Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking

被引:2
|
作者
Wong, Daniel P. G. H. [1 ]
Good, Benjamin H. [1 ,2 ,3 ]
机构
[1] Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Biol, Stanford, CA 94305 USA
[3] Chan Zuckerberg Biohub San Francisco, San Francisco, CA 94158 USA
基金
美国国家卫生研究院;
关键词
FITNESS; ADAPTATION; MICROBIOME; EVOLUTION; SYMBIONT; LEAVES;
D O I
10.1038/s41467-024-45792-0
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Gut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult to characterize in dominant gut species in their complex in vivo environment. Here we show that the fine-scale dynamics of genome-wide transposon libraries can enable quantitative inferences of these in vivo evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains in gnotobiotic mice, we observed positive selection on thousands of cryptic variants - most of which were unrelated to their original gene knockouts. The spectrum of fitness benefits varied between species, and displayed diverse tradeoffs over time and in different dietary conditions, enabling inferences of their underlying function. These results suggest that within-host adaptations arise from an intense competition between numerous contending variants, which can strongly influence their emergent evolutionary tradeoffs.
引用
收藏
页数:14
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