title: The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing.
abstract: OBJECTIVE
  An increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (<1200 g) critically ill infants at three different time points during the first two months of life by using 16S rRNA gene specific sequencing.
  
  
  METHODS
  Stool samples were collected at the age of one week, one month and two months. Bacterial community profiling was done using universal amplification of 16S rRNA gene and 454 pyrosequencing.
  
  
  RESULTS
  The diversity of gut microbiota in preterm neonates in the first week of life was low but increased significantly over two months. The gut microbiota was dominated by facultative anaerobic bacteria (Staphylococcus spp. and Enterobacteriaceae) and lacked colonization with bacteria known to provide resistance against pathogens (Bacteroides, Bifidobacterium, and Lactobacillus) throughout the study. Colonization of Escherichia coli and uncultured Veillionella was positively correlated with maturity. Infants born to mothers with chorioamnionitis had significantly higher bacterial diversity than those without.
  
  
  CONCLUSIONS
  High prevalence and abundance of potentially pathogenic Enterobacteriaceae and Staphylococcaceae with low prevalence and abundance of colonization resistance providing taxa bifidobacteria, Bacteroides and lactobacilli may lead to high infection risk via microbial translocation from the gut. Additionally, our data suggest that maternal chorioamnionitis may have an effect on the diversity of infants' gut microbiota; however, the mechanisms involved remain to be elucidated.
authors.affiliation: Institute of Microbiology; University of Tartu; Tartu, Estonia; Centre for Biology of Integrated Systems; Tallinn University of Technology; Tallinn, Estonia; Competence Centre on Reproductive Medicine and Biology; Tartu, Estonia.
authors.forename: Tiina
authors.initials: T
authors.lastname: Drell
authors.affiliation: Institute of Microbiology; University of Tartu; Tartu, Estonia.
authors.forename: Irja
authors.initials: I
authors.lastname: Lutsar
authors.affiliation: Institute of Microbiology; University of Tartu; Tartu, Estonia.
authors.forename: Jelena
authors.initials: J
authors.lastname: Stšepetova
authors.affiliation: Institute of Microbiology; University of Tartu; Tartu, Estonia.
authors.forename: Ulle
authors.initials: U
authors.lastname: Parm
authors.affiliation: Institute of Microbiology; University of Tartu; Tartu, Estonia; Anaesthesiology and Intensive Care Clinic; Tartu University Hospital; Tartu, Estonia.
authors.forename: Tuuli
authors.initials: T
authors.lastname: Metsvaht
authors.affiliation: Department of Anaesthesiology and Intensive Care; Tallinn Children's Hospital; Tallinn, Estonia.
authors.forename: Mari-Liis
authors.initials: ML
authors.lastname: Ilmoja
authors.affiliation: Centre for Biology of Integrated Systems; Tallinn University of Technology; Tallinn, Estonia.
authors.forename: Jaak
authors.initials: J
authors.lastname: Simm
authors.affiliation: Institute of Microbiology; University of Tartu; Tartu, Estonia.
authors.forename: Epp
authors.initials: E
authors.lastname: Sepp
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D058448:Biota; D016000:Cluster Analysis; D016638:Critical Illness; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D041981:Gastrointestinal Tract / Q000382:microbiology*; D020459:Genes, rRNA; D006801:Humans; D007223:Infant; D052577:Infant, Extremely Low Birth Weight; D007231:Infant, Newborn; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA gene sequencing; extremely low birth weight; gut microbiota; microbiome profiling; preterm neonates