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Riopelle JC, Shamsaddini A, Holbrook MG, Bohrnsen E, Zhang Y, Lovaglio J, Cordova K, Hanley P, Kendall LV, Bosio CM, Schountz T, Schwarz B, Munster VJ, Port JR. Sex differences and individual variability in the captive Jamaican fruit bat (Artibeus jamaicensis) intestinal microbiome and metabolome. Sci Rep 2024; 14:3381. [PMID: 38336916 PMCID: PMC10858165 DOI: 10.1038/s41598-024-53645-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
The intestinal microbiome plays an important role in mammalian health, disease, and immune function. In light of this function, recent studies have aimed to characterize the microbiomes of various bat species, which are noteworthy for their roles as reservoir hosts for several viruses known to be highly pathogenic in other mammals. Despite ongoing bat microbiome research, its role in immune function and disease, especially the effects of changes in the microbiome on host health, remains nebulous. Here, we describe a novel methodology to investigate the intestinal microbiome of captive Jamaican fruit bats (Artibeus jamaicensis). We observed a high degree of individual variation in addition to sex- and cohort-linked differences. The intestinal microbiome was correlated with intestinal metabolite composition, possibly contributing to differences in immune status. This work provides a basis for future infection and field studies to examine in detail the role of the intestinal microbiome in antiviral immunity.
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Affiliation(s)
- Jade C Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Amirhossein Shamsaddini
- Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Myndi G Holbrook
- Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Eric Bohrnsen
- Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Yue Zhang
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kathleen Cordova
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patrick Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Lon V Kendall
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Catharine M Bosio
- Laboratory of Bacteriology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Benjamin Schwarz
- Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
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Liu X, Yu J, Huan Z, Xu M, Song T, Yang R, Zhu W, Jiang J. Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors. BMC Genomics 2024; 25:148. [PMID: 38321370 PMCID: PMC10848473 DOI: 10.1186/s12864-024-10041-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.
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Affiliation(s)
- Xuanzhen Liu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Jianqiu Yu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Zongjin Huan
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Mei Xu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ting Song
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ruilin Yang
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
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Moeller AH, Sanders JG, Sprockett DD, Landers A. Assessing co-diversification in host-associated microbiomes. J Evol Biol 2023; 36:1659-1668. [PMID: 37750599 PMCID: PMC10843161 DOI: 10.1111/jeb.14221] [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: 01/31/2023] [Revised: 08/08/2023] [Accepted: 08/29/2023] [Indexed: 09/27/2023]
Abstract
When lineages of hosts and microbial symbionts engage in intimate interactions over evolutionary timescales, they can diversify in parallel (i.e., co-diversify), producing associations between the lineages' phylogenetic histories. Tests for co-diversification of individual microbial lineages and their hosts have been developed previously, and these have been applied to discover ancient symbioses in diverse branches of the tree of life. However, most host-microbe relationships are not binary but multipartite, in that a single host-associated microbiota can contain many microbial lineages, generating challenges for assessing co-diversification. Here, we review recent evidence for co-diversification in complex microbiota, highlight the limitations of prior studies, and outline a hypothesis testing approach designed to overcome some of these limitations. We advocate for the use of microbiota-wide scans for co-diversifying symbiont lineages and discuss tools developed for this purpose. Tests for co-diversification for simple host symbiont systems can be extended to entire phylogenies of microbial lineages (e.g., metagenome-assembled or isolate genomes, amplicon sequence variants) sampled from host clades, thereby providing a means for identifying co-diversifying symbionts present within complex microbiota. The relative ages of symbiont clades can corroborate co-diversification, and multi-level permutation tests can account for multiple comparisons and phylogenetic non-independence introduced by repeated sampling of host species. Discovering co-diversifying lineages will generate powerful opportunities for interrogating the molecular evolution and lineage turnover of ancestral, host-species specific symbionts within host-associated microbiota.
