Agarooligosaccharides as a novel concept in prebiotics: selective inhibition of Ruminococcus gnavus and Fusobacterium nucleatum while preserving Bifidobacteria, Lactobacillales in vitro, and inhibiting Lachnospiraceae in vivo

Recent studies have linked <i>Ruminococcus gnavus</i> to inflammatory bowel disease and <i>Fusobacterium nucleatum</i> to various cancers. Agarooligosaccharides (AOS), derived from the acid hydrolysis of agar, have shown significant inhibitory effects on the growth of <i>R. gnavus</i> and <i>F. nucleatum</i> at concentrations of 0.1 and 0.2%, respectively. RNA sequencing and quantitative reverse-transcription PCR analyses revealed the downregulation of fatty acid biosynthesis genes (<i>fab</i> genes) in these bacteria when exposed to 0.1% AOS. Furthermore, AOS treatment altered the fatty acid composition of <i>R. gnavus</i> cell membranes, increasing medium-chain saturated fatty acids (C8, C10) and C18 fatty acids while reducing long-chain fatty acids (C14, C16). In contrast, no significant growth inhibition was observed in several strains of Bifidobacteria and Lactobacillales at AOS concentrations of 0.2 and 2%, respectively. Co-culture experiments with <i>R. gnavus</i> and <i>Bifidobacterium longum</i> in 0.2% AOS resulted in <i>B. longum</i> dominating the population, constituting over 96% post-incubation. <i>In vivo</i> studies using mice demonstrated a significant reduction in the Lachnospiraceae family, to which <i>R. gnavus</i> belongs, following AOS administration. Quantitative PCR also showed lower levels of the <i>nan</i> gene, potentially associated with immune disorders, in the AOS group. These findings suggest that AOS may introduce a novel concept in prebiotics by selectively inhibiting potentially pathogenic bacteria while preserving beneficial bacteria such as Bifidobacteria and Lactobacillales.