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Over the past few years, a wealth of investigations has demonstrated that GI helminths interact with the host gut flora, and that such interactions result in modifications of the host immune and metabolic statuses. Nevertheless, whilst selected changes in gut microbial composition are consistently observed in response to GI helminth infections across several host-parasite systems, research in this area to date is largely characterised by inconsistent findings. These discrepancies are particularly evident when data from studies of GI helminth-microbiota interactions conducted in humans from parasite-endemic regions are compared. In this review, we provide an overview of the main sources of variance that affect investigations on helminth-gut microbiota interactions in humans, and propose a series of methodological approaches that, whilst accounting for the inevitable constraints of fieldwork, are aimed at minimising confounding factors and draw biologically meaningful interpretations from highly variable datasets.<\/jats:p>","DOI":"10.1017\/s003118201900088x","type":"journal-article","created":{"date-parts":[[2019,7,1]],"date-time":"2019-07-01T06:25:32Z","timestamp":1561962332000},"page":"1371-1378","update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":35,"title":["Helminths and microbes within the vertebrate gut \u2013 not all studies are created equal"],"prefix":"10.1017","volume":"146","author":[{"given":"Alba","family":"Cort\u00e9s","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura 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