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Little is known about the interplay between the microbiota of parasites and the health of the infected host. Using nematode co-infection of lambs as a proof-of-concept model, the aim of this study was to characterise the microbiomes of nematodes and that of their host, enabling identification of candidate nematode-specific microbiota member(s) that could be exploited as drug development tools or for targeted therapy. Deep\u00a0sequencing techniques were used to elucidate the microbiomes of different life stages of two parasitic nematodes of ruminants, Haemonchus contortus and Teladorsagia circumcincta, as well as that of the co-infected ovine hosts, pre- and post infection. Bioinformatic analyses demonstrated significant differences between the composition of the nematode and ovine microbiomes. The two nematode species also differed significantly. The data indicated a shift in the constitution of the larval nematode microbiome after exposure to the ovine microbiome, and in the ovine intestinal microbial community over time as a result of helminth co-infection. Several bacterial species were identified in nematodes that were absent from their surrounding abomasal environment, the most significant of which included Escherichia coli\/Shigella. The ability to purposefully infect nematode species with engineered E. coli was demonstrated in vitro, validating the concept of using this bacterium as a nematode-specific drug development tool and\/or drug delivery vehicle. To our knowledge, this is the first description of the concept of exploiting a parasite\u2019s microbiome for drug development and treatment purposes.<\/jats:p>","DOI":"10.1038\/s41396-019-0462-4","type":"journal-article","created":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T22:01:00Z","timestamp":1561500060000},"page":"2664-2680","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Microbiome analysis as a platform R&amp;D tool for parasitic nematode disease management"],"prefix":"10.1093","volume":"13","author":[{"given":"Glenn","family":"Hogan","sequence":"first","affiliation":[{"name":"SynBioCentre, University College Cork , Cork, Ireland"},{"name":"Cancer Research@UCC, University College Cork , Cork, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sidney","family":"Walker","sequence":"additional","affiliation":[{"name":"SynBioCentre, University College Cork , Cork, 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