Differential gene expression of K. aerogenes during temperature entrainment

In this study we investigate and compare DEGs of K. aerogenes macrocolonies during temperature entrainment (12:12, 35°C:36°C) and subsequent free running conditions (35°C). The goal of this experiment was to identify rhythmically expressed genes in K. aerogenes, the first human gut commensal bacterium with described circadian clock (Paulose et al. 2016). K. aerogenes circadian clock is sensitive to temperature entrainment (Paulose et al. 2019). To further investigate this temperature entrainment of K. aerogenes we performed RNA sequencing experiment. We identified 48 differentially expressed genes when comparing timepoints ZT6 to ZT18, 427 differentially expressed genes when comparing timepoints ZT6 to CT6, 6 differentially expressed genes between timepoints CT6 and CT18, and 2 differentially expressed genes between timepoints ZT18 and CT18. Overall design: In this study we investigate and compare DGE of K. aerogenes macrocolonies in temperature entrainment and free running conditions We implemented temperature entrainment using 12:12 cycle of 35°C and 36°C for 3 days. Samples were collected on day 3 at Zeitgeber time 6 (ZT6) and ZT18. Then bacteria were released into constant 35°C and samples were collected on day 4 at circadian time 6 (CT6) and CT18.