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Nishida AH, Ochman H. Rates of gut microbiome divergence in mammals. Mol Ecol 2018; 27:1884-1897. [PMID: 29290090 PMCID: PMC5935551 DOI: 10.1111/mec.14473] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/14/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
The variation and taxonomic diversity among mammalian gut microbiomes raises several questions about the factors that contribute to the rates and patterns of change in these microbial communities. By comparing the microbiome compositions of 112 species representing 14 mammalian orders, we assessed how host and ecological factors contribute to microbiome diversification. Except in rare cases, the same bacterial phyla predominate in mammalian gut microbiomes, and there has been some convergence of microbiome compositions according to dietary category across all mammalians lineages except Chiropterans (bats), which possess high proportions of Proteobacteria and tend to be most similar to one another regardless of diet. At lower taxonomic ranks (families, genera, 97% OTUs), bacteria are more likely to be associated with a particular mammalian lineage than with a particular dietary category, resulting in a strong phylogenetic signal in the degree to which microbiomes diverge. Despite different physiologies, the gut microbiomes of several mammalian lineages have diverged at roughly the same rate over the past 75 million years; however, the gut microbiomes of Cetartiodactyla (ruminants, whales, hippopotami) have evolved much faster and those of Chiropterans much slower. Contrary to expectations, the number of dietary transitions within a lineage does not influence rates of microbiome divergence, but instead, some of the most dramatic changes are associated with the loss of bacterial taxa, such as those accompanying the transition from terrestrial to marine lifestyles and the evolution of hominids.
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Affiliation(s)
- Alex H Nishida
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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152
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Sherrill-Mix S, McCormick K, Lauder A, Bailey A, Zimmerman L, Li Y, Django JBN, Bertolani P, Colin C, Hart JA, Hart TB, Georgiev AV, Sanz CM, Morgan DB, Atencia R, Cox D, Muller MN, Sommer V, Piel AK, Stewart FA, Speede S, Roman J, Wu G, Taylor J, Bohm R, Rose HM, Carlson J, Mjungu D, Schmidt P, Gaughan C, Bushman JI, Schmidt E, Bittinger K, Collman RG, Hahn BH, Bushman FD. Allometry and Ecology of the Bilaterian Gut Microbiome. mBio 2018; 9:e00319-18. [PMID: 29588401 PMCID: PMC5874926 DOI: 10.1128/mbio.00319-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022] Open
Abstract
Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (Bilateria) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction.IMPORTANCE The intestinal microbiome of animals is essential for health, contributing to digestion of foods, proper immune development, inhibition of pathogen colonization, and catabolism of xenobiotic compounds. How these communities assemble and persist is just beginning to be investigated. Here we interrogated a set of gut samples from a wide range of animals to investigate the roles of selection and random processes in microbial community construction. We show that the numbers of bacterial species increased with the weight of host organisms, paralleling findings from studies of island biogeography. Communities in larger organisms tended to be more anaerobic, suggesting one mechanism for niche diversification. Nonselective processes enable specific predictions for community structure, but our samples did not match the predictions of the neutral model. Thus, these findings highlight the importance of niche selection in community construction and suggest mechanisms of niche diversification.
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Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin McCormick
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Abigail Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aubrey Bailey
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laurie Zimmerman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jean-Bosco N Django
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, United Kingdom
| | - Christelle Colin
- Projet Primates France, Centre de Conservation pour Chimpanzés, Faranah, Republic of Guinea
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, Kinshasa, Democratic Republic of the Congo
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, USA
| | - Rebeca Atencia
- Tchimpounga Chimpanzee Rehabilitation Center, Jane Goodall Institute, Pointe Noire, Republic of Congo
| | - Debby Cox
- Tchimpounga Chimpanzee Rehabilitation Center, Jane Goodall Institute, Pointe Noire, Republic of Congo
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Volker Sommer
- Department of Anthropology, University College London, London, United Kingdom
| | - Alexander K Piel
- Department of Natural Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Fiona A Stewart
- Department of Natural Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, IDA-Africa, Portland, Oregon, USA
| | - Joe Roman
- Gund Institute for Environment, Rubenstein School for Environment and Natural Resources, University of Vermont, Burlington, Vermont, USA
| | - Gary Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Josh Taylor
- Tulane National Primate Research Center, Tulane University Health Science Center, Covington, Louisiana, USA
| | - Rudolf Bohm
- Tulane National Primate Research Center, Tulane University Health Science Center, Covington, Louisiana, USA
| | - Heather M Rose
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - John Carlson
- Southeast Fisheries Science Center, National Oceanic and Atmospheric Administration Fisheries Service, Panama City, Florida, USA
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute, Kigoma, Tanzania
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Celeste Gaughan
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joyslin I Bushman
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ella Schmidt
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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153
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Pent M, Hiltunen M, Põldmaa K, Furneaux B, Hildebrand F, Johannesson H, Ryberg M, Bahram M. Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies. Environ Microbiol 2018; 20:1641-1650. [DOI: 10.1111/1462-2920.14069] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Mari Pent
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Markus Hiltunen
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Brendan Furneaux
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory; Heidelberg Germany
| | - Hanna Johannesson
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Martin Ryberg
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
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154
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Hale VL, Tan CL, Niu K, Yang Y, Knight R, Zhang Q, Cui D, Amato KR. Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species. MICROBIAL ECOLOGY 2018; 75:515-527. [PMID: 28735426 DOI: 10.1007/s00248-017-1041-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 07/10/2017] [Indexed: 05/16/2023]
Abstract
Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza). Monkeys were housed at five different captive institutes: Panxi Wildlife Rescue Center (Guizhou, China), Beijing Zoo, Beijing Zoo Breeding Center, Singapore Zoo, and Singapore Zoo Primate Conservation Breeding Center. Captive diets varied widely between institutions, but within an institution, all colobine monkey species were fed nearly identical or identical diets. In addition, four monkey species were present at multiple captive institutes. This allowed us to parse the effects of diet and phylogeny in these captive colobines. Gut microbial communities clustered weakly by host species and strongly by diet, and overall, colobine phylogenetic relationships were not reflected in gut microbiota analyses. Core microbiota analyses also identified several key taxa-including microbes within the Ruminococcaceae and Lachnospiraceae families-that were shared by over 90% of the monkeys in this study. Microbial species within these families include many butyrate producers that are important for GI health. These results highlight the importance of diet in captive colobines.
