AUTHOR=Scanu Matteo , Toto Francesca , Petito Valentina , Masi Letizia , Fidaleo Marco , Puca Pierluigi , Baldelli Valerio , Reddel Sofia , Vernocchi Pamela , Pani Giovambattista , Putignani Lorenza , Scaldaferri Franco , Del Chierico Federica 

TITLE=An integrative multi-omic analysis defines gut microbiota, mycobiota, and metabolic fingerprints in ulcerative colitis patients

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=14

YEAR=2024

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2024.1366192

DOI=10.3389/fcimb.2024.1366192

ISSN=2235-2988

ABSTRACT=<sec><title>Background</title><p>Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches.</p></sec><sec><title>Methods</title><p>The 16S rRNA- and ITS2-based metataxonomics and gas chromatography–mass spectrometry/solid phase microextraction (GC–MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis.</p></sec><sec><title>Results</title><p>In the UC cohort, we reported the increase of <italic>Streptococcus</italic>, <italic>Bifidobacterium</italic>, Enterobacteriaceae, TM7-3, <italic>Granulicatella</italic>, <italic>Peptostreptococcus</italic>, <italic>Lactobacillus</italic>, <italic>Veillonella</italic>, <italic>Enterococcus</italic>, <italic>Peptoniphilus</italic>, Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of <italic>Akkermansia</italic>; Ruminococcaceae; <italic>Ruminococcus</italic>; <italic>Gemmiger</italic>; <italic>Methanobrevibacter</italic>; <italic>Oscillospira</italic>; <italic>Coprococus</italic>; <italic>Christensenellaceae</italic>; <italic>Clavispora</italic>; <italic>Vishniacozyma</italic>; <italic>Quambalaria</italic>; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions.</p></sec><sec><title>Conclusion</title><p>In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.</p></sec>