Microbes with higher metabolic independence are enriched in human gut microbiomes under stress

• DOI: 10.7554/elife.89862.1
• Publication Date: 2023-09-08T15:25:05Z
• Authors: Iva Veseli; Yiqun T. Chen; Matthew S. Schechter; Chiara Vanni; Emily C. Fogarty; Andrea R. Watson; Bana Jabri; Ran Blekhman; Amy D. Willis; Michael K. Yu; Antonio Fernàndez...; Jessika Füssel; A. Murat Eren
• Keywords: Dysbiosis

A wide variety of human diseases are associated with loss microbial diversity in the gut, inspiring a great interest diagnostic or therapeutic potential microbiota. However, ecological forces that drive reduction disease states remain unclear, rendering it difficult to ascertain role microbiota emergence severity. One hypothesis explain this phenomenon is diminished as select for populations more fit survive environmental stress caused by inflammation other host factors. Here, we tested on large scale, developing software framework quantify enrichment metabolisms complex metagenomes function diversity. We applied over 400 gut from individuals who healthy diagnosed inflammatory bowel (IBD). found high metabolic independence (HMI) distinguishing characteristic communities IBD. classifier trained using normalized copy numbers 33 HMI-associated modules not only distinguished health versus IBD, but also tracked recovery microbiome following antibiotic treatment, suggesting HMI hallmark stressed environments.