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| ID | Type | Description | Link |
|---|---|---|---|
| MRT-168043 | Other Grant/Funding Number | CIHR |
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| Name | Class |
|---|---|
| Unity Health Toronto | OTHER |
| University of Toronto | OTHER |
| University of Calgary | OTHER |
| Dalhousie University |
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This study is being conducted to investigate how a mother's nutritional status and her gut microbiome during pregnancy contribute to the birth outcomes and health of her baby. The gut microbiome is the totality of microorganisms (e.g. bacteria, viruses, fungi) living in the gastrointestinal tract. This study will focus on pregnant women, 28 years and younger living in the Toronto and greater Toronto area. The focus is on younger women due to their vulnerability to undernutrition. Pregnant participants, and upon delivery, their newborns will be followed throughout pregnancy and for a year afterwards. Throughout this period, the investigators will collect stool samples, rectal swabs, blood samples, health assessments, nutritional and dietary assessments and birth/ labour details. The goal is to define the relationship between a mother's nutritional status and her microbiome dynamics during pregnancy and how they contribute to the birth outcomes and growth of her newborn. With the hypothesis that alterations of the microbiota in the maternal gut (dysbiosis) exacerbated by nutritional status or pathogen exposure during pregnancy, impacts weight gain because of impaired nutrient absorption, leading to corresponding negative birth outcomes.
This project represents the first systematic investigation of the impact of the microbiome on nutritional status during pregnancy in young women and directly aligns with global health initiatives focused on this vulnerable cohort. The goal of the study is to define the relationships between host nutritional status and microbiome dynamics during pregnancy and how they contribute to birth outcomes. The gut microbiome has a profound influence on host nutritional status. Dysbiosis (loss of diversity/beneficial microbes and gain of pathobionts) has emerged as a major factor in the development of undernutrition. Despite the importance of nutrition during pregnancy, few studies have examined the role of the microbiome on maternal health and birth outcomes. Further, little is known concerning the influence of enteric eukaryotic microbes, such as parasites, on the bacterial microbiome and host nutrition.
At the core of this study are two complementary cohorts of young women that provide an exceptional opportunity to obtain longitudinal samples to monitor the dynamic relationships between microbiome community structure and function with gut health and host nutritional status. This registration is for the the Toronto cohort of the study, which will focus on refugee and young adult obstetric clinics in Toronto, a population of specific relevance to undernutrition. This cohort is expected to yield insights into the influence of eukaryotic microbes that are often viewed as asymptomatic. The target demographic of the study is young mothers, 28 years of age and younger, in the Toronto and Greater Toronto Area. The investigators have identified this younger demographic due to the lack of knowledge on the microbiome of young women, and their vulnerability to undernutrition. A second complementary cohort will be based in the Matiari district of Pakistan. This project will yield unprecedented insights into the relationships between prokaryotic and eukaryotic microbes in the gut and their associations with maternal health and birth outcomes.
The central hypothesis of the study is that alterations of the microbiota in the maternal gut (dysbiosis) exacerbated by nutritional status or pathogen exposure during pregnancy, impacts weight gain because of impaired nutrient absorption, leading to corresponding negative birth outcomes.
The study will be a prospective, longitudinal, observational study to investigate the impact and relationship between prokaryotic and eukaryotic microbes in the gut and their association with maternal health and birth outcomes among young women, 28 years of age and younger in the Toronto and Greater Toronto Area. The study will aim to recruit 400 women into two groups based on BMI at time of recruitment (Normal BMI will be defined as between 20 and 24.9 kg/m2 and Low BMI will be defined as less than 20 kg/m2). With a goal of having 200 participants within the normal BMI group and 200 participants within the low BMI group. Although this is the recruitment aim, in the event that the investigators are unable to recruit 200 women with a low BMI, more women will be recruited that fall within the normal BMI range. The study will follow women and their infants over the course of their pregnancy and for a year post-partum, collecting stool, rectal and blood samples, nutritional information, heath assessments, anthropometric measurements and empowerment metrics at different time points.
