Table 3.

Biospecimen type and testing plan

Sample type	Testing plan
Maternal vaginal swab	Vaginal microbiome
Maternal breast milk	sIgA, milk microbiome, metabolomics
Infant/child blood	Innate immune cell function, Treg cell profile, plasma lipidomics, allergen-specific and total IgE, cryopreservation
Infant/child nasal swab	Nasal microbiome, respiratory virus detection (surveillance)
Infant/child nasal illness swab	Respiratory virus detection (illness)
Child nasal brushinga	Transcriptomics
Infant/child stool	Gastrointestinal microbiome
Infant/child urine	Metabolomics
Infant/child skin swab	Skin microbiome
Infant/child saliva	Oral microbiome
Household airborne and vacuum dust	Environmental microbiome (bacterial and fungal)
Drinking water	Environmental microbiome
Barn airborne dust	Environmental microbiome (bacterial and fungal)
Farm milk	Microbiome, metabolomics

sIgA secreted immunoglobulin A, Treg T regulatory cell

^aObtained in subset of participants