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While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of <jats:italic>Sarcoptes scabiei<\/jats:italic>. Here we analyze adult female mite and egg metagenome datasets. The majority of adult mite bacterial reads matched with Enterobacteriaceae (phylum Proteobacteria), followed by Corynebacteriaceae (phylum Actinobacteria). <jats:italic>Klebsiella<\/jats:italic> was the most dominant genus (78%) and <jats:italic>Corynebacterium<\/jats:italic> constituted 9% of the assigned sequences. Scabies mite eggs had a more diverse microbial composition with sequences from Proteobacteria being the most dominant (75%), while Actinobacteria, Bacteroidetes and Firmicutes accounted for 23% of the egg microbiome sequences. DNA sequences of a potential endosymbiont, namely <jats:italic>Streptomyces<\/jats:italic>, were identified in the metagenome sequence data of both life stages. The presence of <jats:italic>Streptomyces<\/jats:italic> was confirmed by conventional PCR. Digital droplet PCR indicated higher <jats:italic>Streptomyces<\/jats:italic> numbers in adult mites compared to eggs. <jats:italic>Streptomyces<\/jats:italic> were localized histologically in the scabies mite gut and faecal pellets by Fluorescent <jats:italic>In Situ<\/jats:italic> Hybridization (FISH). <jats:italic>Streptomyces<\/jats:italic> may have essential symbiotic roles in the scabies parasite intestinal system requiring further investigation.<\/jats:p>","DOI":"10.1038\/s41598-019-47892-0","type":"journal-article","created":{"date-parts":[[2019,8,13]],"date-time":"2019-08-13T10:02:28Z","timestamp":1565690548000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["High-throughput metagenome analysis of the Sarcoptes scabiei internal microbiota and in-situ identification of intestinal Streptomyces sp."],"prefix":"10.1038","volume":"9","author":[{"given":"Pearl M.","family":"Swe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martha","family":"Zakrzewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3123-3718","authenticated-orcid":false,"given":"Rebecca","family":"Waddell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kadaba S.","family":"Sriprakash","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katja","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,8,13]]},"reference":[{"key":"47892_CR1","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/B978-0-12-398457-9.00005-6","volume":"79","author":"K Fischer","year":"2012","unstructured":"Fischer, K., Holt, D., Currie, B. & Kemp, D. 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