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| Measure | Description | Time Frame |
|---|---|---|
| To assess if alterations of the microbiota in the maternal gut (dysbiosis) are associated with changes in maternal gestational weight gain. | The primary endpoint will be the change in maternal gestational weight gain (GWG) during pregnancy, measured between the first (8-20 weeks post-conception) and second time point (30-34 weeks post conception). | 8-20 weeks post-conception, 30-34 weeks post conception |
| Measure | Description | Time Frame |
|---|---|---|
| Anthropometrics: Maternal BMI | calculated using weight and height; BMI = kg/m2 | 8-20 weeks post-conception, 30-34 weeks post-conception, delivery, 3-months post-partum, 6 months post-partum and 12 months post-partum |
| Anthropometrics: Maternal middle upper arm circumference |
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Inclusion Criteria:
Exclusion Criteria:
Biological sex: as the study's primary aim is to investigate pregnancy, participation will be restricted to participants who are biologically female. However, the study is inclusive with respect to gender, including both cis-gendered and trans-gendered participants (biological female-to-male).
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The study population will consist of pregnant women, 28 years of age and younger, living in the Toronto and Greater Toronto Area. The investigators focus on younger women, due to the lack of knowledge about their microbiome and their vulnerability to undernutrition
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| Name | Affiliation | Role |
|---|---|---|
| John Parkinson, PHD | The Hospital for Sick Children | Principal Investigator |
| Shazeen Suleman, MD | Unity Health Toronto | Principal Investigator |
| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| St. Michael's Hospital | Toronto | Canada | ||||
| The Hospital for Sick Children |
In addition to publishing findings in open access journals, the investigators will ensure all sequences and metabolomics datasets are deposited in appropriate public repositories. SOPs, pathogen samples and statistical methods developed through this project will be shared with the IMPACTT research core (https://www.impactt-microbiome.ca/). Microbiome sequence data will be uploaded on the National Centre for Biotechnology Information (NCBI).
The NCBI acts as a central data repository for sequence data. In line with publication standards, the investigators are required to provide access to users who may wish to follow up on analyzing the microbiome data for their own purposes.
The sample analysis information, including the sequencing data and metabolomics data will be de-identified and the patient sequence data will be removed.
All sequence and metabolomics data will be made available within 12 months of study completion Supporting information will be shared at time of request
Supporting information will be shared upon request Sequence and metabolomics datasets will be made available without restriction
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| Type | Includes Protocol | Includes SAP | Includes ICF | Document Label | Document Date | Document Uploaded Date | Document File Name |
|---|---|---|---|---|---|---|---|
| Prot_SAP | Yes | Yes | No | Study Protocol and Statistical Analysis Plan | Oct 6, 2025 |
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| OTHER |
| Aga Khan University | OTHER |
| University of Alberta | OTHER |
| National Institute of Allergy and Infectious Diseases (NIAID) | NIH |
| Canadian Institutes of Health Research (CIHR) | OTHER_GOV |
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The following samples will be collected: blood samples, stool samples and rectal swabs.
Participants will have the option to have their blood samples biobanked for future genetic testing (This would be a separate study application in the future).
