IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-32805-z.html
   My bibliography  Save this article

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome

Author

Listed:
  • Shuqin Zeng

    (Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University)

  • Dhrati Patangia

    (University College Cork
    Moorepark, Fermoy
    University College Cork)

  • Alexandre Almeida

    (University of Cambridge
    European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus)

  • Zhemin Zhou

    (Pasteurien College, Medical College of Soochow University, Soochow University)

  • Dezhi Mu

    (Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University)

  • R. Paul Ross

    (University College Cork
    University College Cork)

  • Catherine Stanton

    (University College Cork
    Moorepark, Fermoy)

  • Shaopu Wang

    (Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University)

Abstract

Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life.

Suggested Citation

  • Shuqin Zeng & Dhrati Patangia & Alexandre Almeida & Zhemin Zhou & Dezhi Mu & R. Paul Ross & Catherine Stanton & Shaopu Wang, 2022. "A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32805-z
    DOI: 10.1038/s41467-022-32805-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-32805-z
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-32805-z?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. Fiona Fouhy & Claire Watkins & Cian J. Hill & Carol-Anne O’Shea & Brid Nagle & Eugene M. Dempsey & Paul W. O’Toole & R. Paul Ross & C. Anthony Ryan & Catherine Stanton, 2019. "Perinatal factors affect the gut microbiota up to four years after birth," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    2. Oonagh E Keag & Jane E Norman & Sarah J Stock, 2018. "Long-term risks and benefits associated with cesarean delivery for mother, baby, and subsequent pregnancies: Systematic review and meta-analysis," PLOS Medicine, Public Library of Science, vol. 15(1), pages 1-22, January.
    3. Junjie Qin & Ruiqiang Li & Jeroen Raes & Manimozhiyan Arumugam & Kristoffer Solvsten Burgdorf & Chaysavanh Manichanh & Trine Nielsen & Nicolas Pons & Florence Levenez & Takuji Yamada & Daniel R. Mende, 2010. "A human gut microbial gene catalogue established by metagenomic sequencing," Nature, Nature, vol. 464(7285), pages 59-65, March.
    4. Christopher J. Stewart & Nadim J. Ajami & Jacqueline L. O’Brien & Diane S. Hutchinson & Daniel P. Smith & Matthew C. Wong & Matthew C. Ross & Richard E. Lloyd & HarshaVardhan Doddapaneni & Ginger A. M, 2018. "Temporal development of the gut microbiome in early childhood from the TEDDY study," Nature, Nature, vol. 562(7728), pages 583-588, October.
    5. Tommi Vatanen & Eric A. Franzosa & Randall Schwager & Surya Tripathi & Timothy D. Arthur & Kendra Vehik & Åke Lernmark & William A. Hagopian & Marian J. Rewers & Jin-Xiong She & Jorma Toppari & Anette, 2018. "The human gut microbiome in early-onset type 1 diabetes from the TEDDY study," Nature, Nature, vol. 562(7728), pages 589-594, October.
    6. Hothorn, Torsten & Hornik, Kurt & van de Wiel, Mark A. & Zeileis, Achim, 2006. "A Lego System for Conditional Inference," The American Statistician, American Statistical Association, vol. 60, pages 257-263, August.
    7. Stephen Nayfach & Zhou Jason Shi & Rekha Seshadri & Katherine S. Pollard & Nikos C. Kyrpides, 2019. "New insights from uncultivated genomes of the global human gut microbiome," Nature, Nature, vol. 568(7753), pages 505-510, April.
    8. Brandon Brooks & Matthew R. Olm & Brian A. Firek & Robyn Baker & Brian C. Thomas & Michael J. Morowitz & Jillian F. Banfield, 2017. "Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome," Nature Communications, Nature, vol. 8(1), pages 1-7, December.
    9. Ohad Manor & Chengzhen L. Dai & Sergey A. Kornilov & Brett Smith & Nathan D. Price & Jennifer C. Lovejoy & Sean M. Gibbons & Andrew T. Magis, 2020. "Health and disease markers correlate with gut microbiome composition across thousands of people," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    10. Yan Shao & Samuel C. Forster & Evdokia Tsaliki & Kevin Vervier & Angela Strang & Nandi Simpson & Nitin Kumar & Mark D. Stares & Alison Rodger & Peter Brocklehurst & Nigel Field & Trevor D. Lawley, 2019. "Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth," Nature, Nature, vol. 574(7776), pages 117-121, October.
    11. Alexandre Almeida & Alex L. Mitchell & Miguel Boland & Samuel C. Forster & Gregory B. Gloor & Aleksandra Tarkowska & Trevor D. Lawley & Robert D. Finn, 2019. "A new genomic blueprint of the human gut microbiota," Nature, Nature, vol. 568(7753), pages 499-504, April.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Shuqin Zeng & Alexandre Almeida & Shiping Li & Junjie Ying & Hua Wang & Yi Qu & R. Paul Ross & Catherine Stanton & Zhemin Zhou & Xiaoyu Niu & Dezhi Mu & Shaopu Wang, 2024. "A metagenomic catalog of the early-life human gut virome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