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Affiliation(s)
- Vanessa L Hale
- Microbiome Program, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA.
| | - Chia L Tan
- San Diego Zoo Institute for Conservation Research, Escondido, CA, 92027, USA
| | - Kefeng Niu
- Fanjingshan National Nature Reserve Administration, Tongren, China
- Department of Life Sciences and Systems Biology, University of Turin, 10123, Turin, Italy
| | - Yeqin Yang
- Fanjingshan National Nature Reserve Administration, Tongren, China
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Qikun Zhang
- Zhejiang Institute of Microbiology, Zhejiang, Hangzhou, China
| | - Duoying Cui
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208, USA
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155
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Mallott EK, Amato KR, Garber PA, Malhi RS. Influence of fruit and invertebrate consumption on the gut microbiota of wild white‐faced capuchins (
Cebus capucinus
). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:576-588. [DOI: 10.1002/ajpa.23395] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/09/2017] [Accepted: 12/13/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Elizabeth K. Mallott
- Department of AnthropologyNorthwestern University1810 Hinman Ave, Evanston Illinois 60208
| | - Katherine R. Amato
- Department of AnthropologyNorthwestern University1810 Hinman Ave, Evanston Illinois 60208
| | - Paul A. Garber
- Department of AnthropologyUniversity of Illinois at Urbana‐Champaign109A Davenport Hall, 607 South Mathews Avenue, Urbana Illinois 61801
| | - Ripan S. Malhi
- Department of AnthropologyUniversity of Illinois at Urbana‐Champaign109A Davenport Hall, 607 South Mathews Avenue, Urbana Illinois 61801
- Carl R Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐Champaign1206 West Gregory Drive, Urbana Illinois 61801
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156
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Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals. PLoS One 2017; 12:e0189404. [PMID: 29281673 PMCID: PMC5744928 DOI: 10.1371/journal.pone.0189404] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/26/2017] [Indexed: 12/21/2022] Open
Abstract
Host diet influences the diversity and metabolic activities of the gut microbiome. Previous studies have shown that the gut microbiome provides a wide array of enzymes that enable processing of diverse dietary components. Because the primary diet of the porcupine, Erethizon dorsatum, is lignified plant material, we reasoned that the porcupine microbiome would be replete with enzymes required to degrade lignocellulose. Here, we report on the bacterial composition in the porcupine microbiome using 16S rRNA sequencing and bioinformatics analysis. We extended this analysis to the microbiomes of 20 additional mammals located in Shubenacadie Wildlife Park (Nova Scotia, Canada), enabling the comparison of bacterial diversity amongst three mammalian taxonomic orders (Rodentia, Carnivora, and Artiodactyla). 16S rRNA sequencing was validated using metagenomic shotgun sequencing on selected herbivores (porcupine, beaver) and carnivores (coyote, Arctic wolf). In the microbiome, functionality is more conserved than bacterial composition, thus we mined microbiome data sets to identify conserved microbial functions across species in each order. We measured the relative gene abundances for cellobiose phosphorylase, endoglucanase, and beta-glucosidase to evaluate the cellulose-degrading potential of select mammals. The porcupine and beaver had higher proportions of genes encoding cellulose-degrading enzymes than the Artic wolf and coyote. These findings provide further evidence that gut microbiome diversity and metabolic capacity are influenced by host diet.
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157
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Abstract
The trillions of microbes living in the gut-the gut microbiota-play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity's near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations. Finally, we propose that this broader phylogenetic perspective is useful for understanding the mechanisms underlying human-microbiome interactions.
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Affiliation(s)
- Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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158
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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: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [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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159
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Ren T, Boutin S, Humphries MM, Dantzer B, Gorrell JC, Coltman DW, McAdam AG, Wu M. Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. MICROBIOME 2017; 5:163. [PMID: 29268780 PMCID: PMC5740981 DOI: 10.1186/s40168-017-0382-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/12/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciurus hudsonicus) population. Red squirrels are territorial, solitary, and live in a highly seasonal environment and therefore represent a very attractive system to study factors that drive the temporal and spatial dynamics of gut microbiota. RESULT For the first time, this study revealed significant spatial patterns of gut microbiota within a host population, suggesting limited dispersal could play a role in shaping and maintaining the structure of gut microbial communities. We also found a remarkable seasonal rhythm in red squirrel's gut microbial composition manifested by a tradeoff between relative abundance of two genera Oscillospira and Corpococcus and clearly associated with seasonal variation in diet availability. Our results show that in nature, environmental factors exert a much stronger influence on gut microbiota than host-associated factors including age and sex. Despite strong environmental effects, we found clear evidence of individuality and maternal effects, but host genetics did not seem to be a significant driver of the gut microbial communities in red squirrels. CONCLUSION Taken together, the results of this study emphasize the importance of external ecological factors rather than host attributes in driving temporal and spatial patterns of gut microbiota in natural environment.
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Affiliation(s)
- Tiantian Ren
- Department of Biology, University of Virginia, Charlottesville, VA USA
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta Canada
| | - Murray M. Humphries
- Department of Natural Resource Sciences, Macdonald Campus, McGill University, Ste-Anne-de-Bellevue, Québec Canada
| | - Ben Dantzer
- Department of Psychology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI USA
| | - Jamieson C. Gorrell
- Biology Department, Vancouver Island University, Nanaimo, British Columbia Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta Canada
| | - Andrew G. McAdam
- Department of Integrative Biology, University of Guelph, Guelph, Ontario Canada
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, VA USA
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160
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van Veelen HPJ, Falcao Salles J, Tieleman BI. Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks. MICROBIOME 2017; 5:156. [PMID: 29191217 PMCID: PMC5709917 DOI: 10.1186/s40168-017-0371-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 11/09/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Working toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and ecological factors shaping their variation. In this study, we described the microbiota in the cloaca, brood patch skin and feathers of two species of birds and the microbial communities in their nest environment. We compared patterns of resemblance between these microbial communities at different levels of biological organisation (species, individual, body part) and investigated the phylogenetic structure to deduce potential microbial community assembly processes. RESULTS Using 16S rRNA gene amplicon data of woodlarks (Lullula arborea) and skylarks (Alauda arvensis), we demonstrated that bird- and nest-associated microbiota showed substantial OTU co-occurrences and shared dominant taxonomic groups, despite variation in OTU richness, diversity and composition. Comparing host species, we uncovered that sympatric woodlarks and skylarks harboured similar microbiota, dominated by Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria. Yet, compared with the nest microbiota that showed little variation, each species' bird-associated microbiota displayed substantial variation. The latter could be partly (~ 20%) explained by significant inter-individual differences. The various communities of the bird's body (cloaca, brood patch skin and feathers) appeared connected with each other and with the nest microbiota (nest lining material and surface soil). Communities were more similar when the contact between niches was frequent or intense. Finally, bird microbiota showed significant phylogenetic clustering at the tips, but not at deeper branches of the phylogeny. CONCLUSIONS Our interspecific comparison suggested that the environment is more important than phylogeny in shaping the bird-associated microbiotas. In addition, variation among individuals and among body parts suggested that intrinsic or behavioural differences among females and spatial heterogeneity among territories contributed to the microbiome variation of larks. Modest but significant phylogenetic clustering of cloacal, skin and feather microbiotas suggested weak habitat filtering in these niches. We propose that lark microbiota may be primarily, but not exclusively, shaped by horizontal acquisition from the regional bacterial pool at the breeding site. More generally, we hypothesise that the extent of ecological niche-sharing by avian (or other vertebrate) hosts may predict the convergence of their microbiota.
