{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T11:43:48Z","timestamp":1786362228429,"version":"build-2736575974"},"reference-count":97,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T00:00:00Z","timestamp":1705017600000},"content-version":"vor","delay-in-days":1522,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,11,12]],"date-time":"2019-11-12T00:00:00Z","timestamp":1573516800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,11,12]],"date-time":"2019-11-12T00:00:00Z","timestamp":1573516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with\u00a0minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome.<\/jats:p>","DOI":"10.1038\/s41396-019-0551-4","type":"journal-article","created":{"date-parts":[[2019,12,16]],"date-time":"2019-12-16T14:51:14Z","timestamp":1576507874000},"page":"609-622","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":54,"title":["Biodiversity of protists and nematodes in the wild nonhuman primate gut"],"prefix":"10.1093","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7170-6017","authenticated-orcid":false,"given":"Allison E","family":"Mann","sequence":"first","affiliation":[{"name":"Department of Botany and Biodiversity Research Centre, University of British Columbia , Vancouver, BC, Canada"},{"name":"Department of Microbiology, Immunology, and Genetics, University of North Texas , 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florent","family":"Mazel","sequence":"additional","affiliation":[{"name":"Department of Botany and Biodiversity Research Centre, University of British Columbia , Vancouver, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew A","family":"Lemay","sequence":"additional","affiliation":[{"name":"Department of Botany and Biodiversity Research Centre, University of British Columbia , Vancouver, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evan","family":"Morien","sequence":"additional","affiliation":[{"name":"Department of Botany and Biodiversity Research Centre, University of British Columbia , Vancouver, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Billy","sequence":"additional","affiliation":[{"name":"Department of Botany and Biodiversity Research Centre, University of British Columbia , Vancouver, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6737-3771","authenticated-orcid":false,"given":"Martin","family":"Kowalewski","sequence":"additional","affiliation":[{"name":"Estacion Biologica Corrientes (MACN-BR)\u2014CONICET , Corrientes, Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8893-9052","authenticated-orcid":false,"given":"Anthony","family":"Di Fiore","sequence":"additional","affiliation":[{"name":"Department of Anthropology, University of Texas Austin , Austin, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9s","family":"Link","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Universidad de los Andes , Bogota, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tony L","family":"Goldberg","sequence":"additional","affiliation":[{"name":"Department of Pathobiological Science, University of Wisconsin-Madison , Madison, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6640-5049","authenticated-orcid":false,"given":"Stacey","family":"Tecot","sequence":"additional","affiliation":[{"name":"School of Anthropology, University of Arizona , Tucson, AZ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea L","family":"Baden","sequence":"additional","affiliation":[{"name":"Department of Anthropology, Hunter College of City University of New York , New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andres","family":"Gomez","sequence":"additional","affiliation":[{"name":"Department of Animal Science, University of Minnesota , St. Paul, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle L","family":"Sauther","sequence":"additional","affiliation":[{"name":"Department of Anthropology, University of Colorado Boulder , Boulder, CO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank P","family":"Cuozzo","sequence":"additional","affiliation":[{"name":"Lajuma Research Centre , Louis Trichardt (Makhado), Lajuma, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gillian A O","family":"Rice","sequence":"additional","affiliation":[{"name":"Department of Anthropology, Dartmouth College , Hanover, NH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5916-418X","authenticated-orcid":false,"given":"Nathaniel J","family":"Dominy","sequence":"additional","affiliation":[{"name":"Department of Anthropology, Dartmouth College , Hanover, NH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Stumpf","sequence":"additional","affiliation":[{"name":"Department