**Background:** Environmental factors are implicated in the onset and exacerbation of inflammatory bowel disease (IBD), and the gut microbiota is known to play a role in IBD pathogenesis. The authors previously reported that approximately half of over 1,000 IBD outpatients experienced seasonal disease exacerbation, particularly in winter. This study aimed to investigate whether the fecal microbiota composition shows seasonal variation in IBD patients and whether such changes are associated with disease activity.
**Methods:** This prospective observational study was conducted at Osaka University Hospital between November 2015 and April 2019. Participants included 39 IBD outpatients (20 ulcerative colitis [UC] and 19 Crohn's disease [CD] patients) and 8 healthy controls (HCs). Exclusion criteria were age under 18 years, treatment with full elemental diet, antibiotic use within 6 months, or prior ostomy surgery. Fecal samples were self-collected by participants in each of four consecutive seasons (March-May=spring, June-August=summer, September-November=autumn, December-February=winter) and preserved at -80°C. Bacterial DNA was extracted using a DNeasy PowerSoil Kit, and the V1-V2 variable region of the 16S rRNA gene was sequenced on the Illumina MiSeq platform with 251-bp paired-end sequencing. Sequences were processed using DADA2 and QIIME2 (version 2020.2) with the Greengenes 13_8 database. Disease activity was assessed using the Crohn's disease activity index (CDAI) for CD and the partial Mayo score (PMS) for UC. Statistical analyses included Tukey's HSD test, Pearson's correlation, Wilcoxon signed-rank test with Bonferroni correction (p<0.0083 considered significant for seasonal comparisons), and Kaplan-Meier curves with log-rank tests for long-term outcomes.
**Key Results:** A total of 188 fecal samples from 47 participants were analyzed. The median (range) CDAI was 83 (59-123) for CD patients and median PMS was 0 (0-1) for UC patients. Alpha-diversity (Shannon index) was significantly lower in IBD patients than HCs, and lower in CD than UC patients, with no seasonal variation in any group. Beta-diversity analysis showed CD and UC clusters were distinct from HC clusters, with significantly greater UniFrac distances in CD patients than UC patients and HCs. At the phylum level, in CD patients, Actinobacteria and TM7 were both significantly more abundant in autumn than in spring and winter (p<0.0083), but not in summer. In UC patients, Actinobacteria was significantly more abundant in autumn than in spring, but TM7 showed no seasonal change. HCs showed no intraseasonal differences. At the genus level, in CD patients, Actinomyces (phylum Actinobacteria) was significantly more abundant in autumn than in spring (p<0.0083), and c_TM7-3;o_;f_;g_ (TM7-3) was significantly more abundant in autumn than in spring and winter (p<0.0083). No seasonal changes in these genera were observed in UC patients or HCs. A strong positive correlation was found between Actinomyces and TM7-3 abundance in CD patients (correlation coefficient 0.7739, p<0.0001), which was significant across all four seasons. A weaker correlation was observed in HCs (correlation coefficient 0.6024, p=0.0003), significant in autumn and winter, while no correlation was found in UC patients. For long-term outcomes, CD patients with high abundance of TM7-3 in autumn (compared to spring) required significantly fewer therapeutic interventions over 3 years than those with low abundance (p<0.05, log-rank test). No significant association was found for Actinomyces seasonal change. There was no correlation between Actinomyces or TM7-3 abundance and CDAI in the short term.
**Clinical Implications:** This study demonstrates that oral commensal bacteria Actinomyces and its symbiont TM7-3 show correlated seasonal fluctuations specifically in the feces of CD patients, with peak abundance in autumn. The finding that increased autumn TM7-3 abundance is associated with better long-term outcomes (fewer therapeutic interventions over 3 years) challenges the initial hypothesis that these bacteria might trigger winter exacerbations and instead suggests a potential protective role. This aligns with recent reports of TM7 having protective effects against inflammatory damage in periodontitis. The results highlight a novel environmental-microbial interaction in CD that may involve oral-to-gut bacterial translocation, though the mechanisms remain unclear. Limitations include the small sample size (n=47), single-center design, relatively stable outpatient population, lack of data on confounders (diet, smoking, alcohol, dental history), and limited one-year observation period. Further research comparing fecal and salivary microbiota, investigating dietary and oral health factors, and extending observation periods is needed to elucidate the mechanisms underlying these seasonal microbial changes and their protective effects in CD.