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Finnegan PM, Garber PA, McKenney AC, Bicca-Marques JC, De la Fuente MF, Abreu F, Souto A, Schiel N, Amato KR, Mallott EK. Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate. mSphere 2024; 9:e0023324. [PMID: 38940510 PMCID: PMC11288025 DOI: 10.1128/msphere.00233-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
The gut microbiome has the potential to buffer temporal variations in resource availability and consumption, which may play a key role in the ability of animals to adapt to a broad range of habitats. We investigated the temporal composition and function of the gut microbiomes of wild common marmosets (Callithrix jacchus) exploiting a hot, dry environment-Caatinga-in northeastern Brazil. We collected fecal samples during two time periods (July-August and February-March) for 2 years from marmosets belonging to eight social groups. We used 16S rRNA gene amplicon sequencing, metagenomic sequencing, and butyrate RT-qPCR to assess changes in the composition and potential function of their gut microbiomes. Additionally, we identified the plant, invertebrate, and vertebrate components of the marmosets' diet via DNA metabarcoding. Invertebrate, but not plant or vertebrate, consumption varied across the year. However, gut microbiome composition and potential function did not markedly vary across study periods or as a function of diet composition. Instead, the gut microbiome differed markedly in both composition and potential function across marmosets residing in different social groups. We highlight the likely role of factors, such as behavior, residence, and environmental heterogeneity, in modulating the structure of the gut microbiome. IMPORTANCE In a highly socially cohesive and cooperative primate, group membership more strongly predicts gut microbiome composition and function than diet.
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Affiliation(s)
- Peter M. Finnegan
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Paul A. Garber
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, China
| | - Anna C. McKenney
- Department of Natural Sciences, Parkland College, Champaign, Illinois, USA
| | - Júlio César Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católicado Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Filipa Abreu
- Comparative BioCognition, Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
| | - Antonio Souto
- Department of Zoology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Nicola Schiel
- Laboratório de Etologia Teórica e Aplicada, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Katherine R. Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elizabeth K. Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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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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Webb SE, Orkin JD, Williamson RE, Melin AD. Activity budget and gut microbiota stability and flexibility across reproductive states in wild capuchin monkeys in a seasonal tropical dry forest. Anim Microbiome 2023; 5:63. [PMID: 38102711 PMCID: PMC10724892 DOI: 10.1186/s42523-023-00280-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/05/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Energy demands associated with pregnancy and lactation are significant forces in mammalian evolution. To mitigate increased energy costs associated with reproduction, female mammals have evolved behavioural and physiological responses. Some species alter activity to conserve energy during pregnancy and lactation, while others experience changes in metabolism and fat deposition. Restructuring of gut microbiota with shifting reproductive states may also help females increase the energy gained from foods, especially during pregnancy. The goal of this study was to examine the relationships among behaviour, gut microbiota composition, and reproductive state in a wild, non-human primate to better understand reproductive ecology. We combined life history data with > 13,000 behavioural scans and 298 fecal samples collected longitudinally across multiple years from 33 white-faced capuchin monkey (Cebus imitator) females. We sequenced the V4 region of the 16S rRNA gene and used the DADA2 pipeline to analyze microbial diversity. We used PICRUSt2 to assess putative functions. RESULTS Reproductive state explained some variation in activity, but overall resting behaviours were relatively stable across pregnancy and lactation. Foraging was less frequent among females in the early stage of nursing compared to the cycling stage, though otherwise remained at comparable levels. Maximum temperature was a strong, significantly positive predictor of resting, while social dominance had a small but significantly negative effect on resting. Ecological variables such as available fruit biomass and rainfall had a small but significantly positive effects on measures of foraging time. Gut microbial community structure, including richness, alpha diversity, and beta diversity remained stable across the reproductive cycle. In pairwise comparisons, pregnant females exhibited increased relative abundances of multiple microbial ASVs, suggesting small changes in relation to reproductive state. Reproductive state was not linked to differential abundance of putative metabolic pathways. CONCLUSIONS Previous data suggest that activity budget and the gut microbiome shifts considerably during reproduction. The present study finds that both activity and gut microbial communities are less associated with reproduction compared to other predictors, including ecological contexts. This suggests that behavioural flexibility and gut microbial community plasticity is contrained by ecological factors in this population. These data contribute to a broader understanding of plasticity and stability in response to physiological shifts associated with mammalian reproduction.
