Zhu Li-Ting, Zhao Lei, Zhu Yue, Xu Xue-Li, Lin Jing-Jing, Duan Yi-Fang, Long Lu, Wu Yang-Yu, Xu Wen-Juan, Chen Jing-Yu, Yin Yu-Han, Obeten Alex Ujong, Huang Qiansheng
Xiamen Key Laboratory of Indoor Air and Health, State Key Laboratory for Ecological Security of Regions and Cities, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
Microbiome. 2025 Mar 11;13(1):72. doi: 10.1186/s40168-025-02029-6.
The responses of the infant gut microbiota to infection significantly disrupt the natural intrahost evolutionary processes of the microbiome. Here, we collected a 16-month longitudinal cohort of infant gut microbiomes affected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Then, we developed a multicriteria approach to identify core interaction network driving community dynamics under environmental disturbances, which we termed the Conserved Variated Interaction Group (CVIgroup).
The CVIgroup showed significant advantages on pinpointing a sparse set associated with the disturbances, as validated both our own and publicly available datasets. Leveraging the Oxford Nanopore Technology, we found this group facilitates the ecosystem's adaptation to environmental disruptions by enhancing the mobility of mobile genetic elements, including the reinforcement of the twin-arginine translocation pathway in response to increased virulence factors. Furthermore, the CVIgroup serves as an effective indicator of ecosystem health. The timescale for the gut microbiota's adaptation extends beyond 10 months. Members of the CVIgroup, such as Bacteroides thetaiotaomicron and Faecalibacterium, exhibit varying degrees of genomic structural variants, which contribute to guiding the community toward a new stable state rather than returning to its original configuration.
Collectively, the CVIgroup offers a snapshot of the gut microbiota's adaptive response to environmental disturbances. The disruption and subsequent adaptation of the gut microbiota in infants after COVID-19 infection underscores the necessity of re-evaluating reference standards in the context of the post-pandemic era. Video Abstract.
婴儿肠道微生物群对感染的反应会显著扰乱微生物组在宿主体内的自然进化过程。在此，我们收集了一个受严重急性呼吸综合征冠状病毒2（SARS-CoV-2）影响的婴儿肠道微生物群的16个月纵向队列。然后，我们开发了一种多标准方法来识别在环境干扰下驱动群落动态的核心相互作用网络，我们将其称为保守可变相互作用组（CVIgroup）。
CVIgroup在确定与干扰相关的稀疏集方面显示出显著优势，这在我们自己的数据集和公开可用的数据集中都得到了验证。利用牛津纳米孔技术，我们发现该组通过增强移动遗传元件的移动性来促进生态系统对环境干扰的适应，包括响应毒力因子增加而强化双精氨酸转运途径。此外，CVIgroup可作为生态系统健康的有效指标。肠道微生物群适应的时间尺度超过10个月。CVIgroup的成员，如多形拟杆菌和粪杆菌，表现出不同程度的基因组结构变异，这有助于引导群落走向新的稳定状态，而不是恢复到其原始构型。
总体而言，CVIgroup提供了肠道微生物群对环境干扰的适应性反应的快照。COVID-19感染后婴儿肠道微生物群的破坏及随后的适应强调了在大流行后时代重新评估参考标准的必要性。视频摘要。
