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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:e23657. [PMID: 38967215 DOI: 10.1002/ajp.23657] [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: 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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Jose L, Lee W, Hanya G, Tuuga A, Goossens B, Tangah J, Matsuda I, Kumar VS. Gut microbial community in proboscis monkeys ( Nasalis larvatus): implications for effects of geographical and social factors. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231756. [PMID: 39050721 PMCID: PMC11265907 DOI: 10.1098/rsos.231756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/23/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024]
Abstract
Recent technological advances have enabled comprehensive analyses of the previously uncharacterized microbial community in the gastrointestinal tracts of numerous animal species; however, the gut microbiota of several species, such as the endangered proboscis monkey (Nasalis larvatus) examined in this study, remains poorly understood. Our study sought to establish the first comprehensive data on the gut microbiota of free-ranging foregut-fermenting proboscis monkeys and to determine how their microbiota are affected locally by environmental factors, i.e. geographical distance, and social factors, i.e. the number of adult females within harem groups and the number of adults and subadults within non-harem groups, in a riverine forest in Sabah, Malaysian Borneo. Using 16S rRNA gene sequencing of 264 faecal samples collected from free-ranging proboscis monkeys, we demonstrated the trend that their microbial community composition is not particularly distinctive compared with other foregut- and hindgut-fermenting primates. The microbial alpha diversity was higher in larger groups and individuals inhabiting diverse vegetation (i.e. presumed to have a diverse diet). For microbial beta diversity, some measures were significant, showing higher values with larger geographical distances between samples. These results suggest that social factors such as increased inter-individual interactions, which can occur with larger groups, as well as physical distances between individuals or differences in dietary patterns, may affect the gut microbial communities.
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Affiliation(s)
- Lilian Jose
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah88400, Malaysia
| | - Wanyi Lee
- National Taiwan University, Taipei10617, Taiwan
- Center for Ecological Research, Kyoto University, Inuyama484-8506, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama484-8506, Japan
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu, Sabah88100, Malaysia
| | - Benoit Goossens
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu, Sabah88100, Malaysia
- Danau Girang Field Centre, Sabah Wildlife Department, Wisma Muis, Kota Kinabalu, Sabah88100, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, CardiffCF10 3AX, UK
| | - Joseph Tangah
- Sabah Forestry Department, Forest Research Centre, Sandakan, Sabah, Malaysia
| | - Ikki Matsuda
- Wildlife Research Center of Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto606-8203, Japan
- Chubu Institute for Advanced Studies, Chubu University, 1200, Matsumoto-cho, Kasugai-shi, Aichi487-8501, Japan
- Chubu University Academy of Emerging Sciences, 1200, Matsumoto-cho, Kasugai-shi, Aichi487-8501, Japan
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah88400, Malaysia
| | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah88400, Malaysia
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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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Bendová B, Bímová BV, Čížková D, Daniszová K, Ďureje Ľ, Hiadlovská Z, Macholán M, Piálek J, Schmiedová L, Kreisinger J. The strength of gut microbiota transfer along social networks and genealogical lineages in the house mouse. FEMS Microbiol Ecol 2024; 100:fiae075. [PMID: 38730559 PMCID: PMC11134300 DOI: 10.1093/femsec/fiae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/23/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The gut microbiota of vertebrates is acquired from the environment and other individuals, including parents and unrelated conspecifics. In the laboratory mouse, a key animal model, inter-individual interactions are severely limited and its gut microbiota is abnormal. Surprisingly, our understanding of how inter-individual transmission impacts house mouse gut microbiota is solely derived from laboratory experiments. We investigated the effects of inter-individual transmission on gut microbiota in two subspecies of house mice (Mus musculus musculus and M. m. domesticus) raised in a semi-natural environment without social or mating restrictions. We assessed the correlation between microbiota composition (16S rRNA profiles), social contact intensity (microtransponder-based social networks), and mouse relatedness (microsatellite-based pedigrees). Inter-individual transmission had a greater impact on the lower gut (colon and cecum) than on the small intestine (ileum). In the lower gut, relatedness and social contact independently influenced microbiota similarity. Despite female-biased parental care, both parents exerted a similar influence on their offspring's microbiota, diminishing with the offspring's age in adulthood. Inter-individual transmission was more pronounced in M. m. domesticus, a subspecies, with a social and reproductive network divided into more closed modules. This suggests that the transmission magnitude depends on the social and genetic structure of the studied population.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | | | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Kristina Daniszová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Ľudovít Ďureje
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Miloš Macholán
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno 603 00, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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Wiley KS, Gregg AM, Fox MM, Lagishetty V, Sandman CA, Jacobs JP, Glynn LM. Contact with caregivers is associated with composition of the infant gastrointestinal microbiome in the first 6 months of life. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24858. [PMID: 37804008 PMCID: PMC10922139 DOI: 10.1002/ajpa.24858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/18/2023] [Accepted: 09/24/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVES Little is known about how physical contact at birth and early caregiving environments influence the colonization of the infant gastrointestinal microbiome. We investigated how infant contact with caregivers at birth and within the first 2 weeks of life relates to the composition of the gastrointestinal microbiome in a sample of U.S. infants (n = 60). METHODS Skin-to-skin and physical contact with caregivers at birth and early caregiving environments were surveyed at 2 weeks postpartum. Stool samples were collected from infants at 2 weeks, 2, 6, and 12 months of age and underwent 16S rRNA sequencing as a proxy for the gastrointestinal microbiome. Associations between early caregiving environments and alpha and beta diversity, and differential abundance of bacteria at the genus level were assessed using PERMANOVA, and negative binomial mixed models in DEseq2. RESULTS Time in physical contact with caregivers explained 10% of variation in beta diversity at 2 weeks' age. The number of caregivers in the first few weeks of life explained 9% of variation in beta diversity at 2 weeks and the number of individuals in physical contact at birth explained 11% of variation in beta diversity at 6 months. Skin-to-skin contact on the day of birth was positively associated with the abundance of eight genera. Infants held for by more individuals had greater abundance of eight genera. DISCUSSION Results reveal a potential mechanism (skin-to-skin and physical contact) by which caregivers influence the infant gastrointestinal microbiome. Our findings contribute to work exploring the social transmission of microbes.
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Affiliation(s)
- Kyle S Wiley
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Andrew M Gregg
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Molly M Fox
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Curt A Sandman
- Department of Psychiatry and Human Behavior, UC Irvine, Irvine, California, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Laura M Glynn
- Department of Psychology, Chapman University, Orange, California, USA
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Rose C, Lund MB, Schramm A, Bilde T, Bechsgaard J. Does ecological drift explain variation in microbiome composition among groups in a social host species? J Evol Biol 2023; 36:1684-1694. [PMID: 37776090 DOI: 10.1111/jeb.14228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 10/01/2023]
Abstract
Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless divergence in microbiome composition among related groups arise. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider Stegodyphus dumicola. We simulated the initiation of new groups by splitting field-collected nests into groups of 1, 3, and 10 individuals respectively, and compared variation in microbiome composition among and within groups after 6 weeks using 16S rRNA gene sequencing. Theory predicts that ecological drift increases with decreasing group size. We found that microbiome composition among single founders was more dissimilar than among individuals kept in groups, supporting this prediction. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Individual founders appear to harbour higher relative abundances of non-core symbionts compared with founders in small groups, some of which are possible pathogens. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.
