to live within different environments, adapt to seasonal changes in diet and maintain performance throughout its entire life history, highlighting the ecological relevance of the gut microbiota. Whilst it is evident that gut microbes can underpin host metabolic plasticity, the causal nature of associations between particular microorganisms and host performance is not always clear unless a manipulative approach has been used. Many studies have focussed on a correlative approach by characterizing microbial community composition, but there is now a need for more experimental studies in both wild and laboratory-based environments, to reveal the true role of gut microbiota in influencing the functioning of their hosts, including its capacity to tolerate environmental change. We highlight areas where these would be particularly fruitful in the context of ecological energetics.
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Affiliation(s)
- Elle C Lindsay
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Neil B Metcalfe
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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Fecal Short-Chain Fatty Acid Concentrations Increase in Newly Paired Male Marmosets (Callithrix jacchus). mSphere 2020; 5:5/5/e00794-20. [PMID: 32938699 PMCID: PMC7494834 DOI: 10.1128/msphere.00794-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
This study addressed a knowledge gap about longitudinal changes in the gut microbiome metabolites during animal pairing. This research in the laboratory common marmoset can control for the confounding factors such as diet and other environmental conditions. Phascolarctobacterium showed the highest contribution to the sex-biased transmission of the female to the male after pairing. Here, we observed the sex difference in the increase in short-chain fatty acid concentration in the feces of newly paired marmosets, which may be caused by the sex-biased gut microbiome transmission after pairing. The role by which the gut microbiome influences host health (e.g., energy equilibrium and immune system) may be partly mediated by short-chain fatty acids, which are bacterial fermentation products from the dietary fibers. However, little is known about longitudinal changes in gut microbiome metabolites during cohabitation alongside social contact. In common marmosets (Callithrix jacchus), the gut microbiome community is influenced by social contact, as newly paired males and females develop convergent microbial profiles. Here, we monitored the dynamics of short-chain fatty acid concentrations in common marmoset feces from the prepairing (PRE) to postpairing (POST) stages. In males, we observed that the concentrations of acetate, propionate, isobutyrate, and isovalerate significantly increased in the POST stage compared to the PRE stage. However, no significant changes were found in females. We further found that the propionate concentration was significantly positively correlated with the abundance of Phascolarctobacterium in the male feces. Thus, the sex difference in the changes in the concentrations of short-chain fatty acids might be related to sex-biased gut microbiome transmission after pairing. We suggest that the significant changes in the gut microbiomes and some short-chain fatty acids of the common marmoset during cohabitation may contribute to physiological homeostasis during pairing. IMPORTANCE This study addressed a knowledge gap about longitudinal changes in the gut microbiome metabolites during animal pairing. This research in the laboratory common marmoset can control for the confounding factors such as diet and other environmental conditions. Phascolarctobacterium showed the highest contribution to the sex-biased transmission of the female to the male after pairing. Here, we observed the sex difference in the increase in short-chain fatty acid concentration in the feces of newly paired marmosets, which may be caused by the sex-biased gut microbiome transmission after pairing.
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Hanya G, Tackmann J, Sawada A, Lee W, Pokharel SS, de Castro Maciel VG, Toge A, Kuroki K, Otsuka R, Mabuchi R, Liu J, Hatakeyama M, Yamasaki E, von Mering C, Shimizu-Inatsugi R, Hayakawa T, Shimizu KK, Ushida K. Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses. MICROBIAL ECOLOGY 2020; 80:459-474. [PMID: 32328670 DOI: 10.1007/s00248-020-01515-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.
