Divergent Resilience of Bacterial and Fungal Gut Microbiota After Colorectal Surgery: Insights From a Prospective Longitudinal Cohort Study

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ABSTRACT The composition of the gut microbiota changes throughout life and is shaped by various external influences, particularly major physiological stressors such as surgery. The extent of these changes and their impact remain poorly understood. This prospective cohort study aimed to investigate changes in the gut microbiota following colorectal surgery and to identify factors that modify these alterations. Paired pre‐ and postoperative stool samples from 59 patients at the University Medical Centre Freiburg were analyzed using 16S rRNA and ITS2 gene sequencing. Analyses included alpha and beta diversity, LEfSe differential feature analysis, network analysis with Louvain clustering, KEGG pathway annotation, and correlation with clinical parameters. Bacterial diversity significantly decreased postoperatively (Shannon index: p < 0.001), while fungal diversity remained largely unchanged (p > 0.05). Beta diversity revealed increased inter‐patient variability in bacterial communities after surgery (PERMANOVA p = 0.001). Preoperative network analyses identified 18 microbial network clusters and interkingdom associations between bacteria and fungi. KEGG pathway mapping showed cluster‐specific metabolic profiles, including enrichment in degradation pathways, antimicrobial resistance mechanisms, and bacterial secretion systems. The contrasting responses of bacterial and fungal communities highlight the importance of considering the entire gut microbiome in perioperative care and suggest a central role for interkingdom interactions in maintaining gut homeostasis during surgical recovery.

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