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Affiliation(s)
- Clémence Rose
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Marie Braad Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jesper Bechsgaard
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Enari H, Enari HS, Fujita S, Kawazoe T, Asai T, Oi T, Kondo T, Uno T, Seki K, Shimada M, Tsuji Y, Langgeng A, MacIntosh A, Suzuki K, Yamada K, Onishi K, Ueno M, Kubo K, Hanya G. Diet-related factors strongly shaped the gut microbiota of Japanese macaques. Am J Primatol 2023; 85:e23555. [PMID: 37766673 DOI: 10.1002/ajp.23555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/08/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large-scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet-related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
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Affiliation(s)
- Wanyi Lee
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Hiroto Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Haruka S Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Shiho Fujita
- Department of Behavioral Physiology and Ecology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tatsuro Kawazoe
- Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Takayuki Asai
- South Kyushu Wildlife Management Center, Kagoshima, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | | | - Takeharu Uno
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Kentaro Seki
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Masaki Shimada
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, Japan
| | - Yamato Tsuji
- Department of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
| | - Abdullah Langgeng
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | - Andrew MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | | | - Kazunori Yamada
- Graduate School of Human Sciences, Osaka University, Suita, Osaka, Japan
| | - Kenji Onishi
- Department of Early Childhood Education, Nara University of Education, Nara, Japan
| | - Masataka Ueno
- Faculty of Applied Sociology, Kindai University, Higashiosaka, Osaka, Japan
| | - Kentaro Kubo
- Cultural Asset Management Division, Board of Education, Oita-City, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
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Cheng Q, Krajmalnik-Brown R, DiBaise JK, Maldonado J, Guest MA, Todd M, Langer SL. Relationship Functioning and Gut Microbiota Composition among Older Adult Couples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085435. [PMID: 37107717 PMCID: PMC10138905 DOI: 10.3390/ijerph20085435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/11/2023] [Accepted: 03/23/2023] [Indexed: 05/11/2023]
Abstract
An emerging area of research extends work on couple functioning and physical health to gut health, a critical marker of general health and known to diminish with age. As a foray into this area, we conducted a pilot study to (1) determine the feasibility of remote data collection, including a fecal sample, from older adult couples, (2) examine within-couple concordance in gut microbiota composition, and (3) examine associations between relationship functioning and gut microbiota composition. Couples (N = 30) were recruited from the community. The participants' demographic characteristics were as follows: M (SD) age = 66.6 (4.8), 53% female, 92% White, and 2% Hispanic. Two of the couples were same-sex. All 60 participants completed self-report measures and supplied a fecal sample for microbiome analysis. Microbial DNA was extracted from the samples, and the 16S rRNA gene V4 region was amplified and sequenced. The results indicated that individuals shared more similar gut microbial composition with their partners than with others in the sample, p < 0.0001. In addition, individuals with better relationship quality (greater relationship satisfaction and intimacy and less avoidant communication) had greater microbial diversity, p < 0.05, a sign of healthier gut microbiota. Further research with a larger and more diverse sample is warranted to elucidate mechanisms.
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Affiliation(s)
- Qiwen Cheng
- Biodesign Center for Health through Microbiomes, Arizona State University, Tempe, AZ 85281, USA; (Q.C.); (R.K.-B.)
| | - Rosa Krajmalnik-Brown
- Biodesign Center for Health through Microbiomes, Arizona State University, Tempe, AZ 85281, USA; (Q.C.); (R.K.-B.)
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85281, USA
| | - John K. DiBaise
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic College of Medicine and Science, Scottsdale, AZ 85259, USA;
| | - Juan Maldonado
- Knowledge Enterprise Genomics Core, Arizona State University, Tempe, AZ 85281, USA;
| | - M. Aaron Guest
- Center for Innovation in Healthy and Resilient Aging, Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA;
| | - Michael Todd
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA
| | - Shelby L. Langer
- Center for Health Promotion and Disease Prevention, Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA
- Correspondence: ; Tel.: +1-602-496-0823
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9
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [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
- grid.418215.b0000 0000 8502 7018Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany ,grid.412889.e0000 0004 1937 0706Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Dominik Schneider
- grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Michael Heistermann
- grid.418215.b0000 0000 8502 7018Endocrinology Laboratory, German Primate Center, Göttingen, Germany
| | - Rolf Daniel
- grid.7450.60000 0001 2364 4210Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Claudia Fichtel
- grid.418215.b0000 0000 8502 7018Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany
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10
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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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11
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Ahmed E, Hens K. Microbiome in Precision Psychiatry: An Overview of the Ethical Challenges Regarding Microbiome Big Data and Microbiome-Based Interventions. AJOB Neurosci 2022; 13:270-286. [PMID: 34379050 DOI: 10.1080/21507740.2021.1958096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
There has been a spurt in both fundamental and translational research that examines the underlying mechanisms of the human microbiome in psychiatric disorders. The personalized and dynamic features of the human microbiome suggest the potential of its manipulation for precision psychiatry in ways to improve mental health and avoid disease. However, findings in the field of microbiome also raise philosophical and ethical questions. From a philosophical point of view, they may yet be another attempt at providing a biological cause for phenomena that ultimately cannot be so easily localized. From an ethical point of view, it is relevant that the human gut microbiome comprises data on the individual's lifestyle, disease history, previous medications, and mental health. Massive datasets of microbiome sequences are collected to facilitate comparative studies to identify specific links between the microbiome and mental health. Although this emerging research domain may show promise for psychiatric patients, it is surrounded by ethical challenges regarding patient privacy, health risks, effects on personal identity, and concerns about responsibility. This narrative overview displays the roles and advances of microbiome research in psychiatry and discusses the philosophical and ethical implications of microbiome big data and microbiome-based interventions for psychiatric patients. We also investigate whether these issues are really "new," or "old wine in new bottles."
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Affiliation(s)
- Eman Ahmed
- University of Antwerp.,Suez Canal University
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12
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Kapsetaki SE, Marquez Alcaraz G, Maley CC, Whisner CM, Aktipis A. Diet, Microbes, and Cancer Across the Tree of Life: a Systematic Review. Curr Nutr Rep 2022; 11:508-525. [PMID: 35704266 PMCID: PMC9197725 DOI: 10.1007/s13668-022-00420-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE OF REVIEW Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator between diet and cancers. Here, we review the work on cancer and the microbiome across species to search for broad patterns of susceptibility associated with different microbial species. RECENT FINDINGS Some microbes, such as Helicobacter bacteria, papillomaviruses, and the carnivore-associated Fusobacteria, consistently induce tumorigenesis in humans and other species. Other microbes, such as the milk-associated Lactobacillus, consistently inhibit tumorigenesis in humans and other species. We systematically reviewed over a thousand published articles and identified links between diet, microbes, and cancers in several species of mammals, birds, and flies. Future work should examine a larger variety of host species to discover new model organisms for human preclinical trials, to better understand the observed variance in cancer prevalence across species, and to discover which microbes and diets are associated with cancers across species. Ultimately, this could help identify microbial and dietary interventions to diagnose, prevent, and treat cancers in humans as well as other animals.
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Affiliation(s)
- Stefania E Kapsetaki
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA.
| | - Gissel Marquez Alcaraz
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA
| | - Corrie M Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - Athena Aktipis
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Psychology, Arizona State University, Tempe, AZ, USA
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13
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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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14
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Hair Microbiome Diversity within and across Primate Species. mSystems 2022; 7:e0047822. [PMID: 35876529 PMCID: PMC9426569 DOI: 10.1128/msystems.00478-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Primate hair and skin are substrates upon which social interactions occur and are host-pathogen interfaces. While human hair and skin microbiomes display body site specificity and immunological significance, little is known about the nonhuman primate (NHP) hair microbiome. Here, we collected hair samples (n = 158) from 8 body sites across 12 NHP species housed at three zoological institutions in the United States to examine the following: (1) the diversity and composition of the primate hair microbiome and (2) the factors predicting primate hair microbiome diversity and composition. If both environmental and evolutionary factors shape the microbiome, then we expect significant differences in microbiome diversity across host body sites, sexes, institutions, and species. We found our samples contained high abundances of gut-, respiratory-, and environment-associated microbiota. In addition, multiple factors predicted microbiome diversity and composition, although host species identity outweighed sex, body site, and institution as the strongest predictor. Our results suggest that hair microbial communities are affected by both evolutionary and environmental factors and are relatively similar across nonhuman primate body sites, which differs from the human condition. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome. IMPORTANCE We created the most comprehensive primate hair and skin data set to date, including data from 12 nonhuman primate species sampled from 8 body regions each. We find that the nonhuman primate hair microbiome is distinct from the human hair and skin microbiomes in that it is relatively uniform-as opposed to distinct-across body regions and is most abundant in gut-, environment-, and respiratory-associated microbiota rather than human skin-associated microbiota. Furthermore, we found that the nonhuman primate hair microbiome varies with host species identity, host sex, host environment, and host body site, with host species identity being the strongest predictor. This result demonstrates that nonhuman primate hair microbiome diversity varies with both evolutionary and environmental factors and within and across primate species. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome.
