1
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Goldman SL, Sanders JG, Sprockett DD, Landers A, Yan W, Moeller AH. Hackflex library preparation enables low-cost metagenomic profiling. bioRxiv 2024:2024.04.23.590092. [PMID: 38712258 PMCID: PMC11071439 DOI: 10.1101/2024.04.23.590092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.
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Affiliation(s)
- Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Abigail Landers
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540
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2
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Zipple MN, Kuo DC, Meng X, Reichard TM, Guess K, Vogt CC, Moeller AH, Sheehan MJ. Sex-specific competitive social feedback amplifies the role of early life contingency in male mice. bioRxiv 2024:2024.04.19.590322. [PMID: 38659792 PMCID: PMC11042324 DOI: 10.1101/2024.04.19.590322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Contingency (or 'luck') in early life plays an important role in shaping individuals' development. When individuals live within larger societies, social experiences may cause the importance of early contingencies to be magnified or dampened. Here we test the hypothesis that competition magnifies the importance of early contingency in a sex-specific manner by comparing the developmental trajectories of genetically identical, free-living mice who either experienced high levels of territorial competition (males) or did not (females). We show that male territoriality results in a competitive feedback loop that magnifies the importance of early contingency and pushes individuals onto divergent, self-reinforcing life trajectories, while the same process appears absent in females. Our results indicate that the strength of sexual selection may be self-limiting, as within-sex competition increases the importance of early life contingency, thereby reducing the ability of selection to lead to evolution. They also demonstrate the potential for contingency to lead to dramatic differences in life outcomes, even in the absence of any underlying differences in ability ('merit').
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3
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Vogt CC, Zipple MN, Sprockett DD, Miller CH, Hardy SX, Arthur MK, Greenstein AM, Colvin MS, Michel LM, Moeller AH, Sheehan MJ. Publisher Correction: Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures. BMC Biol 2024; 22:72. [PMID: 38561721 PMCID: PMC10986037 DOI: 10.1186/s12915-024-01871-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Affiliation(s)
- Caleb C Vogt
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
| | - Matthew N Zipple
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Caitlin H Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Summer X Hardy
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew K Arthur
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Adam M Greenstein
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Melanie S Colvin
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Lucie M Michel
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
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4
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Vogt CC, Zipple MN, Sprockett DD, Miller CH, Hardy SX, Arthur MK, Greenstein AM, Colvin MS, Michel LM, Moeller AH, Sheehan MJ. Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures. BMC Biol 2024; 22:35. [PMID: 38355587 PMCID: PMC10865716 DOI: 10.1186/s12915-024-01809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science. RESULTS Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice. CONCLUSIONS C57 and wild-derived mice individually vary in their social and spatial behaviors which scale to shape overall social organization. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.
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Affiliation(s)
- Caleb C Vogt
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
| | - Matthew N Zipple
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Caitlin H Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Summer X Hardy
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew K Arthur
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Adam M Greenstein
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Melanie S Colvin
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Lucie M Michel
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
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5
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Real MVF, Colvin MS, Sheehan MJ, Moeller AH. Major urinary protein ( Mup) gene family deletion drives sex-specific alterations in the house-mouse gut microbiota. Microbiol Spectr 2024; 12:e0356623. [PMID: 38170981 PMCID: PMC10846032 DOI: 10.1128/spectrum.03566-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024] Open
Abstract
The gut microbiota is shaped by host metabolism. In house mice (Mus musculus), major urinary protein (MUP) pheromone production represents a considerable energy investment, particularly in sexually mature males. Deletion of the Mup gene family shifts mouse metabolism toward an anabolic state, marked by lipogenesis, lipid accumulation, and body mass increases. Given the metabolic implications of MUPs, they may also influence the gut microbiota. Here, we investigated the effect of a deletion of the Mup gene family on the gut microbiota of sexually mature mice. Shotgun metagenomics revealed distinct taxonomic and functional profiles between wild-type and knockout males but not females. Deletion of the Mup gene cluster significantly reduced diversity in microbial families and functions in male mice. Additionally, a species of Ruminococcaceae and several microbial functions, such as transporters involved in vitamin B5 acquisition, were significantly depleted in the microbiota of Mup knockout males. Altogether, these results show that MUPs significantly affect the gut microbiota of house mouse in a sex-specific manner.IMPORTANCEThe community of microorganisms that inhabits the gastrointestinal tract can have profound effects on host phenotypes. The gut microbiota is in turn shaped by host genes, including those involved with host metabolism. In adult male house mice, expression of the major urinary protein (Mup) gene cluster represents a substantial energy investment, and deletion of the Mup gene family leads to fat accumulation and weight gain in males. We show that deleting Mup genes also alters the gut microbiota of male, but not female, mice in terms of both taxonomic and functional compositions. Male mice without Mup genes harbored fewer gut bacterial families and reduced abundance of a species of Ruminococcaceae, a family that has been previously shown to reduce obesity risk. Studying the impact of the Mup gene family on the gut microbiota has the potential to reveal the ways in which these genes affect host phenotypes.
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Affiliation(s)
- Madalena V. F. Real
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Melanie S. Colvin
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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6
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Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Microbial transmission in the social microbiome and host health and disease. Cell 2024; 187:17-43. [PMID: 38181740 PMCID: PMC10958648 DOI: 10.1016/j.cell.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Cameron J A McInroy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Siobhán Harty
- Independent, Tandy Court, Spitalfields, Dublin, Ireland
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK; Department of Computing, University of Turku, Turku, Finland
| | - Neil G O Ibata
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mireia Valles-Colomer
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Katerina V-A Johnson
- Institute of Psychology, Leiden University, Leiden, the Netherlands; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph Henrich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Francesca S Gazzaniga
- Molecular Pathology Unit, Cancer Center, Massachusetts General Hospital Research Institute, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Brunetti AE, Lyra ML, Monteiro JPC, Zurano JP, Baldo D, Haddad CFB, Moeller AH. Convergence of gut microbiota in myrmecophagous amphibians. Proc Biol Sci 2023; 290:20232223. [PMID: 37964521 PMCID: PMC10646458 DOI: 10.1098/rspb.2023.2223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023] Open
Abstract
The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.
