Temporal dynamics of the very premature infant gut dominant microbiota
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)...
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Published in | BMC microbiology Vol. 14; no. 1; p. 325 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
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BioMed Central Ltd
31.12.2014
BioMed Central |
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Abstract | 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.
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.
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. |
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AbstractList | 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 1st to the 8th 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. 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. 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. 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. 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.sup.st to the 8.sup.th week of life in 30 very pre-term infants born before 30 weeks of gestational age. 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. 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. BACKGROUNDThe 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.RESULTSCombining 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.CONCLUSIONSDespite 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. Background : The very-preterm infant gut microbiota is increasingly explored due to its probable role in thedevelopment of life threatening diseases. Results of high-throughput studies validate and renew the interest inapproaches with lower resolution such as PCR-Temporal Temperature Gel Electrophoresis (TTGE) for the follow-upof dominant microbiota dynamics. We report here an extensive longitudinal study of gut colonization in verypreterm infants. We explored by 16S rDNA-based PCR-TTGE a total of 354 stool specimens sampled during routinemonitoring from the 1stto the 8thweek 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-LevelOperational Taxonomic Units (SLOTUs) as well as semi-quantitative estimation of Operational Taxonomic Units (OTUs).Coagulase-negative staphylococci, mainly theStaphylococcus epidermidis, was found in all the infants during the studyperiod and was the most represented (75.7% of the SLOTUs) from the first days of life. Enterococci, present in 60% ofthe infants were early, highly represented and persistent colonizers of the premature gut. LaterEnterobacteriaceaeandthe genusClostridiumappeared and were found in 10 (33%) and 21 infants (70%), respectively. We showed a highrepresentation of Veillonellain 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, Sneathiaand Streptococcuswere observed as transient or persistentcolonizers, each genus being found in a minority of infants. Conclusions : Despite low resolution, PCR-TTGE remains complementary to high-throughput sequencing-basedapproaches because it allows the follow-up of dominant bacteria in gut microbiota in a large longitudinal cohorts ofpreterm neonates. We described the development of pre-term gut microbiota that should be now replaced regardingthe functional role of major OTUs. 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.sup.st to the 8.sup.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. Keywords: Extremely low birth weight Infant, Stool, Microbiota, Follow-up, PCR-TTGE, Diversity, Dynamics, Staphylococcus, Enterococcus, Clostridium, Enterobacteriaceae, Veillonellaceae |
ArticleNumber | 325 |
Audience | Academic |
Author | Jacquot, Aurélien Aujoulat, Fabien Roudière, Laurent Jumas-Bilak, Estelle Filleron, Anne Picaud, Jean-Charles Neveu, Dorine Baum, Thierry-Pascal Marchandin, Hélène |
Author_xml | – sequence: 1 givenname: Fabien surname: Aujoulat fullname: Aujoulat, Fabien email: fabien.aujoulat@univ-montp1.fr organization: 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 – sequence: 2 givenname: Laurent surname: Roudière fullname: Roudière, Laurent email: roudiere-l@chi-frejus-saint-raphael.fr organization: Centre Hospitalier de Fréjus, Laboratoire de bactériologie, 240 avenue de Saint-Lambert BP 110 83608, Fréjus, France. roudiere-l@chi-frejus-saint-raphael.fr – sequence: 3 givenname: Jean-Charles surname: Picaud fullname: Picaud, Jean-Charles email: jean-charles.picaud@chu-lyon.fr organization: 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 – sequence: 4 givenname: Aurélien surname: Jacquot fullname: Jacquot, Aurélien email: a-jacquot@chu-montpellier.fr organization: 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 – sequence: 5 givenname: Anne surname: Filleron fullname: Filleron, Anne email: a-filleron@chu-montpellier.fr, a-filleron@chu-montpellier.fr organization: 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 – sequence: 6 givenname: Dorine surname: Neveu fullname: Neveu, Dorine email: dorine.neveu@univ-montp1.fr organization: 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 – sequence: 7 givenname: Thierry-Pascal surname: Baum fullname: Baum, Thierry-Pascal email: tpbaum.chu.mpt@gmail.com organization: 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 – sequence: 8 givenname: Hélène surname: Marchandin fullname: Marchandin, Hélène email: helene.marchandin@univ-montp1.fr, helene.marchandin@univ-montp1.fr organization: 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 – sequence: 9 givenname: Estelle surname: Jumas-Bilak fullname: Jumas-Bilak, Estelle email: ebilak@univ-montp1.fr, ebilak@univ-montp1.fr organization: Centre Hospitalier Universitaire de Montpellier, Laboratoire d'Hygiène hospitalière, 778, Rue de la Croix Verte, Montpellier, 34000, France. ebilak@univ-montp1.fr |
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Keywords | Enterococcus Clostridium Microbiota PCR-TTGE Veillonellaceae Stool Dynamics Diversity Extremely low birth weight Infant Staphylococcus Follow-up Enterobacteriaceae |
Language | English |
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PublicationDate | 2014-12-31 |
PublicationDateYYYYMMDD | 2014-12-31 |
PublicationDate_xml | – month: 12 year: 2014 text: 2014-12-31 day: 31 |
PublicationDecade | 2010 |
PublicationPlace | England |
PublicationPlace_xml | – name: England – name: London |
PublicationTitle | BMC microbiology |
PublicationTitleAlternate | BMC Microbiol |
PublicationYear | 2014 |
Publisher | BioMed Central Ltd BioMed Central |
Publisher_xml | – name: BioMed Central Ltd – name: BioMed Central |
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Snippet | The very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of... Background The very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of... BACKGROUNDThe very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of... BACKGROUND: The very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results... Background : The very-preterm infant gut microbiota is increasingly explored due to its probable role in thedevelopment of life threatening diseases. Results... |
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SubjectTerms | Analysis Cluster Analysis DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal - chemistry DNA, Ribosomal - genetics Feces - microbiology Gastrointestinal Microbiome Gastrointestinal Tract - microbiology Genetic aspects Health aspects Humans Infant Infant, Newborn Infant, Premature Infants (Premature) Life Sciences Longitudinal Studies Methods Microbiology and Parasitology Microbiota Microbiota (Symbiotic organisms) Molecular Sequence Data Phylogeny Polymerase Chain Reaction Prognosis RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA Time Factors |
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Title | Temporal dynamics of the very premature infant gut dominant microbiota |
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