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For decades, babies were thought to be born germ-free, but recent evidences suggest that they are already exposed to various bacteria  in utero . However, the data on population levels of such pioneer gut bacteria, particularly in context to birth mode, is sparse. We herein aimed to quantify such bacteria from the meconium of 151 healthy term Japanese infants born vaginally or by C-section. Neonatal first meconium was obtained within 24–48 h of delivery; RNA was extracted and subjected to reverse-transcription-quantitative PCR using specific primers for  Clostridium coccoides  group,  C. leptum  subgroup,  Bacteroides fragilis  group,  Atopobium  cluster,  Prevotella, Bifidobacterium ,  Lactobacillus ,  Enterococcus , Enterobacteriaceae,  Staphylococcus ,  Enterococcus ,  Streptococcus ,  C. perfringens , and  C. difficile . We detected several bacterial groups in both vaginally- and cesarean-born infants.  B. fragilis  group, Enterobacteriaceae,  Enterococcus ,  Streptococcus , and  Staphylococcus  were detected in more than 50% of infants, with counts ranging from 10 5  to 10 8  cells/g sample. About 30–35% samples harbored  Bifidobacterium  and  Lactobacillus  (10 4 –10 5  cells/g); whereas  C. coccoides  group,  C. leptum  subgroup and  C. perfringens  were detected in 10–20% infants (10 3 –10 5  cells/g). Compared to vaginally-born babies, cesarean-born babies were significantly less often colonized with  Lactobacillus  genus (6% vs. 37%;  P  = 0.01) and  Lactobacillus gasseri  subgroup (6% vs. 31%;  P  = 0.04). Overall, seven  Lactobacillus  subgroups/species, i.e.,  L. gasseri  subgroup,  L. ruminis  subgroup,  L. casei  subgroup,  L. reuteri  subgroup,  L. sakei  subgroup,  L. plantarum  subgroup, and  L. brevis  were detected in the samples from vaginally-born group, whereas only two members, i.e.,  L. gasseri  subgroup and  L. brevis  were detected in the cesarean group. These data corroborate that several bacterial clades may already be present before birth in term infants’ gut. Further, lower detection rate of lactobacilli in cesarean-born babies suggests that the primary source of lactobacilli in infant gut is mainly from maternal vaginal and–to a lesser extent–anal microbiota during vaginal delivery, and that the colonization by some important  Lactobacillus  species is delayed in babies delivered via cesarean-section.

Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section