title: The neonatal gut harbours distinct bifidobacterial strains.
abstract: BACKGROUND
  Recent studies have described the bifidobacterial composition of neonates at a species level; however, with advancing technologies we can gain insight into the diversity of the bifidobacterial microbiota residing within the infant gut.
  
  
  OBJECTIVE
  To compare species and strain diversity of culturable bifidobacterial populations in faecal samples obtained from healthy term infants on three different feeding regimes.
  
  
  METHODS
  In total, 51 healthy term infants were recruited for this study and divided equally into three different groups (n=17) based on their feeding regime during the first 4 weeks of life. Culturable bifidobacterial populations were analysed at week 1, week 4 and 6 months of age. Isolates were characterised to species level by 16s rRNA-internally transcribed spacer (ITS) gene sequence analysis and to strain level by pulsed field gel electrophoresis (PFGE).
  
  
  RESULTS
  In total,173 bifidobacterial strains were detected across all three groups from 2295 isolates, 42% (72 of 173) of which were detected in the prebiotic-fed group, followed by 30% (52 of 173) and 28% (49 of 173) in the breastfed and non-prebiotic-fed groups, respectively. Surprisingly, only two of the 51 infants harboured an identical bifidobacterial strain which was not present in the other 49 infants. Prebiotic supplementation in the early neonatal period increased the prevalence of Bifidobacterium longum in infants, in addition to promoting strain diversity. B. longum was the dominant species recovered from all three groups during the first 6 months of life, followed by Bifidobacterium breve and Bifidobacterium bifidum.
  
  
  CONCLUSIONS
  This study reveals a hitherto unknown level of diversity at the strain level among bifidobacteria isolated from different infants and the influence prebiotic formula feeding has on the bifidobacterial population.
authors.affiliation: Teagasc Food Research Programme, Moorepark, Co. Cork, Ireland Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, National University of Ireland, Co. Cork, Ireland.
authors.forename: Eoin
authors.initials: E
authors.lastname: Barrett
authors.affiliation: Department of Paediatric and Child Health, University College Cork, National University of Ireland, Co. Cork, Ireland Department of Neonatology, Cork University Maternity Hospital, Co. Cork, Ireland.
authors.forename: A K
authors.initials: AK
authors.lastname: Deshpandey
authors.affiliation: Department of Paediatric and Child Health, University College Cork, National University of Ireland, Co. Cork, Ireland Department of Neonatology, Cork University Maternity Hospital, Co. Cork, Ireland.
authors.forename: C A
authors.initials: CA
authors.lastname: Ryan
authors.affiliation: Department of Paediatric and Child Health, University College Cork, National University of Ireland, Co. Cork, Ireland Department of Neonatology, Cork University Maternity Hospital, Co. Cork, Ireland.
authors.forename: Eugene M
authors.initials: EM
authors.lastname: Dempsey
authors.affiliation: Department of Paediatric and Child Health, University College Cork, National University of Ireland, Co. Cork, Ireland Department of Neonatology, Cork University Maternity Hospital, Co. Cork, Ireland.
authors.forename: Brendan
authors.initials: B
authors.lastname: Murphy
authors.affiliation: Teagasc Food Research Programme, Moorepark, Co. Cork, Ireland Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, National University of Ireland, Co. Cork, Ireland.
authors.forename: L
authors.initials: L
authors.lastname: O'Sullivan
authors.affiliation: Teagasc Food Research Programme, Moorepark, Co. Cork, Ireland Department of Microbiology, University College Cork, National University of Ireland, Co. Cork, Ireland.
authors.forename: C
authors.initials: C
authors.lastname: Watkins
authors.affiliation: Teagasc Food Research Programme, Moorepark, Co. Cork, Ireland Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, National University of Ireland, Co. Cork, Ireland.
authors.forename: R Paul
authors.initials: RP
authors.lastname: Ross
authors.affiliation: Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, National University of Ireland, Co. Cork, Ireland Department of Microbiology, University College Cork, National University of Ireland, Co. Cork, Ireland.
authors.forename: Paul W
authors.initials: PW
authors.lastname: O'Toole
authors.affiliation: Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, National University of Ireland, Co. Cork, Ireland Department of Microbiology, University College Cork, National University of Ireland, Co. Cork, Ireland.
authors.forename: Gerald F
authors.initials: GF
authors.lastname: Fitzgerald
authors.affiliation: Teagasc Food Research Programme, Moorepark, Co. Cork, Ireland Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, National University of Ireland, Co. Cork, Ireland.
authors.forename: Catherine
authors.initials: C
authors.lastname: Stanton
mesh_terms: D001644:Bifidobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001942:Breast Feeding; D016521:Electrophoresis, Gel, Pulsed-Field; D005243:Feces / Q000382:microbiology; D006801:Humans; D007223:Infant; D041943:Infant Formula / Q000737:chemistry; D007231:Infant, Newborn / Q000502:physiology*; D007422:Intestines / Q000382:microbiology*; D056692:Prebiotics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D056692:Prebiotics; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Infant Feeding; Microbiology; Nutrition