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Affiliation(s)
- H Pieter J van Veelen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands.
| | - Joana Falcao Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
| | - B Irene Tieleman
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. box 11103, 9700 CC, Groningen, The Netherlands
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161
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Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes. mSystems 2017; 2:mSystems00132-17. [PMID: 29181448 PMCID: PMC5698494 DOI: 10.1128/msystems.00132-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 02/01/2023] Open
Abstract
The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly. The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = −0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
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162
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Kohl KD, Dearing MD. With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology-An Introduction to the Symposium. Integr Comp Biol 2017; 57:669-673. [PMID: 28992098 DOI: 10.1093/icb/icx103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The role that host-associated microbes play in animal biology is gaining attention in comparative biology. Numerous research groups study the roles that microbes play in human health and nutrition, or in enhancing the production of agricultural animals. However, inclusion of host-associated microbes into research questions of integrative and comparative biology has lagged behind. We hosted a symposium to bring together top researchers in the field of host-associated microbes who also incorporate aspects of integrative and comparative biology. In this introduction, we highlight recent research demonstrating the profound roles that host-associated microbes play in many aspects of animal biology, such as immune function, endocrinology, and even behavior. It is our hope that integrative and comparative biologists will begin to include aspects of host-associated microbes into their research programs, enhancing both the fields of comparative biology and host-microbe interactions.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
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163
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Unraveling the gut microbiome of the long-lived naked mole-rat. Sci Rep 2017; 7:9590. [PMID: 28852094 PMCID: PMC5575099 DOI: 10.1038/s41598-017-10287-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/07/2017] [Indexed: 01/16/2023] Open
Abstract
The naked mole-rat (Heterocephalus glaber) is a subterranean mouse-sized African mammal that shows astonishingly few age-related degenerative changes and seems to not be affected by cancer. These features make this wild rodent an excellent model to study the biology of healthy aging and longevity. Here we characterize for the first time the intestinal microbial ecosystem of the naked mole-rat in comparison to humans and other mammals, highlighting peculiarities related to the specific living environment, such as the enrichment in bacteria able to utilize soil sulfate as a terminal electron acceptor to sustain an anaerobic oxidative metabolism. Interestingly, some compositional gut microbiota peculiarities were also shared with human gut microbial ecosystems of centenarians and Hadza hunter-gatherers, considered as models of a healthy gut microbiome and of a homeostatic and highly adaptive gut microbiota-host relationship, respectively. In addition, we found an enrichment of short-chain fatty acids and carbohydrate degradation products in naked mole-rat compared to human samples. These data confirm the importance of the gut microbial ecosystem as an adaptive partner for the mammalian biology and health, independently of the host phylogeny.
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164
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Pascoe EL, Hauffe HC, Marchesi JR, Perkins SE. Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies. ISME JOURNAL 2017; 11:2644-2651. [PMID: 28800135 DOI: 10.1038/ismej.2017.133] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/21/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
A wealth of human studies have demonstrated the importance of gut microbiota to health. Research on non-human animal gut microbiota is now increasing, but what insight does it provide? We reviewed 650 publications from this burgeoning field (2009-2016) and determined that animals driving this research were predominantly 'domestic' (48.2%), followed by 'model' (37.5%), with least studies on 'wild' (14.3%) animals. Domestic studies largely experimentally perturbed microbiota (81.8%) and studied mammals (47.9%), often to improve animal productivity. Perturbation was also frequently applied to model animals (87.7%), mainly mammals (88.1%), for forward translation of outcomes to human health. In contrast, wild animals largely characterised natural, unperturbed microbiota (79.6%), particularly in pest or pathogen vectoring insects (42.5%). We used network analyses to compare the research foci of each animal group: 'diet' was the main focus in all three, but to different ends: to enhance animal production (domestic), to study non-infectious diseases (model), or to understand microbiota composition (wild). Network metrics quantified model animal studies as the most interdisciplinary, while wild animals incorporated the fewest disciplines. Overall, animal studies, especially model and domestic, cover a broad array of research. Wild animals, however, are the least investigated, but offer under-exploited opportunities to study 'real-life' microbiota.
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Affiliation(s)
- Emily L Pascoe
- Organisms and Environment Division, School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff University, Cardiff, UK.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Michele all' Adige (TN), Italy
| | - Heidi C Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Michele all' Adige (TN), Italy
| | - Julian R Marchesi
- Organisms and Environment Division, School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff University, Cardiff, UK.,Centre for Digestive and Gut Health, Imperial College London, London, UK.,Department of Surgery and Cancer, Imperial College London, London, UK
| | - Sarah E Perkins
- Organisms and Environment Division, School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff University, Cardiff, UK.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Michele all' Adige (TN), Italy
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165
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Morphology of the tongue of Vermilingua (Xenarthra: Pilosa) and evolutionary considerations. J Morphol 2017. [DOI: 10.1002/jmor.20718] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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166
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Baldo L, Pretus JL, Riera JL, Musilova Z, Bitja Nyom AR, Salzburger W. Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes. ISME JOURNAL 2017; 11:1975-1987. [PMID: 28509910 PMCID: PMC5560477 DOI: 10.1038/ismej.2017.62] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/09/2017] [Accepted: 03/14/2017] [Indexed: 02/08/2023]
Abstract
Ecoevolutionary dynamics of the gut microbiota at the macroscale level, that is, in across-species comparisons, are largely driven by ecological variables and host genotype. The repeated explosive radiations of African cichlid fishes in distinct lakes, following a dietary diversification in a context of reduced genetic diversity, provide a natural setup to explore convergence, divergence and repeatability in patterns of microbiota dynamics as a function of the host diet, phylogeny and environment. Here we characterized by 16S rRNA amplicon sequencing the gut microbiota of 29 cichlid species from two distinct lakes/radiations (Tanganyika and Barombi Mbo) and across a broad dietary and phylogenetic range. Within each lake, a significant deviation between a carnivorous and herbivorous lifestyle was found. Herbivore species were characterized by an increased bacterial taxonomic and functional diversity and converged in key compositional and functional community aspects. Despite a significant lake effect on the microbiota structure, this process has occurred with remarkable parallels in the two lakes. A metabolic signature most likely explains this trend, as indicated by a significant enrichment in herbivores/omnivores of bacterial taxa and functions associated with fiber degradation and detoxification of plant chemical compounds. Overall, compositional and functional aspects of the gut microbiota individually and altogether validate and predict main cichlid dietary habits, suggesting a fundamental role of gut bacteria in cichlid niche expansion and adaptation.
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Affiliation(s)
- Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Joan Lluís Pretus
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Zuzana Musilova
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Zoology, Charles University in Prague, Prague, Czech Republic
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167
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Kropáčková L, Těšický M, Albrecht T, Kubovčiak J, Čížková D, Tomášek O, Martin JF, Bobek L, Králová T, Procházka P, Kreisinger J. Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence. Mol Ecol 2017; 26:5292-5304. [PMID: 28401612 DOI: 10.1111/mec.14144] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/05/2017] [Indexed: 01/03/2023]
Abstract
Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM.
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Affiliation(s)
- Lucie Kropáčková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Kubovčiak
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Dagmar Čížková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Oldřich Tomášek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Lukáš Bobek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Tereza Králová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Petr Procházka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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168
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Abstract
The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.