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Affiliation(s)
- Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Abigail Landers
- Department of Microbiology, Cornell University, Ithaca, NY 14850, USA
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Nishida AH, Ochman H. Origins and Evolution of Novel Bacteroides in Captive Apes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563286. [PMID: 37961372 PMCID: PMC10634691 DOI: 10.1101/2023.10.20.563286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bacterial strains evolve in response to the gut environment of their hosts, with genomic changes that influence their interactions with hosts as well as with other members of the gut community. Great apes in captivity have acquired strains of Bacteroides xylanisolvens, which are common within gut microbiome of humans but not typically found other apes, thereby enabling characterization of strain evolution following colonization. Here, we isolate, sequence and reconstruct the history of gene gain and loss events in numerous captive-ape-associated strains since their divergence from their closest human-associated strains. We show that multiple captive-ape-associated B. xylanisolvens lineages have independently acquired gene complexes that encode functions related to host mucin metabolism. Our results support the finding of high genome fluidity in Bacteroides, in that several strains, in moving from humans to captive apes, have rapidly gained large genomic regions that augment metabolic properties not previously present in their relatives.
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Affiliation(s)
- Alexandra H. Nishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
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Malukiewicz J, D'arc M, Dias CA, Cartwright RA, Grativol AD, Moreira SB, Souza AR, Tavares MCH, Pissinatti A, Ruiz-Miranda CR, Santos AFA. Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools. Sci Rep 2023; 13:15679. [PMID: 37735195 PMCID: PMC10514281 DOI: 10.1038/s41598-023-42059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.
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Affiliation(s)
- Joanna Malukiewicz
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, 37077, Germany.
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, SP, 05403-000, Brazil.
| | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Cecilia A Dias
- Centro de Primatologia, Universidade de Brasília, Brasília, Brazil
| | - Reed A Cartwright
- School of Life Sciences and the Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | | | - Silvia Bahadian Moreira
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | | | | | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Rio de Janeiro, Brazil
| | - Carlos R Ruiz-Miranda
- Laboratorio das Ciencias Ambientais, Centro de Biociencias e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - André F A Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Sanders JG, Sprockett DD, Li Y, Mjungu D, Lonsdorf EV, Ndjango JBN, Georgiev AV, Hart JA, Sanz CM, Morgan DB, Peeters M, Hahn BH, Moeller AH. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nat Microbiol 2023:10.1038/s41564-023-01388-w. [PMID: 37169918 DOI: 10.1038/s41564-023-01388-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.
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Affiliation(s)
- Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA, USA
- Department of Anthropology, Emory University, Atlanta, GA, USA
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- School of Natural Sciences, Bangor University, Bangor, UK
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, Kinshasa, Democratic Republic of the Congo
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St Louis, Saint Louis, MO, USA
- Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL, USA
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, Montpellier, France
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
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Dallas JW, Warne RW. Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation. MICROBIAL ECOLOGY 2023; 85:820-838. [PMID: 35316343 DOI: 10.1007/s00248-022-01991-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 05/04/2023]
Abstract
During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.
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Affiliation(s)
- Jason W Dallas
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA.
| | - Robin W Warne
- Department of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL, 62901, USA
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Flynn JK, Ortiz AM, Herbert R, Brenchley JM. Host Genetics and Environment Shape the Composition of the Gastrointestinal Microbiome in Nonhuman Primates. Microbiol Spectr 2023; 11:e0213922. [PMID: 36475838 PMCID: PMC9927375 DOI: 10.1128/spectrum.02139-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
The bacterial component of the gastrointestinal tract microbiome is comprised of hundreds of species, the majority of which live in symbiosis with the host. The bacterial microbiome is influenced by host diet and disease history, and host genetics may additionally play a role. To understand the degree to which host genetics shapes the gastrointestinal tract microbiome, we studied fecal microbiomes in 4 species of nonhuman primates (NHPs) held in separate facilities but fed the same base diet. These animals include Chlorocebus pygerythrus, Chlorocebus sabaeus, Macaca mulatta, and Macaca nemestrina. We also followed gastrointestinal tract microbiome composition in 20 Macaca mulatta (rhesus macaques [RMs]) as they transitioned from an outdoor to indoor environment and compared 6 Chlorocebus pygerythrus monkeys that made the outdoor to indoor transition to their 9 captive-born offspring. We found that genetics can influence microbiome composition, with animals of different genera (Chlorocebus versus Macaca) having significantly different gastrointestinal (GI) microbiomes despite controlled diets. Animals within the same genera have more similar microbiomes, although still significantly different, and animals within the same species have even more similar compositions that are not significantly different. Significant differences were also not observed between wild-born and captive-born Chlorocebus pygerythrus, while there were significant changes in RMs as they transitioned into captivity. Together, these results suggest that the effects of captivity have a larger impact on the microbiome than other factors we examined within a single NHP species, although host genetics does significantly influence microbiome composition between NHP genera and species. IMPORTANCE Our data point to the degree to which host genetics can influence GI microbiome composition and suggest, within primate species, that individual host genetics is unlikely to significantly alter the microbiome. These data are important for the development of therapeutics aimed at altering the microbiome within populations of genetically disparate members of primate species.