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Affiliation(s)
- Andrés E. Brunetti
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Juliane P. C. Monteiro
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Juan P. Zurano
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Puerto Iguazú, Misiones 3370, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
| | - Celio F. B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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9
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Trevelline BK, Sprockett D, DeLuca WV, Andreadis CR, Moeller AH, Tonra CM. Convergent remodelling of the gut microbiome is associated with host energetic condition over long-distance migration. Funct Ecol 2023; 37:2840-2854. [PMID: 38249446 PMCID: PMC10795773 DOI: 10.1111/1365-2435.14430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/25/2023] [Indexed: 01/23/2024]
Abstract
The gut microbiome can be thought of as a virtual organ given its immense metabolic capacity and profound effects on host physiology. Migratory birds are capable of adaptively modulating many aspects of their physiology to facilitate long-distance movements, raising the hypothesis that their microbiome may undergo a parallel remodeling process that helps to meet the energetic demands of migration.To test this hypothesis, we investigated changes in gut microbiome composition and function over the fall migration of the Blackpoll Warbler (Setophaga striata), which exhibits one of the longest known autumnal migratory routes of any songbird and rapidly undergoes extensive physiological remodeling during migration.Overall, our results showed that the Blackpoll Warbler microbiome differed significantly across phases of fall migration. This pattern was driven by a dramatic increase in the relative abundance of Proteobacteria, and more specifically a single 16S rRNA gene amplicon sequence variant belonging to the family Enterobacteriaceae. Further, Blackpoll Warblers exhibited a progressive reduction in microbiome diversity and within-group variance over migration, indicating convergence of microbiome composition among individuals during long-distance migration. Metagenomic analysis revealed that the gut microbiome of staging individuals was enriched in bacterial pathways involved in vitamin, amino acid, and fatty acid biosynthesis, as well as carbohydrate metabolism, and that these pathways were in turn positively associated with host body mass and subcutaneous fat deposits.Together, these results provide evidence that the gut microbiome of migratory birds may undergo adaptive remodeling to meet the physiological and energetic demands of long-distance migration.
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Affiliation(s)
- Brian K. Trevelline
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Daniel Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | | | - Catherine R. Andreadis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Christopher M. Tonra
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
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10
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Real MVF, Colvin MS, Sheehan MJ, Moeller AH. Major urinary protein ( Mup) gene family deletion drives sex-specific alterations on the house mouse gut microbiota. bioRxiv 2023:2023.08.01.551491. [PMID: 37577672 PMCID: PMC10418228 DOI: 10.1101/2023.08.01.551491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The gut microbiota is shaped by host metabolism. In house mice (Mus musculus), major urinary protein (MUP) pheromone production represents a considerable energy investment, particularly in sexually mature males. Deletion of the Mup gene family shifts mouse metabolism towards an anabolic state, marked by lipogenesis, lipid accumulation, and body mass increases. Given the metabolic implications of MUPs, they may also influence the gut microbiota. Here, we investigated the effect of deletion of the Mup gene family on the gut microbiota of sexually mature mice. Shotgun metagenomics revealed distinct taxonomic and functional profiles between wildtype and knockout males, but not females. Deletion of the Mup gene cluster significantly reduced diversity in microbial families and functions in male mice. Additionally, specific taxa of the Ruminococcaceae family, which is associated with gut health and reduced risk of developing metabolic syndrome, and several microbial functions, such as transporters involved in vitamin B5 acquisition, were significantly depleted in the microbiota of Mup-knockout males. Altogether these results show that major urinary proteins significantly affect the gut microbiota of house mouse in a sex-specific manner.
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Affiliation(s)
- Madalena V. F. Real
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Melanie S. Colvin
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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11
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Sprockett DD, Price JD, Juritsch AF, Schmaltz RJ, Real MV, Goldman SL, Sheehan M, Ramer-Tait AE, Moeller AH. Home-site advantage for host species-specific gut microbiota. Sci Adv 2023; 9:eadf5499. [PMID: 37184968 PMCID: PMC10184861 DOI: 10.1126/sciadv.adf5499] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here, we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wild-type (WT) and Rag1-knockout (Rag1-/-) house mice revealed widespread fitness advantages for native gut bacteria. Native bacterial lineages significantly outcompeted non-native lineages in both WT and Rag1-/- mice, indicating home-site advantage for native microbiota independent of host adaptive immunity. However, a minority of native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1-/- hosts, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates home-site advantage for native gut bacteria, consistent with local adaptation of gut microbiota to their mammalian species.
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Affiliation(s)
- Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeffrey D. Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anthony F. Juritsch
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Robert J. Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Madalena V. F. Real
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Michael Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Sanders JG, Yan W, Mjungu D, Lonsdorf EV, Hart JA, Sanz CM, Morgan DB, Peeters M, Hahn BH, Moeller AH. A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes. Genome Biol 2022; 23:212. [PMID: 36224660 PMCID: PMC9558970 DOI: 10.1186/s13059-022-02777-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
Earth's environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.
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Affiliation(s)
- Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 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, 30322, USA
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, MO, USA.,Wildlife Conservation Society, Congo Program, Brazzaville, B.P. 14537, 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, 34090, 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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14
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Abstract
Bacterial strains in the gut microbiota diversified as humans spread across the globe.
