From Home to Classroom: Gut Microbiome Trajectories and Infection Burden in Kindergarten Beginners

<title>Abstract</title> <p> Background The transition to kindergarten represents a major environmental and social shift for young children, often accompanied by an increased burden of infectious diseases. Whether gut microbiota dynamics during this period contribute to the observed morbidity remains largely unexplored. Methods We conducted a four-month longitudinal study in 14 healthy children (aged 24–45 months, 9 males) at three time points: one month before (T1), one month after (T2), and three months after (T3) kindergarten entry. Fecal samples were collected at each time point for full-length 16S rRNA gene sequencing (Nanopore). Infectious disease symptoms, including respiratory, gastrointestinal, and febrile episodes, were monitored through parental reports and kindergarten attendance records. Results Total illness days and healthcare visits increased significantly from T1 to T3 (both <italic>P</italic>  &lt; 0.01). Gut microbiota α-diversity (Shannon, Chao1, Faith’s PD) remained stable from T1 to T2 but increased markedly at T3 ( <italic>P</italic>  &lt; 0.001), coinciding with a compositional shift from <italic>Firmicutes</italic> - and <italic>Bacteroidetes-</italic> enriched to <italic>Proteobacteria</italic> -dominant communities. The expansion of specific opportunistic taxa ( <italic>Hydrogenophaga</italic> sp. <italic>PBC</italic> , <italic>Pseudomonas putida</italic> , <italic>Acinetobacter baumannii</italic> , and <italic>Enterobacter</italic> spp.) correlated positively with total illness days and healthcare visits. Conversely, the keystone species <italic>Bacteroides fragilis</italic> showed consistent negative associations with disease duration and symptom severity. Conclusions Kindergarten entry is associated with progressive gut microbiota restructuring, characterized by delayed diversity expansion and eventual enrichment of <italic>Proteobacteria</italic> . These changes, particularly the depletion of <italic>Bacteroides fragilis</italic> and the proliferation of opportunistic pathobionts, correlate with respiratory and gastrointestinal symptom burden. This suggests that specific gut microbial dynamics may modulate infection susceptibility during this critical transition. The small sample size limits causal inference and generalizability; larger confirmatory studies are needed. Trial registration Not applicable. </p>