Table 1.
Studies demonstrating the importance of the mucosa-associated microbiota in health and diseases.
| Model | Main findings | Ref. | |
|---|---|---|---|
| Steady state | Mouse | - Discovery of the “autochthonous bacterial flora”. Bacterial populations are different between the epithelium and the lumen. | 16–18 |
| Mouse | - Mucosa-associated microbiota is different from the luminal microbiota: Actinobacteria is more abundant in the lumen, while Acidobacteria, Deferribacteres and Proteobacteria are enriched in the mucosa. | 19 | |
| Macaque | - The lumen harbors obligate anaerobes, while mucosa-associated microbiota is enriched in oxygen-tolerant bacteria. | 20 | |
| Pig | - Firmicutes are more abundant in the digesta, while Proteobacteria and Bacteroidetes are enriched in the mucosa. | 21 | |
| Mouse | - In the ascending colon, the digesta is enriched in Bacteroidaceae, Enterococcaceae and Lactobacillaceae, while crypts constitute special niches sheltering Lachnospiraceae and Ruminococcaceae families. | 22 | |
| Mouse & Human | - Lachnospiraceae and Ruminococcaceae are present at the same relative abundance in human biopsies than in the interfold region in mice. Some bacteria are species and region dependent: Faecalibacterium or Subdoligranulum are only detected in human biopsies, while Marvinbryantia is inherent to mice and Butyrivibrio only localized in mice interfold region. | 187 | |
| Mouse | - Identification of the colonic crypt-associated microbiota (CSCM). Lumen is richer in Firmicutes while CSCM is composed of Proteobacteria, aerobic genera (Burkholderiales, Xanthomonadale). | 25 | |
| Mouse & Human | - Acinetobacter genus has a particular tropism for the crypt environment | 25,26 | |
| Mouse | - SFB is a commensal bacterium adherent to the ileal epithelium and playing a symbiotic role. | 89,94,95,99,100,102 | |
| Mouse | - Citrobacter rodentium is able to attach to the intestinal epithelium and grow through the hydrogen peroxide (H2O2) respiration, with a central role played by the NAPDH oxidase NOX1. | 126 | |
| IBD/IBS | Human | - Colonic biopsies from IBD patients are characterized by increased bacterial encroachment and paracellular and vascular permeability. | 56 |
| Human | - E. coli, Clostridium and Bacteroides are enriched in the mucosa of IBD patients compared to controls, while Bifidobacteria is decreased. In active UC disease, E. Coli and Bacteroides are found in the lamina propria. | 58 | |
| Human | - Reduced bacterial diversity is found in the mucosa-associated microbiota of IBD patients compared to controls. | 59,61,62 | |
| Human | - Crohn’s disease recurrence following a partial bowel resection can be predicted by analysis of the ileal mucosa-associated microbiota (role of Gammaproteobacteria, Ruminococcus gnavus and Corynebacterium) | 72 | |
| Human | - Brachyspira is found in the mucosa-associated microbiota of 30–40% IBS patients. | 73 | |
| Human & Mouse | - Faecalibacterium prausnitzii is reduced in IBD patients. Multiple strains, as well as Faecalibacterium prausnitzii supernatant, polymeric extracellular matrix and a purified protein are sufficient to decrease intestinal inflammation in animal models. | 62,188–190 | |
| Human | - Adherent-Invasive Escherichia coli (AIEC) pathobionts (Enterobacteriaceae) are found in the mucosa of 30–40% IBD patients, compared to 5–10% in healthy individuals. | 64,66 | |
| Mouse | - AIEC are flagellated and express a mucinase, which enhance their ability to adhere to and penetrate the intestinal mucus barrier. | 71,191 | |
| Mouse | - Emulsifier-induced colitis is associated with microbiota encroachment, altered microbiota composition and increased pro-inflammatory potential. | 50 | |
| Mouse | - Flagellin immunization increase host-microbiota distance and protect against colitis and obesity. | 184 | |
| Diabetes | Mouse | - Emulsifier-induced metabolic syndrome is associated with microbiota encroachment, altered microbiota composition and increased pro-inflammatory potential. | 50 |
| Mouse | - A complex microbiota containing specific species infiltrating the mucus layer is required for the detrimental effects of emulsifiers. | 144 | |
| Human | - Microbiota encroachment is a feature of metabolic disease, particularly hyperglycemia, in humans. | 51 | |
| Mouse | - Western diet (WD) affects the growth rate and penetrability of the colonic mucus layer. | 131 | |
| - WD-associated deleterious effects are reversed by soluble fiber consumption. | 131,135,140,141 | ||
| Mouse & Human | - Akkermansia muciniphila is a commensal bacterium whose administration strengthens intestinal epithelium integrity and reverse metabolic disorders. | 149,157,161 | |
| Colorectal cancer | Human | - Fusobacterium and Bacteroides fragilis are enriched in biopsies from right-side tumors, while Parvimonas micro is enriched in biopsies from left-side tumors. | 26 |
| Human | - Identification of Fusobacterium nucleatum in biopsies of CRC patients. | 55,80 | |
| Human | - Identification of Enterotoxigenic E. coli and Bacteroides fragilis (ETBF) in colonic mucosa-associated biofilm from familial adenomatous polyposis patients. | 81 |