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Affiliation(s)
- Jacob K. Flynn
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Alexandra M. Ortiz
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Richard Herbert
- Comparative Medicine Branch, NIAID, NIH, Bethesda, Maryland, USA
| | - Jason M. Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
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Bensch HM, Tolf C, Waldenström J, Lundin D, Zöttl M. Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent. Anim Microbiome 2023; 5:9. [PMID: 36765400 PMCID: PMC9912604 DOI: 10.1186/s42523-023-00231-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND In mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species. RESULTS We found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes. CONCLUSION We found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.
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Affiliation(s)
- Hanna M. Bensch
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden ,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| | - Conny Tolf
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Jonas Waldenström
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Daniel Lundin
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Markus Zöttl
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden ,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
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Ni Q, Dong S, Xing B, Zeng B, Kong F, Xu H, Yao Y, Li D, Zhang M, Fan X, Yang D, Yang M, Xie M. Oral and fecal microbiome of confiscated Bengal slow lorises in response to confinement duration. Front Microbiol 2022; 13:941261. [PMID: 36238588 PMCID: PMC9553000 DOI: 10.3389/fmicb.2022.941261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Slow lorises are small arboreal and nocturnal primates. Due to the illegal trade, a large number of slow lorises were confiscated into wildlife sanctuaries or rescue centers. The re-release has been considered a preferable approach for alleviating the captive pressure, but inappropriate and long-term confinement make it difficult to achieve this goal. In this study, we investigated and compared the fecal and oral microbiome of Bengal slow lorises (Nycticebus bengalensis) under long-term captivity (LC) and short-term captivity (SC) groups based on 16s rRNA high-throughput gene sequencing. The oral microbiome displayed higher Chao1 richness but lower Shannon and Simpson indices than the fecal microbiome. The Bengal slow lorises under long-term captivity had abundant pathogenic genera in both gut and oral microbiomes, such as Desulfovibrio, Actinomyces, Capnocytophaga, Neisseria, and Fusobacterium, while some specific bacterial taxa associated with intestinal balance were more enriched in the SC group. Due to the plant gum scarcity in the diet, both groups had a low abundance of Bifidobacterium. Function profile prediction indicated that the LC group was enriched with genetic information processing and metabolism pathways due to the stable food intake. The increased membrane transport and xenobiotic metabolism and degradation functions in the SC group could be explained by the function of the host microbiome in facilitating adaptation to changing environments and diets. The results demonstrated that the oral microbiome had the potential to be used as a regular surveillance tool. Also, current captive management should be improved to ensure reintroduction success.
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Affiliation(s)
- Qingyong Ni
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Qingyong Ni,
| | - Shasha Dong
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bolin Xing
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Fanli Kong
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Diyan Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Deying Yang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingyao Yang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Yaan, China
- Meng Xie,
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11
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Kubovčiak J, Schmiedová L, Albrecht T, Těšický M, Tomášek O, Kauzálová T, Kreisinger J. Within-community variation of interspecific divergence patterns in passerine gut microbiota. Ecol Evol 2022; 12:e9071. [PMID: 35813907 PMCID: PMC9251858 DOI: 10.1002/ece3.9071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota (GM) often exhibit variation between different host species and co-divergence with hosts' phylogeny. Identifying these patterns is a key for understanding the mechanisms that shaped symbiosis between GM and its hosts. Therefore, both GM-host species specificity and GM-host co-divergence have been investigated by numerous studies. However, most of them neglected a possibility that different groups of bacteria within GM can vary in the tightness of their association with the host. Consequently, unlike most of these studies, we aimed to directly address how the strength of GM-host species specificity and GM-host co-divergence vary across different GM clades. We decomposed GM communities of 52 passerine species (394 individuals), characterized by 16S rRNA amplicon sequence variant (ASV) profiles, into monophyletic Binned Taxonomic units (BTUs). Subsequently, we analyzed strength of host species specificity and correlation with host phylogeny separately for resulting BTUs. We found that most BTUs exhibited significant host-species specificity in their composition. Notably, BTUs exhibiting high host-species specificity comprised bacterial taxa known to impact host's physiology and immune system. However, BTUs rarely displayed significant co-divergence with host phylogeny, suggesting that passerine GM evolution is not shaped primarily through a shared evolutionary history between the host and its gut microbes.
