Abstract

Background: Although the gut microbiota is generally recognized to remain relatively stable in healthy individuals, its taxonomic composition still undergoes subtle temporal fluctuations. To systematically characterize these dynamic variations, we adopted “enterotypes” as a macroscopic and practical metric to evaluate the structural dynamics of the intestinal microbial community. Methods: We longitudinally recruited a cohort of healthy adults and collected a total of 72 shotgun metagenomic fecal samples across approximately 40 days. All samples underwent metagenomic sequencing, and subjects were grouped by their predominant enterotypes and longitudinal fluctuation patterns. We evaluated the microbial markers and the longitudinal co-occurrence network topologies of different groups to clarify the potential factors causing gut microbial fluctuations. Results: Longitudinal tracking revealed that those undergoing persistent alterations in microbial communities exhibited diarrhea symptoms, accompanied by markedly greater variability in gut microbiota. The reduction in Alistipes shahii is a potential predictive marker for community instability, exhibiting a cross-validated AUC of 0.824 (95% CI: 0.760–0.888). Furthermore, the co-occurrence network and correlation analysis indicated that fluctuating communities exhibited significantly higher clustering coefficients and denser connectivity among core taxa. Rather than indicating robustness, this dense architecture reflected an increased degree of microbial interdependence within the unstable gut microbial community. Conclusions: This preliminary study discovered candidate bacteria taxa that may serve as indicators of disturbances in the gut microbiota. Furthermore, the hyper-connectivity during continuous fluctuations suggested that increased interdependent microbial relationships meant diminished gut resilience. These results offer a new perspective for detecting early signals of dysbiosis and understanding mechanisms underlying stability of gut microbiota.

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