Prenatal household size and composition are associated with infant fecal bacterial diversity in Cebu, Philippines

Abstract

Objectives The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members. Materials and Methods As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition. Results Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables. Conclusions Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM.

Contact with caregivers is associated with composition of the infant gastrointestinal microbiome in the first 6 months of life

“…In a large, multi‐country study, Lane et al (2019) did not detect associations between household composition and gastrointestinal microbiome diversity, although household size and the presence of extended family were nonlinearly associated with the differential abundance of specific taxa, including Enterobacter and Lactobacillus . Manus et al (2023) reported that prenatal household size predicted Shannon (alpha) diversity in infancy, although the association was negative at 2 weeks of age and positive at 6 months of age. However, Thompson et al (2015) found that infants, aged 2–14 months, enrolled in out‐of‐home daycare had higher diversity and species richness compared to infants cared for at home, as well as significantly greater Lactobacillus and Sutterella .…”

“…For example, Lane et al (2019) sequenced the V1‐V3 region of the 16S rRNA gene, used unrarefied data to generate alpha diversity, used Observed Richness instead of Chao1, and conducted differential abundance tests with the Analysis of Compositions of Microbiomes (ANCOM) rather than DESeq2. Manus et al (2023) sequenced the V4‐V5 region and also used ANCOM. Thompson et al (2015) sequenced the V1‐V2 region of the 16 s rRNA gene and used rarefied data but also used Observed Richness.…”