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Affiliation(s)
- Jan Kubovčiak
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Oldřich Tomášek
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Tereza Kauzálová
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
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12
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de Jonge N, Carlsen B, Christensen MH, Pertoldi C, Nielsen JL. The Gut Microbiome of 54 Mammalian Species. Front Microbiol 2022; 13:886252. [PMID: 35783446 PMCID: PMC9246093 DOI: 10.3389/fmicb.2022.886252] [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: 02/28/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by the prevailing conditions in the gut environment. Community composition has been suggested to have large implications for conservation efforts, and gut health has become of interest for optimizing animal care in captivity. In this study, we explore the gut microbiome of a wide range of animals in the context of conservation biology. The composition of the gut microbial community of 54 mammalian animal species was investigated using 16S rRNA gene amplicon sequencing. The composition of the gut microbiota clearly reflects diet and the structure of the gastrointestinal system, and it is to a certain degree more similar between closely related animals. Specific clusters of taxa were observed across animals of the same species, diet, and gut morphology. The microbiota retained regardless of captivity status is hypothesized to cover important symbiotic relationships with the host, while the remaining part reflects the artificial living conditions and can therefore be used as a future tool for conservation biologists. For five animal species (giraffes, horses, baboons, elephants, and zebras), it was possible to compare the microbiota of wild and captive individuals. Differences were observed in the proportion of microbiota detected between wild and captive specimens of the same animal species. We propose that the gut microbiota harbours important species, which can potentially serve as indicators for the well-being of the animal and the effect of living in captivity.
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Affiliation(s)
- Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Benjamin Carlsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Aalborg Zoo, Aalborg, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- *Correspondence: Jeppe Lund Nielsen
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13
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Li D, Liu C, Abuduaini R, Du M, Wang Y, Zhu H, Chen H, Zhou N, Xin Y, Wu L, Ma J, Zhou Y, Lu Y, Jiang C, Sun Q, Liu S. The monkey microbial biobank brings previously uncultivated bioresources for nonhuman primate and human gut microbiomes. MLIFE 2022; 1:210-217. [PMID: 38817672 PMCID: PMC10989993 DOI: 10.1002/mlf2.12017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/28/2022] [Accepted: 02/19/2022] [Indexed: 06/01/2024]
Abstract
Nonhuman primates (NHPs) such as monkeys are the closest living relatives to humans and are the best available models for causative studies of human health and diseases. Gut microbiomes are intensively involved in host health. In this study, by large-scale cultivation of microbes from fecal samples of monkeys, we obtained previously uncultured bacterial species and constructed a Macaca fascicularis Gut Microbial Biobank (MfGMB). The MfGMB consisted of 250 strains that represent 97 species of 63 genera, 25 families, and 4 phyla. The information of the 250 strains and the genomes of 97 cultured species are publicly accessible. The MfGMB represented nearly 50% of core gut microbial compositions at the genus level and covered over 80% of the KO-based known gut microbiome functions of M. fascicularis. Data mining showed that the bacterial species in the MfGMB were prevalent not only in NHPs gut microbiomes but also in human gut microbiomes. This study will help the understanding and future investigations on how gut microbiomes interact with their mammalian hosts.
