The ability of probiotic strain Escherichia coli O83:K24:H31 to modulate gut homeostasis and immune function after antibiotic-induced dysbiosis

This study examines the impact of broad-spectrum antibiotics (ampicillin 1 g/L, neomycin sulphate 1 g/L, metronidazole 1 g/L, and vancomycin 0.5 g/L) on gut microbiota composition using 16S rDNA metagenomic sequencing in a mouse model. We analyzed how antibiotic treatment affects microbiota diversity and composition, and evaluated whether probiotic strain Escherichia coli O83:K24:H31 (EcO83) can restore microbial homeostasis. Total DNA was extracted from stool samples using the QIAmp Fast DNA Stool Mini Kit (Qiagen), with DNA quality and concentration determined using NanoDrop and agarose gel electrophoresis. 16S rDNA metagenomic NGS libraries were prepared and sequenced at the Institute of Applied Biotechnologies using Illumina MiSeq v3 platform (600 cycles). Only samples passing quality control (A260/280 ratio 1.6-2.1) were used for library preparation. The microbial composition was analyzed using relative abundance, normalizing reads for each taxonomic level to 100% of total classified reads. Our sequencing data reveals significant changes in bacterial populations at phylum, class, and order levels, with notable shifts in Candidatus Saccharibacteria, Deferribacteres, and Flavobacteria abundance. The dataset includes 16S rRNA gene sequencing from 69 stool samples collected across two independent experiments: 31 samples from the first experiment examining immediate response after antibiotic treatment (14-day experiment), and 38 samples from the second experiment evaluating microbiota changes after subsequent probiotic administration with EcO83 on the day of sacrifice.