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15
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Fitzpatrick CR, Toor I, Holmes MM. Colony but not social phenotype or status structures the gut bacteria of a eusocial mammal. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03230-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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16
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Björk JR, Dasari MR, Roche K, Grieneisen L, Gould TJ, Grenier JC, Yotova V, Gottel N, Jansen D, Gesquiere LR, Gordon JB, Learn NH, Wango TL, Mututua RS, Kinyua Warutere J, Siodi L, Mukherjee S, Barreiro LB, Alberts SC, Gilbert JA, Tung J, Blekhman R, Archie EA. Synchrony and idiosyncrasy in the gut microbiome of wild baboons. Nat Ecol Evol 2022; 6:955-964. [PMID: 35654895 PMCID: PMC9271586 DOI: 10.1038/s41559-022-01773-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/20/2022] [Indexed: 01/04/2023]
Abstract
Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments and medications but it could also emerge from fundamental ecological forces that shape microbiota more generally. Here, we leverage extensive gut microbial time series from wild baboons-hosts who experience little interindividual dietary and environmental heterogeneity-to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, baboon microbiota were only weakly synchronized. The strongest synchrony occurred among baboons living in the same social group, probably because group members range over the same habitat and simultaneously encounter the same sources of food and water. However, this synchrony was modest compared to each host's personalized dynamics. In support, host-specific factors, especially host identity, explained, on average, more than three times the deviance in longitudinal dynamics compared to factors shared with social group members and ten times the deviance of factors shared across the host population. These results contribute to mounting evidence that highly idiosyncratic gut microbiomes are not an artefact of modern human environments and that synchronizing forces in the gut microbiome (for example, shared environments, diets and microbial dispersal) are not strong enough to overwhelm key drivers of microbiome personalization, such as host genetics, priority effects, horizontal gene transfer and functional redundancy.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Kim Roche
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec, Canada
- Research Center, Montreal Heart Institute, Montréal, Quebec, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec, Canada
| | - Neil Gottel
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
- The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Nairobi, Kenya
| | - Raphael S Mututua
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - J Kinyua Warutere
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Luis B Barreiro
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jack A Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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17
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Ning Y, Roberts NJ, Qi J, Peng Z, Long Z, Zhou S, Gu J, Hou Z, Yang E, Ren Y, Lang J, Liang Z, Zhang M, Ma J, Jiang G. Inbreeding status and implications for Amur tigers. Anim Conserv 2021. [DOI: 10.1111/acv.12761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Y. Ning
- College of Life Science Jilin Agricultural University Changchun China
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - N. J. Roberts
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - J. Qi
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
- School of Forestry Northeast Forestry University Harbin China
| | - Z. Peng
- School of Basic Medical Sciences Nanchang University Nanchang China
| | - Z. Long
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - S. Zhou
- Heilongjiang Research Institute of Wildlife Harbin China
| | - J. Gu
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - Z. Hou
- College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - E. Yang
- Wildlife Conservation Society Hunchun China
| | - Y. Ren
- Wildlife Conservation Society Hunchun China
| | - J. Lang
- Jilin Hunchun Amur Tiger National Nature Reserve Hunchun China
| | - Z. Liang
- Heilongjiang Laoyeling Amur Tiger National Nature Reserve Dongning China
| | - M. Zhang
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - J. Ma
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - G. Jiang
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
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18
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Lopes S, Calegaro-Marques C, Klain V, Chaves ÓM, Bicca-Marques JC. Necropsies disclose a low helminth parasite diversity in periurban howler monkeys. Am J Primatol 2021; 84:e23346. [PMID: 34783067 DOI: 10.1002/ajp.23346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 11/11/2022]
Abstract
Primate-parasite interactions are often investigated via coprological studies given ethical and conservation restrictions of collecting primate hosts. Yet, these studies are inadequate to recover adult helminths for taxonomic identification and to accurately assess their prevalence, intensity, abundance, and site of infection. Fresh carcasses found in anthropogenic landscapes come as informative and reliable alternatives. In this study, we identified the helminths of brown howler monkeys (Alouatta guariba clamitans) and their sites of infection, and measured their prevalence, intensity, and abundance of infection. We necropsied 18 adult males, 11 adult females, and 7 juvenile males that died in conflicts with the anthropogenic environment (domestic dog attacks, n = 11; electrocutions and road-kills, n = 10 each; unknown, n = 5) in periurban landscapes of southern Brazil between 2013 and 2019. We found three nematodes (Trypanoxyuris minutus, Dipetalonema gracile, and Parabronema bonnei) and one cestode (Bertiella cf. studeri), a diversity estimated to account for a sampling completeness of 99%. Prevalence ranged from 3% for P. bonnei to 100% for T. minutus. Mean abundance ranged from 2 (D. gracile and B. cf. studeri) to 55,116 (T. minutus) and mean intensity of infection ranged from 4 (B. cf. studeri) to 55,116 (T. minutus). Trypanoxyuris minutus sex ratio was strongly male-biased. The intensity of infection with T. minutus was higher in juvenile males and adult females than in adult males. The low parasite diversity and the helminths' mode of transmission are compatible with howlers' arboreality and folivorous-frugivorous diet. The howlers were not infected with soil-transmitted helminth parasites of humans and domestic animals on the ground and probably did not eat invertebrates to complement the diet. Given the lack of evidence of howler health problems, we suggest that the causes of death of the necropsied howlers are the major threats to the long-term conservation of the species at the study periurban landscapes.
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Affiliation(s)
- Stephanie Lopes
- Departamento de Zoologia, Laboratório de Helmintologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cláudia Calegaro-Marques
- Departamento de Zoologia, Laboratório de Helmintologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Vinícius Klain
- Escola de Ciências da Saúde e da Vida, Laboratório de Primatologia, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Óscar M Chaves
- Escola de Ciências da Saúde e da Vida, Laboratório de Primatologia, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Rio Grande do Sul, Brazil.,Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Júlio César Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Laboratório de Primatologia, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Rio Grande do Sul, Brazil
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19
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Cui Z, Holmes AJ, Zhang W, Hu D, Shao Q, Wang Z, Lu J, Raubenheimer D. Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items. Integr Zool 2021; 17:1147-1161. [PMID: 34767280 DOI: 10.1111/1749-4877.12601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Food supply is one of the major drivers of animal behavior, and the gut microbiome is an important mediator between food supply and its effects on physiology. However, predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging. We propose this reflects processes occurring at different scales. Inadequate accounting for the multi-level complexity of nutrition (nutrients, foods, diets) obscures the diet influence on microbiome and subsequently animal. Here, we present a detailed year-round, multi-level analysis of diet and microbiome changes in a wild population of a temperate primate, the rhesus macaque (Macaca mulatta). Total daily food and nutrient intake of 6 male and 6 female macaques was monitored in each of the 4 seasons (total 120 days observations). For each individual, we found significant variation in the microbiome between all 4 seasons. This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of 6 ecological guilds-sets of taxa sharing similar responses to nutrient intake. We conclude that study of diet, microbiome, and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake. Although microbiome response to diet does show variation in species-level taxa in response to food items, there is greater commonality in response at the level of guilds. A goal for microbiome researchers should be to identify genes encoding microbial attributes that can define such guilds.
