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

Jonathan L Golob; Tomiko T Oskotsky; Alice S Tang; Alennie Roldan; Verena Chung; Connie W Y Ha; Ronald J Wong; Kaitlin J Flynn; Antonio Parraga-Leo; Camilla Wibrand; Samuel S Minot; Boris Oskotsky; Gaia Andreoletti; Idit Kosti; Julie Bletz; Amber Nelson; Jifan Gao; Zhoujingpeng Wei; Guanhua Chen; Zheng-Zheng Tang; Pierfrancesco Novielli; Donato Romano; Ester Pantaleo; Nicola Amoroso; Alfonso Monaco; Mirco Vacca; Maria De Angelis; Roberto Bellotti; Sabina Tangaro; Abigail Kuntzleman; Isaac Bigcraft; Stephen Techtmann; Daehun Bae; Eunyoung Kim; Jongbum Jeon; Soobok Joe; Preterm Birth DREAM Community; Kevin R Theis; Sherrianne Ng; Yun S Lee; Patricia Diaz-Gimeno; Phillip R Bennett; David A MacIntyre; Gustavo Stolovitzky; Susan V Lynch; Jake Albrecht; Nardhy Gomez-Lopez; Roberto Romero; David K Stevenson; Nima Aghaeepour; Adi L Tarca; James C Costello; Marina Sirota

doi:10.1016/j.xcrm.2023.101350

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

Cell Rep Med. 2024 Jan 16;5(1):101350. doi: 10.1016/j.xcrm.2023.101350. Epub 2023 Dec 21.

Authors

Jonathan L Golob¹, Tomiko T Oskotsky², Alice S Tang³, Alennie Roldan³, Verena Chung⁴, Connie W Y Ha⁵, Ronald J Wong⁶, Kaitlin J Flynn⁴, Antonio Parraga-Leo⁷, Camilla Wibrand⁸, Samuel S Minot⁹, Boris Oskotsky¹⁰, Gaia Andreoletti³, Idit Kosti³, Julie Bletz⁴, Amber Nelson⁴, Jifan Gao¹¹, Zhoujingpeng Wei¹¹, Guanhua Chen¹¹, Zheng-Zheng Tang¹¹, Pierfrancesco Novielli¹², Donato Romano¹², Ester Pantaleo¹³, Nicola Amoroso¹⁴, Alfonso Monaco¹³, Mirco Vacca¹⁵, Maria De Angelis¹⁵, Roberto Bellotti¹³, Sabina Tangaro¹², Abigail Kuntzleman¹⁶, Isaac Bigcraft¹⁶, Stephen Techtmann¹⁶, Daehun Bae¹⁷, Eunyoung Kim¹⁷, Jongbum Jeon¹⁸, Soobok Joe¹⁸; Preterm Birth DREAM Community; Kevin R Theis¹⁹, Sherrianne Ng²⁰, Yun S Lee²⁰, Patricia Diaz-Gimeno²¹, Phillip R Bennett²⁰, David A MacIntyre²⁰, Gustavo Stolovitzky²², Susan V Lynch²³, Jake Albrecht⁴, Nardhy Gomez-Lopez²⁴, Roberto Romero²⁵, David K Stevenson²⁶, Nima Aghaeepour²⁷, Adi L Tarca²⁸, James C Costello²⁹, Marina Sirota³⁰

Affiliations

¹ 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.
² 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.
³ 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.
⁴ Sage Bionetworks, Seattle, WA, USA.
⁵ Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
⁶ Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; March of Dimes Prematurity Research Center at Stanford University, Stanford, CA, USA.
⁷ 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.
⁸ 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.
⁹ Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA.
¹⁰ Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA.
¹¹ Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.
¹² 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.
¹³ 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.
¹⁴ 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.
¹⁵ Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy.
¹⁶ Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA.
¹⁷ School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
¹⁸ Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
¹⁹ Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA.
²⁰ 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.
²¹ IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain.
²² 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.
²³ 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.
²⁴ 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.
²⁵ 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.
²⁶ Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Center for Academic Medicine, Stanford University School of Medicine, Stanford, CA, USA.
²⁷ 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.
²⁸ 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.
²⁹ Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
³⁰ 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.

Abstract

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.

Keywords: 16S harmonization; DREAM challenge; crowdsourced; machine learning; microbiome; predictive modeling; preterm birth; vaginal microbiome.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Crowdsourcing*
Female
Humans
Infant, Newborn
Microbiota* / genetics
Phylogeny
Pregnancy
Premature Birth*
Vagina

Abstract

Publication types

MeSH terms

Grants and funding