Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid Research Paper Exploring interactions between Blastocystis sp., Strongyloides spp. and the gut microbiomes of wild chimpanzees in Senegal Justinn Renelies-Hamilton a,b, ⁎ , Marc Noguera-Julian c,d , Mariona Parera c , Roger Paredes c,d , Liliana Pacheco b , Elena Dacal e , José M. Saugar e , José M. Rubio e , Michael Poulsen a , Pamela C. Köster e , David Carmena e a Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark b Jane Goodall Institute Spain, Station Biologique Fouta Djallon, Dindéfélo, Kédougou, Senegal c IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain d Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Spain e Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain ARTICLE INFO Keywords: Ape Faecalibacterium Microbiota Methanobrevibacter Pan troglodytes Parasite ABSTRACT Background: Gut parasites exert an important infuence on the gut microbiome, with many studies focusing on the human gut microbiome. It has, however, undergone severe richness depletion. Hygienic lifestyle, antimicrobial treatments and altered gut homeostasis (e.g., chronic infammation) reduce gut microbiome richness and also parasite prevalence; which may confound results. Studying species closely related to humans could help overcome this problem by providing insights into the ancestral relationship between humans, their gut microbiome and their gut parasites. Chimpanzees are a particularly promising model as they have similar gut microbiomes to humans and many parasites infect both species. Aims: We study the interaction between gut microbiome and enteric parasites in chimpanzees. Investigating what novel insights a closely related species can reveal when compared to studies on humans. Methods: Using eighty-seven faecal samples from wild western chimpanzees (Pan troglodytes verus) in Senegal, we combine 16S rRNA gene amplicon sequencing for gut microbiome characterization with PCR detection of parasite taxa (Blastocystis sp., Strongyloides spp., Giardia duodenalis, Cryptosporidium spp., Plasmodium spp., Filariae and Trypanosomatidae). We test for diferences in gut microbiota ecosystem traits and taxonomical composition between Blastocystis and Strongyloides bearing and non-bearing samples. Results: For Blastocystis, twelve diferentially abundant taxa (e.g., Methanobrevibacter), including Prevotella and Ruminococcus-Methanobrevibacter enterotype markers, replicate fndings in humans. However, several richness indices are lower in Blastocystis carriers, contradicting human studies. This indicates Blastocystis, unlike Strongyloides, is associated to a “poor health” gut microbiome, as does the fact that Faecalibacterium, a bacterium with gut protective traits, is absent in Blastocystis-positive samples. Strongyloides was associated to Alloprevotella and fve other taxonomic groups. Each parasite had its unique impact on the gut microbiota indicating parasite- specifc niches. Our results suggest that studying the gut microbiomes of wild chimpanzees could help disen- tangle biological from artefactual associations between gut microbiomes and parasites. 1. Introduction Ecosystems contain multitudes of interacting species. The great ape gut microbiome (GM), home to trillions of prokaryote and eukaryote cells, is no exception. Research into microbiomes is starting to reveal the complex interactions amongst diferent members of the GM and their interplay with hosts: intestinal eukaryotes are associated to particular GM communities (e.g., reviewed in Leung et al., 2018). Blastocystis and Strongyloides, traditionally deemed parasites (Brumpt, 1912; Campbell, 1893), have been described recently, by some, as benefcial members of the GM due to their correlation with certain microbial markers such as α diversity (e.g., reviewed by Stensvold and Van Der Giezen, 2018 and Zaiss and Harris, 2016). GM markers are assumed to refect the ecological states of the microbial ecosystem: for https://doi.org/10.1016/j.meegid.2019.104010 Received 11 March 2019; Received in revised form 2 July 2019; Accepted 18 August 2019 ⁎ Corresponding author at: Universitetsparken 15, Building 3, 1st Floor, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. E-mail address: claxon71@gmail.com (J. Renelies-Hamilton). Infection, Genetics and Evolution 74 (2019) 104010 Available online 20 August 2019 1567-1348/ © 2019 Elsevier B.V. All rights reserved. T