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Affiliation(s)
- Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Moeller AH. Metagenomic signatures of balancing selection in the human gut. Mol Ecol 2022; 32:2582-2591. [PMID: 35445474 PMCID: PMC10061541 DOI: 10.1111/mec.16474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/12/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022]
Abstract
Bacterial lineages that populate the human gut microbiota contend with spatial and temporal fluctuations in numerous environmental variables, including bouts of extreme selective agents such as antibiotics. Oscillations in the adaptive landscape can impose balancing selection on populations, leaving characteristic signatures in the sequence variation of functionally significant genomic loci. Despite their potential importance for gut bacterial adaptation, the metagenomic targets of balancing selection have not been identified. Here, I present population genetic evidence that balancing selection maintains allelic diversity in multidrug efflux pumps of multiple predominant gut bacterial species. Metagenome-wide scans of 566,958 genes from 287 bacterial species represented by 118,617 metagenome-assembled genomes indicated that most genes have been conserved by purifying selection. However, dozens of core open reading frames (CORFs) displayed positive Tajima's D values that deviated significantly from their species' genomic backgrounds, indicating the action of balancing selection. Multidrug efflux pumps (MEPs) from a diversity of bacterial species were significantly enriched among the CORFs with Tajima's D values >3 in industrialized, but not nonindustrialized, human populations. The AcrB subunit of an MEP from Bacteroides dorei displayed the highest Tajima's D of any CORF. Divergent haplotypes of this CORF displayed evidence of positive selection and homology to an Escherichia coli AcrB subunit that binds tetracycline and macrolide antibiotics, suggesting functional significance and implicating medical antibiotics as an agent of selection acting on this locus. Other proteins identified as targets of balancing selection included peptidoglycan/LPS O-acetylases and ion transporters. Intriguingly, the degree of balancing selection acting on gut bacterial species was associated with species abundance in the gut based on metagenomic data, further suggesting fitness benefits of the allelic variation identified.
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Affiliation(s)
- Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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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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Abstract
Bone provides structure to the vertebrate body that allows for movement and mechanical stimuli that enable and the proper development of neighboring organs. Bone morphology and density is also highly heritable. In humans, heritability of bone mineral density has been estimated to be 50-80%. However, genome wide association studies have so far explained only 25% of the variation in bone mineral density, suggesting that a substantial portion of the heritability of bone mineral density may be due to environmental factors. Here we explore the idea that the gut microbiome is a heritable environmental factor that contributes to bone morphology and density. The vertebrae skeleton has evolved over the past ~500 million years in the presence of commensal microbial communities. The composition of the commensal microbial communities has co-evolved with the hosts resulting in species-specific microbial populations associated with vertebrate phylogeny. Furthermore, a substantial portion of the gut microbiome is acquired through familial transfer. Recent studies suggest that the gut microbiome also influences postnatal development. Here we review studies from the past decade in mice that have shown that the presence of the gut microbiome can influence postnatal bone growth regulating bone morphology and density. These studies indicate that the presence of the gut microbiome may increase longitudinal bone growth and appositional bone growth, resulting differences cortical bone morphology in long bones. More surprising, however are recent studies showing that transfer of the gut microbiota among inbred mouse strains with distinct bone phenotypes can alter postnatal development and adult bone morphology. Together these studies support the concept that the gut microbiome is a contributor to skeletal phenotype.
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Affiliation(s)
- Christopher J Hernandez
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA; Hospital for Special Surgery, New York, NY, USA.
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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19
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Goldman SL, Sanders JG, Yan W, Denice A, Cornwall M, Ivey KN, Taylor EN, Gunderson AR, Sheehan MJ, Mjungu D, Lonsdorf EV, Pusey AE, Hahn BH, Moeller AH. Culture-enriched community profiling improves resolution of the vertebrate gut microbiota. Mol Ecol Resour 2022; 22:122-136. [PMID: 34174174 PMCID: PMC8688194 DOI: 10.1111/1755-0998.13456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 01/03/2023]
Abstract
Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.
