Project description:The goal was to assess the impact of carbon source and cross-feeding on transcription profile of both bacteria. R. gnavus was grown in monoculture with glucose (Glc). R. bromii was grown in monoculture with soluble (SS) or resistant (RS) starch. R. bromii and R. gnavus were co-cultured with SS or RS. Total RNA was extracted from a culture sample taken at mid- to late exponential phase of growth. rRNA was depleted and mRNA sequenced. 3 biological replicates were prepared for each condition.
Project description:RNA-seq of Ruminococcus bromii L2-63 and Ruminococcus gnavus ATCC 29149 grown in mono- or co-culture with different carbon sources (glucose, soluble or resistant starch)
Project description:Degradation of complex dietary fibers by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which relies on the amylosome, a specialized cell-bound enzymatic complex. To unravel its structure-function relationship and the interplay among its components, we applied an holistic multilayered approach and found that amylosome combinatorics, resistant starch degradation and enzymatic synergy are regulated at two levels: structural constraints enforcing enzyme proximity and expression-driven shifts in enzyme proportions. Cryo-electron tomography revealed that the amylosome comprises a constitutive extracellular layer extending toward the RS. However, proteomics demonstrated its remodeling across different growth conditions, with Amy4 and Amy16 comprising 60% of the amylosome in response to RS. Structural and biochemical analyses revealed complementarity and synergistic RS degradation by these enzymes, which allow R. bromii to fine-tune its adaptation to dietary fiber and shape colonic metabolism
Project description:Strain Ruminococcus bromii TSDC10.1-1.1 (species Ruminococcus bromii) was isolated from the fecal microbiota of a USA female at time point zero (bacterial isolates were sequenced from this donor on day 0 and 42). The species name was assigned by genome clustering.
Project description:Strain Ruminococcus bromii TSDC17.2-1.3 (species Ruminococcus bromii) was isolated from the fecal microbiota of a USA female at time point zero (bacterial isolates were sequenced from this donor on day 0 and 49). The species name was assigned by genome clustering.
Project description:Strain Ruminococcus bromii TSDC10.2-1.1 (species Ruminococcus bromii) was isolated from the fecal microbiota of a USA female at time point zero (bacterial isolates were sequenced from this donor on day 0 and 42). The species name was assigned by genome clustering.