of Anthropology, University of Illinois at Urbana-Champaign , Urbana, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca J","family":"Lewis","sequence":"additional","affiliation":[{"name":"Department of Anthropology, University of Texas Austin , Austin, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Larissa","family":"Swedell","sequence":"additional","affiliation":[{"name":"Department of Anthropology, Queens College, City University of New York , Flushing, New York, NY, USA"},{"name":"Department of Archaeology, University of Cape Town , Cape Town, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Amato","sequence":"additional","affiliation":[{"name":"Department of Anthropology, Northwestern University , Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Wegener Parfrey","sequence":"additional","affiliation":[{"name":"Department of Botany and Biodiversity Research Centre, University of British Columbia , Vancouver, BC, Canada"},{"name":"Department of Zoology, University of British Columbia , Vancouver, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,11,12]]},"reference":[{"key":"2024011300270025100_CR1","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1007\/s00248-017-1041-8","article-title":"Diet versus phylogeny: a comparison of gut microbiota in captive colobine monkey species","volume":"75","author":"Hale","year":"2018","journal-title":"Microb Ecol."},{"key":"2024011300270025100_CR2","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1038\/s41396-018-0175-0","article-title":"Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes","volume":"13","author":"Amato","year":"2018","journal-title":"ISME J"},{"key":"2024011300270025100_CR3","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1126\/science.1198719","article-title":"Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans","volume":"332","author":"Muegge","year":"2011","journal-title":"Science."},{"key":"2024011300270025100_CR4","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1111\/mec.12501","article-title":"Convergence of gut microbiomes in myrmecophagous mammals","volume":"23","author":"Delsuc","year":"2014","journal-title":"Mol Ecol."},{"key":"2024011300270025100_CR5","doi-asserted-by":"publisher","first-page":"2559","DOI":"10.1038\/s41396-018-0166-1","article-title":"Factors influencing bacterial microbiome composition in a wild non-human primate community in Ta\u00ef National Park, C\u00f4te d\u2019Ivoire","volume":"12","author":"Gogarten","year":"2018","journal-title":"ISME J"},{"key":"2024011300270025100_CR6","doi-asserted-by":"publisher","first-page":"14319","DOI":"10.1038\/ncomms14319","article-title":"Unraveling the processes shaping mammalian gut microbiomes over evolutionary time","volume":"8","author":"Groussin","year":"2017","journal-title":"Nat Commun."},{"key":"2024011300270025100_CR7","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature."},{"issue":"52","key":"2024011300270025100_CR8","doi-asserted-by":"publisher","first-page":"13768","DOI":"10.1073\/pnas.1700122114","article-title":"Dispersal limitation promotes the diversification of the mammalian gut microbiota","volume":"114","author":"Moeller","year":"2017","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2024011300270025100_CR9","doi-asserted-by":"publisher","first-page":"e05224","DOI":"10.7554\/eLife.05224","article-title":"Social networks predict gut microbiome composition in wild baboons","volume":"4","author":"Tung","year":"2015","journal-title":"eLife."},{"key":"2024011300270025100_CR10","doi-asserted-by":"publisher","first-page":"e1500997","DOI":"10.1126\/sciadv.1500997","article-title":"Social behavior shapes the chimpanzee pan-microbiome","volume":"2","author":"Moeller","year":"2016","journal-title":"Sci Adv"},{"key":"2024011300270025100_CR11","volume-title":"Human Parasitology","author":"Bogitsh","year":"2005","edition":"3rd"},{"key":"2024011300270025100_CR12","doi-asserted-by":"publisher","first-page":"e1005039-e","DOI":"10.1371\/journal.ppat.1005039","article-title":"Are human intestinal eukaryotes beneficial or commensals?","volume":"11","author":"Luke\u0161","year":"2015","journal-title":"PLoS Pathog."},{"key":"2024011300270025100_CR13","doi-asserted-by":"publisher","first-page":"1253","DOI":"10.1038\/ismej.2013.21","article-title":"Waiting for the human intestinal eukaryotome","volume":"7","author":"Andersen","year":"2013","journal-title":"ISME J"},{"key":"2024011300270025100_CR14","first-page":"153","article-title":"Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions","volume":"2","author":"Wegener Parfrey","year":"2011","journal-title":"Front Microbiol"},{"key":"2024011300270025100_CR15","doi-asserted-by":"publisher","first-page":"e00201","DOI":"10.1128\/mSystems.00201-17","article-title":"Microbial eukaryotes: a missing link in gut microbiome studies","volume":"3","author":"Laforest-Lapointe","year":"2018","journal-title":"mSystems."