234 - Inclusion of Early Neonatal Timepoint in Longitudinal Skin Microbiome Investigation Reveals Complexity in Shifting Bacterial Abundances During the First Year of Life

Publication Number: 234.5507

Jennifer Schoch, University of Florida College of Medicine, Ponte Vedra Beach, FL, United States; Ryleigh Griffin, National Institutes of Health, Bethesda, MD, United States; Peng Hou, NIAMS/NIH, Bethesda, MD, United States; Mary Bohannon, University of Florida College of Medicine, Gainesville, FL, United States; Han Li, University of Florida College of Medicine, Gainesville, FL, United States; Leslie Parker, University of Florida College of Medicine, Gainesville, FL, United States; Dominick J. Lemas, University of Florida College of Medicine, Gainesville, FL, United States; Heidi H. Kong, NIH/NIAMS, Bethesda, MD, United States

Background: Recent studies have demonstrated that exposure to skin microbes during the early neonatal period may be critical for skin immunity development. Presently, longitudinal investigations into the development of the infant skin microbiome that include this potentially critical period are limited.

Objective: In a pilot study, we used 16S rRNA sequencing to characterize the bacterial communities present on the skin of 4 infant/mother pairs at 2 weeks, 2 months, and 12 months after birth.

Design/Methods: We recruited four infant-mother dyads and collected skin swabs from both mother and infant volar forearms and infant cheeks when the infant was age 2 weeks, 2 months, and 12 months. All subjects provided written informed consent. Sterile flocked swabs were moistened with sterile saline and rubbed on the skin in alternating directions for 20 seconds.

Genomic DNA and amplified target regions were quantified using the Quant-IT™ PicoGreen™ dsDNA Assay Kit. Samples were prepared using KAPA HiFi Polymerase (KAPA Biosystems) to amplify variable regions 1-3 (27F/534R) of the 16S rRNA gene. Sequence reads were merged using FLASH2, truncated to 400 nt and processed using DADA2 (v1.30.0). Taxonomic assignment was based on the Silva database.

Results: The bacterial communities of 2-week-old infant skin displayed site-specific signatures with a general predominance of Firmicutes. At 12 months, infant skin microbiomes displayed a higher relative abundance of Proteobacteria. Beta diversity analysis showed that by 12 months, the bacterial skin microbiomes at the volar forearm of infants began to more closely resemble those of their mothers. Alpha diversity of infant skin microbiomes increased with infant age, trending towards maternal diversity by 12 months. Importantly, the inclusion of the neonatal timepoint (2 weeks) revealed trends in changing relative abundances of common skin bacterial genera, specifically Staphylococcus, to be more complex and variable than previously reported.

Conclusion(s): Taken together, these results emphasize the importance of including early neonatal timepoints when studying the skin microbiome during the first year of life.

Skin microbiomes in infants are skin site-specific as early as 2 weeks of age and transition over first year of life
Fig1.pdf(a) Relative abundance of skin microbiomes of mother-infant pairs at three timepoints. Infant cheek (IC), infant antecubital fossa (IA), maternal antecubital fossa (MA) are shown. For Firmicutes and Actinobacteria, top two most abundant genera are displayed. Within Staphylococcus, selected commensal species are displayed. (b) Principal coordinate analysis (PCoA) of Bray-Curtis. Circles denote IA samples while triangles denote MA samples. Points are colored by timepoint.

Infant skin microbiomes more closely resemble mothers by 12 months of age after undergoing shifts in predominant bacterial taxa
Fig2.pdf(a) Shannon Diversity Index of infant and maternal samples from antecubital fossa at each time point. (b) Relative abundances of selected genera on infant skin at each skin site and time point.