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Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
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169
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Romano M. Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk. Front Microbiol 2017; 8:721. [PMID: 28473829 PMCID: PMC5397478 DOI: 10.3389/fmicb.2017.00721] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/06/2017] [Indexed: 11/17/2022] Open
Abstract
According to a traditional view, the specific diet in vertebrates is one of the key factors structuring the composition of the gut microbiota. In this interpretation, the microbiota assumes a subordinate position, where the larger host shapes, through evolution and its fitness, the taxonomical composition of the hosted microbiota. The present contribution shows how the evolution of herbivory, framed within the new concept of holobiont, the possibility of inter-kingdom crosstalk and its epigenetic effects, could pave the way to a completely reversed interpretation: instead of being passively shaped, the microbiota can mold and shape the general host body structure to increase its fitness. Central elements to consider in this context are the inter-kingdom crosstalk, the possibility of transporting RNAs through nanovesicles in feces from parents to offspring, and the activation of epigenetic processes passed on vertically from generation to generation. The new hypothesis is that the gut microbiota could play a great role in the macroevolutionary dynamics of herbivorous vertebrates, causing directly through host-microbiota dialog of epigenetic nature (i.e., methylation, histone acetylation, etc.), major changes in the organisms phenotype. The vertical exchange of the same microbial communities from parents to offspring, the interaction of these microbes with fairly uniform genotypes, and the socially restricted groups where these processes take place, could all explain the reasons why herbivory has appeared several time (and independently) during the evolution of vertebrates. The new interpretation could also represent a key factor in understanding the convergent evolution of analogous body structures in very distant lineages.
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Affiliation(s)
- Marco Romano
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und BiodiversitätsforschungBerlin, Germany.,Dipartimento di Scienze della Terra, Sapienza Universita di RomaRome, Italy
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170
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Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun 2017; 8:14319. [PMID: 28230052 PMCID: PMC5331214 DOI: 10.1038/ncomms14319] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/08/2016] [Indexed: 12/28/2022] Open
Abstract
Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution. Both host diet and phylogeny have been argued to shape mammalian microbiome communities. Here, the authors show that diet predicts the presence of ancient bacterial lineages in the microbiome, but that co-speciation between more recent bacterial lineages and their hosts may drive associations between microbiome composition and phylogeny.
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Affiliation(s)
- Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Florent Mazel
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Jon G Sanders
- Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, Massachusetts 02138, USA
| | - Chris S Smillie
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA
| | - Sébastien Lavergne
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Wilfried Thuiller
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA
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171
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Crittenden AN, Schnorr SL. Current views on hunter‐gatherer nutrition and the evolution of the human diet. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162 Suppl 63:84-109. [DOI: 10.1002/ajpa.23148] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 11/03/2016] [Accepted: 11/15/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Alyssa N. Crittenden
- Laboratory of Metabolism, Anthropometry, and Nutrition, Department of AnthropologyUniversity of NevadaLas Vegas, Las Vegas Nevada
| | - Stephanie L. Schnorr
- Laboratories of Molecular Anthropology and Microbiome Research, Department of AnthropologyUniversity of OklahomaNorman Oklahoma
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172
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Miller EA, Beasley DE, Dunn RR, Archie EA. Lactobacilli Dominance and Vaginal pH: Why Is the Human Vaginal Microbiome Unique? Front Microbiol 2016; 7:1936. [PMID: 28008325 PMCID: PMC5143676 DOI: 10.3389/fmicb.2016.01936] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/17/2016] [Indexed: 01/09/2023] Open
Abstract
The human vaginal microbiome is dominated by bacteria from the genus Lactobacillus, which create an acidic environment thought to protect women against sexually transmitted pathogens and opportunistic infections. Strikingly, lactobacilli dominance appears to be unique to humans; while the relative abundance of lactobacilli in the human vagina is typically >70%, in other mammals lactobacilli rarely comprise more than 1% of vaginal microbiota. Several hypotheses have been proposed to explain humans' unique vaginal microbiota, including humans' distinct reproductive physiology, high risk of STDs, and high risk of microbial complications linked to pregnancy and birth. Here, we test these hypotheses using comparative data on vaginal pH and the relative abundance of lactobacilli in 26 mammalian species and 50 studies (N = 21 mammals for pH and 14 mammals for lactobacilli relative abundance). We found that non-human mammals, like humans, exhibit the lowest vaginal pH during the period of highest estrogen. However, the vaginal pH of non-human mammals is never as low as is typical for humans (median vaginal pH in humans = 4.5; range of pH across all 21 non-human mammals = 5.4-7.8). Contrary to disease and obstetric risk hypotheses, we found no significant relationship between vaginal pH or lactobacilli relative abundance and multiple metrics of STD or birth injury risk (P-values ranged from 0.13 to 0.99). Given the lack of evidence for these hypotheses, we discuss two alternative explanations: the common function hypothesis and a novel hypothesis related to the diet of agricultural humans. Specifically, with regard to diet we propose that high levels of starch in human diets have led to increased levels of glycogen in the vaginal tract, which, in turn, promotes the proliferation of lactobacilli. If true, human diet may have paved the way for a novel, protective microbiome in human vaginal tracts. Overall, our results highlight the need for continuing research on non-human vaginal microbial communities and the importance of investigating both the physiological mechanisms and the broad evolutionary processes underlying human lactobacilli dominance.
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Affiliation(s)
- Elizabeth A Miller
- Department of Biological Sciences, University of Notre Dame Notre Dame, IN, USA
| | - DeAnna E Beasley
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga Chattanooga, TN, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State UniversityRaleigh, NC, USA; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre Dame, IN, USA; Institute of Primate Research, National Museums of KenyaNairobi, Kenya
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173
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Rascovan N, Huynh H, Chouin G, Adekola K, Georges-Zimmermann P, Signoli M, Desfosses Y, Aboudharam G, Drancourt M, Desnues C. Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth. NPJ Biofilms Microbiomes 2016. [PMID: 28649400 PMCID: PMC5460193 DOI: 10.1038/s41522-016-0008-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ancient dental pulps are highly precious samples because they conserve DNA from humans and blood-borne pathogens for ages. However, little is known about the microbial communities present in dental pulps. Here, we analyzed ancient and modern dental pulp samples from different time periods and geographic regions and found that they are colonized by distinct microbial communities, which can be differentiated from other oral cavity samples. We found that despite the presence of environmental bacteria, ancient dental pulps conserve a clear and well-conserved record of oral microbes. We were able to detect several different oral pathogens in ancient and modern dental pulps, which are commonly associated with periodontal diseases. We thus showed that ancient dental pulps are not only valuable sources of DNA from humans and systemic infections, but also an open window for the study of ancient oral microbiomes.
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Affiliation(s)
- Nicolás Rascovan
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Hong Huynh
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Gérard Chouin
- Lyon G. Tyler Department of History, William & Mary, Virginia, USA
| | - Kolawole Adekola
- Department of Archaeology and Anthropology, University of Ibadan, Ibadan, Nigeria
| | | | - Michel Signoli
- Department of Medicine, Aix Marseille University, UMR 7268 ADES, EFS CNRS, Secteur Nord, Marseille, France
| | - Yves Desfosses
- Department of Medicine, Aix Marseille University, UMR 7268 ADES, EFS CNRS, Secteur Nord, Marseille, France
| | - Gérard Aboudharam
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Michel Drancourt
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Christelle Desnues
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
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174
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Amato KR. Incorporating the gut microbiota into models of human and non-human primate ecology and evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 159:S196-215. [PMID: 26808106 DOI: 10.1002/ajpa.22908] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mammalian gut is home to a diverse community of microbes. Advances in technology over the past two decades have allowed us to examine this community, the gut microbiota, in more detail, revealing a wide range of influences on host nutrition, health, and behavior. These host-gut microbe interactions appear to shape host plasticity and fitness in a variety of contexts, and therefore represent a key factor missing from existing models of human and non-human primate ecology and evolution. However, current studies of the gut microbiota tend to include limited contextual data or are clinical, making it difficult to directly test broad anthropological hypotheses. Here, I review what is known about the animal gut microbiota and provide examples of how gut microbiota research can be integrated into the study of human and non-human primate ecology and evolution with targeted data collection. Specifically, I examine how the gut microbiota may impact primate diet, energetics, disease resistance, and cognition. While gut microbiota research is proliferating rapidly, especially in the context of humans, there remain important gaps in our understanding of host-gut microbe interactions that will require an anthropological perspective to fill. Likewise, gut microbiota research will be an important tool for filling remaining gaps in anthropological research.
