Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

• Published in: Genome Biology Vol. 23; no. 1; pp. 208 - 31
• Main Authors: Ma, Siyuan, Shungin, Dmitry, Mallick, Himel, Schirmer, Melanie, Nguyen, Long H, Kolde, Raivo, Franzosa, Eric, Vlamakis, Hera, Xavier, Ramnik, Huttenhower, Curtis
• Format: Journal Article
• Language: English
• Published: England BioMed Central 03-10-2022; BMC
• Subjects: Batch effect; Biopsy; Dysbacteriosis; Dysbiosis; Gastrointestinal Microbiome; Gene expression; Humans; Inflammatory bowel disease; Inflammatory Bowel Diseases; Intestine; Meta-analysis; Metagenomics; Method; Microbiomes; Microbiota; Population; Population structure; Inflammatory bowel disease; Metagenomics; Dysbiosis; Batch effect; Meta-analysis
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-022-02753-4

Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial taxonomic and functional profiles. Applying it to ten IBD cohorts, we identify consistent associations, including novel taxa such as Acinetobacter and Turicibacter, and additional exposure and interaction effects. A single gradient of dysbiosis severity is favored over discrete types to summarize IBD microbiome population structure. These results provide a benchmark for characterization of IBD and a framework for meta-analysis of any microbial communities.