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Affiliation(s)
- Goro Hanya
- Primate Research Institute, Kyoto University, Inuyama, Japan.
| | - Janko Tackmann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Akiko Sawada
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Chubu University Academy of Emerging Sciences, Kasugai, Japan
| | - Wanyi Lee
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | | | - Akito Toge
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Kota Kuroki
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Ryoma Otsuka
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, Japan
| | - Ryoma Mabuchi
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Jie Liu
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
| | - Eri Yamasaki
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Takashi Hayakawa
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
- Japan Monkey Centre, Inuyama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Japan
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34
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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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35
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Scheelings TF, Moore RJ, Van TTH, Klaassen M, Reina RD. Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history. Anim Microbiome 2020; 2:17. [PMID: 33499954 PMCID: PMC7807503 DOI: 10.1186/s42523-020-00034-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
Background The microbiota plays a critical role in host homeostasis and has been shown to be a major driving force in host evolution. However, our understanding of these important relationships is hampered by a lack of data for many species, and by significant gaps in sampling of the evolutionary tree. In this investigation we improve our understanding of the host-microbiome relationship by obtaining samples from all seven extant species of sea turtle, and correlate microbial compositions with host evolutionary history. Results Our analysis shows that the predominate phyla in the microbiota of nesting sea turtles was Proteobacteria. We also demonstrate a strong relationship between the bacterial phyla SR1 and sea turtle phylogeny, and that sea turtle microbiotas have changed very slowly over time in accordance with their similarly slow phenotypic changes. Conclusions This is one of the most comprehensive microbiota studies to have been performed in a single clade of animals and further improves our knowledge of how microbial populations have influenced vertebrate evolution.
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Affiliation(s)
| | - Robert J Moore
- RMIT University School of Science, Bundoora West Campus, Plenty Rd, Bundoora, Victoria, 3083, Australia
| | - Thi Thu Hao Van
- RMIT University School of Science, Bundoora West Campus, Plenty Rd, Bundoora, Victoria, 3083, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Richard D Reina
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Victoria, 3800, Australia
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Perry WB, Lindsay E, Payne CJ, Brodie C, Kazlauskaite R. The role of the gut microbiome in sustainable teleost aquaculture. Proc Biol Sci 2020; 287:20200184. [PMID: 32372688 PMCID: PMC7282919 DOI: 10.1098/rspb.2020.0184] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Elle Lindsay
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Christopher Brodie
- Ecosystems and Environment Research Centre, University of Salford, Salford M5 4WT, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 5UG, UK
| | - Raminta Kazlauskaite
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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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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Abstract
Investigation of gut microbiome composition and diversity with respect to human personality. Analyses targeted bacterial genera linked to behaviour in animal and human psychiatric studies. Bacterial genera were modelled (using negative binomial regression) with respect to personality. Genera linked to autism are also related to social behaviour in the general population. Sociability is associated with higher diversity, and anxiety and stress with reduced diversity.
The gut microbiome has a measurable impact on the brain, influencing stress, anxiety, depressive symptoms and social behaviour. This microbiome–gut–brain axis may be mediated by various mechanisms including neural, immune and endocrine signalling. To date, the majority of research has been conducted in animal models, while the limited number of human studies has focused on psychiatric conditions. Here the composition and diversity of the gut microbiome is investigated with respect to human personality. Using regression models to control for possible confounding factors, the abundances of specific bacterial genera are shown to be significantly predicted by personality traits. Diversity analyses of the gut microbiome reveal that people with larger social networks tend to have a more diverse microbiome, suggesting that social interactions may shape the microbial community of the human gut. In contrast, anxiety and stress are linked to reduced diversity and an altered microbiome composition. Together, these results add a new dimension to our understanding of personality and reveal that the microbiome–gut–brain axis may also be relevant to behavioural variation in the general population as well as to cases of psychiatric disorders.
