This dataset was collected for a study which examined differences in the gut microbiome within a cohort of 12-month old infants who provided samples either before the start of the COVID-19 pandemic or during the first 9 months of the pandemic. The study also assessed the demographics and health of the infants' primary caregivers, including factors such as race, ethnicity, socioeconomic status, mental health, diet, and lifestyle.

The study timeline is summarized below:

• April 2018 to December 2019: Infants were 3 months old. Caregivers completed demographic and mental health surveys.
• December 2018 to December 2020: Infants were 12 months old. Caregivers completed demographic and mental health surveys over the phone, a food diary for themselves and their infant, and submitted an infant stool sample by mail.

34 caregivers returned stool samples before March 22, 2020 (pre-pandemic group) and 20 caregivers returned stool samples after that date (pandemic group). Group characteristics can be found in Table 1 in the associated publication.