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We investigated whether the stickleback host microbiome depends on ecoevolutionary variables by testing the impact of exposure to the cestode parasite <jats:italic>Schistocephalus solidus<\/jats:italic> with respect to infection success, host genotype, parasite genotype, and parasite microbiome composition. We observed constitutive differences in the microbiome of sticklebacks of different origin, and those differences increased when sticklebacks exposed to the parasite resisted infection. In contrast, the microbiome of successfully infected sticklebacks varied with parasite genotype. More specifically, we revealed that the association between microbiome and immune gene expression increased in infected individuals and varied with parasite genotype. In addition, we showed that <jats:italic>S<\/jats:italic>. <jats:italic>solidus<\/jats:italic> hosts a complex endomicrobiome and that bacterial abundance in the parasite correlates with expression of host immune genes. Within this comprehensive analysis we demonstrated that (i) parasites contribute to modulating the host microbiome through both successful and unsuccessful infection, (ii) when infection is successful, the host microbiome varies with parasite genotype due to genotype\u2010dependent variation in parasite immunomodulation, and (iii) the parasite\u2010associated microbiome is distinct from its host and impacts the host immune response to infection.<\/jats:p>","DOI":"10.1111\/mec.16344","type":"journal-article","created":{"date-parts":[[2022,1,9]],"date-time":"2022-01-09T17:19:46Z","timestamp":1641748786000},"page":"1577-1594","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":47,"title":["Host phenotype and microbiome vary with infection status, parasite genotype, and parasite microbiome composition"],"prefix":"10.1111","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9266-8232","authenticated-orcid":false,"given":"Megan A.","family":"Hahn","sequence":"first","affiliation":[{"name":"School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnes","family":"Piecyk","sequence":"additional","affiliation":[{"name":"Evolutionary Ecology Max Planck Institute for Evolutionary Biology Pl\u00f6n Germany"},{"name":"Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz Centre for Ocean Research Kiel Kiel Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3138-1729","authenticated-orcid":false,"given":"F\u00e1tima","family":"Jorge","sequence":"additional","affiliation":[{"name":"Department of Zoology University of Otago Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Cerrato","sequence":"additional","affiliation":[{"name":"School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Kalbe","sequence":"additional","affiliation":[{"name":"Evolutionary Ecology Max Planck Institute for Evolutionary Biology Pl\u00f6n Germany"},{"name":"Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz Centre for Ocean Research Kiel Kiel Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nolwenn M.","family":"Dheilly","sequence":"additional","affiliation":[{"name":"School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York USA"},{"name":"ANSES Agence Nationale de S\u00e9curit\u00e9 Sanitaire de l\u2019Alimentation de l\u2019Environnement et du Travail \u2010 Laboratoire de Ploufragan\u2010Plouzan\u00e9 Unit\u00e9 G\u00e9n\u00e9tique Virale de Bios\u00e9curit\u00e9 Ploufragan France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,1,27]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2012.174"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/1365-2656.12708"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1086\/590958"},{"key":"e_1_2_10_5_1","first-page":"f1000research","article-title":"Differential expression of RNA\u2010Seq data at the gene level\u2013the DESeq package","volume":"10","author":"Anders S.","year":"2012","journal-title":"EMBL"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.3354\/ame01753"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182000072103"},{"key":"e_1_2_10_8_1","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1007\/978-3-642-30197-1_300","volume-title":"The family Rhodospirillaceae, in the prokaryotes: Alphaproteobacteria and Betaproteobacteria","author":"Baldani J. 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