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Affiliation(s)
- Zhenwei Cui
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Andrew J Holmes
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Wenjuan Zhang
- School of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Dalong Hu
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Qi Shao
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - Zhenlong Wang
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - Jiqi Lu
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - David Raubenheimer
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, China.,Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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20
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Xia W, Zhao M, Wang D, Wang F, Chen H, Liu G, Zhu L, Li D. Invasion and defense of the basic social unit in a nonhuman primate society leads to sexual differences in the gut microbiome. Integr Zool 2021; 17:168-180. [PMID: 34751507 PMCID: PMC9299848 DOI: 10.1111/1749-4877.12608] [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] [Indexed: 12/31/2022]
Abstract
Multilevel society is one of the most complex social systems in natural ecosystems and is a typical feature among some primates. Given the potential connection between social behavior and gut microbiome composition, the multilevel social system could affect the primate gut microbiome. Here, based on long‐term observation (e.g. social unit dynamics, transfer, and behavior), we investigated this potential integrating 16S rRNA gene amplicon sequencing and behavior data in Yunnan snub‐nosed monkeys (Rhinopithecus bieti), which possess a multilevel social group based on one male units (OMUs, each unit with several breeding females and their offspring) and all‐male unit (AMU, several bachelor males residing together). We found that the mean unweighted Unifrac distance between adult males from different OMUs was significantly lower than that between adult females from different OMUs (paired Wilcoxon test, P = 0.007). There was no significant difference in the mean unweighted Unifrac distance between females within the same OMU or between females from different OMUs. These findings indicated the potential connection between the defense and invasion of social units and the gut microbiome community in wild Yunnan snub‐nosed monkeys. We speculated that the resident males of OMUs displaying a significantly higher similarity in the gut microbial community than that of adult females in separate OMUs might be associated with the sexual differences in their interactions and from previously having cohabitated together in the AMU. Therefore, this study suggested that multilevel societies might have an effect on the gut microbial community in this wild nonhuman primate species.
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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
| | - Mei Zhao
- 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
| | - 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
| | - Fan 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
- Mingkef Biotechnology, Hangzhou, China
| | - Guoqi Liu
- Mingkef Biotechnology, Hangzhou, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - 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
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21
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Lopizzo N, Marizzoni M, Begni V, Mazzelli M, Provasi S, Borruso L, Riva MA, Cattaneo A. Social isolation in adolescence and long-term changes in the gut microbiota composition and in the hippocampal inflammation: Implications for psychiatric disorders - Dirk Hellhammer Award Paper 2021. Psychoneuroendocrinology 2021; 133:105416. [PMID: 34593267 DOI: 10.1016/j.psyneuen.2021.105416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 01/03/2023]
Abstract
Exposure to early adverse experiences induces persistent changes in physiological, emotional and behavioural functions predisposing the individual to an enhanced vulnerability to develop different disorders during lifespan. The adverse outcomes depend upon the timing of the stressful experiences, and in this contest, adolescence represents a key sensitive period for brain development. Among the biological systems involved, gut microbiota has recently been proposed to act on the interplay between the stress response, brain functions and immune system, through the gut-brain axis communication. In the current study we aimed to evaluate, in a preclinical model, changes over time in the microbiota community structure in physiological condition and in response to stress during adolescence. We also aimed to correlate the microbiota composition to the inflammatory status in brain. We used the preclinical model of social deprivation in rats during adolescence, based on the lack of all social contacts, for four weeks after weaning, followed by re-socialization until adulthood. We collected fecal samples at different post-natal days to investigate the short- and long-lasting effects of social isolation on gut microbiota composition and we collected brain areas (dorsal and ventral hippocampus) samples at killing to measure a panel of inflammatory and microglia activation markers. 16 S metataxonomic sequencing analysis revealed that microbial changes were influenced by age in both isolated and controls rats, regardless of sex, whereas social isolation impacted the microbial composition in a sex-dependent manner. A multivariate analysis showed that social isolation induced short-term gut microbiota alterations in females but not in males. We also identified several stress-related genera associated with social isolation condition. In brain areas we found a specific inflammatory pattern, in dorsal and ventral hippocampus, that significantly correlated with gut microbiota composition. Overall, in this study we reported a novel sex-specific association between gut microbiota composition and inflammatory response related to social isolation paradigm during adolescence, suggesting that stressful experiences during this sensitive period could have a long-lasting impact on the development of different biological systems that could in turn influence the vulnerability to develop mental disorders later in life.
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Affiliation(s)
- Nicola Lopizzo
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Moira Marizzoni
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy; Laboratory of Neuroimaging and Alzheimer's Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Monica Mazzelli
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Stefania Provasi
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen/Bolzano, piazza Università 5, 39100 Bolzano, Italy
| | - Marco Andrea Riva
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Annamaria Cattaneo
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy.
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22
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Liu G, Guo Z, Liu D, Meng H, Zheng Y, Zhao X, Gu L, Chen Z, Chen X, Li M, Sun J, Ma Z, He H, Yu X, Hu F. Does gut microbiota regulate brooding in geese? ANIM BIOL 2021. [DOI: 10.1163/15707563-bja10059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Domestic geese can reduce the amount of food intake when brooding. Because of the reduction in food intake, the total number of microorganisms in the gut is also reduced. Will this affect the goose’s thinking and make the goose stop brooding and eat food? We hypothesize that gut microbiota affects the brain through a brain–gut peptide and further regulates the breeding behavior of geese. In this study, we evaluated the microbiome related to the goose and transcription groups of brooding and egg production periods. The changes and differences in gut microbiota and gene expression of female geese in different reproduction periods were analyzed, and the possible interaction between them was explored. The results showed that the relative abundance of Faecalibacterium with a growth-promoting effect in the cecum was higher in the egg production group than in the brooding group. Microbial metabolic pathways with significant differences between the two groups were also enriched in the secondary functional groups with different gut microbiota metabolism. The downregulated genes in the egg production group were mainly related to energy metabolism, such as ATP synthesis-related genes. These results suggest that the brooding group’s gut microbiota can make relevant changes according to the reproduction stage of the goose. Since the amount of food taken in is reduced, it can promote the decomposition of the host’s fat. Simultaneously, insulin is also used to deliver messages to the brain; it is necessary to end the brooding behavior at an appropriate time and for eating to start.
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Affiliation(s)
- Guojun Liu
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Zhenhua Guo
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Di Liu
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - He Meng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P.R. China
| | - Yuming Zheng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P.R. China
| | - Xiuhua Zhao
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Lihong Gu
- Hainan Academy of Agricultural Sciences, Institute of Animal Science and Veterinary Medicine, 14 Xingdan Road, Qiongshan District, Haikou, 570203, P.R. China
| | - Zhifeng Chen
- Heilongjiang Academy of Agricultural Sciences, Qiqihare Branch Academy, No. 2 Heyi Road, Qiqihare 161005, P.R. China
| | - Xingyong Chen
- College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiangxi Road, Hefei, 230036, P.R. China
| | - Manyu Li
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Jinyan Sun
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Zhigang Ma
- Heilongjiang Academy of Agricultural Sciences, Qiqihare Branch Academy, No. 2 Heyi Road, Qiqihare 161005, P.R. China
| | - Haijuan He
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Xiaolong Yu
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, No. 368 Xuefu Road, Harbin 150086, P.R. China
| | - Fanghong Hu
- Agricultural and Rural Bureau, Longhexi Road, Liuan, 237006, P.R. China
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23
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Xie M, Zhang S, Xu L, Wu Z, Yuan J, Chen X. Comparison of the Intestinal Microbiota During the Different Growth Stages of Red Swamp Crayfish ( Procambarus clarkii). Front Microbiol 2021; 12:696281. [PMID: 34589066 PMCID: PMC8473915 DOI: 10.3389/fmicb.2021.696281] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/12/2021] [Indexed: 12/21/2022] Open
Abstract
This study aimed to determine the effect of the growth stage of Procambarus clarkii on their intestinal microbiota. Intestinal samples of five different growth stages of P. clarkii (first instar, second instar, third instar, juvenile, and adult) from laboratory culture were analyzed through the Illumina MiSeq high-throughput sequencing platform to determine the intestinal microbiome of crayfish. The alpha diversity decreased along with the growth of the crayfish, with the relative abundance of the microbiota changing among stages; crayfish at closer development stages had a more comparable intestinal microbiota composition. A comparative analysis by principal component analysis and principal coordinate analysis showed that there were significant differences in the intestinal microbiota of crayfish among the different growth stages, except for the first two stages of larval crayfish, and the intestinal microbiota showed a consistent progression pattern from the larval stage to the juvenile stage. Some microbiota showed stage specificity, which might be the characteristic microbiota of different stages of growth. According to FAPROTAX functional clustering analysis, the three stages of larvae were clustered together, while the juvenile and adult stages were clustered separately according to the growth stage, indicating that, in the early stages of larval development, the function of the intestinal flora was similar; as the body grew and developed, the composition and function of the intestinal microbiota also changed.
