title: Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease.
abstract: BACKGROUND
  The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease.
  
  
  RESULTS
  A core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples. Gut microbiota profiles grouped into six distinct clusters, termed preterm gut community types (PGCTs). Each PGCT reflected dominance by the core operational taxonomic units (OTUs), except of PGCT 6, which had high diversity and was dominant in bifidobacteria. While PGCTs 1-5 were present in infants prior to NEC diagnosis, PGCT 6 was comprised exclusively of healthy samples. NEC infants had significantly more PGCT transitions prior to diagnosis. Metabolomic profiling identified significant pathways associated with NEC onset, with metabolites involved in linoleate metabolism significantly associated with NEC diagnosis. Notably, metabolites associated with NEC were the lowest in PGCT 6.
  
  
  CONCLUSIONS
  This is the first study to integrate sequence and metabolomic stool analysis in preterm neonates, demonstrating that NEC does not have a uniform microbial signature. However, a diverse gut microbiome with a high abundance of bifidobacteria may protect preterm infants from disease. These results may inform biomarker development and improve understanding of gut-mediated mechanisms of NEC.
authors.affiliation: Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom. cs12@bcm.edu.|Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA. cs12@bcm.edu.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Stewart
authors.affiliation: Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom.
authors.forename: Nicholas D
authors.initials: ND
authors.lastname: Embleton
authors.affiliation: Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, United Kingdom.
authors.forename: Emma C L
authors.initials: EC
authors.lastname: Marrs
authors.affiliation: Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA.
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Smith
authors.affiliation: Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Nelson
authors.affiliation: Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom.
authors.forename: Bashir
authors.initials: B
authors.lastname: Abdulkadir
authors.affiliation: Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom.
authors.forename: Tom
authors.initials: T
authors.lastname: Skeath
authors.affiliation: Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA.
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Petrosino
authors.affiliation: Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, United Kingdom.
authors.forename: John D
authors.initials: JD
authors.lastname: Perry
authors.affiliation: Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom.
authors.forename: Janet E
authors.initials: JE
authors.lastname: Berrington
authors.affiliation: Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom.|School of Science and Engineering, Teesside University, Middlesbrough, TS1 3BX, United Kingdom.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Cummings
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D020345:Enterocolitis, Necrotizing / Q000378:metabolism / Q000382:microbiology*; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome; D006801:Humans; D007231:Infant, Newborn; D007234:Infant, Premature; D007235:Infant, Premature, Diseases / Q000378:metabolism / Q000382:microbiology*; D019787:Linoleic Acid / Q000378:metabolism; D008137:Longitudinal Studies; D008297:Male; D053858:Metabolic Networks and Pathways; D010802:Phylogeny; D040901:Proteomics / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D019787:Linoleic Acid
keywords: Gut microbiome; Metabolomics; Necrotising enterocolitis; Preterm infant