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Affiliation(s)
- Samantha L. Goldman
- 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
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14850, USA
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Anthony Denice
- Project Chimps, Morganton, GA 30560, USA
- Present address: Chimpanzee Sanctuary Northwest, Cle Elum, WA 98922, USA
| | - Margaret Cornwall
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Kathleen N. Ivey
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
- Present address: Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Emily N. Taylor
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Alex R. Gunderson
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
| | | | - Elizabeth V. Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, LSP 261B, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, 101 Biological Sciences Building, Duke University, Durham, NC 27708, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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20
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Sarkar A, Harty S, Moeller AH, Klein SL, Erdman SE, Friston KJ, Carmody RN. The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2. Trends Mol Med 2021; 27:1115-1134. [PMID: 34756546 PMCID: PMC8492747 DOI: 10.1016/j.molmed.2021.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) continues to exact a devastating global toll. Ascertaining the factors underlying differential susceptibility and prognosis following viral exposure is critical to improving public health responses. We propose that gut microbes may contribute to variation in COVID-19 outcomes. We synthesise evidence for gut microbial contributions to immunity and inflammation, and associations with demographic factors affecting disease severity. We suggest mechanisms potentially underlying microbially mediated differential susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These include gut microbiome-mediated priming of host inflammatory responses and regulation of endocrine signalling, with consequences for the cellular features exploited by SARS-CoV-2 virions. We argue that considering gut microbiome-mediated mechanisms may offer a lens for appreciating differential susceptibility to SARS-CoV-2, potentially contributing to clinical and epidemiological approaches to understanding and managing COVID-19.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Siobhán Harty
- Tandy Court, Spitalfields, Dublin 8, D08 RP20, Ireland
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Susan E Erdman
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karl J Friston
- Wellcome Centre for Human Neuroimaging, University College London, London, UK
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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21
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Houtz JL, Sanders JG, Denice A, Moeller AH. Predictable and host-species specific humanization of the gut microbiota in captive primates. Mol Ecol 2021; 30:3677-3687. [PMID: 34013536 PMCID: PMC10039810 DOI: 10.1111/mec.15994] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Humans and nonhuman primates (NHPs) harbor complex gut microbial communities that affect phenotypes and fitness. The gut microbiotas of wild NHPs reflect their hosts' phylogenetic histories and are compositionally distinct from those of humans, but in captivity the endogenous gut microbial lineages of NHPs can be lost or replaced by lineages found in humans. Despite its potential contributions to gastrointestinal dysfunction, this humanization of the gut microbiota has not been investigated systematically across captive NHP species. Here, we show through comparisons of well-sampled wild and captive populations of apes and monkeys that the fraction of the gut microbiota humanized by captivity varies significantly between NHP species but is remarkably reproducible between captive populations of the same NHP species. Conspecific captive populations displayed significantly greater than expected overlap in the sets of bacterial 16S rRNA gene variants that were differentially abundant between captivity and the wild. This overlap was evident even between captive populations residing on different continents but was never observed between heterospecific captive populations. In addition, we developed an approach incorporating human gut microbiota data to rank NHPs' gut microbial clades based on the propensity of their lineages to be lost or replaced in captivity by lineages found in humans. Relatively few microbial genera displayed reproducible degrees of humanization in different captive host species, but most microbial genera were reproducibly humanized or retained from the wild in conspecific pairs of captive populations. These results demonstrate that the gut microbiotas of captive NHPs display predictable, host-species specific responses to captivity.
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Affiliation(s)
- Jennifer L. Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Anthony Denice
- Project Chimps, Blue Ridge, GA, USA
- Chimpanzee Sanctuary Northwest, Cle Elum, WA, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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22
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Moeller AH. Genomic Expansions in the Human Gut Microbiome. Genome Biol Evol 2021; 13:6319024. [PMID: 34332502 PMCID: PMC8325571 DOI: 10.1093/gbe/evab156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteria inhabiting the human body vary in genome size by over an order of magnitude, but the processes that generate this diversity are poorly understood. Here, we show that evolutionary forces drive divergence in genome size between bacterial lineages in the gut and their closest relatives in other body sites. Analyses of thousands of reference bacterial isolate genomes and metagenome-assembled genomes from the human microbiome indicated that transitions into the gut from other body sites have promoted genomic expansions, whereas the opposite transitions have promoted genomic contractions. Bacterial genomes in the gut are on average ∼127 kb larger than their closest congeneric relatives from other body sites. Moreover, genome size and relative abundance are positively associated within the gut but negatively associated at other body sites. These results indicate that the gut microbiome promotes expansions of bacterial genomes relative to other body sites.
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Affiliation(s)
- Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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23
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Abstract
Human guts are colonized at birth by a limited set of microbes that gradually increases in diversity throughout infancy. A new study reports the opposite pattern in infant chimpanzees, raising questions about how host-microbiota relationships have changed during ape evolution.
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Affiliation(s)
- Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA.
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24
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Sarkar A, Harty S, Johnson KVA, Moeller AH, Carmody RN, Lehto SM, Erdman SE, Dunbar RIM, Burnet PWJ. The role of the microbiome in the neurobiology of social behaviour. Biol Rev Camb Philos Soc 2020; 95:1131-1166. [PMID: 32383208 PMCID: PMC10040264 DOI: 10.1111/brv.12603] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
Microbes colonise all multicellular life, and the gut microbiome has been shown to influence a range of host physiological and behavioural phenotypes. One of the most intriguing and least understood of these influences lies in the domain of the microbiome's interactions with host social behaviour, with new evidence revealing that the gut microbiome makes important contributions to animal sociality. However, little is known about the biological processes through which the microbiome might influence host social behaviour. Here, we synthesise evidence of the gut microbiome's interactions with various aspects of host sociality, including sociability, social cognition, social stress, and autism. We discuss evidence of microbial associations with the most likely physiological mediators of animal social interaction. These include the structure and function of regions of the 'social' brain (the amygdala, the prefrontal cortex, and the hippocampus) and the regulation of 'social' signalling molecules (glucocorticoids including corticosterone and cortisol, sex hormones including testosterone, oestrogens, and progestogens, neuropeptide hormones such as oxytocin and arginine vasopressin, and monoamine neurotransmitters such as serotonin and dopamine). We also discuss microbiome-associated host genetic and epigenetic processes relevant to social behaviour. We then review research on microbial interactions with olfaction in insects and mammals, which contribute to social signalling and communication. Following these discussions, we examine evidence of microbial associations with emotion and social behaviour in humans, focussing on psychobiotic studies, microbe-depression correlations, early human development, autism, and issues of statistical power, replication, and causality. We analyse how the putative physiological mediators of the microbiome-sociality connection may be investigated, and discuss issues relating to the interpretation of results. We also suggest that other candidate molecules should be studied, insofar as they exert effects on social behaviour and are known to interact with the microbiome. Finally, we consider different models of the sequence of microbial effects on host physiological development, and how these may contribute to host social behaviour.