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Affiliation(s)
- Mengqi Xie
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Shiyu Zhang
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Lili Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China
| | - Zhixin Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China.,Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, China
| | - Xiaoxuan Chen
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agriculture University, Wuhan, China
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24
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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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25
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Martínez-Mota R, Righini N, Mallott EK, Gillespie TR, Amato KR. The relationship between pinworm (Trypanoxyuris) infection and gut bacteria in wild black howler monkeys (Alouatta pigra). Am J Primatol 2021; 83:e23330. [PMID: 34529285 DOI: 10.1002/ajp.23330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/17/2021] [Accepted: 09/04/2021] [Indexed: 12/21/2022]
Abstract
Gut bacteria may coexist with other groups of organisms, such as nematode parasites, that inhabit the gastrointestinal tract of primates; however, the possible effects of endoparasites on bacterial communities are frequently overlooked. Here we explored whether infection with Trypanoxyuris, an oxyurid gastrointestinal parasite, is associated with changes in the gut bacterial community of wild black howler monkeys (Alouatta pigra), by comparing gut bacterial communities of consistently infected individuals and individuals that never tested positive for Trypanoxyuris throughout different months across the year. We additionally controlled for other sources of variation reported to influence the primate microbiome including individual identity, social group, and seasonality. Trypanoxyuris infection was not related to differences in gut bacterial alpha diversity, but was weakly associated with differences in gut bacterial community structure. In contrast, among the covariates considered, both individual identity and social group were more strongly associated with variation in the howler gut bacterial community. Our results suggest that gastrointestinal parasites may be associated, to some extent, with shifts in the gut bacterial communities hosted by free-ranging primates, although a causal link still needs to be established. Further studies of wild primate hosts infected with parasite species with different pathogenicity are needed to better elucidate health-related consequences from the parasite-microbiome interplay.
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Affiliation(s)
- Rodolfo Martínez-Mota
- Centro de Investigaciones Tropicales (CITRO), Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Nicoletta Righini
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición (IICAN), Universidad de Guadalajara, Ciudad Guzmán, Jalisco, Mexico
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Thomas R Gillespie
- Department of Environmental Sciences, Program in Population Biology, Ecology, and Evolutionary Biology, Emory University, Atlanta, Georgia, USA.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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26
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Bowen M, Miles C, Hegseth R, Anderson CM, Brandon CS, Langford ML, Wolovich CK. The potential interplay between the glandular microbiome and scent marking behavior in owl monkeys (Aotus nancymaae). Am J Primatol 2021; 83:e23324. [PMID: 34492124 DOI: 10.1002/ajp.23324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 08/18/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022]
Abstract
In mammals, scent marking behavior is a pervasive form of chemical communication that regulates social interactions within and between groups. Glandular microbiota consist of bacterial communities capable of producing chemical cues used in olfactory communication. Despite countless studies on scent marking in primates, few have examined the microbiota associated with glandular secretions. Nancy Ma's owl monkeys (Aotus nancymaae) are nocturnal, socially monogamous primates that frequently scent mark using their subcaudal glands. Previous analyses revealed that unique chemical signatures of Aotus may convey information about sex and age. We used positive reinforcement to sample the subcaudal glands of 23 captive owl monkeys to describe their glandular microbiomes and examine how patterns in these bacterial communities vary with age, sex, rearing environment and/or social group (pair identity). We coupled these analyses with behavioral observations to examine patterns in their scent marking behavior. We isolated 31 bacterial species from Phyla Firmicutes, Proteobacteria, and Actinobacteria, consistent with the dermal and glandular microbiomes of other primates. Several bacterial taxa we identified produce volatile organic compounds, which may contribute to olfactory communication. These bacterial communities are best predicted by an interaction between sex, rearing environment and pair identity rather than any of these variables alone. Within mated pairs of A. nancymaae, males and females scent mark their nest boxes at similar frequencies. In some pairs, rates of scent marking by males and females fluctuated over time in a similar manner. Pairs that had been together longer tended to exhibit the greatest similarities in their rates of scent marking. Together, these findings suggest that scent marking behavior and close social interactions with pair mates in Aotus may influence bacterial transmission and their glandular microbiomes. Chemical communication, including coordinated scent marking, may play a role in strengthening pair bonds, signaling pair status and/or in mate guarding in this socially monogamous primate.
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Affiliation(s)
- Malique Bowen
- Department of Biology, Florida Southern College, Lakeland, Florida, USA
| | - Carly Miles
- Department of Biology, Florida Southern College, Lakeland, Florida, USA
| | - Ryan Hegseth
- Department of Biology, Florida Southern College, Lakeland, Florida, USA
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27
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Lewis CR, Bonham KS, McCann SH, Volpe AR, D’Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, Deoni SCL, Klepac-Ceraj V. Family SES Is Associated with the Gut Microbiome in Infants and Children. Microorganisms 2021; 9:1608. [PMID: 34442687 PMCID: PMC8398307 DOI: 10.3390/microorganisms9081608] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome composition. This study expands on this prior work by examining the association between family socioeconomic status (SES) and host genetics with microbiome composition in infants and children. METHODS Family SES was used to predict a latent variable representing six genera abundances generated from whole-genome shotgun sequencing. A polygenic score derived from a microbiome genome-wide association study was included to control for potential genetic associations. Associations between family SES and microbiome diversity were assessed. RESULTS Anaerostipes, Bacteroides, Eubacterium, Faecalibacterium, and Lachnospiraceae spp. significantly loaded onto a latent factor, which was significantly predicted by SES (p < 0.05) but not the polygenic score (p > 0.05). Our results indicate that SES did not predict alpha diversity but did predict beta diversity (p < 0.001). CONCLUSIONS Our results demonstrate that modifiable environmental factors influence gut microbiome composition at an early age. These results are important as our understanding of gut microbiome influences on health continue to expand.
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Affiliation(s)
- Candace R. Lewis
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Kevin S. Bonham
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
| | - Shelley Hoeft McCann
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
| | - Alexandra R. Volpe
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
| | - Viren D’Sa
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Matt D. De Both
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | | | - Sarah K. Highlander
- Pathogen and Microbiome Division, Translational Genomics Research Institute North (TGen), Flagstaff, AZ 86005, USA;
| | - Sean C. L. Deoni
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- MNCH D&T, Bill and Melinda Gates Foundation, Seattle, WA 98109, USA
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
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28
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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 PMCID: PMC8377764 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
- The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
- Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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29
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Stothart MR, Newman AEM. Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal. Anim Microbiome 2021; 3:46. [PMID: 34225812 PMCID: PMC8256534 DOI: 10.1186/s42523-021-00105-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). RESULTS Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. CONCLUSIONS Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.
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Affiliation(s)
- Mason R. Stothart
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, T2N 4Z6 Canada
| | - Amy E. M. Newman
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, Guelph, N1G 2W1 Canada
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30
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Abstract
Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.
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Eitan S, Madison CA, Kuempel J. The self-serving benefits of being a good host: A role for our micro-inhabitants in shaping opioids' function. Neurosci Biobehav Rev 2021; 127:284-295. [PMID: 33894242 DOI: 10.1016/j.neubiorev.2021.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 04/07/2021] [Accepted: 04/18/2021] [Indexed: 02/07/2023]
Abstract
Opioids are highly efficacious in their ability to relieve pain, but they are liable for abuse, dependence, and addiction. Risk factors to develop opioid use disorders (OUD) include chronic stress, socio-environment, and preexisting major depressive disorders (MDD) and posttraumatic stress disorders (PTSD). Additionally, opioids reduce gut motility, induce loss of gut barrier function, and alter the composition of the trillions of microbes hosted in the gastrointestinal tract, known as the gut microbiota. The microbiota are significant contributors to the reciprocal communication between the central nervous system (CNS) and the gut, termed the gut-brain axis. They have strong influences on their host behaviors, including the ability to cope with stress, sociability, affect, mood, and anxiety. Thus, they are implicated in the etiology of MDD and PTSD. Here we review the latest studies demonstrating that intestinal flora can, directly and indirectly, by affecting sociability levels, responses to stress, and mental state, alter the responses to opioids. It suggests that microbiota can potentially be used to increase the resilience to develop analgesic tolerance and OUD.
