2025年12月17日出版的《自然》杂志发表了美国科学家的一项最新研究成果。来自加州大学的Nandita R. Garud团队发现基因特异性选择性扫描在人类肠道微生物群中普遍存在。

在此，该团队开发了一种新的选择扫描统计数据，称为综合连锁不平衡评分（iLDS），可以检测通过迁移和水平基因转移在宿主微生物群中传播的适应性等位基因的扫描。具体来说，iLDS利用了有害变异与有益变异搭便车的信号。将这一统计数据应用于全球24个人群中约30种最普遍的共生肠道物种，结果显示，物种间有300多次选择性扫描。

该课题组人员发现在碳水化合物代谢相关的位点上有选择性扫描的富集，这表明了对宿主饮食的适应，该课题组人员发现在本土化种群和非本土化种群之间的选择目标有显著差异。其中一个扫过的部位与麦芽糖糊精的代谢有关，麦芽糖糊精是一种合成淀粉，最近已成为本土化饮食中广泛存在的成分。总之，他们的研究结果表明，菌株之间的重组促进了人类肠道共生细菌之间普遍的适应性进化，并强烈暗示宿主饮食和生活方式是关键的选择压力。

据了解，人类肠道微生物群由高度多样化的物种联合体组成，这些物种在宿主体内和宿主之间不断进化。识别许多人类肠道微生物群共同适应的能力不仅可以显示宿主之间共有的选择压力，还可以显示可能影响群落结构和宿主特征的微生物群功能分化的关键驱动因素。然而，适应在人类肠道微生物群中传播的程度是相对未知的。

附：英文原文

Title: Gene-specific selective sweeps are pervasive across human gut microbiomes

Author: Wolff, Richard, Garud, Nandita R.

Issue&Volume: 2025-12-17

Abstract: The human gut microbiome is composed of a highly diverse consortia of species that are continually evolving within and across hosts1,2. The ability to identify adaptations common to many human gut microbiomes would show not only shared selection pressures across hosts but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, the extent to which adaptations have spread across human gut microbiomes is relatively unknown. Here we develop a new selection scan statistic named the integrated linkage disequilibrium score (iLDS) that can detect sweeps of adaptive alleles spreading across host microbiomes by migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with a beneficial variant. Application of the statistic to around 30 of the most prevalent commensal gut species from 24 human populations around the world showed more than 300 selective sweeps across species. We find an enrichment for selective sweeps at loci involved in carbohydrate metabolism, indicative of adaptation to host diet, and we find that the targets of selection differ significantly between industrialized populations and non-industrialized populations. One of these sweeps is at a locus known to be involved in the metabolism of maltodextrin—a synthetic starch that has recently become a widespread component of industrialized diets. In summary, our results indicate that recombination between strains fuels pervasive adaptive evolution among human gut commensal bacteria, and strongly implicate host diet and lifestyle as critical selection pressures.

DOI: 10.1038/s41586-025-09798-y

Source: https://www.nature.com/articles/s41586-025-09798-y