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Affiliation(s)
- Amar Sarkar
- Trinity College, Trinity Street, University of Cambridge, Cambridge, CB2 1TQ, U.K.,Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, Fitzwilliam Street, University of Cambridge, Cambridge, CB2 1QH, U.K
| | - Siobhán Harty
- Institute of Neuroscience, Trinity College Dublin, Dublin 2, Dublin, Ireland.,School of Psychology, Trinity College Dublin, Dublin 2, Dublin, Ireland
| | - Katerina V-A Johnson
- Department of Experimental Psychology, Radcliffe Observatory Quarter, University of Oxford, Oxford, OX2 6GG, U.K.,Pembroke College, University of Oxford, Oxford, OX1 1DW, U.K.,Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, OX3 7JX, U.K
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Corson Hall, Tower Road, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Peabody Museum, 11 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Soili M Lehto
- Psychiatry, University of Helsinki and Helsinki University Hospital, PL 590, FI-00029, Helsinki, Finland.,Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, P.O. Box 6, FI-00014, Helsinki, Finland.,Institute of Clinical Medicine/Psychiatry, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Susan E Erdman
- Division of Comparative Medicine, Massachusetts Institute of Technology, Building 16-825, 77 Massachusetts Avenue, Cambridge, MA, 02139, U.S.A
| | - Robin I M Dunbar
- Department of Experimental Psychology, Radcliffe Observatory Quarter, University of Oxford, Oxford, OX2 6GG, U.K
| | - Philip W J Burnet
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, OX3 7JX, U.K
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25
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Abstract
Every mammalian species harbours a gut microbiota, and variation in the gut microbiota within mammalian species can have profound effects on host phenotypes. In this review, we summarize recent evidence that gut microbiotas have influenced the course of mammalian adaptation and diversification. Associations with gut microbiotas have: (i) promoted the diversification of mammalian species by enabling dietary transitions onto difficult-to-digest carbon sources and toxic food items; (ii) shaped the evolution of adaptive phenotypic plasticity in mammalian species through the amplification of signals from the external environment and from postnatal developmental processes; and (iii) generated selection for host mechanisms, including innate and adaptive immune mechanisms, to control the gut microbiota for the benefit of host fitness. The stability of specific gut microbiotas within host species lineages varies substantially across the mammalian phylogeny, and this variation may alter the ultimate evolutionary outcomes of relationships with gut microbiotas in different mammalian clades. In some mammalian species, including humans, relationships with host species-specific gut microbiotas appear to have led to the evolution of host dependence on the gut microbiota for certain functions. These studies implicate the gut microbiota as a significant environmental factor and selective agent shaping the adaptive evolution of mammalian diet, phenotypic plasticity, gastrointestinal morphology and immunity. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Cornell Institute for Host-Microbe Interaction and Disease, Cornell University, Ithaca, NY 14853, USA
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Abstract
Temperature is a prominent abiotic environmental variable that drives the adaptive trajectories of animal lineages and structures the composition of animal communities. Global temperature regimes are expected to undergo rapid shifts in the next century, yet for many animal taxa we lack an understanding of the consequences of these predicted shifts for animal populations. In this review, we synthesize recent evidence that temperature variation shapes the composition and function of animal gut microbiomes, key regulators of host physiology, with potential consequences for host population responses to climate change. Several recent studies spanning a range of animal taxa, including Chordata, Arthropoda, and Mollusca, have reported repeatable associations between temperature and the community composition and function of the gut microbiome. In several cases, the same microbiome responses to temperature have been observed across distantly related animal taxa, suggesting the existence of conserved mechanisms underlying temperature-induced microbiome plasticity. Extreme temperatures can disrupt the stability of alpha-diversity within the gut microbiomes individual hosts and generate beta-diversity among microbiomes within host populations. Microbiome states resulting from extreme temperatures have been associated, and in some cases causally linked, with both beneficial and deleterious effects on host phenotypes. We propose routes by which temperature-induced changes in the gut microbiome may impact host fitness, including effects on colonization resistance in the gut, on host energy and nutrient assimilation, and on host life history traits. Cumulatively, available data indicate that disruption of the gut microbiome may be a mechanism by which changing temperatures will impact animal fitness in wild-living populations.
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Affiliation(s)
- Juan Sepulveda
- 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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27
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Moeller AH, Suzuki TA, Phifer-Rixey M, Nachman MW. Transmission modes of the mammalian gut microbiota. Science 2018; 362:453-457. [PMID: 30361372 DOI: 10.1126/science.aat7164] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/18/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
Mammals house a diversity of bacteria that affect health in various ways, but the routes by which bacterial lineages are transmitted between hosts remain poorly understood. We experimentally determined microbiota transmission modes by deriving 17 inbred mouse lines from two wild populations and monitoring their gut microbiotas for up to 11 host generations. Individual- and population-level microbiota compositions were maintained within mouse lines throughout the experiment, indicating predominantly vertical inheritance of the microbiota. However, certain bacterial taxa tended to be exchanged horizontally between mouse lines. Consistent with evolutionary theory, the degree of horizontal transmission predicted bacterial genera with pathogenic representatives responsible for human infections and hospitalizations.
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Affiliation(s)
- Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA. .,Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Megan Phifer-Rixey
- Department of Biology, Monmouth University, West Long Branch, NJ 07764, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA. .,Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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28
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Sarkar A, Harty S, Lehto SM, Moeller AH, Dinan TG, Dunbar RIM, Cryan JF, Burnet PWJ. The Microbiome in Psychology and Cognitive Neuroscience. Trends Cogn Sci 2018; 22:611-636. [PMID: 29907531 DOI: 10.1016/j.tics.2018.04.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 02/07/2023]
Abstract
Psychology and microbiology make unlikely friends, but the past decade has witnessed striking bidirectional associations between intrinsic gut microbes and the brain, relationships with largely untested psychological implications. Although microbe-brain relationships are receiving a great deal of attention in biomedicine and neuroscience, psychologists have yet to join this journey. Here, we illustrate microbial associations with emotion, cognition, and social behavior. However, despite considerable enthusiasm and potential, technical and conceptual limitations including low statistical power and lack of mechanistic descriptions prevent a nuanced understanding of microbiome-brain-behavior relationships. Our goal is to describe microbial effects in domains of cognitive significance and the associated challenges to stimulate interdisciplinary research on the contribution of this hidden kingdom to psychological processes.
