Time-restricted feeding and mouse gut microbiome

Time-restricted feeding (TRF) impacts the dynamics of the gut microbiota and improves metabolic health in mice. The relationship between the TRF-induced alterations of the gut microbiota was explored with bacterial taxa as functional units. However, in the gut ecosystem, bacteria with different taxonomic backgrounds interact with each other and form coherent functional groups called guilds, members of which show co-abundant behavior. Here, we clustered the prevalent amplicon sequence variants (ASVs) of the 16S rRNA gene V3-V4 region into 35 co-abundance groups (CAGs). The overall structure of the gut microbiota showed significant concordance between the CAG and the ASV-level data. Then we showed that TRF selectively altered the overall structure of the gut microbiota at the guild level in HFD-fed mice. Furthermore, the CAGs that were promoted by TRF were positively correlated with improvements in glucose metabolism in the HFD-fed mice, while one CAG that was increased in the group with ad libitum access to HFD was associated with impaired glucose metabolism. Furthermore, most of the CAGs that responded to the TRF regime regained diurnal rhythmicity in HFD-fed mice. Together, these data suggest that TRF alleviated HFD-induced detrimental effects on body weight gain and glucose metabolism by altering the overall structure and restoring the diurnal oscillations of the key CAGs in the gut microbiota of HFD-fed mice despite isocaloric food intake.