IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-44720-6.html
   My bibliography  Save this article

Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’

Author

Listed:
  • Jun-Jun She

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Wei-Xin Liu

    (The Chinese University of Hong Kong)

  • Xiao-Ming Ding

    (The First Affiliated Hospital of Xi’an Jiao Tong University
    Xi’an Jiao Tong University)

  • Gang Guo

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Jing Han

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Fei-Yu Shi

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Harry Cheuk-Hay Lau

    (The Chinese University of Hong Kong)

  • Chen-Guang Ding

    (The First Affiliated Hospital of Xi’an Jiao Tong University
    Xi’an Jiao Tong University)

  • Wu-Jun Xue

    (The First Affiliated Hospital of Xi’an Jiao Tong University
    Xi’an Jiao Tong University)

  • Wen Shi

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Gai-Xia Liu

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Zhe Zhang

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Chen-Hao Hu

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Yinnan Chen

    (First Affiliated Hospital of Xi’an Jiao Tong University
    First Affiliated Hospital of Xi’an Jiao Tong University)

  • Chi Chun Wong

    (The Chinese University of Hong Kong)

  • Jun Yu

    (First Affiliated Hospital of Xi’an Jiao Tong University
    The Chinese University of Hong Kong)

Abstract

The microbiome in a specific human organ has been well-studied, but few reports have investigated the multi-organ microbiome as a whole. Here, we aim to analyse the intra-individual inter-organ and intra-organ microbiome in deceased humans. We collected 1608 samples from 53 sites of 7 surface organs (oral cavity, esophagus, stomach, small intestine, appendix, large intestine and skin; n = 33 subjects) and performed microbiome profiling, including 16S full-length sequencing. Microbial diversity varied dramatically among organs, and core microbial species co-existed in different intra-individual organs. We deciphered microbial changes across distinct intra-organ sites, and identified signature microbes, their functional traits, and interactions specific to each site. We revealed significant microbial heterogeneity between paired mucosa-lumen samples of stomach, small intestine, and large intestine. Finally, we established the landscape of inter-organ relationships of microbes along the digestive tract. Therefore, we generate a catalogue of bacterial composition, diversity, interaction, functional traits, and bacterial translocation in human at inter-organ and intra-organ levels.

