title: Temporal dynamics of the very premature infant gut dominant microbiota.
abstract: BACKGROUND
  The very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of high-throughput studies validate and renew the interest in approaches with lower resolution such as PCR-Temporal Temperature Gel Electrophoresis (TTGE) for the follow-up of dominant microbiota dynamics. We report here an extensive longitudinal study of gut colonization in very preterm infants. We explored by 16S rDNA-based PCR-TTGE a total of 354 stool specimens sampled during routine monitoring from the 1(st) to the 8(th) week of life in 30 very pre-term infants born before 30 weeks of gestational age.
  
  
  RESULTS
  Combining comparison with a diversity ladder and sequencing allowed affiliation of 50 Species-Level Operational Taxonomic Units (SLOTUs) as well as semi-quantitative estimation of Operational Taxonomic Units (OTUs). Coagulase-negative staphylococci, mainly the Staphylococcus epidermidis, was found in all the infants during the study period and was the most represented (75.7% of the SLOTUs) from the first days of life. Enterococci, present in 60% of the infants were early, highly represented and persistent colonizers of the premature gut. Later Enterobacteriaceae and the genus Clostridium appeared and were found in 10 (33%) and 21 infants (70%), respectively. We showed a high representation of Veillonella in more than a quarter of the infants and being able to persistently colonize premature gut. The genera Anaerococcus, Aquabacterium, Bacillus, Bifidobacterium, Corynebacterium, Micrococcus, Oceanobacillus, Propionibacterium, Pseudomonas, Rothia, Sarcina, Sneathia and Streptococcus were observed as transient or persistent colonizers, each genus being found in a minority of infants.
  
  
  CONCLUSIONS
  Despite low resolution, PCR-TTGE remains complementary to high-throughput sequencing-based approaches because it allows the follow-up of dominant bacteria in gut microbiota in a large longitudinal cohorts of preterm neonates. We described the development of pre-term gut microbiota that should be now replaced regarding the functional role of major OTUs.
authors.affiliation: Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France. fabien.aujoulat@univ-montp1.fr.
authors.forename: Fabien
authors.initials: F
authors.lastname: Aujoulat
authors.affiliation: Centre Hospitalier de Fréjus, Laboratoire de bactériologie, 240 avenue de Saint-Lambert BP 110 83608, Fréjus, France. roudiere-l@chi-frejus-saint-raphael.fr.
authors.forename: Laurent
authors.initials: L
authors.lastname: Roudière
authors.affiliation: Hospices Civil de Lyon, Service de Néonatalogie, 103, Grande-Rue de la Croix-Rousse, Lyon, Cedex 04, 69317, France. jean-charles.picaud@chu-lyon.fr.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Picaud
authors.affiliation: Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Lapeyronie, Département Urgences pédiatriques, 371, Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France. a-jacquot@chu-montpellier.fr.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Jacquot
authors.affiliation: Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France. a-filleron@chu-montpellier.fr.|Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Service de néo-natalogie, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France. a-filleron@chu-montpellier.fr.
authors.forename: Anne
authors.initials: A
authors.lastname: Filleron
authors.affiliation: Centre Hospitalier Universitaire de Montpellier, Département d'Information Médicale, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France. dorine.neveu@univ-montp1.fr.
authors.forename: Dorine
authors.initials: D
authors.lastname: Neveu
authors.affiliation: Centre Hospitalier Universitaire de Montpellier, Département d'Information Médicale, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France. tpbaum.chu.mpt@gmail.com.
authors.forename: Thierry-Pascal
authors.initials: TP
authors.lastname: Baum
authors.affiliation: Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France. helene.marchandin@univ-montp1.fr.|Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, Montpellier, Cedex 5, 34295, France. helene.marchandin@univ-montp1.fr.
authors.forename: Hélène
authors.initials: H
authors.lastname: Marchandin
authors.affiliation: Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France. ebilak@univ-montp1.fr.|Centre Hospitalier Universitaire de Montpellier, Laboratoire d'Hygiène hospitalière, 778, Rue de la Croix Verte, Montpellier, 34000, France. ebilak@univ-montp1.fr.
authors.forename: Estelle
authors.initials: E
authors.lastname: Jumas-Bilak
mesh_terms: D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007234:Infant, Premature; D008137:Longitudinal Studies; D064307:Microbiota; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S