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Affiliation(s)
- Shoshana Eitan
- Behavioral and Cellular Neuroscience, Department of Psychological and Brain Sciences, Texas A&M University, 4235 TAMU, College Station, TX, 77843, USA.
| | - Caitlin A Madison
- Behavioral and Cellular Neuroscience, Department of Psychological and Brain Sciences, Texas A&M University, 4235 TAMU, College Station, TX, 77843, USA
| | - Jacob Kuempel
- Behavioral and Cellular Neuroscience, Department of Psychological and Brain Sciences, Texas A&M University, 4235 TAMU, College Station, TX, 77843, 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: 52] [Impact Index Per Article: 17.3] [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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Baniel A, Amato KR, Beehner JC, Bergman TJ, Mercer A, Perlman RF, Petrullo L, Reitsema L, Sams S, Lu A, Snyder-Mackler N. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas. MICROBIOME 2021; 9:26. [PMID: 33485388 PMCID: PMC7828014 DOI: 10.1186/s40168-020-00977-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/07/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes in food availability and diet. However, outside of dietary shifts, other potential environmental drivers of gut microbial composition have rarely been investigated, particularly in organisms living in their natural environments. RESULTS Here, we generated the largest wild nonhuman primate gut microbiome dataset to date to identify the environmental drivers of gut microbial diversity and function in 758 samples collected from wild Ethiopian geladas (Theropithecus gelada). Because geladas live in a cold, high-altitude environment and have a low-quality grass-based diet, they face extreme thermoregulatory and energetic constraints. We tested how proxies of food availability (rainfall) and thermoregulatory stress (temperature) predicted gut microbiome composition of geladas. The gelada gut microbiome composition covaried with rainfall and temperature in a pattern that suggests distinct responses to dietary and thermoregulatory challenges. Microbial changes were driven by differences in the main components of the diet across seasons: in rainier periods, the gut was dominated by cellulolytic/fermentative bacteria that specialized in digesting grass, while during dry periods the gut was dominated by bacteria that break down starches found in underground plant parts. Temperature had a comparatively smaller, but detectable, effect on the gut microbiome. During cold and dry periods, bacterial genes involved in energy, amino acid, and lipid metabolism increased, suggesting a stimulation of fermentation activity in the gut when thermoregulatory and nutritional stress co-occurred, and potentially helping geladas to maintain energy balance during challenging periods. CONCLUSION Together, these results shed light on the extent to which gut microbiota plasticity provides dietary and metabolic flexibility to the host, and might be a key factor to thriving in changing environments. On a longer evolutionary timescale, such metabolic flexibility provided by the gut microbiome may have also allowed members of Theropithecus to adopt a specialized diet, and colonize new high-altitude grassland habitats in East Africa. Video abstract.
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Affiliation(s)
- Alice Baniel
- Department of Anthropology, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
| | - Jacinta C Beehner
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Anthropology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Thore J Bergman
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arianne Mercer
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA
| | - Rachel F Perlman
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Lauren Petrullo
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Laurie Reitsema
- Department of Anthropology, University of Georgia, Athens, GA, 30602, USA
| | - Sierra Sams
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Noah Snyder-Mackler
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85281, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.
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Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States. mSystems 2020; 5:5/6/e00834-20. [PMID: 33144313 PMCID: PMC7646528 DOI: 10.1128/msystems.00834-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis). Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes. IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).
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Li Y, Chen T, Liang J, Li Y, Huang Z. Seasonal variation in the gut microbiota of rhesus macaques inhabiting limestone forests of southwest Guangxi, China. Arch Microbiol 2020; 203:787-798. [PMID: 33057745 DOI: 10.1007/s00203-020-02069-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Data on the gut microbiota of animals can provide new insights into dietary ecology of hosts, consequently assisting in understanding their adaptation strategy and evolutionary potential. We studied the gut microbiota composition and function of the wild rhesus macaques (Macaca mulatta) using 16S rRNA sequencing method. Our results revealed that the gut microbiota of the wild rhesus macaques was dominated by Firmicutes, Bacteroidetes, and Spirochaetes. Diversity and richness of gut microbiota were higher during the dry season than the rainy season. Specifically, higher proportions of Firmicutes, Tenericutes, Cyanobacteria, and unclassified bacteria at the phylum level and more Coprococcus at the genus level were detected in the dry season. Predictive functional analysis showed that pathways associated with carbohydrate metabolism and drug resistance (antimicrobial and antineoplastic) were richer in the dry season. These seasonal differences in microbiota could be due to their heavier dependence on leaf-based diet in the dry season. Additionally, macaques in limestone forests had a higher percentage of Spirochaetes, probably suggesting that the proportion of fruits in dietary composition also play an important role in the gut microbiota. We concluded that diet was strongly linked to the diversity, composition, and function of the gut microbiota in the wild groups of rhesus macaques living in the limestone forest, highlighting the importance of diet in the gut microbiota of macaques and the need to conduct further study on the adaptation strategy in response of environmental changes in the ground of gut microbiota.
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Affiliation(s)
- 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, No. 15 Yu Cai Road, Guilin, China
| | - Ting Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China
| | - Jipeng Liang
- Administration Centre of Guangxi Chongzuo White-headed Langur National Nature Reserve, Chongzuo, China
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China.
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, No. 15 Yu Cai Road, Guilin, China.
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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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Abstract
Understanding the interactions between host behavior and microbiome dynamics remains an outstanding priority in the field of microbial ecology. Here, we provide the reader with a simple example of how the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut). Seasonal dynamics in symbiotic microbiomes have been investigated in a number of vertebrates and are mainly caused by changes in the diet (in the gut microbiome) or the living environment (in the skin microbiome). Most amphibian microbiome studies focus on the skin, whereas internal microbiome structure and dynamics are often overlooked. The present study investigated the seasonal dynamics in three types of symbiotic microbiomes (the skin, stomach, and gut) across four wild frog species, belonging to different families, in May and October. The frogs harbored more water source microbes in May than in October. On the contrary, the frogs harbored more soil source microbes in October than in May. The frog species investigated tend to live in a water environment in May to maintain body surface humidity at high environmental temperatures and to breed. In October, these four species prefer to live on the land, as the environmental temperature decreases, to prepare for hibernation in caves or under stones. Thus, seasonal changes in the wild amphibian symbiotic microbiome may be caused by the difference in microbe transmission from their living environment due to specific behaviors. This study demonstrated that the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut). We revealed the potential association between specific behaviors in poikilothermic animals and host symbiotic microbiomes. IMPORTANCE Understanding the interactions between host behavior and microbiome dynamics remains an outstanding priority in the field of microbial ecology. Here, we provide the reader with a simple example of how the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut).
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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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Williams CL, Garcia-Reyero N, Martyniuk CJ, Tubbs CW, Bisesi JH. Regulation of endocrine systems by the microbiome: Perspectives from comparative animal models. Gen Comp Endocrinol 2020; 292:113437. [PMID: 32061639 DOI: 10.1016/j.ygcen.2020.113437] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023]
Abstract
The microbiome regulates endocrine systems and influences many aspects of hormone signaling. Using examples from different animal taxa, we highlight the state of the science in microbiome research as it relates to endocrinology and endocrine disruption research. Using a comparative approach discussing fish, birds, and mammals, we demonstrate the bidirectional interaction between microbiota and hormone systems, presenting concepts that include (1) gastrointestinal microbiome regulation of the neuroendocrine feeding axis; (2) stress hormones and microbial communities; (3) the role of site-specific microbiota in animal reproduction; (4) microbiome effects on the neuroendocrine systems and behavior; and (5) novel mechanisms of endocrine disruption through the microbiome. This mini-review demonstrates that hormones can directly affect the richness and diversity of microbiota and conversely, microbiota can influence hormone production and mediate their functions in animals. In addition, microbiota can influence the action of a diverse range of neurotransmitters and neuropeptides in the central nervous system, which can lead to behavioral disruptions. As many animals have species-specific reproductive behaviors, it is important to understand how shifts in the microbiota relate to these complex interactions between sexes. This is especially important for captive animals on specialized diets, and there are significant implications for microbiome research in conservation and reproductive biology. For example, microbial metabolites may modify motility of gametes or modulate hormone-receptor interactions in reproductive tissues. Thus, efforts to incorporate metabolomics into the science of microbiome-endocrine relationships, both those produced by the host and those generated from microbial metabolism, are increasingly needed. These concepts have fostered an exciting emerging era in comparative endocrinology.