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175
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Ellegaard KM, Engel P. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota. Front Microbiol 2016; 7:1475. [PMID: 27708630 PMCID: PMC5030217 DOI: 10.3389/fmicb.2016.01475] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/05/2016] [Indexed: 12/31/2022] Open
Abstract
Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.
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Affiliation(s)
- Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
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176
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Ren T, Kahrl AF, Wu M, Cox RM. Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards. Mol Ecol 2016; 25:4793-804. [PMID: 27497270 DOI: 10.1111/mec.13796] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022]
Abstract
Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct 'ecomorphs' related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk-crown, trunk-ground, grass-bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk-ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species.
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Affiliation(s)
- Tiantian Ren
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA
| | - Ariel F Kahrl
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA
| | - Martin Wu
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA
| | - Robert M Cox
- Department of Biology, University of Virginia, PO Box 400328, Charlottesville, VA, 22904, USA.
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177
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Hoang KL, Morran LT, Gerardo NM. Experimental Evolution as an Underutilized Tool for Studying Beneficial Animal-Microbe Interactions. Front Microbiol 2016; 7:1444. [PMID: 27679620 PMCID: PMC5020044 DOI: 10.3389/fmicb.2016.01444] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/30/2016] [Indexed: 11/29/2022] Open
Abstract
Microorganisms play a significant role in the evolution and functioning of the eukaryotes with which they interact. Much of our understanding of beneficial host–microbe interactions stems from studying already established associations; we often infer the genotypic and environmental conditions that led to the existing host–microbe relationships. However, several outstanding questions remain, including understanding how host and microbial (internal) traits, and ecological and evolutionary (external) processes, influence the origin of beneficial host–microbe associations. Experimental evolution has helped address a range of evolutionary and ecological questions across different model systems; however, it has been greatly underutilized as a tool to study beneficial host–microbe associations. In this review, we suggest ways in which experimental evolution can further our understanding of the proximate and ultimate mechanisms shaping mutualistic interactions between eukaryotic hosts and microbes. By tracking beneficial interactions under defined conditions or evolving novel associations among hosts and microbes with little prior evolutionary interaction, we can link specific genotypes to phenotypes that can be directly measured. Moreover, this approach will help address existing puzzles in beneficial symbiosis research: how symbioses evolve, how symbioses are maintained, and how both host and microbe influence their partner’s evolutionary trajectories. By bridging theoretical predictions and empirical tests, experimental evolution provides us with another approach to test hypotheses regarding the evolution of beneficial host–microbe associations.
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Affiliation(s)
- Kim L Hoang
- Department of Biology, O. Wayne Rollins Research Center, Emory University Atlanta, GA, USA
| | - Levi T Morran
- Department of Biology, O. Wayne Rollins Research Center, Emory University Atlanta, GA, USA
| | - Nicole M Gerardo
- Department of Biology, O. Wayne Rollins Research Center, Emory University Atlanta, GA, USA
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178
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Schnorr SL, Sankaranarayanan K, Lewis CM, Warinner C. Insights into human evolution from ancient and contemporary microbiome studies. Curr Opin Genet Dev 2016; 41:14-26. [PMID: 27507098 DOI: 10.1016/j.gde.2016.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA.
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179
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Colston TJ, Jackson CR. Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown. Mol Ecol 2016; 25:3776-800. [DOI: 10.1111/mec.13730] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Timothy J. Colston
- Department of Biology The University of Mississippi University MS 38677 USA
| | - Colin R. Jackson
- Department of Biology The University of Mississippi University MS 38677 USA
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180
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Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems 2016; 1:mSystems00021-16. [PMID: 27822526 PMCID: PMC5069758 DOI: 10.1128/msystems.00021-16] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/05/2016] [Indexed: 01/10/2023] Open
Abstract
Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive. Immediate freezing at −20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods—95% ethanol, FTA cards, and the OMNIgene Gut kit—can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates. However, even the worst methods, including those with no fixative, were able to reveal microbiome differences between species at 8 weeks and between individuals after a week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than interindividual variation (although use of a single method within a study is strongly recommended to reduce batch effects). Encouragingly for FTA cards, the differences caused by this method are systematic and can be detrended. As in other studies, we strongly caution against the use of 70% ethanol. The results, spanning 15 individuals and over 1,200 samples, provide our most comprehensive view to date of storage effects on stool and provide a paradigm for the future studies of other sample types that will be required to provide a global view of microbial diversity and its interaction among humans, animals, and the environment. IMPORTANCE Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive.
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181
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Ren T, Grieneisen LE, Alberts SC, Archie EA, Wu M. Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons. Environ Microbiol 2016; 18:1312-25. [PMID: 25818066 PMCID: PMC5941927 DOI: 10.1111/1462-2920.12852] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 12/18/2022]
Abstract
Gut bacterial communities play essential roles in host biology, but to date we lack information on the forces that shape gut microbiota between hosts and over time in natural populations. Understanding these forces in wild primates provides a valuable comparative context that enriches scientific perspectives on human gut microbiota. To this end, we tested predictors of gut microbial composition in a well-studied population of wild baboons. Using cross-sectional and longitudinal samples collected over 13 years, we found that baboons harbour gut microbiota typical of other omnivorous primates, albeit with an especially high abundance of Bifidobacterium. Similar to previous work in humans and other primates, we found strong effects of both developmental transitions and diet on gut microbial composition. Strikingly, baboon gut microbiota appeared to be highly dynamic such that samples collected from the same individual only a few days apart were as different from each other as samples collected over 10 years apart. Despite the dynamic nature of baboon gut microbiota, we identified a set of core taxa that is common among primates, supporting the hypothesis that microbiota codiversify with their host species. Our analysis identified two tentative enterotypes in adult baboons that differ from those of humans and chimpanzees.
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Affiliation(s)
- Tiantian Ren
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Laura E. Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46617 USA
| | - Susan C. Alberts
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
- Department of Biology, Duke University, Durham, NC 27708 USA
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46617 USA
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
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182
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Soverini M, Quercia S, Biancani B, Furlati S, Turroni S, Biagi E, Consolandi C, Peano C, Severgnini M, Rampelli S, Brigidi P, Candela M. The bottlenose dolphin (Tursiops truncatus) faecal microbiota. FEMS Microbiol Ecol 2016; 92:fiw055. [DOI: 10.1093/femsec/fiw055] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 12/31/2022] Open
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183
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Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas. Naturwissenschaften 2016; 103:25. [DOI: 10.1007/s00114-016-1348-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/08/2016] [Accepted: 02/12/2016] [Indexed: 12/27/2022]
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184
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Bittleston LS, Pierce NE, Ellison AM, Pringle A. Convergence in Multispecies Interactions. Trends Ecol Evol 2016; 31:269-280. [PMID: 26858111 DOI: 10.1016/j.tree.2016.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/05/2016] [Accepted: 01/12/2016] [Indexed: 12/29/2022]
Abstract
The concepts of convergent evolution and community convergence highlight how selective pressures can shape unrelated organisms or communities in similar ways. We propose a related concept, convergent interactions, to describe the independent evolution of multispecies interactions with similar physiological or ecological functions. A focus on convergent interactions clarifies how natural selection repeatedly favors particular kinds of associations among species. Characterizing convergent interactions in a comparative context is likely to facilitate prediction of the ecological roles of organisms (including microbes) in multispecies interactions and selective pressures acting in poorly understood or newly discovered multispecies systems. We illustrate the concept of convergent interactions with examples: vertebrates and their gut bacteria; ectomycorrhizae; insect-fungal-bacterial interactions; pitcher-plant food webs; and ants and ant-plants.