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Affiliation(s)
- Danhua Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Chang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Rexiding Abuduaini
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Mengxuan Du
- State Key Laboratory of Microbial BiotechnologyShandong UniversityQingdaoChina
| | - Yujing Wang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Haizhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Honghe Chen
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yuhua Xin
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- China General Microorganism Culture Collection, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Linhuan Wu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate NeurobiologyCAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Institute of NeuroscienceShanghaiChina
| | - Juncai Ma
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate NeurobiologyCAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Institute of NeuroscienceShanghaiChina
| | - Yuguang Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- China General Microorganism Culture Collection, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Yong Lu
- Microbial Resources and Big Data Center, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Microbial Resources and Big Data Center, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Qiang Sun
- Microbial Resources and Big Data Center, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Shuang‐Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial BiotechnologyShandong UniversityQingdaoChina
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14
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Dillard BA, Chung AK, Gunderson AR, Campbell-Staton SC, Moeller AH. Humanization of wildlife gut microbiota in urban environments. eLife 2022; 11:76381. [PMID: 35638605 PMCID: PMC9203057 DOI: 10.7554/elife.76381] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Urbanization is rapidly altering Earth's environments, demanding investigation of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans), crested anole lizards (Anolis cristatellus), and white-crowned sparrows (Zonotrichia leucophrys) acquire gut microbiota constituents found in humans, including gut bacterial lineages associated with urbanization in humans. Comparisons of urban and rural wildlife and human populations revealed significant convergence of gut microbiota among urban populations relative to rural populations. All bacterial lineages overrepresented in urban wildlife relative to rural wildlife and differentially abundant between urban and rural humans were also overrepresented in urban humans relative to rural humans. Remarkably, the bacterial lineage most overrepresented in urban anoles was a Bacteroides sequence variant that was also the most significantly overrepresented in urban human populations. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.
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Affiliation(s)
- Brian A Dillard
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, United States
| | | | | | | | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, United States
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15
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Houtz JL, Taff CC, Vitousek MN. Gut Microbiome as a Mediator of Stress Resilience: A Reactive Scope Model Framework. Integr Comp Biol 2022; 62:41-57. [PMID: 35544275 DOI: 10.1093/icb/icac030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stress resilience is defined as the ability to rebound to a homeostatic state after exposure to a perturbation. Organisms modulate various physiological mediators to respond to unpredictable changes in their environment. The gut microbiome is a key example of a physiological mediator that coordinates a myriad of host functions including counteracting stressors. Here, we highlight the gut microbiome as a mediator of host stress resilience in the framework of the reactive scope model. The reactive scope model integrates physiological mediators with unpredictable environmental changes to predict how animals respond to stressors. We provide examples of how the gut microbiome responds to stressors within the four ranges of the reactive scope model (i.e., predictive homeostasis, reactive homeostasis, homeostatic overload, and homeostatic failure). We identify measurable metrics of the gut microbiome that could be used to infer the degree to which the host is experiencing chronic stress, including microbial diversity, flexibility, and gene richness. The goal of this perspective piece is to highlight the underutilized potential of measuring the gut microbiome as a mediator of stress resilience in wild animal hosts.
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Affiliation(s)
- Jennifer L Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Conor C Taff
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Maren N Vitousek
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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16
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The gut microbiome of exudivorous marmosets in the wild and captivity. Sci Rep 2022; 12:5049. [PMID: 35322053 PMCID: PMC8942988 DOI: 10.1038/s41598-022-08797-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/08/2022] [Indexed: 12/14/2022] Open
Abstract
Mammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild. Marmosets represent another group of dietary specialists, exudivores that eat plant exudates, but whose microbiome remains relatively less studied. The common occurrence of gastrointestinal distress in captive marmosets prompted us to study the Callithrix gut microbiome composition and predictive function through bacterial 16S ribosomal RNA V4 region sequencing. We sampled 59 wild and captive Callithrix across four species and their hybrids. Host environment had a stronger effect on the gut microbiome than host taxon. Wild Callithrix gut microbiomes were enriched for Bifidobacterium, which process host-indigestible carbohydrates. Captive marmoset guts were enriched for Enterobacteriaceae, a family containing pathogenic bacteria. While gut microbiome function was similar across marmosets, Enterobacteriaceae seem to carry out most functional activities in captive host guts. More diverse bacterial taxa seem to perform gut functions in wild marmosets, with Bifidobacterium being important for carbohydrate metabolism. Captive marmosets showed gut microbiome composition aspects seen in human gastrointestinal diseases. Thus, captivity may perturb the exudivore gut microbiome, which raises implications for captive exudivore welfare and calls for husbandry modifications.
