The goal of this prospective longitudinal cohort study is to examine how the human microbiome of pregnant women-including bacteria and fungi in the gastrointestinal tract, vaginal canal, skin, and breastmilk-may influence infant gut inflammation, measured by fecal calprotectin (FCP) levels, and to identify factors that could inform dietary interventions to improve infant health outcomes. Specifically, the study aims to determine which maternal gut microbiome characteristics and dietary patterns during pregnancy are associated with elevated FCP levels in infants, and which infant gut microbiota compositions and dietary factors are linked to high FCP levels. Researchers will compare microbiome signatures and dietary factors in pregnant women and their infants with active or inactive IBD, as well as non-IBD controls, to identify microbial patterns that may predict infant gut inflammation. Participants will provide fecal samples at all study timepoints, one vaginal swab during the third trimester of pregnancy, and optional breastmilk and breast skin swab samples. They will also complete 3-day diet recalls using a smartphone app and participate in a longitudinal follow-up over 12 months after birth to monitor dietary patterns, microbiome profiles, and gut inflammation in both mother and infant.

Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition that often presents during reproductive years, with approximately 25% of IBD patients having children after diagnosis. IBD during pregnancy can negatively impact infant health, as infants born to parents with IBD frequently exhibit higher fecal calprotectin (FCP) levels, a marker of gastrointestinal inflammation. Elevated FCP levels have been associated with increased risks of asthma, eczema, and IBD later in life. The purpose of this study is to examine how the maternal gut microbiome, diet, and breastmilk composition influence infant FCP levels and to identify factors that may guide dietary interventions to improve infant health outcomes. Specifically, the study aims to: (1) identify pregnancy-related maternal gut microbiota and dietary factors linked to elevated infant FCP levels, (2) determine infant gut microbiota and dietary factors associated with high FCP levels, (3) validate a supervised machine learning model capable of predicting high FCP levels in infants at 1 year of age using microbiota and dietary data, and (4) characterize human milk oligosaccharide (HMO) composition in breastmilk of mothers with and without IBD and its association with infant gut microbiota and FCP levels. This prospective study will evaluate changes in microbiota and dietary habits during and after pregnancy among maternal IBD patients (with active or quiescent disease) and non-IBD controls and their infants. Participants will be recruited during pregnancy (1st, 2nd, and early 3rd trimesters), and data and samples will be collected at four timepoints: 3rd trimester (week 34-35), 2 weeks postpartum, 3 months postpartum, and 1 year postpartum. Collected data will include 3-day dietary recalls, maternal and infant stool samples (for microbiota composition and FCP levels), optional breastmilk and breast skin swabs, vaginal swabs, and pregnancy and infant outcomes. These data will be integrated into a machine learning model to predict high infant FCP levels at 1 year, considering known covariates and factors identified in this study. The primary outcome is to determine the association between maternal gut microbiota composition-specifically the abundance of anti-inflammatory bacteria such as Faecalibacterium and Bifidobacterium-during the third trimester and early postpartum period, and infant FCP levels at 3 months and 1 year, accounting for maternal adherence to Mediterranean dietary patterns. Secondary outcomes include developing and validating a machine learning model for predicting elevated infant FCP at 1 year, characterizing and comparing HMO profiles between IBD and non-IBD mothers and their associations with infant gut microbiota and FCP levels, comparing pregnancy outcomes between mothers with ulcerative colitis, Crohn's disease, and non-IBD controls-including the impact of IBD therapy and mode of delivery-and examining the associations between maternal diet, microbiota composition (gut, skin, and vaginal), and pregnancy and infant outcomes across all study timepoints.

Inclusion Criteria:

All patients

• Pregnant individuals ≥19 years recruited during their first, second or early third trimester.
• Own or have regular access to a smartphone compatible with the study smartphone application RXFood.

IBD patients

● A documented IBD diagnosis (CD or UC) with active or quiescent disease.

Non-IBD controls ● Absence of IBD.

Exclusion Criteria:

All patients

• Inability to provide consent
• Previous gastrointestinal cancer or bowel surgery
• Renal disease
• HIV/AIDS or other serious infection
• Fetal chromosomal or structural abnormalities
• Other immune-mediated diseases (e.g., multiple sclerosis, rheumatoid arthritis, primary sclerosing cholangitis)
• Prebiotic, probiotic or postbiotic supplements in the month prior to first sample collection
• Gastroenteritis during or 1 month before the first sample collection
• Travel outside of Canada and the United States in the month prior to first sample collection

IBD patients

● Pregnant individuals with active perianal or extra-intestinal disease in IBD

The investigators aim to have a total of 80 pregnant participants enrolled before week 35 of gestation. Patient grouping for recruitment is as follows:Group 1: 40 pregnant participants with a confirmed diagnosis of IBD, including either Crohn's Disease (CD) or Ulcerative Colitis (UC). Participants will have varying disease severity levels as determined by their gastroenterologist using standardized scoring systems: SES-CD (Simple Endoscopic Score for Crohn's Disease) for CD patients and Mayo score for UC patients.Group 2: 40 Control Pregnant individuals without a diagnosis of IBD, matched as controls for comparison.