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O’Brien SL, Tammone MN, Cuello PA, Lacey EA. Facultative sociality in a subterranean rodent, the highland tuco-tuco (Ctenomys opimus). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Understanding why social relationships vary among conspecifics is central to studies of animal behaviour. For many species, patterns of space use provide important insights into social behaviour. To characterize the social organization of the highland tuco-tuco (Ctenomys opimus), we used visual observations and radiotelemetry to quantify spatial relationships among adults in a population at Laguna de los Pozuelos, Jujuy Province, Argentina. Specifically, we sought to confirm anecdotal reports that these subterranean rodents are social, meaning that adults share burrow systems and nest sites. Our data indicate that the animals live in spatially distinct groups, although the number of individuals per group varies markedly. Although these relationships were robust with regard to location (above vs. below ground) and type of data (visual vs. telemetry), some groups identified during the daytime fissioned during the night. We suggest that the population of C. opimus at Pozuelos is facultatively social, meaning that individuals display predictable, adaptive differences in social relationships with conspecifics. More generally, our findings add to the growing number of subterranean species of rodents recognized as social, thereby generating new opportunities for comparative studies of these animals aimed at assessing the causes and consequences of variation in social organization.
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Affiliation(s)
- Shannon L O’Brien
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Mauro N Tammone
- INIBIOMA-CONICET and Programa de Estudios Aplicados a la Conservación del Parque Nacional Nanhuel Huapi (CENAC-PHHN, CONICET), Rio Negro, Argentina
| | - Pablo A Cuello
- Instituto Argentino de Investigaciones de Zonas Aridas (IADIZA-CCT CONICET), Mendoza, Argentina
| | - Eileen A Lacey
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, USA
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Woodhams DC, Bletz MC, Becker CG, Bender HA, Buitrago-Rosas D, Diebboll H, Huynh R, Kearns PJ, Kueneman J, Kurosawa E, LaBumbard BC, Lyons C, McNally K, Schliep K, Shankar N, Tokash-Peters AG, Vences M, Whetstone R. Host-associated microbiomes are predicted by immune system complexity and climate. Genome Biol 2020; 21:23. [PMID: 32014020 PMCID: PMC6996194 DOI: 10.1186/s13059-019-1908-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. RESULTS Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate. CONCLUSIONS Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.
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Affiliation(s)
- Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Molly C. Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - C. Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Hayden A. Bender
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Daniel Buitrago-Rosas
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Hannah Diebboll
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Roger Huynh
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Patrick J. Kearns
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Jordan Kueneman
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Emmi Kurosawa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | | | - Casandra Lyons
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Kerry McNally
- School for the Environment, University of Massachusetts, Boston, MA 02125 USA
- Animal Health Department, New England Aquarium, Boston, MA 02110 USA
| | - Klaus Schliep
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Nachiket Shankar
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Amanda G. Tokash-Peters
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, RN1, Butare, Rwanda
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
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Sherwin E, Bordenstein SR, Quinn JL, Dinan TG, Cryan JF. Microbiota and the social brain. Science 2019; 366:366/6465/eaar2016. [DOI: 10.1126/science.aar2016] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sociability can facilitate mutually beneficial outcomes such as division of labor, cooperative care, and increased immunity, but sociability can also promote negative outcomes, including aggression and coercion. Accumulating evidence suggests that symbiotic microorganisms, specifically the microbiota that reside within the gastrointestinal system, may influence neurodevelopment and programming of social behaviors across diverse animal species. This relationship between host and microbes hints that host-microbiota interactions may have influenced the evolution of social behaviors. Indeed, the gastrointestinal microbiota is used by certain species as a means to facilitate communication among conspecifics. Further understanding of how microbiota influence the brain in nature may be helpful for elucidating the causal mechanisms underlying sociability and for generating new therapeutic strategies for social disorders in humans, such as autism spectrum disorders (ASDs).
