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The ability of trophozoites to interact and digest gut bacteria is apparently important for multiplication of the parasite and its pathogenicity; however the contribution of resident bacterial flora is not well understood. We quantified the population of <jats:italic>Bacteroides<\/jats:italic>, <jats:italic>Bifidobacterium, Ruminococcus, Lactobacillus, Clostridium leptum subgroup, Clostridium coccoides subgroup, Eubacterium, Campylobacter, Methanobrevibacter smithii<\/jats:italic> and Sulphur reducing bacteria using genus specific primers in healthy (N\u2009=\u200922) vs amebic patients (<jats:italic>E. histolytica<\/jats:italic> positive, N\u2009=\u200917) stool samples by Real-time PCR.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Absolute quantification of <jats:italic>Bacteroides<\/jats:italic> (p\u2009=\u2009.001), <jats:italic>Closrtridium coccoides<\/jats:italic> subgrou<jats:italic>p<\/jats:italic> (p\u2009=\u20090.002), <jats:italic>Clostridium leptum<\/jats:italic> subgroup (p\u2009=\u20090.0001), <jats:italic>Lactobacillus<\/jats:italic> (p\u2009=\u20090.037), <jats:italic>Campylobacter<\/jats:italic> (p\u2009=\u20090.0014) and <jats:italic>Eubacterium<\/jats:italic> (p\u2009=\u20090.038) show significant drop in their population however, significant increase in <jats:italic>Bifdobacterium<\/jats:italic> (p\u2009=\u20090.009) was observed where as the population of <jats:italic>Ruminococcus<\/jats:italic> (p\u2009=\u20090.33) remained unaltered in healthy vs amebic patients (<jats:italic>E. histolytica<\/jats:italic> positive). We also report high prevalence of <jats:italic>nimE<\/jats:italic> gene in stool samples of both healthy volunteers and amebic patients. No significant decrease in <jats:italic>nimE<\/jats:italic> gene copy number was observed before and after the treatment with antiamebic drug.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our results show significant alteration in predominant gut bacteria in <jats:italic>E. histolytica<\/jats:italic> infected individuals. The frequent episodes of intestinal amoebic dysentery thus result in depletion of few predominant genera in gut that may lead to poor digestion and absorption of food in intestine. It further disturbs the homeostasis between gut epithelium and bacterial flora. The decrease in beneficial bacterial population gives way to dysbiosis of gut bacteria which may contribute to final outcome of the disease. Increase in the copy number of <jats:italic>nimE<\/jats:italic> gene harboring bacteria in our population reflects possible decrease in the availability of metronidazole drug during treatment of amoebiasis.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2180-12-183","type":"journal-article","created":{"date-parts":[[2012,8,22]],"date-time":"2012-08-22T08:14:09Z","timestamp":1345623249000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":91,"title":["Real-time analysis of gut flora in Entamoeba histolytica infected patients of Northern India"],"prefix":"10.1186","volume":"12","author":[{"given":"Anil Kumar","family":"Verma","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ravi","family":"Verma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vineet","family":"Ahuja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaishree","family":"Paul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2012,8,22]]},"reference":[{"key":"1809_CR1","doi-asserted-by":"crossref","first-page":"880","DOI":"10.4269\/ajtmh.2006.75.880","volume":"75","author":"R Rani","year":"2006","unstructured":"Rani R, Murthy RS, Bhattacharya S, Ahuja V, Rizvi MA, Paul J: Changes in Bacterial profile during amebiasis: Demonstration of anaerobic bacteria in ALA pus samples. 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