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Affiliation(s)
- Amar Sarkar
- Department of Experimental Psychology, University of Oxford, Oxford, UK; Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, UK; Trinity College, University of Cambridge, Cambridge, UK.
| | - Siobhán Harty
- Department of Experimental Psychology, University of Oxford, Oxford, UK; Trinity College Institute of Neuroscience and School of Psychology, Trinity College Dublin, Dublin 2, Ireland
| | - Soili M Lehto
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland; Institute of Clinical Medicine / Psychiatry, University of Eastern Finland, Kuopio, Finland; Department of Psychiatry, Kuopio University Hospital, Kuopio, Finland
| | - Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, USA
| | - Timothy G Dinan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - Robin I M Dunbar
- Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - John F Cryan
- Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience University College Cork, Cork, Ireland
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Moeller AH, Suzuki TA, Lin D, Lacey EA, Wasser SK, Nachman MW. Dispersal limitation promotes the diversification of the mammalian gut microbiota. Proc Natl Acad Sci U S A 2017; 114:13768-13773. [PMID: 29229828 PMCID: PMC5748161 DOI: 10.1073/pnas.1700122114] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The gut bacterial communities of mammals have profound effects on host fitness, but the processes that generate and maintain gut bacterial diversity remain poorly understood. We mapped compositional variation (i.e., β-diversity) in the gut microbiotas of 136 pairs of wild mammalian species living throughout the Americas to assess how the distribution of mammals across geographic space influences the diversification of their gut bacteria. Comparing the gut microbiotas of sympatric and allopatric mammalian populations provided insights into the flow of gut bacteria within and between mammalian communities, revealing that spatial limits on bacterial dispersal promote β-diversity between the gut microbiotas of mammalian species. Each geographic locale displayed a unique gut-microbiota composition that could not be fully explained by the diets and phylogenetic histories of the resident mammalian hosts, indicating that some gut bacteria are geographically restricted. Across the western hemisphere, the compositional overlap between the gut microbiotas of allopatric mammalian populations decayed exponentially with the geographic distance separating the hosts. The relationship between geographic distances among hosts and compositional differences among their gut microbiotas was independent of dietary and phylogenetic divergence among hosts. Within mammalian communities, we observed widespread sharing of gut bacteria between predator-prey host-species pairs, indicating horizontal transfer of gut bacteria through mammalian food chains. Collectively, these results indicate that compositional differences between the gut microbiotas of mammalian taxa are generated and maintained by limits to bacterial dispersal imposed by physical distance between hosts.
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Affiliation(s)
- Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720;
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Dana Lin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Eileen A Lacey
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Samuel K Wasser
- Center for Conservation Biology, University of Washington, Seattle, WA 98195
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
- Department of Integrative Biology, University of California, Berkeley, CA 94720
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30
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Abstract
Mammals harbor complex assemblages of gut bacteria that are deeply integrated with their hosts' digestive, immune, and neuroendocrine systems. Recent work has revealed that there has been a substantial loss of gut bacterial diversity from humans since the divergence of humans and chimpanzees. This bacterial depauperation began in humanity's ancient evolutionary past and has accelerated in recent years with the advent of modern lifestyles. Today, humans living in industrialized societies harbor the lowest levels of gut bacterial diversity of any primate for which metagenomic data are available, a condition that may increase risk of infections, autoimmune disorders, and metabolic syndrome. Some missing gut bacteria may remain within under-sampled human populations, whereas others may be globally extinct and unrecoverable.
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Affiliation(s)
- Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, 2538 Channing Way, Berkley, CA 94720, United States.
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31
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Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, Muller MN, Pusey AE, Peeters M, Hahn BH, Ochman H. Cospeciation of gut microbiota with hominids. Science 2016; 353:380-2. [PMID: 27463672 DOI: 10.1126/science.aaf3951] [Citation(s) in RCA: 355] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/02/2016] [Indexed: 12/14/2022]
Abstract
The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations. Divergence times of these cospeciating gut bacteria are congruent with those of hominids, indicating that nuclear, mitochondrial, and gut bacterial genomes diversified in concert during hominid evolution. This study identifies human gut bacteria descended from ancient symbionts that speciated simultaneously with humans and the African apes.
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Affiliation(s)
- Andrew H Moeller
- Department of Integrative Biology, 2506 Speedway A5000, University of Texas at Austin, Austin, TX 78712, USA. Miller Institute for Basic Research in Science, 2536 Channing Way, University of California, Berkeley, CA 94720, USA
| | | | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Alexander V Georgiev
- Department of Anthropology, Northwestern University, 1810 Hinman Avenue, Evanston, IL 60208, USA. Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, LSP 261B, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, MSC01-1040, Albuquerque, NM 87131, USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology, 101 Biological Sciences Building, Duke University, Durham, NC 27708, USA
| | - Martine Peeters
- Institut de Recherche pour le Développement, University of Montpellier, 34394 Montpellier, France
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, 409 Johnson Pavilion, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Ochman
- Department of Integrative Biology, 2506 Speedway A5000, University of Texas at Austin, Austin, TX 78712, USA.