},{"key":"2024011300270025100_CR16","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.pt.2018.02.004","article-title":"Associations between gut microbiota and common luminal intestinal parasites","volume":"34","author":"Stensvold","year":"2018","journal-title":"Trends Parasitol"},{"issue":"2","key":"2024011300270025100_CR17","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1073\/pnas.0707221105","article-title":"Ecological rules governing helminth microparasite coinfection","volume":"105","author":"Graham","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2024011300270025100_CR18","doi-asserted-by":"publisher","first-page":"843","DOI":"10.3389\/fmicb.2018.00843","article-title":"Parasite-microbiota interactions with the vertebrate gut: synthesis through an ecological lens","volume":"9","author":"Leung","year":"2018","journal-title":"Front Microbiol"},{"key":"2024011300270025100_CR19","doi-asserted-by":"publisher","first-page":"e1005658","DOI":"10.1371\/journal.pgen.1005658","article-title":"Variation in Rural African gut microbiota is strongly correlated with colonization by entamoeba and subsistence","volume":"11","author":"Morton","year":"2015","journal-title":"PLOS Genet."},{"key":"2024011300270025100_CR20","doi-asserted-by":"publisher","first-page":"e00007","DOI":"10.1128\/mSystems.00007-18","article-title":"Asymptomatic intestinal colonization with protist blastocystis is strongly associated with distinct microbiome ecological patterns","volume":"3","author":"Nieves-Ram\u00edrez","year":"2018","journal-title":"mSystems."},{"key":"2024011300270025100_CR21","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/s40168-019-0644-3","article-title":"Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies","volume":"7","author":"Yason","year":"2019","journal-title":"Microbiome."},{"key":"2024011300270025100_CR22","doi-asserted-by":"publisher","first-page":"eaap7399-p","DOI":"10.1126\/sciadv.aap7399","article-title":"Manipulation of host and parasite microbiotas: survival strategies during chronic nematode infection","volume":"4","author":"White","year":"2018","journal-title":"Sci Adv"},{"key":"2024011300270025100_CR23","doi-asserted-by":"publisher","first-page":"249","DOI":"10.15698\/mic2018.05.631","article-title":"Microbial competition between Escherichia coli and Candida albicans reveals a soluble fungicidal factor","volume":"5","author":"Cabral","year":"2018","journal-title":"Microb Cell."},{"key":"2024011300270025100_CR24","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1038\/ismej.2008.76","article-title":"Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces","volume":"2","author":"Scanlan","year":"2008","journal-title":"ISME J"},{"key":"2024011300270025100_CR25","doi-asserted-by":"publisher","first-page":"e66019-e","DOI":"10.1371\/journal.pone.0066019","article-title":"Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents","volume":"8","author":"Hoffmann","year":"2013","journal-title":"PloS One."},{"key":"2024011300270025100_CR26","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s40168-017-0373-4","article-title":"The gut mycobiome of the Human Microbiome Project healthy cohort","volume":"5","author":"Nash","year":"2017","journal-title":"Microbiome."},{"key":"2024011300270025100_CR27","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1093\/sysbio\/syy001","article-title":"Using phylogenomic data to expore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case","volume":"67","author":"Reis","year":"2018","journal-title":"Syst Biol"},{"key":"2024011300270025100_CR28","doi-asserted-by":"publisher","first-page":"6006","DOI":"10.1073\/pnas.1119506109","article-title":"Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution","volume":"109","author":"Steiper","year":"2012","journal-title":"PNAS."},{"key":"2024011300270025100_CR29","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1023\/A:1015520830318","article-title":"Evolution of primate social systems","volume":"23","author":"Kappeler","year":"2002","journal-title":"Int J Primatol"},{"key":"2024011300270025100_CR30","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1007\/s10764-012-9618-z","article-title":"Evolution of multilevel social systems in nonhuman primates and humans","volume":"33","author":"Grueter","year":"2012","journal-title":"Int J Primatol"},{"key":"2024011300270025100_CR31","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1016\/j.mehy.2011.06.019","article-title":"Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune diseases","volume":"77","author":"Bilbo","year":"2011","journal-title":"Med Hypotheses."