Diet Induced Alteration of the Murine Intestinal Microbiome After Antibiotic Ablation

Abstract

Background and Objective We detected a dominant non-cultivatable gram-positive coccobacillus associated with cultivatable yeast in feces of mice treated with a cocktail of broad-spectrum antibiotics while being fed a partially defined mouse chow that is commonly used for nutritional studies. The goal of this study was to determine the identity of the non-cultivatable grampositive coccobacillus. Methods Fecal samples were analyzed by Gram stain, quantitative flow cytometry, next generation sequencing of the V3 or V4 regions of the 16S rRNA gene, fluorescence microscopy, and sequence analysis of the tuf gene, which can distinguish among Streptococcus and Staphylococcus genera. Results Fecal samples from antibiotic-treated mice displayed a tenfold decline in bacterial cell number. High-throughput sequencing of the variable regions of the 16S rRNA gene and tuf gene sequencing identified the major phylotype as Lactococcus. Lactococcus did not grow from fecal cultures, although Enterococcus casseliflavus did grow, which was a confounding finding. The mouse chow was heavily contaminated with non-viable Lactococcus. Appearance of intestinal yeast was dependent on the specific chow, although yeast was not detected in the chow. Conclusion Dead bacteria in food can modulate the intestinal microbiome. Whether and how food-derived dead bacteria alter intestinal physiology needs to be determined.