title: Factors influencing the composition of the intestinal microbiota in early infancy.
abstract: OBJECTIVE
  The aim of this study was to examine the contribution of a broad range of external influences to the gut microbiotic composition in early infancy.
  
  
  METHODS
  Fecal samples from 1032 infants at 1 month of age, who were recruited from the KOALA Birth Cohort Study in the Netherlands, were subjected to quantitative real-time polymerase chain reaction assays for the enumeration of bifidobacteria, Escherichia coli, Clostridium difficile, Bacteroides fragilis group, lactobacilli, and total bacterial counts. Information on potential determinants of the gut microbiotic composition was collected with repeated questionnaires. The associations between these factors and the selected gut bacteria were analyzed with univariate and multivariate analyses.
  
  
  RESULTS
  Infants born through cesarean section had lower numbers of bifidobacteria and Bacteroides, whereas they were more often colonized with C difficile, compared with vaginally born infants. Exclusively formula-fed infants were more often colonized with E coli, C difficile, Bacteroides, and lactobacilli, compared with breastfed infants. Hospitalization and prematurity were associated with higher prevalence and counts of C difficile. Antibiotic use by the infant was associated with decreased numbers of bifidobacteria and Bacteroides. Infants with older siblings had slightly higher numbers of bifidobacteria, compared with infants without siblings.
  
  
  CONCLUSIONS
  The most important determinants of the gut microbiotic composition in infants were the mode of delivery, type of infant feeding, gestational age, infant hospitalization, and antibiotic use by the infant. Term infants who were born vaginally at home and were breastfed exclusively seemed to have the most "beneficial" gut microbiota (highest numbers of bifidobacteria and lowest numbers of C difficile and E coli).
authors.affiliation: Department of Epidemiology, Nutrition and Toxicology Research Institute Maastricht, Maastricht University, PO Box 616, 6200 MD Maastricht, Netherlands. j.penders@epid.unimaas.nl
authors.forename: John
authors.initials: J
authors.lastname: Penders
authors.forename: Carel
authors.initials: C
authors.lastname: Thijs
authors.forename: Cornelis
authors.initials: C
authors.lastname: Vink
authors.forename: Foekje F
authors.initials: FF
authors.lastname: Stelma
authors.forename: Bianca
authors.initials: B
authors.lastname: Snijders
authors.forename: Ischa
authors.initials: I
authors.lastname: Kummeling
authors.forename: Piet A
authors.initials: PA
authors.lastname: van den Brandt
authors.forename: Ellen E
authors.initials: EE
authors.lastname: Stobberingh
mesh_terms: D000328:Adult; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D000935:Antifungal Agents / Q000494:pharmacology; D001419:Bacteria / Q000302:isolation & purification*; D001441:Bacteroides fragilis / Q000302:isolation & purification; D001644:Bifidobacterium / Q000302:isolation & purification; D001942:Breast Feeding; D002585:Cesarean Section; D016360:Clostridioides difficile / Q000302:isolation & purification; D015331:Cohort Studies; D036861:Delivery, Obstetric; D004926:Escherichia coli / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology*; D005260:Female; D005334:Fever / Q000453:epidemiology; D005865:Gestational Age; D006700:Home Childbirth; D006760:Hospitalization; D006801:Humans; D007223:Infant; D007225:Infant Food; D007231:Infant, Newborn; D007422:Intestines / Q000382:microbiology*; D007778:Lactobacillus / Q000302:isolation & purification; D008297:Male; D009426:Netherlands; D011247:Pregnancy; D011446:Prospective Studies; D035781:Siblings; D013045:Species Specificity; D011795:Surveys and Questionnaires
chemical_list: D000900:Anti-Bacterial Agents; D000935:Antifungal Agents