Scientific Reports (2024)
Hyun Sik Kim, Shin Ju Oh, Byung Kwon Kim, Ji Eun Kim, Bo-Hyung Kim, Young-Kyu Park, Bo-Gie Yang, Jae-Yun Lee, Jin-Woo Bae & Chang Kyun Lee
Summary
연구 필요성
- IBD (Crohn’s disease and ulcerative colitis) is increasing rapidly in Asia, including Korea, but most gut microbiome studies have been conducted in Western populations.
- Previous Asian studies were limited by small sample sizes, lack of healthy controls, or lack of detailed functional annotation.
- Therefore, a large cohort with ethnicity-matched healthy controls is needed to characterize both taxonomic and functional microbiome signatures of IBD.
연구 목
- To characterize the taxonomic and functional gut microbiome signature of Korean IBD patients compared with healthy controls matched for ethnicity and lifestyle.
- To identify a small set of microbial markers that can discriminate healthy vs IBD, healthy vs CD, healthy vs UC, and CD vs UC.
실험 방법
- Fecal samples from 640 participants were collected (117 healthy controls, 223 CD, 300 UC). Patients were in a stable phase, and healthy controls were strictly screened.
- 16S rRNA (V3-V4) sequencing on Illumina MiSeq; preprocessing with DADA2, Skewer and Mothur; taxonomy assigned with SILVA.
- Alpha and beta diversity (UniFrac, PERMANOVA) were analyzed.
- Differential abundance was tested with MaAsLin2, adjusted for age, sex, BMI, smoking, alcohol, stool consistency and disease activity.
- Functions (KO, EC, KEGG and MetaCyc pathways) were predicted with PICRUSt2, and a functional dysbiosis score was calculated.
- Random forest models were built to select diagnostic marker genera, evaluated by AUROC.
주요 결과
- Alpha diversity was lower in IBD, most in CD. Within CD, diversity fell further in stricturing/penetrating behavior.
- Beta diversity differed significantly between groups, but effect sizes were small (R2 about 1-5%).
- Many SCFA-producing genera (e.g., Agathobacter, Blautia, Lachnospira) were depleted in both CD and UC. Only Escherichia-Shigella increased significantly in CD, and no genus increased in both diseases.
- Predicted functional profiles of CD were widely scattered compared with healthy controls (Healthy vs CD R2 about 0.14).
- Virulence-related pathways (shigellosis, bacterial invasion of epithelial cells, LPS biosynthesis, secretion system) and a taurine-cysteine-H2S pathway were enriched in CD.
- Functional dysbiosis was found in about 5% of healthy, 50% of CD and 22% of UC.
- 2-3 genera discriminated groups with AUROC 0.845 (Healthy vs IBD), 0.860 (Healthy vs CD), 0.826 (Healthy vs UC) and 0.718 (CD vs UC).
Take home message
- Korean IBD patients show a distinct gut microbiome signature, with Escherichia-Shigella expansion and enrichment of virulence and H2S-producing pathways as hallmarks of CD dysbiosis.
- A small panel of 2-3 genera may serve as a low-cost, non-invasive diagnostic aid, but validation in independent cohorts is needed.
Points helpful for my research
- This paper helped to understand a practical workflow for biomarker discovery: MaAsLin2 to select candidate genera, followed by a random forest model evaluated by AUROC.