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Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H. Social behavior shapes the chimpanzee pan-microbiome. Sci Adv 2016; 2:e1500997. [PMID: 26824072 PMCID: PMC4730854 DOI: 10.1126/sciadv.1500997] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/19/2015] [Indexed: 05/21/2023]
Abstract
Animal sociality facilitates the transmission of pathogenic microorganisms among hosts, but the extent to which sociality enables animals' beneficial microbial associations is poorly understood. The question is critical because microbial communities, particularly those in the gut, are key regulators of host health. We show evidence that chimpanzee social interactions propagate microbial diversity in the gut microbiome both within and between host generations. Frequent social interaction promotes species richness within individual microbiomes as well as homogeneity among the gut community memberships of different chimpanzees. Sampling successive generations across multiple chimpanzee families suggests that infants inherited gut microorganisms primarily through social transmission. These results indicate that social behavior generates a pan-microbiome, preserving microbial diversity across evolutionary time scales and contributing to the evolution of host species-specific gut microbial communities.
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Affiliation(s)
- Andrew H. Moeller
- Department of Integrative Biology, University of California, Berkeley, 1005 Valley Life Sciences Building #3101, Berkeley, CA 94720, USA
| | - Steffen Foerster
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Building, Durham, NC 27708, USA
| | - Michael L. Wilson
- Department of Anthropology, University of Minnesota, 301 19th Avenue South, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108 USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences Building, Durham, NC 27708, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, Philadelphia, PA 19104, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, 2506 Speedway A5000, Austin, TX 78712, USA
- Corresponding author. E-mail:
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33
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Barbian HJ, Li Y, Ramirez M, Klase Z, Lipende I, Mjungu D, Moeller AH, Wilson ML, Pusey AE, Lonsdorf EV, Bushman FD, Hahn BH. Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees. Am J Primatol 2015; 80. [PMID: 26676710 DOI: 10.1002/ajp.22515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/20/2015] [Accepted: 12/01/2015] [Indexed: 12/17/2022]
Abstract
Enteric dysbiosis is a characteristic feature of progressive human immunodeficiency virus type 1 (HIV-1) infection but has not been observed in simian immunodeficiency virus (SIVmac)-infected macaques, including in animals with end-stage disease. This has raised questions concerning the mechanisms underlying the HIV-1 associated enteropathy, with factors other than virus infection, such as lifestyle and antibiotic use, implicated as playing possible causal roles. Simian immunodeficiency virus of chimpanzees (SIVcpz) is also associated with increased mortality in wild-living communities, and like HIV-1 and SIVmac, can cause CD4+ T cell depletion and immunodeficiency in infected individuals. Given the central role of the intestinal microbiome in mammalian health, we asked whether gut microbial constituents could be identified that are indicative of SIVcpz status and/or disease progression. Here, we characterized the gut microbiome of SIVcpz-infected and -uninfected chimpanzees in Gombe National Park, Tanzania. Subjecting a small number of fecal samples (N = 9) to metagenomic (shotgun) sequencing, we found bacteria of the family Prevotellaceae to be enriched in SIVcpz-infected chimpanzees. However, 16S rRNA gene sequencing of a larger number of samples (N = 123) failed to show significant differences in both the composition and diversity (alpha and beta) of gut bacterial communities between infected (N = 24) and uninfected (N = 26) chimpanzees. Similarly, chimpanzee stool-associated circular virus (Chi-SCV) and chimpanzee adenovirus (ChAdV) identified by metagenomic sequencing were neither more prevalent nor more abundant in SIVcpz-infected individuals. However, fecal samples collected from SIVcpz-infected chimpanzees within 5 months before their AIDS-related death exhibited significant compositional changes in their gut bacteriome. These data indicate that SIVcpz-infected chimpanzees retain a stable gut microbiome throughout much of their natural infection course, with a significant destabilization of bacterial (but not viral) communities observed only in individuals with known immunodeficiency within the last several months before their death. Am. J. Primatol. 80:e22515, 2018. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Hannah J Barbian
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Miguel Ramirez
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zachary Klase
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania
| | | | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Andrew H Moeller
- Department of Integrative Biology, University of California, Berkeley, California.,Miller Institute for Basic Research, University of California, Berkeley, California
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota.,Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Elizabeth V Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, Pennsylvania
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
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Moeller AH, Peeters M, Ayouba A, Ngole EM, Esteban A, Hahn BH, Ochman H. Stability of the gorilla microbiome despite simian immunodeficiency virus infection. Mol Ecol 2015; 24:690-7. [PMID: 25545295 DOI: 10.1111/mec.13057] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 12/17/2014] [Accepted: 12/19/2014] [Indexed: 01/04/2023]
Abstract
Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we examine the effects of SIVgor, a close relative of SIVcpz of chimpanzees and HIV-1 of humans, on the gut bacterial communities residing within wild gorillas, revealing that gorilla gut microbiomes are exceptionally robust to SIV infection. In contrast to the microbiomes of HIV-1-infected humans and SIVcpz-infected chimpanzees, SIVgor-infected gorilla microbiomes exhibit neither rises in the frequencies of opportunistic pathogens nor elevated rates of microbial turnover within individual hosts. Regardless of SIV infection status, gorilla microbiomes assort into enterotypes, one of which is compositionally analogous to those identified in humans and chimpanzees. The other gorilla enterotype appears specialized for a leaf-based diet and is enriched in environmentally derived bacterial genera. We hypothesize that the acquisition of this gorilla-specific enterotype was enabled by lowered immune system control over the composition of the microbiome. Our results indicate differences between the pathology of SIVgor and SIVcpz/HIV-1 infections, demonstrating the utility of investigating host microbial ecology as a means for studying disease in wild primates of high conservation priority.