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Affiliation(s)
- Leonora S Bittleston
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Aaron M Ellison
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA 01366, USA
| | - Anne Pringle
- Departments of Bacteriology and Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
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185
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Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun 2016; 7:10516. [PMID: 26839246 PMCID: PMC4742810 DOI: 10.1038/ncomms10516] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022] Open
Abstract
Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.
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Affiliation(s)
- Elisabeth M. Bik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Elizabeth K. Costello
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexandra D. Switzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | - Randall S. Wells
- Sarasota Dolphin Research Program, Chicago Zoological Society, c/o Mote Marine Laboratory, Sarasota, Florida 34236, USA
| | - Kevin P. Carlin
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA
| | - Eric D. Jensen
- Space and Naval Warfare Systems Center Pacific, San Diego, California 92152, USA
| | - Stephanie Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University School of Medicine, Stanford, California 94305, USA
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186
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Giatsis C, Sipkema D, Smidt H, Heilig H, Benvenuti G, Verreth J, Verdegem M. The impact of rearing environment on the development of gut microbiota in tilapia larvae. Sci Rep 2015; 5:18206. [PMID: 26658351 PMCID: PMC4676014 DOI: 10.1038/srep18206] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 11/13/2015] [Indexed: 02/08/2023] Open
Abstract
This study explores the effect of rearing environment on water bacterial communities (BC) and the association with those present in the gut of Nile tilapia larvae (Oreochromis niloticus, Linnaeus) grown in either recirculating or active suspension systems. 454 pyrosequencing of PCR-amplified 16S rRNA gene fragments was applied to characterize the composition of water, feed and gut bacteria communities. Observed changes in water BC over time and differences in water BCs between systems were highly correlated with corresponding water physico-chemical properties. Differences in gut bacterial communities during larval development were correlated with differences in water communities between systems. The correlation of feed BC with those in the gut was minor compared to that between gut and water, reflected by the fact that 4 to 43 times more OTUs were shared between water and gut than between gut and feed BC. Shared OTUs between water and gut suggest a successful transfer of microorganisms from water into the gut, and give insight about the niche and ecological adaptability of water microorganisms inside the gut. These findings suggest that steering of gut microbial communities could be possible through water microbial management derived by the design and functionality of the rearing system.
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Affiliation(s)
- Christos Giatsis
- Aquaculture and Fisheries Group, Wageningen University, PO Box 338, 6708 WD Wageningen, the Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Giulia Benvenuti
- Bioprocess Engineering, AlgaePARC, Wageningen University, PO Box 16, 6700 AA Wageningen, the Netherlands
| | - Johan Verreth
- Aquaculture and Fisheries Group, Wageningen University, PO Box 338, 6708 WD Wageningen, the Netherlands
| | - Marc Verdegem
- Aquaculture and Fisheries Group, Wageningen University, PO Box 338, 6708 WD Wageningen, the Netherlands
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187
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Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia 2015; 180:717-33. [DOI: 10.1007/s00442-015-3507-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 11/02/2015] [Indexed: 01/01/2023]
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188
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Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nat Commun 2015; 6:8285. [PMID: 26393325 PMCID: PMC4595633 DOI: 10.1038/ncomms9285] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 08/04/2015] [Indexed: 12/21/2022] Open
Abstract
Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood. Diet appears to be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique gut microbiomes with surprising parallels in functional capacity and higher level taxonomy to those of terrestrial herbivores. These similarities likely reflect a shared role for fermentative metabolisms despite a shift in primary carbon sources from plant-derived to animal-derived polysaccharides, such as chitin. In contrast, protein catabolism and essential amino acid synthesis pathways in baleen whale microbiomes more closely resemble those of terrestrial carnivores. Our results demonstrate that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut. Diet is a major factor determining the composition of gut microbiota in mammals, while host evolutionary history seems to play an unclear role. Here, Sanders et al. show that baleen whales, which prey on animals, harbour a unique gut microbiome with similarities to those of terrestrial herbivores.
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189
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Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, Suen G. Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environ Microbiol 2015; 18:1391-402. [DOI: 10.1111/1462-2920.13022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 01/03/2023]
Affiliation(s)
| | - Paul J. Weimer
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
- US Department of Agriculture; Agricultural Research Service; Madison WI 53706 USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Garret Suen
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
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190
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Zepeda Mendoza ML, Sicheritz-Pontén T, Gilbert MTP. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform 2015; 16:745-58. [PMID: 25673291 PMCID: PMC4570204 DOI: 10.1093/bib/bbv001] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Indexed: 01/19/2023] Open
Abstract
DNA-based taxonomic and functional profiling is widely used for the characterization of organismal communities across a rapidly increasing array of research areas that include the role of microbiomes in health and disease, biomonitoring, and estimation of both microbial and metazoan species richness. Two principal approaches are currently used to assign taxonomy to DNA sequences: DNA metabarcoding and metagenomics. When initially developed, each of these approaches mandated their own particular methods for data analysis; however, with the development of high-throughput sequencing (HTS) techniques they have begun to share many aspects in data set generation and processing. In this review we aim to define the current characteristics, goals and boundaries of each field, and describe the different software used for their analysis. We argue that an appreciation of the potential and limitations of each method can help underscore the improvements required by each field so as to better exploit the richness of current HTS-based data sets.
