Stratification of Intestinal Microbes with Unique Transcriptional Pattern and Metabolism in the Outer Layer of Intestinal Mucus

The mammalian lower intestinal tract harbors great density and diversity of commensal microbes, and a physical gel-like barrier named mucus is adopted in terms of limiting direct contact of commensal bacteria to host during host-microbes coevolution. The inner mucus layer with its tight compiled structure is impenetrable to bacteria, whereas a comparable dose of bacteria to luminal contents are living in the colonic outer mucus layer. We asked whether the outer mucus layer was a separate microbial niche regarding bacterial kinetics and behaviors. Our data show that the outer mucus layer had different representations of microbes compare to adjacent luminal contents, and the exchange between the two compartments was very limited due to immobility of bacteria in mucus layer. Furthermore, by comparing the transcriptional and metabolic patterns of two model bacterial species, Escherichia coli and Bacteroides thetaiotaomicron, with exceedingly different mucolytic capability, we showed mucus and contents associated bacteria differentially shaped their metabolic pattern to adapt to the nutrients accessible in the two compartments. This was not limited to the carbon source, including host-derived phospholipids for E. coli and host or dietary glycans for B. theta, but also included essential minerals. Intensive study of host-microbial mutualism in outer mucus layer is important to uncover the mechanism in clinic diseases as the mucus associated bacteria have a physical nearby impacts to the host.