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Affiliation(s)
- Eoin Sherwin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN, USA
| | - John L. Quinn
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Sciences, University College Cork, Cork, Ireland
| | - John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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Kuthyar S, Manus MB, Amato KR. Leveraging non-human primates for exploring the social transmission of microbes. Curr Opin Microbiol 2019; 50:8-14. [PMID: 31585390 DOI: 10.1016/j.mib.2019.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/16/2019] [Accepted: 09/02/2019] [Indexed: 12/15/2022]
Abstract
Host social interactions can provide multiple complex pathways for microbial transmission. Here, we suggest non-human primates as models to study the social transmission of commensal or mutualistic microbes due to their high sociality, wide range of group compositions and dominance structures, and diverse group interactions. Microbial sharing from social interactions can positively impact host health by promoting microbial diversity and influencing immunity. Microbes may also drive their own transmission by shaping host behavior, which could lead to fitness benefits for both microbes and hosts. Variation in patterns of social interactions at both the individual and group scale make non-human primates an ideal system to explore the relationship between social behavior, microbial sharing, and their impact on host health and evolution.
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Affiliation(s)
- Sahana Kuthyar
- Department of Anthropology, Northwestern University, Evanston, IL 60208, United States
| | - Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, IL 60208, United States
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL 60208, United States.
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43
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Lane AA, McGuire MK, McGuire MA, Williams JE, Lackey KA, Hagen EH, Kaul A, Gindola D, Gebeyehu D, Flores KE, Foster JA, Sellen DW, Kamau-Mbuthia EW, Kamundia EW, Mbugua S, Moore SE, Prentice AM, Kvist LJ, Otoo GE, Rodríguez JM, Ruiz L, Pareja RG, Bode L, Price WJ, Meehan CL. Household composition and the infant fecal microbiome: The INSPIRE study. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:526-539. [PMID: 31012086 DOI: 10.1002/ajpa.23843] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/01/2019] [Accepted: 04/07/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Establishment and development of the infant gastrointestinal microbiome (GIM) varies cross-culturally and is thought to be influenced by factors such as gestational age, birth mode, diet, and antibiotic exposure. However, there is little data as to how the composition of infants' households may play a role, particularly from a cross-cultural perspective. Here, we examined relationships between infant fecal microbiome (IFM) diversity/composition and infants' household size, number of siblings, and number of other household members. MATERIALS AND METHODS We analyzed 377 fecal samples from healthy, breastfeeding infants across 11 sites in eight different countries (Ethiopia, The Gambia, Ghana, Kenya, Peru, Spain, Sweden, and the United States). Fecal microbial community structure was determined by amplifying, sequencing, and classifying (to the genus level) the V1-V3 region of the bacterial 16S rRNA gene. Surveys administered to infants' mothers identified household members and composition. RESULTS Our results indicated that household composition (represented by the number of cohabitating siblings and other household members) did not have a measurable impact on the bacterial diversity, evenness, or richness of the IFM. However, we observed that variation in household composition categories did correspond to differential relative abundances of specific taxa, namely: Lactobacillus, Clostridium, Enterobacter, and Klebsiella. DISCUSSION This study, to our knowledge, is the largest cross-cultural study to date examining the association between household composition and the IFM. Our results indicate that the social environment of infants (represented here by the proxy of household composition) may influence the bacterial composition of the infant GIM, although the mechanism is unknown. A higher number and diversity of cohabitants and potential caregivers may facilitate social transmission of beneficial bacteria to the infant gastrointestinal tract, by way of shared environment or through direct physical and social contact between the maternal-infant dyad and other household members. These findings contribute to the discussion concerning ways by which infants are influenced by their social environments and add further dimensionality to the ongoing exploration of social transmission of gut microbiota and the "old friends" hypothesis.