More information on sample analysis can be found in section 10 of the protocol
Measured in cm |
| 8-20 weeks post-conception, 30-34 weeks post-conception, 3-months post-partum,and 12 months post-partum |
| Anthropometrics: Maternal triceps skinfold thickness | Measured in cm | 8-20 weeks post-conception, 30-34 weeks post-conception, 3-months post-partum, and 12 months post-partum |
| Anthropometrics: Maternal height | Measured in cm | 8-20 weeks post conception, 30-34 weeks post conception, delivery, 3 months post-partum and 12 months post partum |
| Anthropometrics: Maternal weight | Measured in kg | 8-20 weeks post conception, 30-34 weeks post conception, delivery, 3 months post-partum and 12 months post-partum |
| Maternal blood biomarkers | Concentration of HB + MCV, ferritin, and CRP | 8-20 weeks post-conception, 30-34 weeks post-conception, and 12 months post-partum |
| Infant blood biomarkers | Concentration of HB + MCV, ferritin, and CRP | 12 months |
| Infant sex | Female or Male | Determined at delivery |
| Infant morbidity | Assessed through infant health assessment questionnaires | 3 months, 6 months and 12 months |
| Maternal morbidity | Assessed through health assessment questionnaires | 8-20 weeks post-conception, 30-34 weeks post-conception, 3 months post-partum, 6 months post-partum and 12 months post-partum |
| Infant growth: weight | Measured in kg | within 24 hours of birth, 3 months, 6 months and 12 months |
| Infant growth: length | Measured in cm | within 24 hours of birth, 3 months, 6 months and 12 months |
| Infant growth: head circumference | Measured in cm | within 24 hours of birth, 3 months, 6 months and 12 months |
| Infant growth: mid upper arm circumference | Measured in cm | within 24 hours of birth, 3 months, 6 months and 12 months |
| Infant growth: triceps skinfold thickness | Measured in cm | within 24 hours of birth, 3 months, 6 months and 12 months |
| Infant Gestational age | Will be documented at baseline visit. | 8-20 weeks post conception |
| Breast feeding: amount and initiation of complementary feeding | Based off of WHO 2010 Guidelines: Indicators for assessing infant and young child feeding practices (Part 2 Measurement) | within 24 hours of birth, 3 months, 6 months and 12 months |
| Maternal age | 28 years or younger | Documented at 8-20 weeks post-conception |
| Reported maternal medication use | [Questionnaire] | 8-20 weeks post-conception, 30-34 weeks post-conception, within 24 hours of delivery, 3-months post-partum, 6 months post-partum and 12 months post-partum |
| Reported Infant medication use | [Questionnaire] | within 24 hours of birth, 3 months, 6 months and 12 months |
| Maternal dietary intake | Assessed through ASA 24 HR Dietary Recall system, completed 2x each time point | 8-20 weeks post conception, 30-34 weeks post conception and 12 months post partum |
| Dietary diversity | Minimum Dietary Diversity Score for Women (MDD-W) | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post-partum and 12 months post partum |
| Household annual food insecurity | Food insecurity will be assessed using the Household Food Insecurity Access Scale (HFIAS) | 3 months post-partum and 12 months post-partum |
| Self-efficacy | Self-efficacy will be measured using the Generalized Self-Efficacy scale, developed by Schwarzer and Jerusalem | 3 months post-partum and 12 months post partum |
| Perceived decision making | Questions pertaining to perceived decision-making are from the Pakistan Demographic and Health Survey (PDHS) | 3 months post-partum and 12 months post partum |
| Perceived social support | Perceived social support will be measured using the Multi-dimensional Scale of Perceived Social Support (MSPSS), developed by Zimet et al. | 3 months post-partum and 12 months post partum |
| Maternal demographics | Questions pertaining to demographic data are adapted from the Pakistan Demographic and Health Survey (PDHS) | 8-20 weeks post-conception |
| Food insecurity | Questionnaire developed by Hager, E.R., et al., Development and validity of a 2-item screen to identify families at risk for food insecurity. | 8-20 weeks post conception, 3 months post partum and 12 months post partum |
| Perceived parental stress | Perceived parental stress will be measured using the Perceived Stress Scale (PSS-10) | 3 months post-partum and 12 months post partum |
| Preterm birth | noted in labor and birth chart review | Within 24 hours of birth |
| Stillbirth | noted in labor and birth chart review | Within 24 hours of birth |
| Small for gestational age | noted in labor and birth chart review | Within 24 hours of birth |
| Large for gestational age | noted in labor and birth chart review | Within 24 hours of birth |
| Birth size: length | Measured in cm | within 24 hours of birth |
| Birth size: head circumference | Measured in cm | within 24 hours of birth |
| Birth size: weight | Measured in kg | within 24 hours of birth |
