{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T11:52:23Z","timestamp":1774525943370,"version":"3.50.1"},"reference-count":55,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T00:00:00Z","timestamp":1760054400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Ministry of Health of Russia, State assignment","award":["124021600069-3"],"award-info":[{"award-number":["124021600069-3"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Intestinal bacterial dysbiosis develops in a number of immune-mediated disorders. Fecal microbiota transfer (FMT) is considered a potentially efficient tool for restoration of the patient\u2019s gut microbiota. The aim of our study was to trace the time course of dominant bacterial populations and some Enterobacteria phages in patients with GVHD and Crohn\u2019s disease after FMT procedure. Patients and methods: We observed 12 patients with intestinal graft-versus-host disease (GVHD), and 15 persons with Crohn\u2019s disease after massive anti-infectious treatment. FMT was performed by a standard protocol using oral capsules administered for 2 days. Fecal bacteriome was assessed by 16S rRNA sequencing. Viral sequences were identified by NGS with a customized primer set. Plasma citrulline levels were measured in order to assess enterocyte damage in the patients. Results: Complete clinical response to FMT was observed in 5 of 12 GVHD patients and 10 of 15 Crohn\u2019s disease cases. Before FMT, most anaerobic Bacillota were exhausted in both Crohn\u2019s disease patients and GVHD. Following FMT, Akkermansia ratios tended to decrease within 30 days in Crohn\u2019s disease, along with higher Faecalibacteria, Romboutsia, and Dialister ratios than in GVHD, thus suggesting lesser damage to anaerobic microbiota in Crohn\u2019s disease. Increased contents of facultative anaerobes (Enterococcus and E. coli) was detected in GVHD patients after FMT. Fecal virome changes in Crohn\u2019s disease after FMT included early transient decrease in Caudoviricetes with a rise in Lederbergvirus and Eganvirus ratios at later terms. In GVHD patients, reverse correlations were revealed between E. coli and E. coli-hosted Eganvirus species. Intestinal damage assessed by low plasma citrulline levels was associated with fecal Klebsiella expansion, being more pronounced in GVHD than in Crohn\u2019s disease. Clinical response to FMT in GVHD patients correlated with increased plasma citrulline and lower Eganvirus abundance. Future studies will concern specific relations between fecal bacteriome and virome reconstitution following FMT in gut GVHD and other immune-mediated intestinal disorders.<\/jats:p>","DOI":"10.3390\/microorganisms13102337","type":"journal-article","created":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:50:16Z","timestamp":1760107816000},"page":"2337","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Changes in Gut Phageome and Bacteriome Following Fecal Microbiota Transfer in Patients with Intestinal Graft-Versus-Host Disease and Crohn\u2019s Disease"],"prefix":"10.3390","volume":"13","author":[{"given":"Alexei B.","family":"Chukhlovin","sequence":"first","affiliation":[{"name":"R.Gorbacheva Memorial Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0736-1269","authenticated-orcid":false,"given":"Oleg V.","family":"Goloshchapov","sequence":"additional","affiliation":[{"name":"R.Gorbacheva Memorial Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oksana B.","family":"Shchukina","sequence":"additional","affiliation":[{"name":"R.Gorbacheva Memorial Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandra M.","family":"Kharitidis","sequence":"additional","affiliation":[{"name":"R.Gorbacheva Memorial Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander A.","family":"Zhloba","sequence":"additional","affiliation":[{"name":"R.Gorbacheva Memorial Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2278-8391","authenticated-orcid":false,"given":"Tatiana F.","family":"Subbotina","sequence":"additional","affiliation":[{"name":"R.Gorbacheva Memorial Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9546-7831","authenticated-orcid":false,"given":"Aleksey V.","family":"Kusakin","sequence":"additional","affiliation":[{"name":"Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3427-6593","authenticated-orcid":false,"given":"Oleg V.","family":"Kosarev","sequence":"additional","affiliation":[{"name":"Saint Petersburg Mining University, 199106 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viktoria V.","family":"Tsai","sequence":"additional","affiliation":[{"name":"Serbalab Laboratory, 199106 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1791-7045","authenticated-orcid":false,"given":"Roman S.","family":"Kalinin","sequence":"additional","affiliation":[{"name":"Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yury A.","family":"Eismont","sequence":"additional","affiliation":[{"name":"Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia"},{"name":"Serbalab Laboratory, 199106 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0091-2224","authenticated-orcid":false,"given":"Oleg S.","family":"Glotov","sequence":"additional","affiliation":[{"name":"Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1159\/000538303","article-title":"Fecal microbiota transfer in acute graft-versus-host disease following allogeneic stem cell transplantation","volume":"40","author":"Weber","year":"2024","journal-title":"Visc. 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