Fig. 1: Gut mucosal microbiome.

a (Left) The mouse colon consists of dense mucosal communities, as shown in the heat maps of bacterial density taken from lumen cross-sections. (Right) Mucosal communities in the mouse colon are compositionally diverse. Each dye refers to a different taxon. Adapted with permission from ref. ⁴². Copyright (2017) National Academy of Sciences. b (Top-left) In a healthy mouse gut, biofilm retains an integrated continuous structure over gut topographies; (top-right) in the diseased state, biofilm consists of dissociated aggregates. Gray stains host nuclei, green dyes glycoproteins, and yellow shows bacteria stained by 16S ribosomal DNA fluorescence in situ hybridization. Adapted with permission from ref. ⁸. Copyright (2018) Springer Nature. (bottom-left) The formation of a biofilm helps to maintain a homeostasis state; (bottom-right) the depletion of the biofilm layer makes the intestinal tissue exposed to pathogenic attacks (red bacteria), resulting in dysbiosis; this further causes inflammation by stimulating immune cells. c Schematic of microbial metabolic interactions in a biofilm. Biofilm bacteria interact through the uptake of nutrients and exchange of metabolic by-products.