| Birth defects | Assessed within 24 hours of birth | within 24 hours of birth |
| Delivery assessment | Assessed within 24 hours of birth | within 24 hours of birth |
| Infant dietary intake: NutricheQ Questionnaire | NutricheQ questionnaire: a tool designed for toddlers aged 1 to 3 years of age, with a focus on markers for inadequate or excessive intake and dietary imbalances | 12 months |
| Maternal stool biomarkers: Calprotectin, Lipocalin and Claudin 15 | Markers in the stool for intestinal mass, inflammation, and gut permeability and circulating lipopolysaccharide, among other markers | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Infant Stool biomarkers: Calprotectin, Lipocalin and Claudin 15 | Markers in the stool for intestinal mass, inflammation, and gut permeability and circulating lipopolysaccharide, among other markers | 3 months and 12 months |
| Maternal: incidence of pathobionts | As identified through 16S, 18S and ITS rDNA surveys | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Infant: incidence of pathobionts | As identified through 16S, 18S and ITS rDNA surveys | 3 months and 12 months |
| Maternal: metabolomic profile of stool (metabolites involved in central metabolism as analysed by Mass Spectrometry) | Analysis of the core metabolites involved in central metabolism. These metabolites will be analysed through Mass Spec and include short chain fatty acids, amino acids, intermediates in energy metabolism and nucleotide biosynthesis | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Maternal gut bacteria profile as measured through 16S rDNA sequence surveys | measured through 16S rDNA sequence surveys | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Maternal: blood metallomics profile as measured through ICP-MS (https://www.metabolomicscentre.ca/new_service/25) | TMIC Metallomics Platform to be used. | 8-20 weeks post conception, 30-34 weeks post conception, and 12 months post partum |
| Infant: blood metallomics profile as measured through ICP-MS (https://www.metabolomicscentre.ca/new_service/25) | Through TMIC platform | 12 months |
| Infant: gut bacterial profile as measured through 16S rDNA sequence surveys | measured through 16S rDNA sequence surveys | 3 and 12 months post partum |
| Maternal metabolic pathway expression profile as measured through whole microbiome RNASeq (metatranscriptomics) | measured through whole microbiome RNASeq (metatranscriptomics) | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Infant eukaryotic microbiome profile as measured through 18S and ITS rDNA sequence surveys | measured through 18S and ITS rDNA sequence surveys | 3 months and 12 months |
| Maternal eukaryotic microbiome profile as measured through 18S and ITS rDNA sequence surveys | measured through 18S and ITS rDNA sequence surveys | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Maternal bacterial gene expression profile as measured through whole microbiome RNASeq (metatranscriptomics) | The output of these analyses are readouts of microbial gene expression detailing biochemical activities as well as the taxa responsible. | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Maternal: microbiome taxonomic alpha and beta diversity | To define taxonomic diversity, species profiles from 16S, 18S and ITS rDNA data will be clustered to identify differences in community structure across samples. Alpha diversity will be measured through indices such as Chao, Shannon and Simpson indices. Beta diversity will be measured through standard indices such as Bray-Curtis distances. | 8-20 weeks post conception, 30-34 weeks post conception, 3 months post partum and 12 months post partum |
| Infant: microbiome taxonomic alpha and beta diversity | To define taxonomic diversity, species profiles from 16S, 18S and ITS rDNA data will be clustered to identify differences in community structure across samples. Alpha diversity will be measured through indices such as Chao, Shannon and Simpson indices. Beta diversity will be measured through standard indices such as Bray-Curtis distances. | 3 months and 12 months |
| Toronto |
| Canada |
| Apr 22, 2026 |
| Prot_SAP_004.pdf |
| ICF | No | No | Yes | Informed Consent Form | Dec 30, 2024 | Apr 22, 2026 | ICF_005.pdf |
| ID | Term |
|---|---|
| D011248 | Pregnancy Complications |
| D010272 | Parasitic Diseases |
| D003141 | Communicable Diseases |
| D044342 | Malnutrition |
| D007228 | Infant Nutrition Disorders |
| D001942 | Breast Feeding |
| ID | Term |
|---|---|
| D005261 | Female Urogenital Diseases and Pregnancy Complications |
| D000091642 | Urogenital Diseases |
| D007239 | Infections |
| D020969 | Disease Attributes |
| D010335 | Pathologic Processes |
| D013568 | Pathological Conditions, Signs and Symptoms |
| D009748 | Nutrition Disorders |
| D009750 | Nutritional and Metabolic Diseases |
| D005247 | Feeding Behavior |
| D001519 | Behavior |
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