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Volume 13
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10.3390/microorganisms13102337
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Changes in Gut Phageome and Bacteriome Following Fecal Microbiota Transfer in Patients with Intestinal Graft-Versus-Host Disease and Crohn’s Disease

by
Alexei B. Chukhlovin
1,*,
Oleg V. Goloshchapov
1,
Oksana B. Shchukina
1,
Aleksandra M. Kharitidis
1,
Alexander A. Zhloba
1,
Tatiana F. Subbotina
1,
Aleksey V. Kusakin
2,
Oleg V. Kosarev
3,
Viktoria V. Tsai
4,
Roman S. Kalinin
2,
Yury A. Eismont
2,4 and
Oleg S. Glotov
2
1
R.Gorbacheva Memorial Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, 197022 St. Petersburg, Russia
2
Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
3
Saint Petersburg Mining University, 199106 St. Petersburg, Russia
4
Serbalab Laboratory, 199106 St. Petersburg, Russia
*
Author to whom correspondence should be addressed.
Microorganisms 2025, 13(10), 2337; https://doi.org/10.3390/microorganisms13102337
Submission received: 11 August 2025 / Revised: 27 September 2025 / Accepted: 5 October 2025 / Published: 10 October 2025
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 3rd Edition)
Versions Notes

Abstract

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’s 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’s disease after FMT procedure. Patients and methods: We observed 12 patients with intestinal graft-versus-host disease (GVHD), and 15 persons with Crohn’s 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’s disease cases. Before FMT, most anaerobic Bacillota were exhausted in both Crohn’s disease patients and GVHD. Following FMT, Akkermansia ratios tended to decrease within 30 days in Crohn’s disease, along with higher Faecalibacteria, Romboutsia, and Dialister ratios than in GVHD, thus suggesting lesser damage to anaerobic microbiota in Crohn’s disease. Increased contents of facultative anaerobes (Enterococcus and E.coli) was detected in GVHD patients after FMT. Fecal virome changes in Crohn’s 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’s 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.
Keywords: fecal microbiota transplantation; virome; bacteriophages; Enterobacteriaceae; next-generation sequencing; plasma citrulline; graft-versus-host disease; Crohn’s disease fecal microbiota transplantation; virome; bacteriophages; Enterobacteriaceae; next-generation sequencing; plasma citrulline; graft-versus-host disease; Crohn’s disease

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MDPI and ACS Style

Chukhlovin, A.B.; Goloshchapov, O.V.; Shchukina, O.B.; Kharitidis, A.M.; Zhloba, A.A.; Subbotina, T.F.; Kusakin, A.V.; Kosarev, O.V.; Tsai, V.V.; Kalinin, R.S.; et al. Changes in Gut Phageome and Bacteriome Following Fecal Microbiota Transfer in Patients with Intestinal Graft-Versus-Host Disease and Crohn’s Disease. Microorganisms 2025, 13, 2337. https://doi.org/10.3390/microorganisms13102337

AMA Style

Chukhlovin AB, Goloshchapov OV, Shchukina OB, Kharitidis AM, Zhloba AA, Subbotina TF, Kusakin AV, Kosarev OV, Tsai VV, Kalinin RS, et al. Changes in Gut Phageome and Bacteriome Following Fecal Microbiota Transfer in Patients with Intestinal Graft-Versus-Host Disease and Crohn’s Disease. Microorganisms. 2025; 13(10):2337. https://doi.org/10.3390/microorganisms13102337

Chicago/Turabian Style

Chukhlovin, Alexei B., Oleg V. Goloshchapov, Oksana B. Shchukina, Aleksandra M. Kharitidis, Alexander A. Zhloba, Tatiana F. Subbotina, Aleksey V. Kusakin, Oleg V. Kosarev, Viktoria V. Tsai, Roman S. Kalinin, and et al. 2025. "Changes in Gut Phageome and Bacteriome Following Fecal Microbiota Transfer in Patients with Intestinal Graft-Versus-Host Disease and Crohn’s Disease" Microorganisms 13, no. 10: 2337. https://doi.org/10.3390/microorganisms13102337

APA Style

Chukhlovin, A. B., Goloshchapov, O. V., Shchukina, O. B., Kharitidis, A. M., Zhloba, A. A., Subbotina, T. F., Kusakin, A. V., Kosarev, O. V., Tsai, V. V., Kalinin, R. S., Eismont, Y. A., & Glotov, O. S. (2025). Changes in Gut Phageome and Bacteriome Following Fecal Microbiota Transfer in Patients with Intestinal Graft-Versus-Host Disease and Crohn’s Disease. Microorganisms, 13(10), 2337. https://doi.org/10.3390/microorganisms13102337

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