Abstract Background Gut microbiota perturbations are linked to ulcerative colitis (UC), but mechanistic data tying specific microbial functions to disease activity are limited. Current insights largely derive from culture independent sequencing methods which cannot distinguish viable from non-viable organisms and provide only inferred, rather than experimentally verified, functional potential. High throughput culturomics combines anaerobic culturing with sequencing to recover viable, and disease-associated isolates that permit direct phenotypic testing. Hydrogen sulphide (H2S) is a microbial by-product implicated in UC through direct epithelial injury and inhibition of colonocyte butyrate utilisation. We applied culturomics to patients with ulcerative proctitis (UP) enrolled in the UP-FMT trial to i) identify isolates associated with active disease in vivo and ii) map the taxonomic distribution of H2S production Methods Baseline stool and rectal mucosal biopsies from patients with active ulcerative proctitis in the UP-FMT pilot study were homogenised and cultured anaerobically on a variety of bacteriological media. After incubation, individual colonies were subcultured in broth and used as template for full-length 16S rRNA PCR and sequencing for taxonomic assignment. Isolates were phenotyped for H2S production from organic (L-cysteine) and inorganic (thiosulphate) sulphur sources, and phylogenetic patterns in this trait were explored. Results Baseline stool and/or mucosal samples were collected from 13 patients. In total 7,125 isolates were obtained with culturing, yielding 5,192 high-quality full-length 16S sequences and 380 species-level OTUs. We identified 141 putative novel species (104 from stool, 61 from mucosa). Multiple clades, particularly within Bacillota and Bacteroidata, consisted exclusively of mucosa-derived isolates. H2S production was widely distributed across diverse taxa, spanning Bacillota, Bacteroidata, Eggerthela related clades (actinomycetota) and Escherichia-related clades (Proteobacteria), as well as previously described sulphate reducers such as Desulfovibrio piger. Isolates of the same species frequently displayed divergent H2S production phenotypes. Conclusion Anaerobic culturomics can recover a rich collection of stool and mucosa-associated isolates from patients with UC, enabling direct functional phenotyping of disease associated microbes. H2S production is not confined to classical sulphate-reducing species but is widely distributed across taxa and enriched at the inflamed mucosal surface. Hydrogen sulphide production may therefore be influenced by ecological context and modifiable functions rather than taxonomic classification alone. References: 1. Raja SS, Costello SP, Rayner CK, Day A, Portmann L, Uylaki W, Wheeler R, Saxon S, Tucker EC, Fon J, Edwards S, Young RB, Forster SC, Goodsall T, Bryant RV. Examining the role of fecal microbiota transplantation for inducing remission in resistant ulcerative proctitis and distal ulcerative colitis (ulcerative proctitis-fecal microbiota transplantation). J Crohns Colitis. 2025 Nov 8;19(10):jjaf169. doi: 10.1093/ecco-jcc/jjaf169. PMID: 40973482. 2. Pitcher MC, Cummings JH. Hydrogen sulphide: a bacterial toxin in ulcerative colitis? Gut. 1996 Jul;39(1):1-4. doi: 10.1136/gut.39.1.1. PMID: 8881797; PMCID: PMC1383219. 3. Ivan Kushkevych, Dani Dordević, Monika Vítězová,Possible synergy effect of hydrogen sulfide and acetate produced by sulfate-reducing bacteria on inflammatory bowel disease development,Journal of Advanced Research,Volume 27,2021,Pages 71-78, Conflict of interest: Dr. Raja, Sreecanth: Research Support from The Hospital Research Foundation Costello, Samuel: Employee: BiomeBank Shareholder: BiomeBank, Microbiotica Research funds and speakers fees: Janssen, Ferring, MSD, Microbiotica Rayner, Chris: CKR has received research funding from AstraZeneca, Merck Sharp & Dohme, Eli Lilly and Company, Novartis, and Sanofi and has participated in advisory boards for Allergan (now AbbVie) and Glyscend. Wheeler, Reuben: No conflict of interest Uylaki, Wendy: No Conflicts Young, Remy: No conflict of interest Forster, Samuel: SCF is a consultant to BiomeBank, Australia. Day, Alice: Research Support from The Hospital Research Foundation and Michelle McGrath Fellowship, consultancy fees from Biome Bank, Ferring, AbbVie. Bibb, Lyndsay: No conflict of interest Bryant, Robert Venning: Robert V. Bryant has received grant/research support/speaker honoraria/advisory board fees from AbbVie, Ferring, Janssen, Shire, Takeda, GlaxoSmithKline, Bristol Myers Squibb, and Emerge Health and is a shareholder in Biomebank.
Raja et al. (Thu,) studied this question.