RT Journal Article
SR Electronic
T1 Delivery mode impacts newborn gut colonization efficiency
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.01.29.919993
DO 10.1101/2020.01.29.919993
A1 Caroline Mitchell
A1 Larson Hogstrom
A1 Allison Bryant
A1 Agnes Bergerat
A1 Avital Cher
A1 Shawna Pochan
A1 Penelope Herman
A1 Maureen Carrigan
A1 Karen Sharp
A1 Curtis Huttenhower
A1 Eric S. Lander
A1 Hera Vlamakis
A1 Ramnik J. Xavier
A1 Moran Yassour
YR 2020
UL http://biorxiv.org/content/early/2020/01/29/2020.01.29.919993.abstract
AB Delivery mode is the variable with the greatest influence on the infant gut microbiome composition in the first few months of life. Children born by Cesarean section (C-section) lack species from the Bacteroides genus in their gut microbial community, and this difference can be detectable until 6-18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome, as children born by C-section do not pass through the birth canal; however, Bacteroides species are not common members of the vaginal microbiome, thus this explanation seems inadequate. Here, we set out to re-evaluate this hypothesis by collecting rectal and vaginal samples before delivery from 73 mothers with paired stool from their infants in the first two weeks of life. We compared microbial profiles of infants born by planned, pre-labor C-section to those born by emergent, post-labor surgery (where the child was in the birth canal, but eventually delivered through an abdominal incision), and found no significant differences in the microbiome between these two groups. Both groups showed the characteristic signature lack of Bacteroides species, despite their difference in exposure to the birth canal. Surprisingly, this signature was only evident in samples from week two of life, but not in the first week. Children born by C-section often had high abundance of Bacteroides in their first few days of life, but these were not stable colonizers of the infant gut, as they were not detectable by week two. Finally, we used metagenomic sequencing to compare microbial strains in maternal vaginal and rectal samples and samples from their infants; we found evidence for mother-to-child transmission of rectal rather than vaginal strains. These results challenge birth canal exposure as the dominant factor in infant gut microbiome establishment and implicate colonization efficiency rather than exposure as a dictating factor of the newborn gut microbiome composition.