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Using conserved and pathogen-specific primers we performed a cross-kingdom analysis of bacterial, fungal, protistan and archaeal communities of I. scapularis nymphs (N = 105) collected from southern Vermont, USA. The bacterial community was dominated by a Rickettsia and several environmental taxa commonly reported in I. scapularis, as well as the human pathogens B. burgdorferi and Anaplasma phagocytophilum, agent of human granulocytic anaplasmosis. With the fungal primer set we detected primarily plant- and litter-associated taxa and &gt;18% of sequences were Malassezia, a fungal genus associated with mammalian skin. Two 18S rRNA gene primer sets, intended to target protistan communities, returned mostly Ixodes DNA as well as the wildlife pathogen Babesia odocoilei (7% of samples), a Gregarines species (14%) and a Spirurida nematode (18%). Data from pathogen-specific and conserved primers were consistent in terms of prevalence and identification. We measured B. burgdorferi presence\/absence and load and found that bacterial beta diversity varied based on B. burgdorferi presence\/absence. Load was weakly associated with bacterial community composition. We identified taxa associated with B. burgdorferi infection that should be evaluated for their role in vector colonization by pathogens.<\/jats:p>","DOI":"10.1093\/femsec\/fiz167","type":"journal-article","created":{"date-parts":[[2019,11,12]],"date-time":"2019-11-12T20:10:41Z","timestamp":1573589441000},"source":"Crossref","is-referenced-by-count":27,"title":["Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load"],"prefix":"10.1093","volume":"95","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2956-4251","authenticated-orcid":false,"given":"William J","family":"Landesman","sequence":"first","affiliation":[{"name":"Department of Biology, University of Bridgeport, Charles Dana Hall, 169 University Ave., Bridgeport, CT 06604, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth","family":"Mulder","sequence":"additional","affiliation":[{"name":"Department of Mathematics, The Long Trail School, 1045 Kirby Hollow Road, Dorset, VT 05251, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L Page","family":"Fredericks","sequence":"additional","affiliation":[{"name":"Department of Entomology, University of Illinois at Urbana-Champaign, 320 Morrill Hall, 505 S. Goodwin Ave., Urbana, IL 61801, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian F","family":"Allan","sequence":"additional","affiliation":[{"name":"Department of Entomology, University of Illinois at Urbana-Champaign, 320 Morrill Hall, 505 S. 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