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Affiliation(s)
- Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
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35
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Moeller AH, Shilts M, Li Y, Rudicell RS, Lonsdorf EV, Pusey AE, Wilson ML, Hahn BH, Ochman H. SIV-induced instability of the chimpanzee gut microbiome. Cell Host Microbe 2014; 14:340-5. [PMID: 24034619 DOI: 10.1016/j.chom.2013.08.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/25/2013] [Accepted: 08/09/2013] [Indexed: 02/01/2023]
Abstract
Simian immunodeficiency virus of chimpanzees (SIVcpz) is the ancestor of human immunodeficiency virus type 1 (HIV-1), the etiologic agent of acquired immunodeficiency syndrome (AIDS) in humans. Like HIV-1-infected humans, SIVcpz-infected chimpanzees can develop AIDS-like symptoms. Because SIVcpz/HIV-1 may disrupt regulation of the gut microbiome and because it has not been possible to sample individual humans pre- and postinfection, we investigated the influence of infection on gut communities through long-term monitoring of chimpanzees from Gombe National Park, Tanzania. SIVcpz infection accelerated the rate of change in gut microbiota composition within individuals for periods of years after the initial infection and led to gut communities marked by high frequencies of pathogen-containing bacterial genera absent from SIVcpz-negative individuals. Our results indicate that immune function maintains temporally stable gut communities that are lost when individuals become infected with SIVcpz.
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Affiliation(s)
- Andrew H Moeller
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA
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36
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Moeller AH, Peeters M, Ndjango JB, Li Y, Hahn BH, Ochman H. Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res 2013; 23:1715-20. [PMID: 23804402 PMCID: PMC3787267 DOI: 10.1101/gr.154773.113] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/19/2013] [Indexed: 12/18/2022]
Abstract
The gut microbial communities within great apes have been shown to reflect the phylogenetic history of their hosts, indicating codiversification between great apes and their gut microbiota over evolutionary timescales. But because the great apes examined to date represent geographically isolated populations whose diets derive from different sources, it is unclear whether this pattern of codiversification has resulted from a long history of coadaptation between microbes and hosts (heritable factors) or from the ecological and geographic separation among host species (environmental factors). To evaluate the relative influences of heritable and environmental factors on the evolution of the great ape gut microbiota, we assayed the gut communities of sympatric and allopatric populations of chimpanzees, bonobos, and gorillas residing throughout equatorial Africa. Comparisons of these populations revealed that the gut communities of different host species can always be distinguished from one another but that the gut communities of sympatric chimpanzees and gorillas have converged in terms of community composition, sharing on average 53% more bacterial phylotypes than the gut communities of allopatric hosts. Host environment, independent of host genetics and evolutionary history, shaped the distribution of bacterial phylotypes across the Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria, the four most common phyla of gut bacteria. Moreover, the specific patterns of phylotype sharing among hosts suggest that chimpanzees living in sympatry with gorillas have acquired bacteria from gorillas. These results indicate that geographic isolation between host species has promoted the evolutionary differentiation of great ape gut bacterial communities.
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Affiliation(s)
- Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Martine Peeters
- Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, 34394 Montpellier Cedex 5, France
| | - Jean-Basco Ndjango
- Faculties of Sciences, University of Kisangani, Kisangani, BP 2012, Democratic Republic of the Congo
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Howard Ochman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
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37
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Abstract
Surveys of humans from around the world have revealed differences in gut microbiota composition among geographically separated populations. But because humans from the same regions often share common ancestry as well as dietary and cultural habits, most studies have not been able to differentiate among the effects of heritable factors and external factors on the composition of the gut microbiota. Here we discuss how the analysis of gut microbial communities of chimpanzees residing in Gombe Stream National Park has provided an unprecedented opportunity to measure the effects of external factors while controlling for heritable factors. The differences in gut microbiota composition between separated host populations of chimpanzees are due almost entirely to external factors, with the contribution of heritable factors to intraspecific variation in gut microbiota composition being too small to detect. The dominant influence of external factors in generating differences among the gut microbiota of our closest relatives lends promise to the possibility of manipulating the composition of the gut microbiome within human hosts. These results highlight the need for controlled studies that isolate the roles of specific external factors, such as diet, cultural practices and geography, in generating differences in the gut microbiota composition.
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López-Giráldez F, Moeller AH, Townsend JP. Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. Biomed Res Int 2013; 2013:621604. [PMID: 23878813 PMCID: PMC3708382 DOI: 10.1155/2013/621604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/03/2013] [Indexed: 11/17/2022]
Abstract
Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.
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Affiliation(s)
- Francesc López-Giráldez
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Jeffrey P. Townsend
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
- Department of Biostatistics, Yale University, 135 College Street, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, 300 George Street, Yale University, New Haven, CT 06520, USA
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Moeller AH, Degnan PH, Pusey AE, Wilson ML, Hahn BH, Ochman H. Chimpanzees and humans harbour compositionally similar gut enterotypes. Nat Commun 2013; 3:1179. [PMID: 23149725 PMCID: PMC3520023 DOI: 10.1038/ncomms2159] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 09/03/2012] [Indexed: 01/17/2023] Open
Abstract
Microbes inhabiting the human gastrointestinal tract tend to adopt one of three characteristic community structures, called ‘enterotypes’, each of which is overrepresented by a distinct set of bacterial genera. Here, we report that the gut microbiotae of chimpanzees also assort into enterotypes and that these chimpanzee enterotypes are compositionally analogous to those of humans. Through the analysis of longitudinal samples, we show that the microbial signatures of the enterotypes are stable over time, but that individual hosts switch between enterotypes over periods longer than a year. These results support the hypothesis that enterotypic variation was present in populations of great apes before the divergence of humans and chimpanzees.
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Affiliation(s)
- Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
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Moeller AH, Townsend JP. Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates. Mol Phylogenet Evol 2011; 60:271-2. [PMID: 21558010 DOI: 10.1016/j.ympev.2011.04.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/15/2011] [Accepted: 04/26/2011] [Indexed: 01/15/2023]
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