Effect of Entamoeba histolytica infection on gut microbial diversity and composition in diarrhoeal patients from New Delhi

During amoebiasis, colonization of the gut by Entamoeba histolytica can lead to alterations of the host microbiota. In this study we have compared the gut microbiota of patients of amoebiasis with healthy controls using 16S rRNA gene variable regions, (V1-V3) and (V3-V5) of the bacterial genome. From this 16S rRNA gene amplicon data one paired end and two single end data sets were selected and compared by the number of OTUs obtained, sequence count and diversity analysis. Our results showed that the V1-V3- paired end data set gave the maximum number of OTUs in comparison to the two single end data sets studied. The amoebiasis patient samples showed a significant drop in richness in the alpha diversity measurements and lower intra group similarity compared to the healthy controls. Bacteria of genus Prevotella, Sutterella and Collinsella were more abundant in healthy controls whereas Escherichia, Klebsiella and Ruminococcus were more abundant in the E. histolytica positive patients. All the healthy controls harboured bacteria belonging to Faecalibacterium, Prevotella, Ruminococcus, Subdoligranulum and Escherichia genera while all the E. histolytica positive patients samples contained genus Enterobacter.