},{"key":"2024011300270025100_CR32","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/icb.1996.60","article-title":"IgE, allergies and helminth parasites: a new perspective on an old conundrum","volume":"74","author":"Bell","year":"1996","journal-title":"Immunol Cell Biol"},{"key":"2024011300270025100_CR33","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1086\/586717","article-title":"Intensity of intestinal infection with multiple worm species is related to regulatory cytokine output and immune hyporesponsiveness","volume":"197","author":"Turner","year":"2008","journal-title":"J Infect Dis"},{"key":"2024011300270025100_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/cei.12269","article-title":"Microbial \u2018old friends\u2019, immunoregulation and socioeconomic status","volume":"177","author":"Rook","year":"2014","journal-title":"Clin Exp Immunol"},{"key":"2024011300270025100_CR35","doi-asserted-by":"publisher","first-page":"e51146","DOI":"10.1371\/journal.pone.0051146","article-title":"Insights from characterizing extinct human gut microbiomes","volume":"7","author":"Tito","year":"2012","journal-title":"PLOS One."},{"key":"2024011300270025100_CR36","doi-asserted-by":"publisher","first-page":"6505","DOI":"10.1038\/ncomms7505","article-title":"Subsistence strategies in traditional societies distinguish gut microbiomes","volume":"6","author":"Obregon-Tito","year":"2015","journal-title":"Nat Commun."},{"key":"2024011300270025100_CR37","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.nmni.2018.10.009","article-title":"Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals","volume":"27","author":"Angelakis","year":"2018","journal-title":"New Microbes New Infect"},{"key":"2024011300270025100_CR38","doi-asserted-by":"crossref","first-page":"e00127","DOI":"10.1128\/mSystems.00127-16","article-title":"Microbiome Helper: a custom and streamlined workflow for microbiome research","volume":"2","author":"Comeau","year":"2017","journal-title":"mSystems"},{"issue":"11","key":"2024011300270025100_CR39","doi-asserted-by":"publisher","first-page":"e27492","DOI":"10.1371\/journal.pone.0027492","article-title":"Arctic Ocean Microbial Community Structure before and after the 2007 Record Sea Ice Minimum","volume":"6","author":"Comeau","year":"2011","journal-title":"PLoS ONE"},{"key":"2024011300270025100_CR40","first-page":"10","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnetjournal"},{"key":"2024011300270025100_CR41","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","article-title":"PEAR: a fast and accurate Illumina Paired-End reAd mergeR","volume":"30","author":"Zhang","year":"2014","journal-title":"Bioinformatics"},{"key":"2024011300270025100_CR42","doi-asserted-by":"publisher","first-page":"e2584-e","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ."},{"key":"2024011300270025100_CR43","doi-asserted-by":"publisher","first-page":"e1420-e","DOI":"10.7717\/peerj.1420","article-title":"Swarm v2: highly-scalable and high-resolution amplicon clustering","volume":"3","author":"Mah\u00e9","year":"2015","journal-title":"PeerJ."},{"key":"2024011300270025100_CR44","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat Methods."},{"key":"2024011300270025100_CR45","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2024011300270025100_CR46","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2024011300270025100_CR47","doi-asserted-by":"publisher","first-page":"e1004957","DOI":"10.1371\/journal.pcbi.1004957","article-title":"MEGAN community edition\u2014interactive exploration and analysis of large-scale microbiome sequencing data","volume":"12","author":"Huson","year":"2016","journal-title":"PLOS Comput Biol"},{"key":"2024011300270025100_CR48","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon","year":"2017","journal-title":"Int J Syst Evol Microbiol"},{"key":"2024011300270025100_CR49","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"2024011300270025100_CR50","volume-title":"R: a language and environment for statistical computing","author":"R Development Core Team.","year":"2008"},{"key":"2024011300270025100_CR51","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1111\/j.1654-1103.2003.tb02228.x","article-title":"VEGAN, a package of R functions for community ecology","volume":"14","author":"Dixon","year":"2003","journal-title":"J Veg Sci"},{"key":"2024011300270025100_CR52","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2018","journal-title":"Bioinformatics."