Oxygen-responsive bacterial glycosphingolipid links symbiont fitness and immune development in neonatal host.
Symbiotic gut bacteria must re-establish themselves in every host generation, yet the molecular strategies enabling this inheritance remain poorly understood. Here, we show that Bacteroides fragilis uses a membrane glycolipid, alpha-galactosylceramide (BfaGC), to colonize the neonatal gut. Genome-wide fitness profiling revealed that BfaGC biosynthesis is selectively required during early life, when transient oxygenation creates a physiological bottleneck for strict anaerobes. Mechanistically, BfaGC reduces membrane proton permeability, sustaining the proton-motive force that supports aerobic respiration. This oxygen-responsive adaptation simultaneously generates a host-facing immunomodulatory signal that calibrates neonatal natural killer T (NKT) cell development, linking bacterial fitness to immune maturation through a single metabolite. The same mechanism also enables niche expansion by enterotoxigenic strains, revealing context-dependent consequences. Notably, this strategy is distinct among gut Bacteroidales: other prominent members synthesize a different sphingolipid subclass supporting broader fitness, implying divergent evolutionary strategies. Our findings provide time-resolved insight into how bacterial metabolites shape host-microbiota symbiosis across development.