Gut microbiota modulation in response to combination of Escherichia coli Nissle 1917 and sugars: Lessons from comparative analysis of fecal microbiota of two healthy donors from 2019-2021

The Escherichia coli Nissle 1917 strain (EcN) has shown its probiotic efficacy against many enteric pathogenic bacteria infecting human, including Vibrio cholerae, either alone or in combination with prebiotics. Understanding of these mechanisms of infection control requires the basic knowledge of probiotic mediated gut microbial community alterations especially in presence of different prebiotics. The present study has used the ex-vivo microbiota model and Next Generation Sequencing techniques to demonstrate the effect of EcN along with different sugars, namely glucose, galactose and starch, on the human gut microbiome community composition. The microbiome compositional changes have been observed at two different time-points, set one and a half years apart, in fecal slurries obtained from two donors. The study has indicated that the extent of microbiome alterations varies with different carbohydrate prebiotics and EcN probiotic and most of the alterations are broadly dependent upon the existing gut microbial community structure of the donors. The major distinct compositional changes have been found in the conditions where glucose and starch were administered, both with and without EcN, in spite of the inter-donor microbial community variation. Several of these microbiome component variations also remain consistent for both the time-points, including genus like Bacteroides, Prevotella and Lactobacillus. Altogether, the present study has shown the effectiveness of EcN along with glucose and starch towards specific changes of microbial community alterations independent of initial microbial composition. This type of model study can be implemented for hypothesis testing in case of therapeutic and prophylactic use of probiotic and prebiotic combinations.