},{"key":"2024011300270025100_CR53","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLOS One."},{"key":"2024011300270025100_CR54","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot 2: elegant graphics for data analysis","author":"Wickham","year":"2016"},{"key":"2024011300270025100_CR55","volume-title":"Inferring phylogenies","author":"Felsenstein","year":"2004"},{"key":"2024011300270025100_CR56","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1111\/j.2041-210X.2010.00044.x","article-title":"Phylogenetic signal and linear regression on species data","volume":"1","author":"Revell","year":"2010","journal-title":"Methods Ecol Evol"},{"key":"2024011300270025100_CR57","first-page":"2010","article-title":"MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package","volume":"1","author":"Hadfield","year":"2010","journal-title":"J Stat Softw"},{"key":"2024011300270025100_CR58","doi-asserted-by":"publisher","first-page":"e00097","DOI":"10.1128\/mSystems.00097-18","article-title":"Is host filtering the main driver of phylosymbiosis across the tree of life?","volume":"3","author":"Mazel","year":"2018","journal-title":"mSystems."},{"key":"2024011300270025100_CR59","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1111\/jeu.12249","article-title":"Expanding the entamoeba universe: new hosts yield novel ribosomal lineages","volume":"63","author":"Jacob","year":"2016","journal-title":"J Eukaryot Microbiol"},{"key":"2024011300270025100_CR60","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.actatropica.2012.12.011","article-title":"Variable geographic distribution of Blastocystis subtypes and its potential implications","volume":"126","author":"Alfellani","year":"2013","journal-title":"Acta Trop."},{"key":"2024011300270025100_CR61","doi-asserted-by":"publisher","first-page":"e2005849","DOI":"10.1371\/journal.pbio.2005849","article-title":"EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution","volume":"16","author":"del Campo","year":"2018","journal-title":"PLOS Biol"},{"key":"2024011300270025100_CR62","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2024011300270025100_CR63","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2024011300270025100_CR64","volume-title":"Proceedings of the 16th International Parallel and Distributed Processing Symposium","author":"Clement","year":"2002"},{"key":"2024011300270025100_CR65","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"popart: full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol Evol"},{"key":"2024011300270025100_CR66","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1093\/molbev\/msr238","article-title":"Last of the human protists: the phylogeny and genetic diversity of iodamoeba","volume":"29","author":"Stensvold","year":"2011","journal-title":"Mol Biol Evol"},{"key":"2024011300270025100_CR67","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.1128\/AEM.01996-06","article-title":"Quantitative and qualitative \u03b2 diversity measures lead to different insights into factors that structure microbial communities","volume":"73","author":"Lozupone","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"2024011300270025100_CR68","doi-asserted-by":"publisher","first-page":"105","DOI":"10.3114\/sim.2007.58.05","article-title":"Biodiversity in the Cladosporium herbarum complex (Davidiellaceae, Capnodiales), with standardisation of methods for Cladosporium taxonomy and diagnostics","volume":"58","author":"Schubert","year":"2007","journal-title":"Stud Mycol"},{"key":"2024011300270025100_CR69","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/S1055-7903(03)00010-1","article-title":"Phylogenetic significance of morphological characters in the taxonomy of Pestalotiopsis species","volume":"27","author":"Jeewon","year":"2003","journal-title":"Mol Phylogenet Evol"},{"key":"2024011300270025100_CR70","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/j.protis.2010.09.003","article-title":"\u201cSlime Molds\u201d among the Tubulinea (Amoebozoa): molecular systematics and taxonomy of Copromyxa","volume":"162","author":"Brown","year":"2011","journal-title":"Protist."},{"key":"2024011300270025100_CR71","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1007\/s12223-011-0053-x","article-title":"The ciliate, Troglodytella abrassarti, contributes to polysaccharide hydrolytic activities in the chimpanzee colon","volume":"56","author":"Profousov\u00e1","year":"2011","journal-title":"Folia Microbiol."