Community-wide adaptive evolution of gut bacteria during dietary transitions
Diet exerts selection on bacterial species within the mammalian gut microbiota1,2,3,4,5, but the extent, modes, genomic bases, and repeatability of gut bacterial adaptive evolution in response to dietary variation within hosts are poorly understood. Here, we show that within-host dietary transitions drive ubiquitous and highly reproducible adaptive evolution of gut bacterial populations. We…
A recent study reveals that gut bacteria within mammals undergo adaptive evolution in response to dietary transitions. Researchers examined gut microbiota from isogenic mice, which were either switched from low-fat/high-carbohydrate diets to high-fat/low-carbohydrate diets or remained on their ancestral diet.
The analysis of allele-frequency dynamics in these gut bacteria showed that dietary changes induced parallel allele-frequency shifts in 61 out of 62 core bacterial species within five months. In contrast, no significant parallelism was observed in the control group of mice maintained on their original diet. This suggests that the gut microbiota of these mice were undergoing deterministic adaptive evolutionary responses to the dietary shifts.
Adaptation occurred through various mechanisms, including strain sorting and changes at the gene level. The gene-wise responses were particularly enriched in certain gene families and functions, such as those involved in invertases. Culturing experiments revealed a DNA switch in Phocaeicola sartorii, which localized a promoter sequence upstream of cell-surface glycan foraging genes. This switch was found to be localized in all replicates of mice switched to a high-fat/low-carbohydrate diet.
These findings provide evidence of widespread gut bacterial adaptive evolution driven by within-host dietary variation.
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