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Affiliation(s)
- Avery A Lane
- Department of Anthropology, Washington State University, Pullman, Washington
| | - Michelle K McGuire
- School of Family and Consumer Sciences, University of Idaho, Moscow, Idaho
| | - Mark A McGuire
- Department of Animal and Veterinary Science, University of Idaho, Moscow, Idaho
| | - Janet E Williams
- Department of Animal and Veterinary Science, University of Idaho, Moscow, Idaho
| | - Kimberly A Lackey
- School of Family and Consumer Sciences, University of Idaho, Moscow, Idaho
| | - Edward H Hagen
- Department of Anthropology, Washington State University, Pullman, Washington
| | - Abhishek Kaul
- Department of Mathematics and Statistics, Washington State University, Pullman, Washington
| | - Debela Gindola
- Department of Anthropology, Hawassa University, Hawassa, Ethiopia
| | - Dubale Gebeyehu
- Department of Anthropology, Hawassa University, Hawassa, Ethiopia
| | - Katherine E Flores
- Department of Anthropology, Washington State University, Pullman, Washington
| | - James A Foster
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Daniel W Sellen
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Samwel Mbugua
- Department of Human Nutrition, Egerton University, Nakuru, Kenya
| | - Sophie E Moore
- Department of Women and Children's Health, King's College London, London, United Kingdom.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.,MRC International Nutrition Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Gloria E Otoo
- Department of Nutrition and Food Science, University of Ghana, Accra, Ghana
| | - Juan M Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain
| | - Lorena Ruiz
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain.,Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain
| | | | - Lars Bode
- Department of Pediatrics, and Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, California
| | - William J Price
- Statistical Programs, College of Agriculture and Life Sciences, University of Idaho, Moscow, Idaho
| | - Courtney L Meehan
- Department of Anthropology, Washington State University, Pullman, Washington
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44
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Martin MA. Biological Anthropology in 2018: Grounded in Theory, Questioning Contexts, Embracing Innovation. AMERICAN ANTHROPOLOGIST 2019. [DOI: 10.1111/aman.13233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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45
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Greene LK, Bornbusch SL, McKenney EA, Harris RL, Gorvetzian SR, Yoder AD, Drea CM. The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs. Am J Primatol 2019; 81:e22974. [PMID: 30932230 DOI: 10.1002/ajp.22974] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/22/2022]
Abstract
Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host-microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to this topic, each of which relies on the diversity of Malagasy lemurs (representing a total of 19 species) and the comparative approach applied across scales of analysis. In Study 1, we compare gut microbial membership across 14 species in the wild to test the relative importance of host phylogeny and feeding strategy in mediating microbiome structure. Whereas host phylogeny strongly predicted community composition, the same feeding strategies shared by distant relatives did not produce convergent microbial consortia, but rather shaped microbiomes in host lineage-specific ways, particularly in folivores. In Study 2, we compare 14 species of wild and captive folivores, frugivores, and omnivores, to highlight the importance of captive populations for advancing gut microbiome research. We show that the perturbational effect of captivity is mediated by host feeding strategy and can be mitigated, in part, by modified animal management. In Study 3, we examine various scent-gland microbiomes across three species in the wild or captivity and show them to vary by host species, sex, body site, and a proxy of social status. These rare data provide support for the bacterial fermentation hypothesis in olfactory signal production and implicate steroid hormones as mediators of microbial community structure. We conclude by discussing the role of scale in comparative microbial studies, the links between feeding strategy and host-microbiome coadaptation, the underappreciated benefits of captive populations for advancing conservation research, and the need to consider the entirety of an animal's microbiota. Ultimately, these studies will help move the field from exploratory to hypothesis-driven research.
