Table 4.

Data collection and terminology considerations for pregnancy and infant microbiome studies

MATERNAL CONSIDERATIONS
Domain	Exposures	Timing
Demographics	Age at study entry; Ethnicity; Socioeconomic status; Parity; Health conditions (especially allergic or immune disease)	At recruitment
Antibiotic use	Indication; Type; Duration of use; Number of Courses	Within 6 months of conception, during pregnancy and/or during delivery
Probiotic use	Type/Strain; Frequency of use; Duration of use	Within 6 months of conception and during pregnancy
Anthropometry	Weight; Height; BMI; GWG. Ideal: Waist-To-Hip Ratio; Body Composition (Fat Mass; Fat-Free Mass)	At conception and across pregnancy Ideal: at least thrice in pregnancy
Dietary intake	Dietary patterns; Nutrient intake; Dietary Diversity; Fiber intake; Dietary Supplement Intake (type, frequency and duration of use)	Within 6 months of conception and during pregnancy Ideal: at least twice in pregnancy
Diabetes status	Diagnosis of type I or type II diabetes mellitus prior to conception; Diagnosis of GDM; Diagnosis of Insulin Resistance; Metformin use; Insulin use	At conception and across pregnancy
Mental health	Stress; Self-Efficacy; Mental Illness (Depression; Anxiety; Others)	At conception and during pregnancy Ideal: at least twice in pregnancy
Medications (e.g. PPIs, steroids)	Indication; Type; Duration; Number of Courses	Within 6 months of conception, during pregnancy and/or during delivery
Others as specific/pertinent to research questions, e.g. sleep, household size, social support, health literacy, air pollution, pet ownership, etc.		As relevant to outcomes of interest
INFANT CONSIDERATIONS
Domain	Exposures	Timing
Demographics	Gender; Gestational Age; Siblings (Number; Ages)	At birth
Birth mode	Vaginal delivery; Surgically assisted delivery; Spontaneous or Induced; Indication for cesarean delivery, if applicable)	At birth
Antibiotic use	Indication; Type; Duration of use; Number of Courses	At birth and any exposure across the first 1,000 days
Probiotic use	Type/Strain; Frequency of use; Duration of use; Indication (if applicable)	Any exposure across the first 1,000 days
Anthropometry	Weight; Length; Weight-for-Length Ideal: Body Composition (Fat Mass; Fat-Free Mass)	At birth, 6 months, 12 months and 24 months Ideal: whenever dietary intake is assessed
Breastmilk or Formula feeding	Breastfeeding; Formula-feeding; Mixed-feeding; Duration of Exclusive Breastfeeding; Total Duration of Any Breastfeeding; Total Duration of Formula-Feeding; Type of Formula (Standard; Hydrolyzed; Prebiotic-Containing)	From birth and across the first 1,000 days, at least four times (e.g. 0–3 months, 4–6 months, 8–12 months and 12–24 months)
Solid food intake	Age at Introduction to Solids; Dietary patterns; Nutrient intake; Dietary Diversity; Fiber intake; Texture	From 4 to 24 months, at least three times (e.g. 4–6 months, 8–12 months and 12–24 months)
Medications	Indication; Type; Duration; Number of Courses	At birth and any exposure across the first 1,000 days
Others as specific/pertinent to research questions, e.g. neurocognitive development, sleep, household size, air pollution, pet ownership, etc.		As relevant to outcomes of interest
METHODOLOGICAL CONSIDERATIONS
Domain	Outcomes/considerations
Overall design	Recruitment methods and dropout rates clearly described; Comparisons made between participants and those lost to follow up, by exposure status; Main potential confounders are identified and accounted for in study design and analysis; Randomization and concealment occur where possible.
Terminology	Concepts or terms used to describe the gut microbiome should be consistent across studies.
Microbiome analysis	Use of culture independent methodology (e.g. 16S rRNA gene sequencing, metagenomic sequencing); Measures of composition (e.g. total bacterial counts, relative abundance); Measure of diversity (e.g. Shannon and Simpson indices) and richness (e.g. Chao1); Appropriate OTU classification (to amplicon sequence variants, or metagenomic strains); Use of compositional data analytical approaches; Clear reporting of methodologies used and limitations of same.
Sampling frequency	Longitudinal measurement across the first 1,000 days, with most infant samples after 2 weeks, e.g., Mothers in early pregnancy (0–12 weeks); Mothers in late pregnancy (32–40 weeks); Infants at 1–3 months (prior to introduction of solids); Infants at 4–6 months (when solids have been introduced); Infants at 9–12 months (increasing dietary diversity and complexity, possible weaning formula and/or breastfeeding, introduction of other milks).

BMI = Body Mass Index; GWG = Gestational Weight Gain; GDM = Gestational Diabetes Mellitus; PPI = Proton Pump Inhibitor; OTU = Operational Taxonomic Unit.