IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-53454-4.html
   My bibliography  Save this article

The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission

Author

Listed:
  • Marwan E. Majzoub

    (UNSW)

  • Sudarshan Paramsothy

    (University of Sydney
    Concord Repatriation General Hospital)

  • Craig Haifer

    (UNSW
    St Vincent’s Hospital)

  • Rohit Parthasarathy

    (UNSW)

  • Thomas J. Borody

    (Centre for Digestive Diseases)

  • Rupert W. Leong

    (University of Sydney
    Concord Repatriation General Hospital)

  • Michael A. Kamm

    (St Vincent’s Hospital
    University of Melbourne)

  • Nadeem O. Kaakoush

    (UNSW)

Abstract

Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.

Suggested Citation

  • Marwan E. Majzoub & Sudarshan Paramsothy & Craig Haifer & Rohit Parthasarathy & Thomas J. Borody & Rupert W. Leong & Michael A. Kamm & Nadeem O. Kaakoush, 2024. "The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53454-4
    DOI: 10.1038/s41467-024-53454-4
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-53454-4
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-53454-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Lingling Wang & Haobin Yao & Daniel C. Morgan & Kam Shing Lau & Suet Yi Leung & Joshua W. K. Ho & Wai K. Leung, 2023. "Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Yuko Sato & Koji Atarashi & Damian R. Plichta & Yasumichi Arai & Satoshi Sasajima & Sean M. Kearney & Wataru Suda & Kozue Takeshita & Takahiro Sasaki & Shoki Okamoto & Ashwin N. Skelly & Yuki Okamura , 2021. "Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians," Nature, Nature, vol. 599(7885), pages 458-464, November.
    3. Alejandro Reyes & Matthew Haynes & Nicole Hanson & Florent E. Angly & Andrew C. Heath & Forest Rohwer & Jeffrey I. Gordon, 2010. "Viruses in the faecal microbiota of monozygotic twins and their mothers," Nature, Nature, vol. 466(7304), pages 334-338, July.
    4. Koen Wortelboer & Patrick A. Jonge & Torsten P. M. Scheithauer & Ilias Attaye & E. Marleen Kemper & Max Nieuwdorp & Hilde Herrema, 2023. "Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Youwen Qin & Xin Tong & Wei-Jian Mei & Yanshuang Cheng & Yuanqiang Zou & Kai Han & Jiehai Yu & Zhuye Jie & Tao Zhang & Shida Zhu & Xin Jin & Jian Wang & Huanming Yang & Xun Xu & Huanzi Zhong & Liang X, 2024. "Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Qi Zhao & Man-Yun Dai & Ruo-Yue Huang & Jing-Yi Duan & Ting Zhang & Wei-Min Bao & Jing-Yi Zhang & Shao-Qiang Gui & Shu-Min Xia & Cong-Ting Dai & Ying-Mei Tang & Frank J. Gonzalez & Fei Li, 2023. "Parabacteroides distasonis ameliorates hepatic fibrosis potentially via modulating intestinal bile acid metabolism and hepatocyte pyroptosis in male mice," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Shao-Ming Gao & Han-Lan Fei & Qi Li & Li-Ying Lan & Li-Nan Huang & Peng-Fei Fan, 2024. "Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Romina Bonomini-Gnutzmann & Julio Plaza-Díaz & Carlos Jorquera-Aguilera & Andrés Rodríguez-Rodríguez & Fernando Rodríguez-Rodríguez, 2022. "Effect of Intensity and Duration of Exercise on Gut Microbiota in Humans: A Systematic Review," IJERPH, MDPI, vol. 19(15), pages 1-17, August.
    5. Juan Salazar & Pablo Durán & María P. Díaz & Maricarmen Chacín & Raquel Santeliz & Edgardo Mengual & Emma Gutiérrez & Xavier León & Andrea Díaz & Marycarlota Bernal & Daniel Escalona & Luis Alberto Pa, 2023. "Exploring the Relationship between the Gut Microbiota and Ageing: A Possible Age Modulator," IJERPH, MDPI, vol. 20(10), pages 1-24, May.
    6. Christine Tara Peterson, 2024. "Gut Microbiota-Mediated Biotransformation of Medicinal Herb-Derived Natural Products: A Narrative Review of New Frontiers in Drug Discovery," J, MDPI, vol. 7(3), pages 1-22, September.
    7. Diana P. Baquero & Sofia Medvedeva & Camille Martin-Gallausiaux & Nika Pende & Anna Sartori-Rupp & Stéphane Tachon & Thierry Pedron & Laurent Debarbieux & Guillaume Borrel & Simonetta Gribaldo & Mart , 2024. "Stable coexistence between an archaeal virus and the dominant methanogen of the human gut," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    8. Ethan A. Older & Jian Zhang & Zachary E. Ferris & Dan Xue & Zheng Zhong & Mary K. Mitchell & Michael Madden & Yuzhen Wang & Hexin Chen & Prakash Nagarkatti & Mitzi Nagarkatti & Daping Fan & Melissa El, 2024. "Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    9. Suguru Nishijima & Naoyoshi Nagata & Yuya Kiguchi & Yasushi Kojima & Tohru Miyoshi-Akiyama & Moto Kimura & Mitsuru Ohsugi & Kohjiro Ueki & Shinichi Oka & Masashi Mizokami & Takao Itoi & Takashi Kawai , 2022. "Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53454-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.