Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
Department of Biology, Stanford University, Stanford, CA, 94305, USA.
Nat Commun. 2023 Nov 6;14(1):7146. doi: 10.1038/s41467-023-42769-3.
Gut microbiota can evolve within their hosts on human-relevant timescales, but little is known about how these changes influence (or are influenced by) the composition of their local community. Here, by combining ecological and evolutionary analyses of a large cohort of human gut metagenomes, we show that the short-term evolution of the microbiota is linked with shifts in its ecological structure. These correlations are not simply explained by expansions of the evolving species, and often involve additional fluctuations in distantly related taxa. We show that similar feedbacks naturally emerge in simple resource competition models, even in the absence of cross-feeding or predation. These results suggest that the structure and function of host microbiota may be shaped by their local evolutionary history, which could have important implications for personalized medicine and microbiome engineering.
肠道微生物组可以在人类相关的时间尺度内于宿主中进化，但人们对这些变化如何影响（或受其影响）其局部群落组成知之甚少。在这里，我们通过对大量人类肠道宏基因组进行生态和进化分析，表明微生物组的短期进化与生态结构的变化有关。这些相关性并不仅仅可以用进化物种的扩张来解释，而且通常还涉及到与进化物种关系较远的分类单元的额外波动。我们表明，即使在没有互养或捕食的情况下，简单的资源竞争模型也会自然产生类似的反馈，这些结果表明，宿主微生物组的结构和功能可能受到其局部进化历史的影响，这可能对个性化医学和微生物组工程具有重要意义。
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