{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T22:04:41Z","timestamp":1780956281499,"version":"3.54.1"},"reference-count":48,"publisher":"Cambridge University Press (CUP)","issue":"1","license":[{"start":{"date-parts":[[2019,9,23]],"date-time":"2019-09-23T00:00:00Z","timestamp":1569196800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/www.cambridge.org\/core\/terms"}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Parasitology"],"published-print":{"date-parts":[[2020,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The presence of bacterial DNA in <jats:italic>Dientamoeba fragilis<\/jats:italic> DNA extracts from culture poses a substantial challenge to sequencing the <jats:italic>D. fragilis<\/jats:italic> genome. However, elimination of bacteria from <jats:italic>D. fragilis<\/jats:italic> cultures has proven difficult in the past, presumably due to its dependence on some unknown prokaryote\/s. This study explored options for removal of bacteria from <jats:italic>D. fragilis<\/jats:italic> cultures and for the generation of genome sequence data from <jats:italic>D. fragilis<\/jats:italic>. DNA was extracted from human faecal samples and xenic <jats:italic>D. fragilis<\/jats:italic> cultures. Extracts were subjected to 16S ribosomal DNA bacterial diversity profiling. Xenic <jats:italic>D. fragilis<\/jats:italic> cultures were then subject to antibiotic treatment regimens that systematically removed bacterial species depending on their membrane structure (Gram-positive or Gram-negative) and aerobic requirements. The impact of these treatments on cultures was assessed by 16S amplicon sequencing. Prior to antibiotic treatment, the cultures were dominated by Gram-negative bacteria. Addition of meropenem to cultures eliminated anaerobic Gram-negative bacteria, but it also led to protozoan death after 5 days incubation. The seeding of meropenem resistant <jats:italic>Klebsiella pneumoniae<\/jats:italic> strain KPC-2 into cultures before treatment by meropenem prevented death of <jats:italic>D. fragilis<\/jats:italic> cells beyond this 5 day period, suggesting that one or more species of Gram-negative bacteria may be an essential nutritional requirement for <jats:italic>D. fragilis<\/jats:italic>. Gram-positive cells were completely eliminated using vancomycin without affecting trophozoite growth. Finally, this study shows that genome sequencing of <jats:italic>D. fragilis<\/jats:italic> is feasible following bacterial elimination from cultures as the result of the major advances occurring in bioinformatics. We provide evidence on this fact by successfully sequencing the <jats:italic>D. fragilis<\/jats:italic> 28S large ribosomal DNA subunit gene using culture-derived DNA.<\/jats:p>","DOI":"10.1017\/s0031182019001173","type":"journal-article","created":{"date-parts":[[2019,8,27]],"date-time":"2019-08-27T07:08:34Z","timestamp":1566889714000},"page":"29-38","update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":5,"title":["Diversity profiling of xenic cultures of <i>Dientamoeba fragilis<\/i> following systematic antibiotic treatment and prospects for genome sequencing"],"prefix":"10.1017","volume":"147","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6753-0557","authenticated-orcid":false,"given":"Rory","family":"Gough","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8711-2408","authenticated-orcid":false,"given":"Joel","family":"Barratt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damien","family":"Stark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Ellis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2019,9,23]]},"reference":[{"key":"S0031182019001173_ref2","doi-asserted-by":"publisher","DOI":"10.1093\/ajcp\/16.6.380"},{"key":"S0031182019001173_ref42","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2013.10.013"},{"key":"S0031182019001173_ref8","doi-asserted-by":"publisher","DOI":"10.1080\/00034983.1936.11684951"},{"key":"S0031182019001173_ref6","doi-asserted-by":"publisher","DOI":"10.1016\/j.protis.2015.06.002"},{"key":"S0031182019001173_ref21","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.31.6.907-912.1976"},{"key":"S0031182019001173_ref24","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(15)00293-5"},{"key":"S0031182019001173_ref17","doi-asserted-by":"publisher","DOI":"10.1126\/science.1110591"},{"key":"S0031182019001173_ref5","doi-asserted-by":"publisher","DOI":"10.4161\/gmic.2.1.14755"},{"key":"S0031182019001173_ref19","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01466-18"},{"key":"S0031182019001173_ref48","doi-asserted-by":"publisher","DOI":"10.2165\/00003495-199550010-00007"},{"key":"S0031182019001173_ref9","first-page":"17","article-title":"Part 1: The human gut microbiome in health and disease","volume":"13","author":"Bull","year":"2014","journal-title":"Integrative Medicine: A Clinician's Journal"},{"key":"S0031182019001173_ref37","doi-asserted-by":"publisher","DOI":"10.1038\/nrc.2017.13"},{"key":"S0031182019001173_ref20","first-page":"9","article-title":"PAST: Paleontological Statistics Software Package for Education and Data Analysis","volume":"4","author":"Hammer","year":"2001","journal-title":"Palaeontologia Electronica"},{"key":"S0031182019001173_ref31","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182012000145"},{"key":"S0031182019001173_ref16","doi-asserted-by":"publisher","DOI":"10.2307\/3277781"},{"key":"S0031182019001173_ref14","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.38.5.1157"},{"key":"S0031182019001173_ref18","unstructured":"Giske, CG , Martinez-Martinez, L , Canton, R , Stefani, S , Skov, R , Glupczynski, Y , Nordmann, PN , Wootton, M , Miriagou, V , Simonsen, GS , Zemlickova, H , Cohen-Stuart, J and Gniadkowski, M (2017) EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical and\/or epidemiological importance. 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