Abstract
BACKGROUND: 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). RESULTS: 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. CONCLUSIONS: 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.