Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.

16S harmonization DREAM challenge crowdsourced machine learning microbiome predictive modeling preterm birth vaginal microbiome

Journal

Cell reports. Medicine
ISSN: 2666-3791
Titre abrégé: Cell Rep Med
Pays: United States
ID NLM: 101766894

Informations de publication

Date de publication:
21 Dec 2023
Historique:
received: 28 03 2023
revised: 15 09 2023
accepted: 01 12 2023
medline: 23 12 2023
pubmed: 23 12 2023
entrez: 22 12 2023
Statut: aheadofprint

Résumé

Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; <37 weeks) or (2) early preterm birth (ePTB; <32 weeks) from 9 vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from public raw data via phylogenetic harmonization. The predictive models are validated on two independent unpublished datasets representing 331 samples from 148 pregnant individuals. The top-performing models (among 148 and 121 submissions from 318 teams) achieve area under the receiver operator characteristic (AUROC) curve scores of 0.69 and 0.87 predicting PTB and ePTB, respectively. Alpha diversity, VALENCIA community state types, and composition are important features in the top-performing models, most of which are tree-based methods. This work is a model for translation of microbiome data into clinically relevant predictive models and to better understand preterm birth.

Identifiants

DOI: 10.1016/j.xcrm.2023.101350 PMID: 38134931
pubmed: 38134931
pii: S2666-3791(23)00567-0
doi: 10.1016/j.xcrm.2023.101350
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

101350

Informations de copyright

Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests S.V.L. is a board member at, holds stock in, and consults for Siolta Therapeutics. She also consults for the Atria Academy of Science and Medicine and for Sanofi. J.C.C. is co-founder of PrecisionProfile and OncoRx Insights. N.Aghaeepour. is a member of the scientific advisory boards of January AI, Parallel Bio, Celine Therapeutics, and WellSim Biomedical Technologies and is a paid consultant for Mara BioSystems. J.G. and M.S. have filed a patent related to the phylotype generation process.

Auteurs

Jonathan L Golob (JL)

Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA. Electronic address: golobj@umich.edu.

Tomiko T Oskotsky (TT)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA. Electronic address: tomiko.oskotsky@ucsf.edu.

Alice S Tang (AS)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.

Alennie Roldan (A)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.

Verena Chung (V)

Sage Bionetworks, Seattle, WA, USA.

Connie W Y Ha (CWY)

Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.

Ronald J Wong (RJ)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; March of Dimes Prematurity Research Center at Stanford University, Stanford, CA, USA.

Kaitlin J Flynn (KJ)

Sage Bionetworks, Seattle, WA, USA.

Antonio Parraga-Leo (A)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain; IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain.

Camilla Wibrand (C)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.

Samuel S Minot (SS)

Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Boris Oskotsky (B)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA.

Gaia Andreoletti (G)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.

Idit Kosti (I)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.

Julie Bletz (J)

Sage Bionetworks, Seattle, WA, USA.

Amber Nelson (A)

Sage Bionetworks, Seattle, WA, USA.

Jifan Gao (J)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.

Zhoujingpeng Wei (Z)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.

Guanhua Chen (G)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.

Zheng-Zheng Tang (ZZ)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.

Pierfrancesco Novielli (P)

Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy.

Donato Romano (D)

Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy.

Ester Pantaleo (E)

Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy.

Nicola Amoroso (N)

Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Bari, Italy.

Alfonso Monaco (A)

Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy.

Mirco Vacca (M)

Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy.

Maria De Angelis (M)

Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy.

Roberto Bellotti (R)

Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy.

Sabina Tangaro (S)

Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy.

Abigail Kuntzleman (A)

Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA.

Isaac Bigcraft (I)

Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA.

Stephen Techtmann (S)

Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA.

Daehun Bae (D)

School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.

Eunyoung Kim (E)

School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.

Jongbum Jeon (J)

Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.

Soobok Joe (S)

Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.

Kevin R Theis (KR)

Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA.

Sherrianne Ng (S)

Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

Yun S Lee (YS)

Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

Patricia Diaz-Gimeno (P)

IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain.

Phillip R Bennett (PR)

Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

David A MacIntyre (DA)

Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

Gustavo Stolovitzky (G)

Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA; Thomas J. Watson Research Center, IBM, Yorktown Heights, NY, USA; Sema4, Stamford, CT, USA.

Susan V Lynch (SV)

Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.

Jake Albrecht (J)

Sage Bionetworks, Seattle, WA, USA.

Nardhy Gomez-Lopez (N)

Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA.

Roberto Romero (R)

Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Detroit Medical Center, Detroit, MI, USA; Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA.

David K Stevenson (DK)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Center for Academic Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Nima Aghaeepour (N)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA, USA.

Adi L Tarca (AL)

Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA.

James C Costello (JC)

Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.

Marina Sirota (M)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA. Electronic address: marina.sirota@ucsf.edu.

Classifications MeSH