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Affiliation(s)
- Lydia K Greene
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Sally L Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Rachel L Harris
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Sarah R Gorvetzian
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, North Carolina
| | - Christine M Drea
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Department of Biology, Duke University, Durham, North Carolina
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Perofsky AC, Lewis RJ, Meyers LA. Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals. THE ISME JOURNAL 2019; 13:50-63. [PMID: 30108305 PMCID: PMC6299109 DOI: 10.1038/s41396-018-0251-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/03/2018] [Accepted: 07/19/2018] [Indexed: 12/14/2022]
Abstract
The gut microbiomes of mammals appear to mirror their hosts' phylogeny, suggesting host-driven microbial community assembly. Yet, much of this evidence stems from comparative studies of distinct wild or captive populations that lack data for disentangling the relative influences of shared phylogeny and environment. Here, we present phylogenetic and multivariate analyses of gut microbiomes from six sympatric (i.e., co-occurring) mammal species inhabiting a 1-km2 area in western Madagascar-three lemur and three non-primate species-that consider genetic, dietary, and ecological predictors of microbiome functionality and composition. Host evolutionary history, indeed, appears to shape gut microbial patterns among both closely and distantly related species. However, we also find that diet-reliance on leaves versus fruit-is the best predictor of microbiome similarity among closely related lemur species, and that host substrate use-ground versus tree-constrains horizontal transmission via incidental contact with feces, with arboreal species harboring far more distinct communities than those of their terrestrial and semi-terrestrial counterparts.
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Affiliation(s)
- Amanda C Perofsky
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Rebecca J Lewis
- Department of Anthropology, The University of Texas at Austin, Austin, TX, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Santa Fe Institute, Santa Fe, NM, USA
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Affiliation(s)
- Bethany J Hoye
- School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Andy Fenton
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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48
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Coordinated change at the colony level in fruit bat fur microbiomes through time. Nat Ecol Evol 2018; 3:116-124. [DOI: 10.1038/s41559-018-0731-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 10/24/2018] [Indexed: 12/26/2022]
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49
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Social context modulates digestive efficiency in greylag geese (Anser anser). Sci Rep 2018; 8:16498. [PMID: 30405171 PMCID: PMC6220252 DOI: 10.1038/s41598-018-34337-3] [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: 05/08/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
In group-living animals, social context is known to modulate physiology, behaviour and reproductive output as well as foraging and nutritional strategies. Here we investigate the digestive efficiency of 38 individuals belonging to different social categories of a semi-feral and individually marked flock of greylag geese (Anser anser). During 9 consecutive days in winter 2017, when the ground was fully covered with snow (i.e. no grass or other natural forage available) and the accessible food was standardized, 184 individual droppings were collected and analysed to estimate the apparent digestibility of organic matter (ADOM). Lignin was used as an indigestible internal marker in the food and droppings. The digestive efficiency was higher in pairs with offspring as compared to pairs without offspring or unpaired birds. Furthermore, individuals with high ADOM were more likely to breed successfully in the following season than those with low ADOM. Our findings demonstrate that social status modulates digestive efficiency, probably via a chain of physiological mechanisms including a dampened stress response in individuals enjoying stable social relationships with and social support by their family members (i.e. their own pair-partner and offspring). Our findings underline the importance of the social network in modulating physiology, such as digestive efficiency, and ultimately reproductive success.
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50
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Abstract
PURPOSE OF THE REVIEW As the science of the microbiome advances, social epidemiologists can contribute to understanding how the broader social environment shapes the microbiome over the life course. This review summarizes current research and describes potential mechanisms of the social epidemiology of the microbiome. RECENT FINDINGS Most existing literature linking the social environment and the microbiome comes from animal models, focused on the impact of social interactions and psychosocial stress. Suggestive evidence of the importance of early life exposures, health behaviors, and the built environment also point to the importance of the social environment for the microbiome in humans. SUMMARY Social epidemiology as a field is well poised to contribute expertise in theory and measurement of the broader social environment to this new area, and to consider both the upstream and downstream mechanisms by which this environment gets "under the skin" and "into the gut." As population-level microbiome data becomes increasingly available, we encourage investigation of the multi-level determinants of the microbiome and how the microbiome may link the social environment and health.
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Affiliation(s)
- Jennifer Beam Dowd
- Department of Global Health and Social Medicine, King’s College London, The Strand, London, WC2R 2LS UK
- Epidemiology and Biostatistics, CUNY Graduate School of Public Health and Health Policy, 55 W 125th St, New York, NY 10027 USA
| | - Audrey Renson
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Dr, Chapel Hill, NC 27599 USA
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