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191
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Mariadassou M, Pichon S, Ebert D. Microbial ecosystems are dominated by specialist taxa. Ecol Lett 2015; 18:974-82. [DOI: 10.1111/ele.12478] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/14/2015] [Accepted: 06/29/2015] [Indexed: 12/20/2022]
Affiliation(s)
| | - Samuel Pichon
- Universität Basel, Zoologisches Institut; Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Universität Basel, Zoologisches Institut; Vesalgasse 1 4051 Basel Switzerland
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192
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Frank SC, Steyaert SM, Swenson JE, Storch I, Kindberg J, Barck H, Zedrosser A. A "clearcut" case? Brown bear selection of coarse woody debris and carpenter ants on clearcuts. FOREST ECOLOGY AND MANAGEMENT 2015; 348:164-173. [PMID: 26190890 PMCID: PMC4459689 DOI: 10.1016/j.foreco.2015.03.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 06/02/2023]
Abstract
Forest management alters habitat characteristics, resulting in various effects among and within species. It is crucial to understand how habitat alteration through forest management (e.g. clearcutting) affects animal populations, particularly with unknown future conditions (e.g. climate change). In Sweden, brown bears (Ursus arctos) forage on carpenter ants (Camponotus herculeanus) during summer, and may select for this food source within clearcuts. To assess carpenter ant occurrence and brown bear selection of carpenter ants, we sampled 6999 coarse woody debris (CWD) items within 1019 plots, of which 902 were within clearcuts (forests ⩽30 years of age) and 117 plots outside clearcuts (forests >30 years of age). We related various CWD and site characteristics to the presence or absence of carpenter ant galleries (nests) and bear foraging sign at three spatial scales: the CWD, plot, and clearcut scale. We tested whether both absolute and relative counts (the latter controlling for the number of CWD items) of galleries and bear sign in plots were higher inside or outside clearcuts. Absolute counts were higher inside than outside clearcuts for galleries (mean counts; inside: 1.8, outside: 0.8). CWD was also higher inside (mean: 6.8) than outside clearcuts (mean: 4.0). However, even after controlling for more CWD inside clearcuts, relative counts were higher inside than outside clearcuts for both galleries (mean counts; inside: 0.3, outside: 0.2) and bear sign (mean counts; inside: 0.03, outside: 0.01). Variables at the CWD scale best explained gallery and bear sign presence than variables at the plot or clearcut level, but bear selection was influenced by clearcut age. CWD circumference was important for both carpenter ant and bear sign presence. CWD hardness was most important for carpenter ant selection. However, the most important predictor for bear sign was the presence or absence of carpenter ant galleries. Bears had a high foraging "success" rate (⩾88%) in foraging CWD where galleries also occurred, which was assessed by summing CWD items with the concurrence of bear sign and galleries, divided by the sum of all CWD with bear sign. Clearcuts appeared to increase the occurrence of a relatively important summer food item, the carpenter ant, on Swedish managed forests for the brown bear. However, the potential benefit of this increase can only be determined from a better understanding of the seasonal and interannual variation of the availability and use of other important brown bear food items, berries (e.g. Vaccinium myrtillus and Empetrum spp.), as well as other primary needs for bears (e.g. secure habitat and denning habitat), within the landscape mosaic of managed forests.
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Affiliation(s)
- Shane C. Frank
- Faculty of Arts and Sciences, Department of Environmental and Health Studies, Telemark University College, Bø NO-3800, Norway
| | - Sam M.J.G. Steyaert
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, As NO-1432, Norway
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, As NO-1432, Norway
- Norwegian Institute for Nature Research, PO Box 5685 Sluppen, NO-7485 Trondheim, Norway
| | - Ilse Storch
- Chair of Wildlife Ecology and Management, Faculty of Environment and Natural Resources, University of Freiburg, D-79085 Freiburg, Germany
| | - Jonas Kindberg
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå SE-90183, Sweden
| | - Hanna Barck
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå SE-90183, Sweden
| | - Andreas Zedrosser
- Faculty of Arts and Sciences, Department of Environmental and Health Studies, Telemark University College, Bø NO-3800, Norway
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193
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Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense). PLoS One 2015; 10:e0132860. [PMID: 26168244 PMCID: PMC4500556 DOI: 10.1371/journal.pone.0132860] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/18/2015] [Indexed: 01/01/2023] Open
Abstract
The gut microbial community is one of the richest and most complex ecosystems on earth, and the intestinal microbes play an important role in host development and health. Next generation sequencing approaches, which rapidly produce millions of short reads that enable the investigation on a culture independent basis, are now popular for exploring microbial community. Currently, the gut microbiome in fresh water shrimp is unexplored. To explore gut microbiomes of the oriental river prawn (Macrobrachium nipponense) and investigate the effects of host genetics and habitats on the microbial composition, 454 pyrosequencing based on the 16S rRNA gene were performed. We collected six groups of samples, including M. nipponense shrimp from two populations, rivers and lakes, and one sister species (M. asperulum) as an out group. We found that Proteobacteria is the major phylum in oriental river prawn, followed by Firmicutes and Actinobacteria. Compositional analysis showed microbial divergence between the two shrimp species is higher than that between the two populations of one shrimp species collected from river and lake. Hierarchical clustering also showed that host genetics had a greater impact on the divergence of gut microbiome than host habitats. This finding was also congruent with the functional prediction from the metagenomic data implying that the two shrimp species still shared the same type of biological functions, reflecting a similar metabolic profile in their gut environments. In conclusion, this study provides the first investigation of the gut microbiome of fresh water shrimp, and supports the hypothesis of host species-specific signatures of bacterial community composition.
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194
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Vendl C, Frei S, Dittmann MT, Furrer S, Osmann C, Ortmann S, Munn A, Kreuzer M, Clauss M. Digestive physiology, metabolism and methane production of captive Linné's two-toed sloths (Choloepus didactylus
). J Anim Physiol Anim Nutr (Berl) 2015; 100:552-64. [DOI: 10.1111/jpn.12356] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- C. Vendl
- Clinic for Zoo Animals, Exotic Pets and Wildlife; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
| | - S. Frei
- Clinic for Zoo Animals, Exotic Pets and Wildlife; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
| | - M. T. Dittmann
- Clinic for Zoo Animals, Exotic Pets and Wildlife; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
- ETH Zurich; Institute of Agricultural Sciences; Zurich Switzerland
| | | | | | - S. Ortmann
- Leibniz Institute for Zoo and Wildlife Research (IZW); Berlin Germany
| | - A. Munn
- School of Biological Sciences; University of Wollongong; Wollongong NSW Australia
| | - M. Kreuzer
- ETH Zurich; Institute of Agricultural Sciences; Zurich Switzerland
| | - M. Clauss
- Clinic for Zoo Animals, Exotic Pets and Wildlife; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
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195
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Liberti J, Sapountzis P, Hansen LH, Sørensen SJ, Adams RMM, Boomsma JJ. Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts. Mol Ecol 2015; 24:3151-69. [PMID: 25907143 PMCID: PMC5008137 DOI: 10.1111/mec.13216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 02/01/2023]
Abstract
Bacterial symbionts are important fitness determinants of insects. Some hosts have independently acquired taxonomically related microbes to meet similar challenges, but whether distantly related hosts that live in tight symbiosis can maintain similar microbial communities has not been investigated. Varying degrees of nest sharing between Megalomyrmex social parasites (Solenopsidini) and their fungus-growing ant hosts (Attini) from the genera Cyphomyrmex, Trachymyrmex and Sericomyrmex allowed us to address this question, as both ant lineages rely on the same fungal diet, interact in varying intensities and are distantly related. We used tag-encoded FLX 454 pyrosequencing and diagnostic PCR to map bacterial symbiont diversity across the Megalomyrmex phylogenetic tree, which also contains free-living generalist predators. We show that social parasites and hosts share a subset of bacterial symbionts, primarily consisting of Entomoplasmatales, Bartonellaceae, Acinetobacter, Wolbachia and Pseudonocardia and that Entomoplasmatales and Bartonellaceae can co-infect specifically associated combinations of hosts and social parasites with identical 16S rRNA genotypes. We reconstructed in more detail the population-level infection dynamics for Entomoplasmatales and Bartonellaceae in Megalomyrmex symmetochus guest ants and their Sericomyrmex amabilis hosts. We further assessed the stability of the bacterial communities through a diet manipulation experiment and evaluated possible transmission modes in shared nests such as consumption of the same fungus garden food, eating of host brood by social parasites, trophallaxis and grooming interactions between the ants, or parallel acquisition from the same nest environment. Our results imply that cohabiting ant social parasites and hosts may obtain functional benefits from bacterial symbiont transfer even when they are not closely related.
