Characterization of infant decal, maternal oral, and human milk microbiomes using 454 pyrosequencing

Mara Adrianne Riley

Objectives and hypotheses The objective of this study was to characterize the bacteria found in infant feces, maternal oral swabs, human milk, and formula using 454 pyrosequencing. We hypothesized that (1) infant feces is not sterile at birth, (2) fecal bacterial diversity increases with time, (3) structure of the fecal bacterial community shifts with time, (4) human milk and maternal oral swabs harbor a diverse microbial presence, and (5) human milk microbial community structure is more like that of infant feces than maternal oral swabs. Methods Infant fecal, human milk, formula, and maternal oral samples were obtained from 12 exclusively breastfed/breastfeeding and 2 exclusively formula-fed/formula feeding infant/mother pairs at 5 time points during the first 2 mo after birth. Samples were analyzed using 454 pyrosequencing (Roche Titanium FLX chemistry) using primers for the V1-V3 region of bacterial 16S rRNA gene. Results The infant fecal samples were found to contain microbial communities at birth which changed dramatically during the first few days of life. The most abundant bacteria found in meconium were Comamonas, Leuconostoc, and Lactococcus; Bacteroides, Veillonella, vi Parabacteroides, Escherichia/Shigella, and Streptococcus represented 51% of fecal bacteria at all remaining time points. Milk and oral samples also harbored diverse microbial communities with high relative abundances of Staphylococcus and/or Streptococcus. Conclusions In summary, our data confirm previous reports that meconium is not sterile, infant fecal microbiota change considerably in the first few days of life, and that fecal microbiota fluctuate for the first 2 mo of life; however, this microbial diversity decreased with time. Our data also support previous studies documenting bacteria in human milk. Maternal oral samples also contain a diverse microbial community, as previously reported. Milk microbial communities, however, were not found to be similar to those of infant feces. We also found preliminary evidence that infant formula is not sterile, and that feeding mode and possibly maternal antibiotic use influence the infant fecal microbiome. Additional work is needed to sequence the microbiota of other sample sites found on mother/infant pairs, such as infant oral cavity and maternal skin and to investigate their relationships with health.

Characterization of infant decal, maternal oral, and human milk microbiomes using 454 pyrosequencing

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