},{"key":"2024011300270025100_CR72","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1094\/PHYTO-99-3-0227","article-title":"Small subunit rDNA-Based phylogeny of the tylenchida sheds light on relationships among some high-impact plant-parasitic nematodes and the evolution of plant feeding","volume":"99","author":"Holterman","year":"2009","journal-title":"Phytopathology."},{"key":"2024011300270025100_CR73","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.1080\/00222930600929285","article-title":"Observations on a Geocentrophora sp. (Lecithoepitheliata) flatworm from forest soils in Nova Scotia","volume":"40","author":"Adl","year":"2006","journal-title":"J Nat Hist"},{"key":"2024011300270025100_CR74","volume-title":"Biology of Turbellaria and some related flatworms","author":"Raikova","year":"1995"},{"key":"2024011300270025100_CR75","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1111\/j.1365-2435.2010.01696.x","article-title":"A hitchhiker\u2019s guide to a crowded syconium: how do fig nematodes find the right ride?","volume":"24","author":"Krishnan","year":"2010","journal-title":"Funct Ecol"},{"key":"2024011300270025100_CR76","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1002\/(SICI)1098-2345(1998)45:3&lt;263::AID-AJP3&gt;3.0.CO;2-U","article-title":"Feeding ecology of the black howler monkey (Alouatta pigra) in Northern Belize","volume":"45","author":"Silver","year":"1998","journal-title":"Am J Primatol"},{"key":"2024011300270025100_CR77","doi-asserted-by":"publisher","first-page":"2341","DOI":"10.1007\/s00436-017-5519-6","article-title":"New Entamoeba group in howler monkeys (Alouatta spp.) associated with parasites of reptiles","volume":"116","author":"Villanueva-Garc\u00eda","year":"2017","journal-title":"Parasitol Res."},{"key":"2024011300270025100_CR78","first-page":"21","article-title":"Verreaux\u2019s sifaka (Propithecus verreauxi) and ring-tailed lemur (Lemur catta) endoparasitism at the Bez\u00e0 Mahafaly special reserve","volume":"8","author":"Loudon","year":"2013","journal-title":"Madag Conserv Dev"},{"key":"2024011300270025100_CR79","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1023\/B:IJOP.0000023577.32587.0b","article-title":"Effects of seasonal water scarcity on the ranging behavior or Eulemur fulvus rufus","volume":"25","author":"Scholz","year":"2004","journal-title":"Int J Primatol"},{"key":"2024011300270025100_CR80","volume-title":"Primates in perspective","author":"Swedell","year":"2011","edition":"2nd"},{"key":"2024011300270025100_CR81","doi-asserted-by":"publisher","first-page":"20190431","DOI":"10.1098\/rspb.2019.0431","article-title":"Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species","volume":"286","author":"Grieneisen","year":"2019","journal-title":"Proc R Soc B"},{"key":"2024011300270025100_CR82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/ajpa.22559","article-title":"Gelada feeding ecology in an intact ecosystem at Guassa, Ethiopia: variability over time and implications for theropith and hominin dietary evolution","volume":"155","author":"Fashing","year":"2014","journal-title":"Am J Phys Anthropol"},{"key":"2024011300270025100_CR83","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/s10329-010-0194-6","article-title":"Behavior of geladas and other endemic wildlife during a desert locust outbreak at Guassa, Ethiopia: ecological and conservation implications","volume":"51","author":"Fashing","year":"2010","journal-title":"Primates."},{"key":"2024011300270025100_CR84","doi-asserted-by":"publisher","first-page":"e0180431","DOI":"10.1371\/journal.pone.0180431","article-title":"Gastrointestinal parasite infections and self-medication in wild chimpanzees surviving in degraded forest fragments within an agricultural landscape mosaic in Uganda","volume":"12","author":"McLennan","year":"2017","journal-title":"PLOS One."},{"key":"2024011300270025100_CR85","doi-asserted-by":"publisher","first-page":"e51144","DOI":"10.1371\/journal.pone.0051144","article-title":"Monkeys in the middle: parasite transmission through the social network of a wild primate","volume":"7","author":"MacIntosh","year":"2012","journal-title":"PLOS One."},{"key":"2024011300270025100_CR86","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.vetpar.2017.12.002","article-title":"Entamoeba histolytica infection in wild lemurs associated with proximity to humans","volume":"249","author":"Ragazzo","year":"2018","journal-title":"Vet Parasitol."