    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. Li Zhang & Karen R. Jonscher & Zuyuan Zhang & Yi Xiong & Ryan S. Mueller & Jacob E. Friedman & Chongle Pan, 2022. "Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Shuqin Zeng & Alexandre Almeida & Shiping Li & Junjie Ying & Hua Wang & Yi Qu & R. Paul Ross & Catherine Stanton & Zhemin Zhou & Xiaoyu Niu & Dezhi Mu & Shaopu Wang, 2024. "A metagenomic catalog of the early-life human gut virome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Fiona B. Tamburini & Dylan Maghini & Ovokeraye H. Oduaran & Ryan Brewster & Michaella R. Hulley & Venesa Sahibdeen & Shane A. Norris & Stephen Tollman & Kathleen Kahn & Ryan G. Wagner & Alisha N. Wade, 2022. "Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. Bin Zhu & David J. Edwards & Katherine M. Spaine & Laahirie Edupuganti & Andrey Matveyev & Myrna G. Serrano & Gregory A. Buck, 2024. "The association of maternal factors with the neonatal microbiota and health," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    5. Aneta Słabuszewska-Jóźwiak & Jacek Krzysztof Szymański & Michał Ciebiera & Beata Sarecka-Hujar & Grzegorz Jakiel, 2020. "Pediatrics Consequences of Caesarean Section—A Systematic Review and Meta-Analysis," IJERPH, MDPI, vol. 17(21), pages 1-17, October.
    6. Justine Tanoey & Christina Baechle & Hermann Brenner & Andreas Deckert & Julia Fricke & Kathrin Günther & André Karch & Thomas Keil & Alexander Kluttig & Michael Leitzmann & Rafael Mikolajczyk & Nadia, 2022. "Birth Order, Caesarean Section, or Daycare Attendance in Relation to Child- and Adult-Onset Type 1 Diabetes: Results from the German National Cohort," IJERPH, MDPI, vol. 19(17), pages 1-14, August.
    7. Julien Tap & Franck Lejzerowicz & Aurélie Cotillard & Matthieu Pichaud & Daniel McDonald & Se Jin Song & Rob Knight & Patrick Veiga & Muriel Derrien, 2023. "Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    8. Chan Yeong Kim & Junyeong Ma & Insuk Lee, 2022. "HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    9. Thomas A. Auchtung & Christopher J. Stewart & Daniel P. Smith & Eric W. Triplett & Daniel Agardh & William A. Hagopian & Anette G. Ziegler & Marian J. Rewers & Jin-Xiong She & Jorma Toppari & Åke Lern, 2022. "Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    10. Shaojun Pan & Chengkai Zhu & Xing-Ming Zhao & Luis Pedro Coelho, 2022. "A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    11. Chiranjib Chakraborty & Ashish Ranjan Sharma & Garima Sharma & Manojit Bhattacharya & Sang-Soo Lee, 2023. "Exploring the status of global terrestrial and aquatic microbial diversity through ‘Biodiversity Informatics’," Environment, Development and Sustainability: A Multidisciplinary Approach to the Theory and Practice of Sustainable Development, Springer, vol. 25(10), pages 10567-10598, October.
    12. Diletta Maria Francesca Ingrosso & Maria Teresa Quarta & Alessia Quarta & Francesco Chiarelli, 2023. "Prevention of Type 1 Diabetes in Children: A Worthy Challenge?," IJERPH, MDPI, vol. 20(11), pages 1-15, May.
    13. Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    14. Ziye Wang & Ronghui You & Haitao Han & Wei Liu & Fengzhu Sun & Shanfeng Zhu, 2024. "Effective binning of metagenomic contigs using contrastive multi-view representation learning," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    15. Mingyue Cheng & Shuai Luo & Peng Zhang & Guangzhou Xiong & Kai Chen & Chuanqi Jiang & Fangdian Yang & Hanhui Huang & Pengshuo Yang & Guanxi Liu & Yuhao Zhang & Sang Ba & Ping Yin & Jie Xiong & Wei Mia, 2024. "A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    16. Sigal Leviatan & Saar Shoer & Daphna Rothschild & Maria Gorodetski & Eran Segal, 2022. "An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    17. Eric W. Seabloom & Maria C. Caldeira & Kendi F. Davies & Linda Kinkel & Johannes M. H. Knops & Kimberly J. Komatsu & Andrew S. MacDougall & Georgiana May & Michael Millican & Joslin L. Moore & Luis I., 2023. "Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    18. Ruairi C. Robertson & Thaddeus J. Edens & Lynnea Carr & Kuda Mutasa & Ethan K. Gough & Ceri Evans & Hyun Min Geum & Iman Baharmand & Sandeep K. Gill & Robert Ntozini & Laura E. Smith & Bernard Chasekw, 2023. "The gut microbiome and early-life growth in a population with high prevalence of stunting," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    19. Jae-Chang Cho, 2021. "Human microbiome privacy risks associated with summary statistics," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-11, April.
    20. Joe J. Lim & Christian Diener & James Wilson & Jacob J. Valenzuela & Nitin S. Baliga & Sean M. Gibbons, 2023. "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes," Nature Communications, Nature, vol. 14(1), pages 1-13, 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:13:y:2022:i:1:d:10.1038_s41467-022-32805-z. 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.