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17
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Abstract
In mammals, the composition of the gut microbiota is associated with host phylogenetic history, and host-lineage specific microbiota have been shown, in some cases, to contribute to fitness-related traits of their hosts. However, in primates, captivity can disrupt the native microbiota through a process of humanization in which captive hosts acquire gut microbiota constituents found in humans. Despite the potential importance of this process for the health of captive hosts, the degree to which captivity humanizes the gut microbiota of other mammalian taxa has not been explored. Here, we analyzed hundreds of published gut microbiota profiles generated from wild and captive hosts spanning seven mammalian families to investigate the extent of humanization of the gut microbiota in captivity across the mammalian phylogeny. Comparisons of these hosts revealed compositional convergence between captive mammal and human gut microbiota in the majority of mammalian families examined. This convergence was driven by a diversity of microbial lineages, including members of the Archaea, Clostridium, and Bacteroides. However, the gut microbiota of two families—Giraffidae and Bovidae—were remarkably robust to humanization in captivity, showing no evidence of gut microbiota acquisition from humans relative to their wild confamiliars. These results demonstrate that humanization of the gut microbiota is widespread in captive mammals, but that certain mammalian lineages are resistant to colonization by human-associated gut bacteria.
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Affiliation(s)
- Brian K Trevelline
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, United States.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
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18
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Petrullo L, Baniel A, Jorgensen MJ, Sams S, Snyder-Mackler N, Lu A. The early life microbiota mediates maternal effects on offspring growth in a nonhuman primate. iScience 2022; 25:103948. [PMID: 35265817 PMCID: PMC8898918 DOI: 10.1016/j.isci.2022.103948] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/06/2022] [Accepted: 02/15/2022] [Indexed: 01/13/2023] Open
Abstract
Maternal parity can impact offspring growth, but the mechanisms driving this effect are unclear. Here, we test the hypothesis that vertically transmitted microbiota may be one potential mechanism. We analyzed 118 fecal and milk samples from mother-offspring vervet monkey dyads across the first 6 months of life. Despite poorer milk production, offspring born to low parity females grew larger than their counterparts. These offspring exhibited reduced alpha diversity in the first days of life, stronger seeding of maternal milk microbiota, Bacteroides fragilis dominance, and a greater abundance of glycan utilization pathways. Moreover, the attainment of greater body mass by 6 months of age was mediated by reduced early life alpha diversity and B. fragilis dominance. This work demonstrates that the establishment of a specialized, milk-oriented gut microbiota promotes infant growth and suggests an evolutionarily conserved developmental role of B. fragilis in primates.
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Affiliation(s)
- Lauren Petrullo
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109, USA,Corresponding author
| | - Alice Baniel
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA,School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Matthew J. Jorgensen
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Sierra Sams
- Paragon Genomics, Hayward, CA 94545, USA,Department of Psychology, University of Washington, Seattle, WA 98195, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA,School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA,Department of Psychology, University of Washington, Seattle, WA 98195, USA,Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
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19
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Diaz J, Reese AT. Possibilities and limits for using the gut microbiome to improve captive animal health. Anim Microbiome 2021; 3:89. [PMID: 34965885 PMCID: PMC8715647 DOI: 10.1186/s42523-021-00155-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/18/2021] [Indexed: 12/13/2022] Open
Abstract
Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.
