Dataset Information

Structure of Chimpanzee Gut Microbiomes across Tropical Africa.

ABSTRACT: Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.

SUBMITTER: Bueno de Mesquita CP

PROVIDER: S-EPMC8269259 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Structure of Chimpanzee Gut Microbiomes across Tropical Africa.

Bueno de Mesquita Clifton P CP Nichols Lauren M LM Gebert Matthew J MJ Vanderburgh Caihong C Bocksberger Gaëlle G Lester Jack D JD Kalan Ammie K AK Dieguez Paula P McCarthy Maureen S MS Agbor Anthony A Álvarez Varona Paula P Ayimisin Ayuk Emmanuel AE Bessone Mattia M Chancellor Rebecca R Cohen Heather H Coupland Charlotte C Deschner Tobias T Egbe Villard Ebot VE Goedmakers Annemarie A Granjon Anne-Céline AC Grueter Cyril C CC Head Josephine J Hernandez-Aguilar R Adriana RA Jeffery Kathryn J KJ Jones Sorrel S Kadam Parag P Kaiser Michael M Lapuente Juan J Larson Bradley B Marrocoli Sergio S Morgan David D Mugerwa Badru B Mulindahabi Felix F Neil Emily E Niyigaba Protais P Pacheco Liliana L Piel Alex K AK Robbins Martha M MM Rundus Aaron A Sanz Crickette M CM Sciaky Lilah L Sheil Douglas D Sommer Volker V Stewart Fiona A FA Ton Els E van Schijndel Joost J Vergnes Virginie V Wessling Erin G EG Wittig Roman M RM Ginath Yuh Yisa Y Yurkiw Kyle K Zuberbühler Klaus K Gogarten Jan F JF Heintz-Buschart Anna A Muellner-Riehl Alexandra N AN Boesch Christophe C Kühl Hjalmar S HS Fierer Noah N Arandjelovic Mimi M Dunn Robert R RR

mSystems 20210622 3

Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which ...[more]

PMID: 34156289

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Project description:BackgroundTop-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents.ResultsThe aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation.ConclusionThis study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.

Dataset Information

Structure of Chimpanzee Gut Microbiomes across Tropical Africa.

Publications

Structure of Chimpanzee Gut Microbiomes across Tropical Africa.

Similar Datasets

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