Journal
ISME COMMUNICATIONS
Volume 1, Issue 1, Pages -Publisher
SPRINGERNATURE
DOI: 10.1038/s43705-021-00003-5
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Funding
- Fondation Andr et Henriette Losch
- CORE programme [CORE/15/BM/104040, CORE/C15/SR/10404839, CORE Junior/14/BM/8066232, AFR PHD-2013-5824125, AFR PHD-2014-1/7934898]
- Fondation Andre et Henriette Losch
- Luxembourg National Research Fund (FNR) [CORE/15/BM/104040, CORE/C15/SR/10404839, CORE Junior/14/BM/8066232, AFR PHD-2013-5824125, AFR PHD-2014-1/7934898, ATTRACT/A09/03]
- European Research Council [ERC-CoG 863664]
- Luxembourg National Research Fund [PRIDE17/11823097]
- Synergia grant through the Swiss National Science Foundation [CRSII5_180241]
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig of the German Research Foundation [FZT 118 - 202548816]
- Integrated BioBank of Luxembourg under the Personalised Medicine Consortium Diabetes programme
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The study found distinct enrichments of certain microbial populations in infants born by Caesarean section delivery at 1 year of age, while other microbes were found at higher levels in the vaginal delivery group. Additionally, immune cell stimulation with CSD extracts resulted in higher levels of tumour necrosis factor alpha compared to VD extracts. The results demonstrate persistent effects at 1 year of age due to differences in gut microbiome colonization based on birth mode.
Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-& alpha;) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation.
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