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Affiliation(s)
- Shasta E Webb
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Joseph D Orkin
- Département d'anthropologie, Université de Montréal, 3150 Rue Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Rachel E Williamson
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada.
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Pfau M, Degregori S, Johnson G, Tennenbaum SR, Barber PH, Philson CS, Blumstein DT. The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231305. [PMID: 37830026 PMCID: PMC10565414 DOI: 10.1098/rsos.231305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]
Abstract
The gut microbiome has a well-documented relationship with host fitness. Greater microbial diversity and abundance of specific microbes have been associated with improved fitness outcomes. Intestinal microbes also may be associated with patterns of social behaviour. However, these associations have been largely studied in captive animal models; we know less about microbiome composition as a potential driver of individual social behaviour and position in the wild. We used linear mixed models to quantify the relationship between fecal microbial composition, diversity and social network traits in a wild population of yellow-bellied marmots (Marmota flaviventer). We focused our analyses on microbes previously linked to sociability and neurobehavioural alterations in captive rodents, primates and humans. Using 5 years of data, we found microbial diversity (Shannon-Wiener and Faith's phylogenetic diversity) has a modest yet statistically significant negative relationship with the number of social interactions an individual engaged in. We also found a negative relationship between Streptococcus spp. relative abundance and two social network measures (clustering coefficient and embeddedness) that quantify an individual's position relative to others in their social group. These findings highlight a potentially consequential relationship between microbial composition and social behaviour in a wild social mammal.
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Affiliation(s)
- Madison Pfau
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Sam Degregori
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Gina Johnson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Stavi R. Tennenbaum
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Conner S. Philson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
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5
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Roche CE, Montague MJ, Wang J, Dickey AN, Ruiz-Lambides A, Brent LJN, Platt ML, Horvath JE. Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques. Microbiol Spectr 2023; 11:e0297423. [PMID: 37750731 PMCID: PMC10580906 DOI: 10.1128/spectrum.02974-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
While skin microbes are known to mediate human health and disease, there has been minimal research on the interactions between skin microbiota, social behavior, and year-to-year effects in non-human primates-important animal models for translational biomedical research. To examine these relationships, we analyzed skin microbes from 78 rhesus macaques living on Cayo Santiago Island, Puerto Rico. We considered age, sex, and social group membership, and characterized social behavior by assessing dominance rank and patterns of grooming as compared to nonsocial behaviors. To measure the effects of a shifting environment, we sampled skin microbiota (based on sequence analysis of the 16S rRNA V4 region) and assessed weather across sampling periods between 2013 and 2015. We hypothesized that, first, monkeys with similar social behavior and/or in the same social group would possess similar skin microbial composition due, in part, to physical contact, and, second, microbial diversity would differ across sampling periods. We found significant phylum-level differences between social groups in the core microbiome as well as an association between total grooming rates and alpha diversity in the complete microbiome, but no association between microbial diversity and measures of rank or other nonsocial behaviors. We also identified alpha and beta diversity differences in microbiota and differential taxa abundance across two sampling periods. Our findings indicate that social dynamics interact with yearly environmental changes to shape the skin microbiota in rhesus macaques, with potential implications for understanding the factors affecting the microbiome in humans, which share many biological and social characteristics with these animals. IMPORTANCE Primate studies are valuable for translational and evolutionary insights into the human microbiome. The majority of primate microbiome studies focus on the gut, so less is known about the factors impacting the microbes on skin and how their links affect health and behavior. Here, we probe the impact of social interactions and the yearly environmental changes on food-provisioned, free-ranging monkeys living on a small island. We expected animals that lived together and groomed each other would have more similar microbes on their skin, but surprisingly found that the external environment was a stronger influence on skin microbiome composition. These findings have implications for our understanding of the human skin microbiome, including potential manipulations to improve health and treat disease.
