Molecular mechanisms of complex-type N-glycan breakdown and metabolism by the human intestinal bacterium Barnesiella intestinihominis.

Intestinal bacteria play a crucial role in human health, for example, by maintaining immune and metabolic homeostasis and protecting against pathogens. Survival in the human intestine depends on the bacterium's ability to utilize complex carbohydrates. Some species are known to use host-derived glycans; for example, Bifidobacteria can utilize O-glycan of mucin. However, there are few studies on intestinal bacteria utilizing host-derived N-glycan. Here, we identified the mechanism underlying the breakdown and utilization of complex-type N-glycan by the human intestinal bacterium Barnesiella intestinihominis. A growth assay showed that B. intestinihominis can utilize complex-type N-glycan as a carbon source, while RNA-seq analysis identified enzymes and transporters involved in the mechanism of N-glycan breakdown. In particular, the expression of three genes encoding glycoside hydrolase 85 endo-β-N-acetylglucosaminidase (endo-BIN1, endo-BIN2, and endo-BIN3) rose markedly in bacterial cells cultured in complex-type N-glycoprotein medium. We also found that the susC and susD genes, encoding the SusC/SusD membrane complex, form a gene cluster with endo-BIN genes, suggesting that SusC/SusD is involved in transportation of the glycan into the cell. Other genes encoding exo-type glycoside hydrolase enzymes showed elevated expression in cells grown in complex-type N-glycoprotein medium, suggesting that these enzymes function in further degradation of glycan for metabolism by the bacterium. Collectively, these findings suggest the survival strategy of an intestinal bacterium that has a unique metabolic pathway to use host-derived complex-type N-glycan as a nutrient.