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Affiliation(s)
- Jessica Diaz
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Aspen T Reese
- Section of Ecology, Behavior, and Evolution, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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20
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Thingholm LB, Bang C, Rühlemann MC, Starke A, Sicks F, Kaspari V, Jandowsky A, Frölich K, Ismer G, Bernhard A, Bombis C, Struve B, Rausch P, Franke A. Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans. BMC Microbiol 2021; 21:276. [PMID: 34635060 PMCID: PMC8504008 DOI: 10.1186/s12866-021-02337-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ancestors. The lowered microbial diversity within the gut of westernized populations has also been associated with different kinds of chronic inflammatory diseases in humans. To further deepen our knowledge on phylogenetic and ecologic impacts on human health and fitness, we established the herein presented biobank as well as its comprehensive microbiota analysis. In total, 368 stool samples from 38 different animal species, including Homo sapiens, belonging to four diverse mammalian orders were collected at seven different locations and analyzed by 16S rRNA gene amplicon sequencing. Comprehensive data analysis was performed to (i) determine the overall impact of host phylogeny vs. diet, location, and ecology and to (ii) examine the general pattern of fecal bacterial diversity across captive mammals and humans. By using a controlled study design with captive mammals we could verify that host phylogeny is the most dominant driver of mammalian gut microbiota composition. However, the effect of ecology appears to be able to overcome host phylogeny and should therefore be studied in more detail in future studies. Most importantly, our study could observe a remarkable decrease of Spirochaetes and Prevotella in westernized humans and platyrrhines, which is probably not only due to diet, but also to the social behavior and structure in these communities. Our study highlights the importance of phylogenetic relationship and ecology within the evolution of mammalian fecal microbiota composition. Particularly, the observed decrease of Spirochaetes and Prevotella in westernized communities might be associated to lifestyle dependent rapid evolutionary changes, potentially involved in the establishment of dysbiotic microbiomes, which promote the etiology of chronic diseases.
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Affiliation(s)
- Louise B Thingholm
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Annika Starke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany
| | - Florian Sicks
- Tierpark Berlin-Friedrichsfelde GmbH, Berlin, Germany
| | - Verena Kaspari
- Tierparkvereinigung Neumuenster e.V, Neumuenster, Germany
| | | | | | | | | | - Claudia Bombis
- Tierpark Hagenbeck Gemeinnützige Gesellschaft mbH, Hamburg, Germany
| | - Barbara Struve
- Leintalzoo Schwaigern, Freudenmühle 1, 74193, Schwaigern, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Campus Kiel, Rosalind-Franklin-Str, 12, 24105, Kiel, Germany. .,University Hospital Schleswig Holstein (UKSH), Campus Kiel, Kiel, Germany.
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21
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Nishida AH, Ochman H. Captivity and the co-diversification of great ape microbiomes. Nat Commun 2021; 12:5632. [PMID: 34561432 PMCID: PMC8463570 DOI: 10.1038/s41467-021-25732-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Wild great apes harbor clades of gut bacteria that are restricted to each host species. Previous research shows the evolutionary relationships among several host-restricted clades mirror those of great-ape species. However, processes such as geographic separation, host-shift speciation, and host-filtering based on diet or gut physiology can generate host-restricted bacterial clades and mimic patterns of co-diversification across host species. To gain insight into the distribution of host-restricted taxa, we examine captive great apes living under conditions where sharing of bacterial strains is readily possible. Here, we show that increased sampling of wild and captive apes identifies additional host-restricted lineages whose relationships are not concordant with the host phylogeny. Moreover, the gut microbiomes of captive apes converge through the displacement of strains that are restricted to their wild conspecifics by human-restricted strains. We demonstrate that host-restricted and co-diversifying bacterial strains in wild apes lack persistence and fidelity in captive environments.
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Affiliation(s)
- Alex H Nishida
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
- Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Howard Ochman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
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22
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Mallott EK, Amato KR. Butyrate-production pathway abundances are similar in human and nonhuman primate gut microbiomes. Mol Biol Evol 2021; 39:6372698. [PMID: 34542625 PMCID: PMC8763029 DOI: 10.1093/molbev/msab279] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Over the course of human evolution, shifts in dietary practices such as meat-eating and cooking, have resulted in reduced fiber intake, a trend that has been exaggerated more recently in industrialized populations. Reduced fiber consumption is associated with a loss of gut microbial taxa that degrade fiber, particularly butyrate. Therefore, this dietary shift in humans may have altered the abundance of microbial genes involved in butyrate production. This study uses a gene-targeted alignment approach to quantify the abundance of butyrate production pathway genes from published wild nonhuman primate and human gut metagenomes. Surprisingly, humans have higher diversity and relative abundances of butyrate production pathways compared with all groups of nonhuman primates except cercopithecoids. Industrialized populations of humans also differ only slightly in butyrate pathway abundance from nonindustrialized populations. This apparent resilience of butyrate production pathways to shifts in human diet across both evolutionary and modern populations may signal an evolutionary shift in host–microbe interactions in humans that increased SCFA production. Such a shift could have contributed to meeting the increased energy requirements of humans relative to nonhuman primates.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208, USA;
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208, USA;
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