The Influence of Bifidobacteria and Lactobacilli on mouse microbiota

Commensal bacteria, such as bifidobacteria and lactobacilli, have beneficial effects on the host by modulating the immune system, strengthening the intestinal barrier, and inhibiting the growth of pathogenic microorganisms. Therefore, studying gut microbiota is important research area. The main methods for identifying microbial diversity are 16S rRNA gene sequence analysis and whole genome sequencing (WGS). The aim of our study was to compare sequencing methods using two platforms, Illumina and Oxford Nanopore Technologies (ONT), to determine the most effective method for analyzing the composition of gut microbiota. During the experiment, we studied the effect of two commensal strains, Lacticaseibacillus rhamnosus K32 and Bifidobacterium Teenis 150, on the intestinal microbiota of C57BL/6 mice. While sequencing the 16S rRNA gene on ONT we did a comparative analysis of the efficiency of filtering bacterial diversity using 5 primer combinations. All primer combinations revealed the same bacterial alpha-diversity. However, one combination (bif27F - 1492R) appeared to be more specific in identifying certain species, resulting in a distinct biodiversity profile. The results show that Illumina mainly identify the Bacteroidota, and ONT - Firmicutes. The results also showed a high degree of correlation between data obtained by using the same platform and different types of DNA quality. However, WGS data obtained from Illumina and ONT platforms have a high level of similarity. Using pooled data with dual-platform sequencing allows carrying out a more complete assessment of bacterial diversity. The results shows that the introduction of commensal strains to mice changed the composition of their intestinal microflora, including the increasing number of bacteria with a beneficial effect on health.