title: Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort.
abstract: The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192﻿) from 1 to 24 weeks of age.
  
  
  
  V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. The metabolomic profile of infant urine at 4 weeks of age was also examined by LC-MS.
  
  
  
  Full-term (FT), spontaneous vaginally delivered (SVD) infants' microbiota remained stable at both phylum and genus levels during the 24-week period examined. FT Caesarean section (CS) infants displayed an increased faecal abundance of Firmicutes (p < 0.01) and lower abundance of Actinobacteria (p < 0.001) after the first week of life compared to FT-SVD infants. FT-CS infants gradually progressed to harbouring a microbiota closely resembling FT-SVD (which remained stable) by week 8 of life, which was maintained at week 24. The gut microbiota of preterm (PT) infants displayed a significantly greater abundance of Proteobacteria compared to FT infants (p < 0.001) at week 1. Metabolomic analysis of urine at week 4 indicated PT-CS infants have a functionally different metabolite profile than FT (both CS and SVD) infants. Co-inertia analysis showed co-variation between the urine metabolome and the faecal microbiota of the infants. Tryptophan and tyrosine metabolic pathways, as well as fatty acid and bile acid metabolism, were found to be affected by delivery mode and gestational age.
  
  
  
  These findings confirm that mode of delivery and gestational age both have significant effects on early neonatal microbiota composition. There is also a significant difference between the metabolite profile of FT and PT infants. Prolonged breastfeeding was shown to have a significant effect on the microbiota composition of FT-CS infants at 24 weeks of age, but interestingly not on that of FT-SVD infants. Twins had more similar microbiota to one another than between two random infants, reflecting the influence of similarities in both host genetics and the environment on the microbiota.﻿.
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.|APC Microbiome Institute, University College Cork, Cork, Ireland.
authors.forename: Cian J
authors.initials: CJ
authors.lastname: Hill
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.|APC Microbiome Institute, University College Cork, Cork, Ireland.
authors.forename: Denise B
authors.initials: DB
authors.lastname: Lynch
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.|APC Microbiome Institute, University College Cork, Cork, Ireland.|Teagasc Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland.
authors.forename: Kiera
authors.initials: K
authors.lastname: Murphy
authors.affiliation: Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'adige, Italy.
authors.forename: Marynka
authors.initials: M
authors.lastname: Ulaszewska
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.
authors.forename: Ian B
authors.initials: IB
authors.lastname: Jeffery
authors.affiliation: Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland.
authors.forename: Carol Anne
authors.initials: CA
authors.lastname: O'Shea
authors.affiliation: Teagasc Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland.
authors.forename: Claire
authors.initials: C
authors.lastname: Watkins
authors.affiliation: Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland.
authors.forename: Eugene
authors.initials: E
authors.lastname: Dempsey
authors.affiliation: Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'adige, Italy.
authors.forename: Fulvio
authors.initials: F
authors.lastname: Mattivi
authors.affiliation: Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'adige, Italy.
authors.forename: Kieran
authors.initials: K
authors.lastname: Tuohy
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.|APC Microbiome Institute, University College Cork, Cork, Ireland.
authors.forename: R Paul
authors.initials: RP
authors.lastname: Ross
authors.affiliation: APC Microbiome Institute, University College Cork, Cork, Ireland.|Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland.
authors.forename: C Anthony
authors.initials: CA
authors.lastname: Ryan
authors.affiliation: School of Microbiology, University College Cork, Cork, Ireland.|APC Microbiome Institute, University College Cork, Cork, Ireland.
authors.forename: Paul W
authors.initials: PW
authors.lastname: O' Toole
authors.affiliation: APC Microbiome Institute, University College Cork, Cork, Ireland. Catherine.stanton@teagasc.ie.|Teagasc Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland. Catherine.stanton@teagasc.ie.
authors.forename: Catherine
authors.initials: C
authors.lastname: Stanton
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001942:Breast Feeding; D002585:Cesarean Section; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D005260:Female; D000069196:Gastrointestinal Microbiome; D006801:Humans; D007231:Infant, Newborn; D055432:Metabolomics / Q000379:methods; D010802:Phylogeny; D011247:Pregnancy; D047928:Premature Birth / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D014556:Urine / Q000737:chemistry*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S