Exploring the Early-Life Microbiomes of Preterm Infants and Their Childhood Health Outcomes (The BLOOM Study): Protocol for a Prospective, Observational Cohort Study.

Michelle R Asbury, Andrea Guedez, Jessica Lee, Emily M Mercer, Fatimoh Kasaba, Zahra Rangipour, James D Kellner, Thierry Lacaze-Masmonteil, Jumana Samara, Lara M Leijser, Catherine Lebel, Hussein Zein, Leonora Hendson, Luis Murguía Favela, Kelly McNagny, Gerald F Giesbrecht, Laura Sycuro, Belal Alshaikh, Marie-Claire Arrieta

Journal: JMIR research protocols 2026;15():e95658

PMID: 42612036

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Abstract

BACKGROUND

Establishment of the gut microbiome during the first years of life is critically important for long-term health and development. In preterm infants, microbial colonization is disrupted due to their developmental immaturity and the myriad of pre- and postnatal exposures. Unfortunately, this places them at an elevated risk for adverse health outcomes into childhood (eg, asthma and impaired neurodevelopment). Understanding the developmental trajectory of the microbiome in preterm infants, the factors predicting these microbial patterns, and the links to childhood health can offer opportunities to develop interventions and optimize health.

OBJECTIVE

BLOOM (Begin a Life of Health With Observation and Optimization of the Microbiome) is a prospective, observational cohort study that aims to examine how early-life microbiomes shape the health and development of preterm infants into childhood (eg, asthma and neurodevelopment).

METHODS

Infants (<37 weeks gestation) and their families are recruited from 4 neonatal intensive care units in Calgary, Alberta, Canada. Maternal stool and weekly infant stool, urine, and human milk samples are collected during the first 2 months postnatally; participants are then followed up at 3 months, 1 year, and 3 years corrected age for continued data (eg, nutrition, medications, medical history, and home environment) and sample collection (stool, urine, nasal swabs, hair, and blood). Additional clinical testing (eg, allergen skin prick test) and questionnaires (eg, Ages & Stages Questionnaires, Third Edition) are administered to assess health outcomes and developmental milestones.

RESULTS

Study recruitment and data/sample collection for BLOOM commenced in 2019; as of May 2026, we have enrolled 245 participants, and recruitment is ongoing. An initial characterization of early-life microbiome profiles for the first 105 infants enrolled in BLOOM was published online in December 2025.

CONCLUSIONS

BLOOM is a large, comprehensive prospective cohort study and biobank aimed at measuring the microbiome development of preterm-born children. This cohort will address significant research priorities through characterizing the patterns of microbiome development in preterm infants over the first 3 years postnatally and correlating these with health outcomes (eg, immune development, asthma and allergy risks, and neurodevelopment). It is anticipated that the results can be leveraged to identify factors and altered microbiome patterns underlying disease risk, design intervention strategies (eg, microbial therapeutics) for later clinical testing, and generate novel hypotheses of possible underlying mechanisms linking microbiome development to health.

© Marie-Claire Arrieta, Andrea Guedez, Belal Alshaikh, Catherine Lebel, Emily M Mercer, Fatimoh Kasaba, Gerald Giesbrecht, Hussein Zein, James Kellner, Jumana Samara, Lara Leijser, Laura Sycuro, Leonora Hendson, Luis Murguia Favela, Michelle Asbury, Thierry Lacaze-Masmontiel, Zahra Rangipour, Jessica Lee, Kelly McNagny. Originally published in JMIR Research Protocols (https://www.researchprotocols.org).

Address: Department of Physiology & Pharmacology, University of Calgary, 3330 Hospital Dr NW, HRIC Room 4A25, Calgary, AB, T2N 1N4, Canada, 1 403-220-7803, 1 403-220-7803.; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Section of Hematology and Immunology, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada.; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.; Section of Hematology and Immunology, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada.; Biomedical Research Centre, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.; Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.

DOI: 10.2196/95658

MeSH Terms: Humans, Prospective Studies, Infant, Newborn, Infant, Premature, Infant, Female, Gastrointestinal Microbiome, Male, Child, Preschool, Alberta, Microbiota, Child Development, Feces