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Affiliation(s)
- Joanito Liberti
- Centre for Social EvolutionDepartment of BiologyUniversity of CopenhagenUniversitetsparken 15DK‐2100CopenhagenDenmark
| | - Panagiotis Sapountzis
- Centre for Social EvolutionDepartment of BiologyUniversity of CopenhagenUniversitetsparken 15DK‐2100CopenhagenDenmark
| | - Lars H. Hansen
- Molecular Microbial Ecology GroupDepartment of BiologyUniversity of CopenhagenUniversitetsparken 15DK‐2100CopenhagenDenmark
- Present address: Environmental Microbial Genomics GroupDepartment of Environmental ScienceAarhus UniversityDK‐4000RoskildeDenmark
| | - Søren J. Sørensen
- Molecular Microbial Ecology GroupDepartment of BiologyUniversity of CopenhagenUniversitetsparken 15DK‐2100CopenhagenDenmark
| | - Rachelle M. M. Adams
- Centre for Social EvolutionDepartment of BiologyUniversity of CopenhagenUniversitetsparken 15DK‐2100CopenhagenDenmark
- Department of EntomologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
| | - Jacobus J. Boomsma
- Centre for Social EvolutionDepartment of BiologyUniversity of CopenhagenUniversitetsparken 15DK‐2100CopenhagenDenmark
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196
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Li Y, Guo W, Han S, Kong F, Wang C, Li D, Zhang H, Yang M, Xu H, Zeng B, Zhao J. The evolution of the gut microbiota in the giant and the red pandas. Sci Rep 2015; 5:10185. [PMID: 25985413 PMCID: PMC4434948 DOI: 10.1038/srep10185] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/01/2015] [Indexed: 11/12/2022] Open
Abstract
The independent dietary shift from carnivore to herbivore with over 90% being bamboo
in the giant and the red pandas is of great interests to biologists. Although
previous studies have shown convergent evolution of the giant and the red pandas at
both morphological and molecular level, the evolution of the gut microbiota in these
pandas remains largely unknown. The goal of this study was to determine whether the
gut microbiota of the pandas converged due to the same diet, or diverged. We
characterized the fecal microbiota from these two species by pyrosequencing the 16S
V1–V3 hypervariable regions using the 454 GS FLX Titanium platform. We also
included fecal samples from Asian black bears, a species phylogenetically closer to
the giant panda, in our analyses. By analyzing the microbiota from these 3 species
and those from other carnivores reported previously, we found the gut microbiotas of
the giant pandas are distinct from those of the red pandas and clustered closer to
those of the black bears. Our data suggests the divergent evolution of the gut
microbiota in the pandas.
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Affiliation(s)
- Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Shushu Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Ya'an, Sichuan 611830 China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Ya'an, Sichuan 611830 China
| | - Heming Zhang
- China Conservation and Research Center for the Giant Panda, Ya'an, Sichuan 611830 China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Huailiang Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jiangchao Zhao
- Department of Pediatrics and Communicable Disease, University of Michigan, Ann Arbor, Michigan 48109, United States of America
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197
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Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes. PLoS One 2015; 10:e0127462. [PMID: 25978452 PMCID: PMC4433246 DOI: 10.1371/journal.pone.0127462] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/15/2015] [Indexed: 12/20/2022] Open
Abstract
The gut microbiota structure reflects both a host phylogenetic history and a signature of adaptation to the host ecological, mainly trophic niches. African cichlid fishes, with their array of closely related species that underwent a rapid dietary niche radiation, offer a particularly interesting system to explore the relative contribution of these two factors in nature. Here we surveyed the host intra- and interspecific natural variation of the gut microbiota of five cichlid species from the monophyletic tribe Perissodini of lake Tanganyika, whose members transitioned from being zooplanktivorous to feeding primarily on fish scales. The outgroup riverine species Astatotilapia burtoni, largely omnivorous, was also included in the study. Fusobacteria, Firmicutes and Proteobacteria represented the dominant components in the gut microbiota of all 30 specimens analysed according to two distinct 16S rRNA markers. All members of the Perissodini tribe showed a homogenous pattern of microbial alpha and beta diversities, with no significant qualitative differences, despite changes in diet. The recent diet shift between zooplantkon- and scale-eaters simply reflects on a significant enrichment of Clostridium taxa in scale-eaters where they might be involved in the scale metabolism. Comparison with the omnivorous species A. burtoni suggests that, with increased host phylogenetic distance and/or increasing herbivory, the gut microbiota begins differentiating also at qualitative level. The cichlids show presence of a large conserved core of taxa and a small set of core OTUs (average 13–15%), remarkably stable also in captivity, and putatively favoured by both restricted microbial transmission among related hosts (putatively enhanced by mouthbrooding behavior) and common host constraints. This study sets the basis for a future large-scale investigation of the gut microbiota of cichlids and its adaptation in the process of the host adaptive radiation.
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198
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Variation in koala microbiomes within and between individuals: effect of body region and captivity status. Sci Rep 2015; 5:10189. [PMID: 25960327 PMCID: PMC4426690 DOI: 10.1038/srep10189] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/25/2015] [Indexed: 12/24/2022] Open
Abstract
Metagenomic analysis of 16S ribosomal RNA has been used to profile microbial communities at high resolution, and to examine their association with host diet or diseases. We examined the oral and gut microbiome composition of two captive koalas to determine whether bacterial communities are unusual in this species, given that their diet consists almost exclusively of Eucalyptus leaves. Despite a highly specialized diet, koala oral and gut microbiomes were similar in composition to the microbiomes from the same body regions of other mammals. Rectal swabs contained all of the diversity present in faecal samples, along with additional taxa, suggesting that faecal bacterial communities may merely subsample the gut bacterial diversity. Furthermore, the faecal microbiomes of the captive koalas were similar to those reported for wild koalas, suggesting that captivity may not compromise koala microbial health. Since koalas frequently suffer from ocular diseases caused by Chlamydia infection, we also examined the eye microbiome composition of two captive koalas, establishing the healthy baseline for this body part. The eye microbial community was very diverse, similar to other mammalian ocular microbiomes but with an unusually high representation of bacteria from the family Phyllobacteriaceae.
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199
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Yuan ML, Dean SH, Longo AV, Rothermel BB, Tuberville TD, Zamudio KR. Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise. Mol Ecol 2015; 24:2521-36. [PMID: 25809385 DOI: 10.1111/mec.13169] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 12/12/2022]
Abstract
Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal-associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.
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Affiliation(s)
- Michael L Yuan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA; Archbold Biological Station, Venus, FL, 33960, USA
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200
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Hale VL, Tan CL, Knight R, Amato KR. Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks. J Microbiol Methods 2015; 113:16-26. [PMID: 25819008 DOI: 10.1016/j.mimet.2015.03.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/24/2015] [Accepted: 03/24/2015] [Indexed: 02/07/2023]
Abstract
Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at -80 °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2 weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8 weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at -20 °C, freezing at -80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8weeks) prior to microbial extraction and analysis.
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Affiliation(s)
- Vanessa L Hale
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA.
| | - Chia L Tan
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science & Engineering, University of California San Diego, La Jolla, California 92093, USA.
| | - Katherine R Amato
- Department of Anthropology, University of Colorado, Boulder, CO 80309, USA.
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