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Affiliation(s)
- Candace L Williams
- Reproductive Sciences, San Diego Zoo Global Institute for Conservation Research, Escondido, CA 92027, USA.
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS 39180, USA
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Christopher W Tubbs
- Reproductive Sciences, San Diego Zoo Global Institute for Conservation Research, Escondido, CA 92027, USA
| | - Joseph H Bisesi
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
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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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Zhu L, Clayton JB, Suhr Van Haute MJ, Yang Q, Hassenstab HR, Mustoe AC, Knights D, Benson AK, French JA. Sex Bias in Gut Microbiome Transmission in Newly Paired Marmosets (Callithrix jacchus). mSystems 2020; 5:e00910-19. [PMID: 32209720 PMCID: PMC7093826 DOI: 10.1128/msystems.00910-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/10/2020] [Indexed: 01/28/2023] Open
Abstract
Social behavior can alter the microbiome composition via transmission among social partners, but there have been few controlled experimental studies of gut microbiome transmission among social partners in primates. We collected longitudinal fecal samples from eight unrelated male-female pairs of marmoset monkeys prior to pairing and for 8 weeks following pairing. We then sequenced 16S rRNA to characterize the changes in the gut microbiome that resulted from the pairing. Marmoset pairs had a higher similarity in gut microbiome communities after pairing than before pairing. We discovered sex differences in the degrees of change in gut microbiome communities following pairing. Specifically, the gut microbiome communities in males exhibited greater dissimilarity from the prepairing stage (baseline) than the gut microbiome communities in females. Conversely, females showed a gradual stabilization in the rate of the gut microbiome community turnover. Importantly, we found that the male fecal samples harbored more female-source gut microbes after pairing, especially early in pairing (paired test, P < 0.05), possibly linked to sex bias in the frequencies of social behavior. From this controlled study, we report for the first time that pair-living primates undergo significant changes in gut microbiome during pairing and that females transmit more microbes to their partners than males do. The potential biases influencing which microbes are transmitted on the basis of sex and whether they are due to sex biases in other behavioral or physiological features need to be widely investigated in other nonhuman primates and humans in the future.IMPORTANCE In this controlled study, we collected longitudinal fecal samples from 16 male and female marmoset monkeys for 2 weeks prior to and for 8 weeks after pairing in male-female dyads. We report for the first time that marmoset monkeys undergo significant changes to the gut microbiome following pairing and that these changes are sex-biased; i.e., females transmit more microbes to their social partners than males do. Marmosets exhibit pair bonding behavior such as spatial proximity, physical contact, and grooming, and sex biases in these behavioral patterns may contribute to the observed sex bias in social transmission of gut microbiomes.
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Affiliation(s)
- Lifeng Zhu
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mallory J Suhr Van Haute
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Qinnan Yang
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Haley R Hassenstab
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Aaryn C Mustoe
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Psychology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew K Benson
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jeffrey A French
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Psychology, University of Nebraska at Omaha, Omaha, Nebraska, USA
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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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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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44
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Björk JR, Dasari M, Grieneisen L, Archie EA. Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. Am J Primatol 2019; 81:e22970. [PMID: 30941803 PMCID: PMC7193701 DOI: 10.1002/ajp.22970] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/05/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022]
Abstract
To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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45
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Garber PA, Mallott EK, Porter LM, Gomez A. The gut microbiome and metabolome of saddleback tamarins (Leontocebus weddelli): Insights into the foraging ecology of a small-bodied primate. Am J Primatol 2019; 81:e23003. [PMID: 31190348 DOI: 10.1002/ajp.23003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/07/2019] [Accepted: 05/12/2019] [Indexed: 12/23/2022]
Abstract
Body mass is a strong predictor of diet and nutritional requirements across a wide range of mammalian taxa. In the case of small-bodied primates, because of their limited gut volume, rapid food passage rate, and high metabolic rate, they are hypothesized to maintain high digestive efficiency by exploiting foods rich in protein, fats, and readily available energy. However, our understanding of the dietary requirements of wild primates is limited because little is known concerning the contributions of their gut microbiome to the breakdown and assimilation of macronutrients and energy. To study how the gut microbiome contributes to the feeding ecology of a small-bodied primate, we analyzed the fecal microbiome composition and metabolome of 22 wild saddleback tamarins (adult body mass 360-390 g) in Northern Bolivia. Samples were analyzed using high-throughput Illumina sequencing of the 16 S rRNA gene V3-V5 regions, coupled with GC-MS metabolomic profiling. Our analysis revealed that the distal microbiome of Leontocebus weddelli is largely dominated by two main bacterial genera: Xylanibacter and Hallella (34.7 ± 14.7 and 22.6 ± 12.4%, respectively). A predictive analysis of functions likely carried out by bacteria in the tamarin gut demonstrated the dominance of membrane transport systems and carbohydrate metabolism as the predominant metabolic pathways. Moreover, given a fecal metabolome composed mainly of glucose, fructose, and lactic acid (21.7 ± 15.9%, 16.5 ± 10.7%, and 6.8 ± 5.5%, respectively), the processing of highly fermentable carbohydrates appears to play a central role in the nutritional ecology of these small-bodied primates. Finally, the results also show a potential influence of environmentally-derived bacteria in colonizing the tamarin gut. These results indicate high energetic turnover in the distal gut of Weddell's saddleback tamarin, likely influenced by dominant bacterial taxa that facilitate dietary dependence on highly digestible carbohydrates present in nectar, plant exudates, and ripe fruits.
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Affiliation(s)
- Paul A Garber
- Department of Anthropology and Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | | | - Leila M Porter
- Department of Anthropology, Northern Illinois University, DeKalb, Illinois
| | - Andres Gomez
- Department of Animal Science, Integrated Animal Systems Biology Team, University of Minnesota, Minnesota
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46
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Orkin JD, Webb SE, Melin AD. Small to modest impact of social group on the gut microbiome of wild Costa Rican capuchins in a seasonal forest. Am J Primatol 2019; 81:e22985. [PMID: 31081233 DOI: 10.1002/ajp.22985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/13/2019] [Accepted: 04/14/2019] [Indexed: 12/18/2022]
Abstract
The horizontal transmission of pathogenic and beneficial microbes has implications for health and development of socially living animals. Social group is repeatedly implicated as an important predictor of gut microbiome structure among primates, with individuals in neighboring social groups exhibiting distinct microbiomes. Here we examine whether group membership is a predictor of gut microbiome structure and diversity across three groups of white-faced capuchins (Cebus capucinus imitator) inhabiting a seasonal Costa Rican forest. We collected 62 fecal samples from 18 adult females during four sampling bouts. Sampling bouts spanned the dry-to-wet-to-dry seasonal transitions. To investigate gut microbial composition, we sequenced the V4 region of the 16S rRNA gene. We used the DADA2 pipeline to assign amplicon sequence variants and the RDP database to classify taxa. Our findings are: 1) gut microbiomes of capuchins clustered by social group in the late dry season, but this pattern was less evident in other sampling bouts; 2) social group was a significant variable in a PERMANOVA test of beta diversity, but it accounted for less variation than season; 3) social group was not an important predictor of abundance for the ten most abundant microbial taxa in capuchins; 4) when examining log2-fold abundances of microbes between social groups, there were significant differences in some pairwise comparisons. While this is suggestive of group-wide differences, individual variation may have a strong impact and should be assessed in future studies. Overall, we found a minor impact of social group membership on the gut microbiota of wild white-faced capuchins. Future research including home range overlap and resource use, as well as fine-scale investigation of individual variation, will further elucidate patterns of socially structured microbes.
