title: Longitudinal Survey of Microbiota in Hospitalized Preterm Very-Low-Birth-Weight Infants.
abstract: OBJECTIVE
  The aim of the present study was to examine the changes in bacteria in hospitalized preterm infants during the first month of life.
  
  
  METHODS
  Rectal swabs were collected daily from 12 preterm infants. DNA was extracted from swabs from day of birth and weekly thereafter. Bacterial taxa were identified with next generation sequencing using universal bacterial primers targeted at the 16S ribosomal DNA on a 454 Roche titanium platform. Sequences were clustered into operational taxonomic units, and taxonomy was assigned against the Greengenes databank using Quantitative Insights Into Microbial Ecology version 1.4. Quantitative polymerase chain reaction was used to determine the abundance of Bifidobacterium spp. Functional assessment of the microbiome was performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt).
  
  
  RESULTS
  Average birth weight and gestational age were 1055 g and 28 weeks, respectively. There were 6 to 35 different bacterial families identified in the day-of-birth samples, unrelated to the mode of delivery. Richness decreased through hospitalization (week 1, 16.9 ± 7.7 vs weeks 3-5, 10.7 ± 3.4, P < 0.001). The Shannon diversity index demonstrated the lowest diversity at birth, an increase at week 2, followed by a rapid decline at weeks 3 to 5, suggesting the development of a more uniform microbiota composition after 2 weeks of stay at a neonatal intensive care unit. Enterobacteriaceae, Staphylococcaceae, and Enterococcaceae constituted the majority of the bacterial families. Bifidobacterium spp were infrequently detected at extremely low levels. PICRUSt analysis revealed the enhancement of peroxisome, PPAR, and adipocytokine signaling; plant-pathogen interaction; and aminobenzoate degradation pathways in week 1 samples.
  
  
  CONCLUSIONS
  Our results suggest that although preterm infants have individualized microbiota that are detectable at birth, the differences decrease during the neonatal intensive care unit hospitalization with increasing prominence of pathogenic microbiota.
authors.affiliation: *Rush University Medical Center, Chicago, IL †Texas Department of State Health Services, Austin ‡Research and Testing Laboratory, Lubbock, TX §University of Illinois at Chicago, Chicago ||WakeMed Health and Hospitals, Raleigh, NC.
authors.forename: Aloka L
authors.initials: AL
authors.lastname: Patel
authors.forename: Ece A
authors.initials: EA
authors.lastname: Mutlu
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.forename: Lars
authors.initials: L
authors.lastname: Koenig
authors.forename: Stefan
authors.initials: S
authors.lastname: Green
authors.forename: Andrew
authors.initials: A
authors.lastname: Jakubowicz
authors.forename: Janet
authors.initials: J
authors.lastname: Mryan
authors.forename: Phillip
authors.initials: P
authors.lastname: Engen
authors.forename: Louis
authors.initials: L
authors.lastname: Fogg
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Chen
authors.forename: Xavier
authors.initials: X
authors.lastname: Pombar
authors.forename: Paula P
authors.initials: PP
authors.lastname: Meier
authors.forename: Ali
authors.initials: A
authors.lastname: Keshavarzian
mesh_terms: D001419:Bacteria / Q000254:growth & development*; D001724:Birth Weight; D004269:DNA, Bacterial / Q000032:analysis; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D005865:Gestational Age; D059014:High-Throughput Nucleotide Sequencing; D006760:Hospitalization; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007234:Infant, Premature; D019102:Infant, Very Low Birth Weight; D007363:Intensive Care Units, Neonatal; D008137:Longitudinal Studies; D008297:Male; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S