Metagenomic analysis of microbes benefiting from mucin degradation in the mouse colon

The secreted mucus layer that covers the mammalian intestine acts both as a physical barrier to prevent bacteria from penetrating the epithelium as well as a nutrient source that supports the growth of a subset of gut microbes. The equilibrium between mucus production and degradation in health can easily be disrupted upon expansion of mucus degraders. Overgrowth of bacteria that degrade mucin, the primary component in mucus, can lead to mucus thinning and barrier defects that make the host susceptible to pathogen invasion, inflammation or cancer. Despite their importance for health, a comprehensive catalog of bacteria degrading mucin in vivo is still lacking. Using a robust optofluidic platform for automated sorting of SIP-labeled microbial cells, bacteria involved in mucin-degradation in the mouse colon have been sorted. Cells present in the sorted fractions were sequenced and the generated mini-metagenomes analyzed.