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Affiliation(s)
| | - Michael J. Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - JiCi Wang
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Allison N. Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Angelina Ruiz-Lambides
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Lauren J. N. Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, United Kingdom
| | - Michael L. Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Marketing Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie E. Horvath
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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6
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Sawada A, Hayakawa T, Kurihara Y, Lee W, Hanya G. Seasonal responses and host uniqueness of gut microbiome of Japanese macaques in lowland Yakushima. Anim Microbiome 2022; 4:54. [PMID: 36163043 PMCID: PMC9513907 DOI: 10.1186/s42523-022-00205-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
Background Changes in the gut microbial composition is an important response to cope with the seasonal fluctuations in the environment such as food availability. We examined the bacterial gut microbiome of the wild nonhuman primate, Japanese macaque (Macaca fuscata) in Yakushima over 13 months by noninvasive continuous sampling from three identified adult females. Results Dietary composition varied considerably over the study period and displayed marked shifts with the seasons. Feeding of leaves, fruits, and invertebrates were their main foods for at least one month. Diet had a significant influence on the gut microbiome. We also confirmed significant effect of host uniqueness in the gut microbiome among the three macaques. Leaf-dominated diet shaped unique gut microbiome structures where the macaques had the highest alpha diversity and their gut microbiome was enriched with Spirochaetes and Tenericutes. Diet-related differences in the putative function were detected, such as a differentially abundant urea cycle during the leaf-feeding season. Conclusion Both diet and host individuality exerted similar amounts of effect on gut microbe community composition. Major bacterial taxa showed a similar response to monthly fluctuations of fruit and invertebrate feeding, which was largely opposite to that of leaf feeding. The main constituents of fruits and invertebrates are both digestible with the enzyme of the host animals, but that of leaves is not available as an energy source without the aid of the fermentation of the gut microbiome. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00205-9.
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7
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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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Grassotti TT, Kothe CI, Prichula J, Mohellibi N, Mann MB, Wagner PGC, Campos FS, Campos AAS, Frazzon J, Frazzon APG. Fecal bacterial communities of wild black capuchin monkeys ( Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100048. [PMID: 34841339 PMCID: PMC8610302 DOI: 10.1016/j.crmicr.2021.100048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/19/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria ( χ ¯ = 80.54%), followed by Firmicutes ( χ ¯ = 12.14%), Actinobacteria ( χ ¯ = 4.60%), and Bacteriodetes ( χ ¯ = 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates.
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Key Words
- FROGS, Find Rapidly OTUs with Galaxy Solution
- FastQC, Fast Quality Control
- Fecal microbiota
- HTS, high-throughput sequencing
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MultiQC, Multi Quality Control
- OTUs, Operational Taxonomic Units
- PGMTM, Personal Genome Machine
- PICRUSt2, Phylogenetic Investigation of Communities by Reconstruction of Unobserved State
- Primate conservation
- Proteobacteria
- Robust capuchins
- SCS, Santa Cruz do Sul
- SSC, São Sebastião do Caí
- SSU, Small Subunit rRNA gene
- Wild south Brazilian primates
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Affiliation(s)
- Tiela Trapp Grassotti
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Janira Prichula
- Department of Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, RS, Brazil
| | - Nacer Mohellibi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Michele Bertoni Mann
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Fabricio Souza Campos
- Laboratory of Bioinformatics and Biotechnology, Campus de Gurupi, Federal University of Tocantins, Gurupi, TO, Brazil; Federal University of Tocantins, Federal University of Tocantins, Palmas, TO, Brazil
| | | | - Jeverson Frazzon
- Biochemistry and Molecular Biology of Microorganisms Laboratory, Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Paula Guedes Frazzon
- Post-Graduation Program in Agricultural and Environmental Microbiology, Microbiology, Immunology, and Parasitology Department, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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9
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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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10
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Yarlagadda K, Razik I, Malhi RS, Carter GG. Social convergence of gut microbiomes in vampire bats. Biol Lett 2021; 17:20210389. [PMID: 34727703 PMCID: PMC8563296 DOI: 10.1098/rsbl.2021.0389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
The 'social microbiome' can fundamentally shape the costs and benefits of group-living, but understanding social transmission of microbes in free-living animals is challenging due to confounding effects of kinship and shared environments (e.g. highly associated individuals often share the same spaces, food and water). Here, we report evidence for convergence towards a social microbiome among introduced common vampire bats, Desmodus rotundus, a highly social species in which adults feed only on blood, and engage in both mouth-to-body allogrooming and mouth-to-mouth regurgitated food sharing. Shotgun sequencing of samples from six zoos in the USA, 15 wild-caught bats from a colony in Belize and 31 bats from three colonies in Panama showed that faecal microbiomes were more similar within colonies than between colonies. To assess microbial transmission, we created an experimentally merged group of the Panama bats from the three distant sites by housing these bats together for four months. In this merged colony, we found evidence that dyadic gut microbiome similarity increased with both clustering and oral contact, leading to microbiome convergence among introduced bats. Our findings demonstrate that social interactions shape microbiome similarity even when controlling for past social history, kinship, environment and diet.
