Dual RNA-seq of gut commensal bacterium B. thetaiotaomicron during colonisation of colonocyte Transwell model and RNA-seq in iron-limiting conditions

Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized or adapts during colonization of the host. Here, we identify a small noncoding RNA (IroR) that mediates iron homeostasis.

We performed dual RNA-seq of WT B. thetaiotaomicron during colonisation of a Transwell model (HT29-MTX-E12 -an immortalized cell line differentiated into goblet-like cells). RNA seq was done for the host and two bacterial subpopulations; adherent (within the mucous layer) and supernatant (within the media suspension). Further RNA-seq experiments were done with RNA extracted from cultures grown in BHIS media, supplemented with BPS to induce irion-limitation.