},{"key":"2024011300270025100_CR87","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1016\/j.ijpara.2017.11.008","article-title":"Diversity of Entamoeba spp. in African great apes and humans: an insight from Illumina MiSeq high-throughput sequencing","volume":"48","author":"Vl\u010dkov\u00e1","year":"2018","journal-title":"Int J Parasitol"},{"key":"2024011300270025100_CR88","first-page":"19","article-title":"An evaluation of the oral microbiome and potential zoonoses of the southern thick-tailed or greater galago (Otolemur crassicaudatus). African","volume":"11","author":"Kotze","year":"2016","journal-title":"Primates."},{"key":"2024011300270025100_CR89","doi-asserted-by":"publisher","first-page":"e49805","DOI":"10.1371\/journal.pone.0049805","article-title":"Seasonal effects on great ape health: a case study of wild chimpanzees and western gorillas","volume":"7","author":"Masi","year":"2012","journal-title":"PLOS One."},{"key":"2024011300270025100_CR90","doi-asserted-by":"publisher","first-page":"e1438","DOI":"10.1002\/wsbm.1438","article-title":"The mammalian mycobiome: a complex system in a dynamic relationship with the host","volume":"11","author":"Lai","year":"2019","journal-title":"Wiley Interdiscip Rev Syst Biol Med"},{"key":"2024011300270025100_CR91","doi-asserted-by":"publisher","first-page":"e00092","DOI":"10.1128\/mSphere.00092-18","article-title":"Investigating colonization of the healthy adult gastrointestinal tract by fungi","volume":"3","author":"Auchtung","year":"2018","journal-title":"mSphere."},{"key":"2024011300270025100_CR92","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.3389\/fmicb.2019.01575","article-title":"Longitudinal survey of fungi in the human gut: its profiling, phenotyping, and colonization","volume":"10","author":"Raimondi","year":"2019","journal-title":"Front Microbiol"},{"key":"2024011300270025100_CR93","doi-asserted-by":"publisher","first-page":"4251","DOI":"10.1128\/aem.61.12.4251-4257.1995","article-title":"Yeast succession in the Amazon fruit Parahancornia amapa as resource partitioning among Drosophila spp","volume":"61","author":"Morais","year":"1995","journal-title":"Appl Environ Microbiol"},{"key":"2024011300270025100_CR94","doi-asserted-by":"publisher","first-page":"e34233","DOI":"10.1371\/journal.pone.0034233","article-title":"Increased gut permeability and microbiota change associate with mesenteric fat inflammation and metabolic dysfunction in diet-induced obese mice","volume":"7","author":"Lam","year":"2012","journal-title":"PLOS One."},{"key":"2024011300270025100_CR95","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/2049-2618-1-3","article-title":"Stool substitute transplant therapy for the eradication of Clostridium difficile infection: \u2018RePOOPulating\u2019 the gut","volume":"1","author":"Petrof","year":"2013","journal-title":"Microbiome."},{"key":"2024011300270025100_CR96","doi-asserted-by":"publisher","first-page":"3654","DOI":"10.1038\/ncomms4654","article-title":"Gut microbiome of the Hadza hunter-gatherers","volume":"5","author":"Schnorr","year":"2014","journal-title":"Nat Commun"},{"key":"2024011300270025100_CR97","doi-asserted-by":"crossref","first-page":"14691","DOI":"10.1073\/pnas.1005963107","article-title":"Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa","volume":"107","author":"De","year":"2010","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["The ISME Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41396-019-0551-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41396-019-0551-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/ismej\/article-pdf\/14\/2\/609\/55526451\/41396_2019_article_551.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/www.nature.com\/articles\/s41396-019-0551-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/academic.oup.com\/ismej\/article-pdf\/14\/2\/609\/55526451\/41396_2019_article_551.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T18:08:36Z","timestamp":1707934116000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismej\/article\/14\/2\/609-622\/7474908"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,12]]},"references-count":97,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,2,1]]}},"URL":"https:\/\/doi.org\/10.1038\/s41396-019-0551-4","relation":{},"ISSN":["1751-7362","1751-7370"],"issn-type":[{"value":"1751-7362","type":"print"},{"value":"1751-7370","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,2]]},"published":{"date-parts":[[2019,11,12]]},"assertion":[{"value":"16 May 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 August 2019","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 September 2019","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 November 2019","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with ethical standards"}},{"value":"The authors declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}