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Affiliation(s)
- Karthik Yarlagadda
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Imran Razik
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Ripan S. Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gerald G. Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
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11
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Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, Del Campo J, Cheves Hernandez S, Di Fiore A, Fontsere C, Hodgson JA, Janiak MC, Kuderna LFK, Lizano E, Martin MP, Niimura Y, Perry GH, Valverde CS, Tang J, Warren WC, de Magalhães JP, Kawamura S, Marquès-Bonet T, Krawetz R, Melin AD. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proc Natl Acad Sci U S A 2021; 118:e2010632118. [PMID: 33574059 PMCID: PMC7896301 DOI: 10.1073/pnas.2010632118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.
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Affiliation(s)
- Joseph D Orkin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T38 6A8, Canada
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19146
| | - Daniela Tejada-Martinez
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
- Doctorado en Ciencias mención Ecología y Evolución, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - Marc de Manuel
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | - Javier Del Campo
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | | | - Anthony Di Fiore
- Department of Anthropology and Primate Molecular Ecology and Evolution Laboratory, University of Texas at Austin, Austin, TX 78712
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, 170901 Cumbayá, Ecuador
| | - Claudia Fontsere
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | - Jason A Hodgson
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T38 6A8, Canada
- School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, United Kingdom
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Maria Pia Martin
- Kids Saving the Rainforest Wildlife Rescue Center, 60601 Quepos, Costa Rica
| | - Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | | | - Jia Tang
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Wesley C Warren
- Division of Animal Sciences, School of Medicine, University of Missouri, Columbia, MO 65211
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-8562 Chiba, Japan
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Consejo Superior de Investigaciones Cientificas, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies, 08010 Barcelona, Spain
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Roman Krawetz
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB T38 6A8, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T38 6A8, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T38 6A8, Canada
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12
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Melin AD, Hogan JD, Campos FA, Wikberg E, King‐Bailey G, Webb S, Kalbitzer U, Asensio N, Murillo‐Chacon E, Cheves Hernandez S, Guadamuz Chavarria A, Schaffner CM, Kawamura S, Aureli F, Fedigan L, Jack KM. Primate life history, social dynamics, ecology, and conservation: Contributions from long‐term research in Área de Conservación Guanacaste, Costa Rica. Biotropica 2020. [DOI: 10.1111/btp.12867] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and Archaeology University of Calgary Calgary AB Canada
- Verhaltensökologie & Soziobiologie Deutsches Primatenzentrum – Leibniz‐Institut für Primatenforschung Göttingen Germany
| | - Jeremy D. Hogan
- Department of Anthropology and Archaeology University of Calgary Calgary AB Canada
| | | | - Eva Wikberg
- Department of Anthropology Tulane University New Orleans LA USA
| | | | - Shasta Webb
- Department of Anthropology and Archaeology University of Calgary Calgary AB Canada
| | - Urs Kalbitzer
- Department of Anthropology McGill University Montreal QC Canada
| | - Norberto Asensio
- Departamento de Psicología Social y Metodología de las Ciencias del Comportamiento Universidad del País Vasco Bilbao Spain
| | | | | | | | | | - Shoji Kawamura
- Department of Integrated Biosciences The University of Tokyo Kashiwa Japan
| | - Filippo Aureli
- Instituto de Neuroetología Universidad Veracruzana Xalapa Mexico
- Research Centre in Evolutionary Anthropology and Palaeoecology Liverpool John Moores University Liverpool UK
| | - Linda Fedigan
- Department of Anthropology and Archaeology University of Calgary Calgary AB Canada
| | - Katharine M. Jack
- Department of Anthropology University of Texas at San Antonio San Antonio TX USA
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13
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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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