Suggested Citation

  • Jun-Jun She & Wei-Xin Liu & Xiao-Ming Ding & Gang Guo & Jing Han & Fei-Yu Shi & Harry Cheuk-Hay Lau & Chen-Guang Ding & Wu-Jun Xue & Wen Shi & Gai-Xia Liu & Zhe Zhang & Chen-Hao Hu & Yinnan Chen & Chi, 2024. "Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-44720-6
    DOI: 10.1038/s41467-024-44720-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-44720-6
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-44720-6?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. Huang Lin & Merete Eggesbø & Shyamal Das Peddada, 2022. "Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Huang Lin & Shyamal Das Peddada, 2020. "Analysis of compositions of microbiomes with bias correction," Nature Communications, Nature, vol. 11(1), pages 1-11, 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. Estelle E. Clerc & Jean-Baptiste Raina & Johannes M. Keegstra & Zachary Landry & Sammy Pontrelli & Uria Alcolombri & Bennett S. Lambert & Valerio Anelli & Flora Vincent & Marta Masdeu-Navarro & Andrea, 2023. "Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Osama Al-Dalahmah & Michael G. Argenziano & Adithya Kannan & Aayushi Mahajan & Julia Furnari & Fahad Paryani & Deborah Boyett & Akshay Save & Nelson Humala & Fatima Khan & Juncheng Li & Hong Lu & Yu S, 2023. "Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Bryan P. Brown & Colin Feng & Ramla F. Tanko & Shameem Z. Jaumdally & Rubina Bunjun & Smritee Dabee & Anna-Ursula Happel & Melanie Gasper & Donald D. Nyangahu & Maricianah Onono & Gonasagrie Nair & Th, 2023. "Copper intrauterine device increases vaginal concentrations of inflammatory anaerobes and depletes lactobacilli compared to hormonal options in a randomized trial," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Guy Amit & Amir Bashan, 2023. "Top-down identification of keystone taxa in the microbiome," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Muntsa Rocafort & David B. Gootenberg & Jesús M. Luévano & Jeffrey M. Paer & Matthew R. Hayward & Juliet T. Bramante & Musie S. Ghebremichael & Jiawu Xu & Zoe H. Rogers & Alexander R. Munoz & Samson O, 2024. "HIV-associated gut microbial alterations are dependent on host and geographic context," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    6. Huang Lin & Merete Eggesbø & Shyamal Das Peddada, 2022. "Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    7. Andrew Baldi & Sabine Braat & Mohammed Imrul Hasan & Cavan Bennett & Marilou Barrios & Naomi Jones & Gemma Moir-Meyer & Imadh Abdul Azeez & Stephen Wilcox & Mohammad Saiful Alam Bhuiyan & Ricardo Atai, 2024. "Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    8. M. Büttner & J. Ostner & C. L. Müller & F. J. Theis & B. Schubert, 2021. "scCODA is a Bayesian model for compositional single-cell data analysis," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    9. Zachary D. Wallen & Ayse Demirkan & Guy Twa & Gwendolyn Cohen & Marissa N. Dean & David G. Standaert & Timothy R. Sampson & Haydeh Payami, 2022. "Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    10. Kotaro Soeda & Takayoshi Sasako & Kenichiro Enooku & Naoto Kubota & Naoki Kobayashi & Yoshiko Matsumoto Ikushima & Motoharu Awazawa & Ryotaro Bouchi & Gotaro Toda & Tomoharu Yamada & Takuma Nakatsuka , 2023. "Gut insulin action protects from hepatocarcinogenesis in diabetic mice comorbid with nonalcoholic steatohepatitis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    11. Aarthi Ravikrishnan & Indrik Wijaya & Eileen Png & Kern Rei Chng & Eliza Xin Pei Ho & Amanda Hui Qi Ng & Ahmad Nazri Mohamed Naim & Jean-Sebastien Gounot & Shou Ping Guan & Jasinda Lee Hanqing & Lihua, 2024. "Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    12. Jonathan W. Lo & Domenico Cozzetto & James L. Alexander & Nathan P. Danckert & Matthew Madgwick & Naomi Knox & Jillian Yong Xin Sieh & Marton Olbei & Zhigang Liu & Hajir Ibraheim & Jesus Miguens Blanc, 2023. "Immune checkpoint inhibitor-induced colitis is mediated by polyfunctional lymphocytes and is dependent on an IL23/IFNγ axis," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    13. 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.
    14. Karen D. Corbin & Elvis A. Carnero & Blake Dirks & Daria Igudesman & Fanchao Yi & Andrew Marcus & Taylor L. Davis & Richard E. Pratley & Bruce E. Rittmann & Rosa Krajmalnik-Brown & Steven R. Smith, 2023. "Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    15. Patrick A. Jonge & Koen Wortelboer & Torsten P. M. Scheithauer & Bert-Jan H. Born & Aeilko H. Zwinderman & Franklin L. Nobrega & Bas E. Dutilh & Max Nieuwdorp & Hilde Herrema, 2022. "Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    16. Fahad Paryani & Ji-Sun Kwon & Christopher W. Ng & Kelly Jakubiak & Nacoya Madden & Kenneth Ofori & Alice Tang & Hong Lu & Shengnan Xia & Juncheng Li & Aayushi Mahajan & Shawn M. Davidson & Anna O. Bas, 2024. "Multi-omic analysis of Huntington’s disease reveals a compensatory astrocyte state," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    17. Barbara B. Warner & Bruce A. Rosa & I. Malick Ndao & Phillip I. Tarr & J. Philip Miller & Sarah K. England & Joan L. Luby & Cynthia E. Rogers & Carla Hall-Moore & Renay E. Bryant & Jacqueline D. Wang , 2023. "Social and psychological adversity are associated with distinct mother and infant gut microbiome variations," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    18. Gertrude Ecklu-Mensah & Candice Choo-Kang & Maria Gjerstad Maseng & Sonya Donato & Pascal Bovet & Bharathi Viswanathan & Kweku Bedu-Addo & Jacob Plange-Rhule & Prince Oti Boateng & Terrence E. Forrest, 2023. "Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    19. Smitha Sukumar & Fang Wang & Carra A. Simpson & Cali E. Willet & Tracy Chew & Toby E. Hughes & Michelle R. Bockmann & Rosemarie Sadsad & F. Elizabeth Martin & Henry W. Lydecker & Gina V. Browne & Kyli, 2023. "Development of the oral resistome during the first decade of life," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    20. Shulei Wang, 2023. "Robust differential abundance test in compositional data," Biometrika, Biometrika Trust, vol. 110(1), pages 169-185.

    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_s41467-024-44720-6. 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.