Gene expression of lactobacilli in murine forestomach biofilms

Lactobacilli populate the gastro-intestinal tract of vertebrates, and are used in food fermentations and as probiotics. Lactobacilli are also major constituents of stable biofilms in the forestomach of rodents. In order to investigate the lifestyle of these biofilm lactobacilli in C57BL/6 mice, we applied metatranscriptomics to analyse gene expression (assessed by mRNA) and community composition (assessed by rRNA). Lactobacillales were the major biofilm inhabitants (62-82% of rRNA reads), followed by Clostridiales (8-31% of rRNA reads). To identify mRNA transcripts specific for the forestomach, we compared forestomach and hindgut metatranscriptomes. Gene expression of the biofilm microbiota was characterized by high abundance of transcripts related to glucose and maltose utilization, peptide degradation, and amino acid transport, indicating their major catabolic and anabolic pathways. The microbiota transcribed genes encoding pathways enhancing oxidative stress (glutathione synthesis) and acid tolerance. Various pathways, including metabolite formation (urea degradation, arginine pathway, -aminobutyrate) and cell wall modification (DltA, cyclopropane-fatty-acyl-phospholipid synthase), contributed to acid tolerance, as judged from the transcript profile. In addition, the biofilm microbiota expressed numerous genes encoding extracellular proteins involved in adhesion and/or biofilm formation (e.g. MucBP, glycosyl hydrolase families 68 and 70). This study shed light on the lifestyle and specific adaptations of lactobacilli in the murine forestomach that might also be relevant for lactobacilli biofilms in other vertebrates, including humans.