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Affiliation(s)
- Joseph Daniel Orkin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta
| | - Shasta Ellen Webb
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta
| | - Amanda Dawn Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta.,Department of Medical Genetics, University of Calgary, Calgary, Alberta
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47
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Pafčo B, Sharma AK, Petrželková KJ, Vlčková K, Todd A, Yeoman CJ, Wilson BA, Stumpf R, White BA, Nelson KE, Leigh S, Gomez A. Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:575-585. [PMID: 31025322 DOI: 10.1002/ajpa.23842] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 04/05/2019] [Accepted: 04/06/2019] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Environmental and ecological factors, such as geographic range, anthropogenic pressure, group identity, and feeding behavior are known to influence the gastrointestinal microbiomes of great apes. However, the influence of individual host traits such as age and sex, given specific dietary and social constraints, has been less studied. The objective of this investigation was to determine the associations between an individual's age and sex on the diversity and composition of the gut microbiome in wild western lowland gorillas. MATERIALS AND METHODS Publicly available 16S rRNA data generated from fecal samples of different groups of Gorilla gorilla gorilla in the Central African Republic were downloaded and bioinformatically processed. The groups analyzed included habituated, partially habituated and unhabituated gorillas, sampled during low fruit (dry, n = 28) and high fruit (wet, n = 82) seasons. Microbial community analyses (alpha and beta diversity and analyses of discriminant taxa), in tandem with network-wide approaches, were used to (a) mine for specific age and sex based differences in gut bacterial community composition and to (b) asses for gut community modularity and bacterial taxa with potential functional roles, in the context of seasonal food variation, and social group affiliation. RESULTS Both age and sex significantly influenced gut microbiome diversity and composition in wild western lowland gorillas. However, the largest differences were observed between infants and adults in habituated groups and between adults and immature gorillas within all groups, and across dry and wet seasons. Specifically, although adults always showed greater bacterial richness than infants and immature gorillas, network-wide analyses showed higher microbial community complexity and modularity in the infant gorilla gut. Sex-based microbiome differences were not evident among adults, being only detected among immature gorillas. CONCLUSIONS The results presented point to a dynamic gut microbiome in Gorilla spp., associated with ontogeny and individual development. Of note, the gut microbiomes of breastfeeding infants seemed to reflect early exposure to complex, herbaceous vegetation. Whether increased compositional complexity of the infant gorilla gut microbiome is an adaptive response to an energy-limited diet and an underdeveloped gut needs to be further tested. Overall, age and sex based gut microbiome differences, as shown here, maybe mainly attributed to access to specific feeding sources, and social interactions between individuals within groups.
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Affiliation(s)
- Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Ashok K Sharma
- Department of Animal Science, University of Minnesota Twin Cities, St. Paul, Minnesota
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Klára Vlčková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,School of Microbiology and APC Microbiome Ireland, Food Science Building, University College Cork, Cork, Ireland
| | | | - Carl J Yeoman
- Department of Animal & Range Sciences, Montana State University, Bozeman, Montana
| | - Brenda A Wilson
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois.,Department of Microbiology, University of Illinois, Urbana, Illinois
| | - Rebecca Stumpf
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois.,Department of Anthropology, University of Illinois, Urbana, Illinois
| | - Bryan A White
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois
| | | | - Steven Leigh
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois.,Department of Anthropology, University of Colorado, Boulder, Colorado
| | - Andres Gomez
- Department of Animal Science, University of Minnesota Twin Cities, St. Paul, Minnesota
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48
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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: 22] [Impact Index Per Article: 4.4] [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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49
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Goodfellow CK, Whitney T, Christie DM, Sicotte P, Wikberg EC, Ting N. Divergence in gut microbial communities mirrors a social group fission event in a black-and-white colobus monkey (Colobus vellerosus). Am J Primatol 2019; 81:e22966. [PMID: 30920682 DOI: 10.1002/ajp.22966] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/11/2019] [Accepted: 02/16/2019] [Indexed: 12/16/2022]
Abstract
Host behavior and social factors have increasingly been implicated in structuring the composition of gut microbial communities. In social animals, distinct microbial communities characterize different social groups across a variety of taxa, although little longitudinal research has been conducted that demonstrates how this divergence occurs. Our study addresses this question by characterizing the gut microbial composition of an African Old World monkey, the black-and-white colobus (Colobus vellerosus), before and after a social group fission event. Gut microbial taxonomic composition of these monkeys was profiled using the V-4 hypervariable region of the bacterial 16S ribosomal RNA gene, and pairwise-relatedness values were calculated for all individuals using 17 short tandem repeat loci and partial pedigree information. The two social groups in this study were found to harbor distinct microbial signatures after the fission event from which they emerged, while these communities were not divergent in the same individuals before this event. Three genera were found to differ in abundance between the two new social groups: Parabacteroides, Coprococcus, and Porphyromonadaceae. Additionally, although this fission happened partially along lines of relatedness, relatedness did not structure the differences that we found. Taken together, this study suggests that distinct gut microbial profiles can emerge in social groups in <1 year and recommends further work into more finely mapping the timescales, causes, and potentially adaptive effects of this recurring trend toward distinct group microbial signatures.
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Affiliation(s)
- Claire K Goodfellow
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon.,Department of Biology, University of Oregon, Eugene, Oregon
| | - Tabor Whitney
- Department of Biology, University of Oregon, Eugene, Oregon
| | - Diana M Christie
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon.,Department of Anthropology, University of Oregon, Eugene, Oregon
| | - Pascale Sicotte
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Eva C Wikberg
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas
| | - Nelson Ting
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon.,Department of Anthropology, University of Oregon, Eugene, Oregon
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50
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Reveles KR, Patel S, Forney L, Ross CN. Age-related changes in the marmoset gut microbiome. Am J Primatol 2019; 81:e22960. [PMID: 30802990 DOI: 10.1002/ajp.22960] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 01/01/2023]
Abstract
The gut microbiome is known to play a significant role in human health but its role in aging remains unclear. The objective of this study was to compare the gut microbiome composition between young adult and geriatric non-human primates (marmosets) as a model of human health and disease. Stool samples were collected from geriatric (8+ years) and young adult males (2-5 years). Stool 16S ribosomal RNA V4 sequences were amplified and sequenced on the Illumina MiSeq platform. Sequences were clustered into operational taxonomic units and classified via Mothur's Bayesian classifier referenced against the Greengenes database. A total of 10 young adult and 10 geriatric marmosets were included. Geriatric marmosets had a lower mean Shannon diversity compared with young marmosets (3.15 vs. 3.46; p = 0.0191). Geriatric marmosets had a significantly higher mean abundance of Proteobacteria (0.22 vs. 0.09; p = 0.0233) and lower abundance of Firmicutes (0.15 vs. 0.19; p = 0.0032) compared with young marmosets. Geriatric marmosets had a significantly higher abundance of Succinivibrionaceae (0.16 vs. 0.01; p = 0.0191) and lower abundance of Porphyromonadaceae (0.07 vs. 0.11; p = 0.0494). In summary, geriatric marmosets had significantly altered microbiome diversity and composition compared with young adult marmosets. Further studies are needed to test microbiome-targeted therapies to improve healthspan and lifespan.
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Affiliation(s)
- Kelly R Reveles
- Phamacotherapy Division, College of Pharmacy, The University of Texas at Austin, Austin, Texas.,Pharmacotherapy Education & Research Center, University of Texas Health San Antonio, San Antonio, Texas
| | - Shrina Patel
- Phamacotherapy Division, College of Pharmacy, The University of Texas at Austin, Austin, Texas.,Pharmacotherapy Education & Research Center, University of Texas Health San Antonio, San Antonio, Texas
| | - Larry Forney
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Corinna N Ross
- Department of Science and Mathematics, Texas A&M University San Antonio, San Antonio, Texas.,Barshop Institute for Longevity and Aging Research, University of Texas Health San Antonio, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
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