Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants
Identifieur interne : 006C63 ( Ncbi/Merge ); précédent : 006C62; suivant : 006C64Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants
Auteurs : S. S. Al-Shehri [Australie, Arabie saoudite] ; E. L. Sweeney [Australie] ; D. M. Cowley [Australie] ; H. G. Liley [Australie] ; P. D. Ranasinghe [Australie] ; B. G. Charles [Australie] ; P. N. Shaw [Australie] ; D. Vagenas [Australie] ; J. A. Duley [Australie] ; C. L. Knox [Australie]Source :
- Scientific Reports [ 2045-2322 ] ; 2016.
Abstract
Url:
DOI: 10.1038/srep38309
PubMed: 27922070
PubMed Central: 5138828
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Al-Shehri</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>School of Applied Medical Sciences, Taif University</institution>, Taif, 21974,<country>Saudi Arabia</country></nlm:aff><country xml:lang="fr">Arabie saoudite</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sweeney, E L" sort="Sweeney, E L" uniqKey="Sweeney E" first="E. L." last="Sweeney">E. L. Sweeney</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>The Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology</institution>, Brisbane, 4059,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Cowley, D M" sort="Cowley, D M" uniqKey="Cowley D" first="D. M." last="Cowley">D. M. Cowley</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Mater Research Institute, The University of Queensland</institution>, Woolloongabba, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liley, H G" sort="Liley, H G" uniqKey="Liley H" first="H. G." last="Liley">H. G. Liley</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Mater Research Institute, The University of Queensland</institution>, Woolloongabba, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ranasinghe, P D" sort="Ranasinghe, P D" uniqKey="Ranasinghe P" first="P. D." last="Ranasinghe">P. D. Ranasinghe</name><affiliation wicri:level="1"><nlm:aff id="a5"><institution>Queensland University of Technology, Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences</institution>, 4001,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Charles, B G" sort="Charles, B G" uniqKey="Charles B" first="B. G." last="Charles">B. G. Charles</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Shaw, P N" sort="Shaw, P N" uniqKey="Shaw P" first="P. N." last="Shaw">P. N. Shaw</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Vagenas, D" sort="Vagenas, D" uniqKey="Vagenas D" first="D." last="Vagenas">D. Vagenas</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>The Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology</institution>, Brisbane, 4059,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Duley, J A" sort="Duley, J A" uniqKey="Duley J" first="J. A." last="Duley">J. A. Duley</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Mater Research Institute, The University of Queensland</institution>, Woolloongabba, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Knox, C L" sort="Knox, C L" uniqKey="Knox C" first="C. L." last="Knox">C. L. Knox</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>The Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology</institution>, Brisbane, 4059,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27922070</idno><idno type="pmc">5138828</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5138828</idno><idno type="RBID">PMC:5138828</idno><idno type="doi">10.1038/srep38309</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000838</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000838</idno><idno type="wicri:Area/Pmc/Curation">000838</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000838</idno><idno type="wicri:Area/Pmc/Checkpoint">000779</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000779</idno><idno type="wicri:Area/Ncbi/Merge">006C63</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants</title><author><name sortKey="Al Shehri, S S" sort="Al Shehri, S S" uniqKey="Al Shehri S" first="S. S." last="Al-Shehri">S. S. Al-Shehri</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>School of Applied Medical Sciences, Taif University</institution>, Taif, 21974,<country>Saudi Arabia</country></nlm:aff><country xml:lang="fr">Arabie saoudite</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sweeney, E L" sort="Sweeney, E L" uniqKey="Sweeney E" first="E. L." last="Sweeney">E. L. Sweeney</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>The Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology</institution>, Brisbane, 4059,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Cowley, D M" sort="Cowley, D M" uniqKey="Cowley D" first="D. M." last="Cowley">D. M. Cowley</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Mater Research Institute, The University of Queensland</institution>, Woolloongabba, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liley, H G" sort="Liley, H G" uniqKey="Liley H" first="H. G." last="Liley">H. G. Liley</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Mater Research Institute, The University of Queensland</institution>, Woolloongabba, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ranasinghe, P D" sort="Ranasinghe, P D" uniqKey="Ranasinghe P" first="P. D." last="Ranasinghe">P. D. Ranasinghe</name><affiliation wicri:level="1"><nlm:aff id="a5"><institution>Queensland University of Technology, Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences</institution>, 4001,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Charles, B G" sort="Charles, B G" uniqKey="Charles B" first="B. G." last="Charles">B. G. Charles</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Shaw, P N" sort="Shaw, P N" uniqKey="Shaw P" first="P. N." last="Shaw">P. N. Shaw</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Vagenas, D" sort="Vagenas, D" uniqKey="Vagenas D" first="D." last="Vagenas">D. Vagenas</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>The Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology</institution>, Brisbane, 4059,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Duley, J A" sort="Duley, J A" uniqKey="Duley J" first="J. A." last="Duley">J. A. Duley</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Mater Research Institute, The University of Queensland</institution>, Woolloongabba, 4102,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Knox, C L" sort="Knox, C L" uniqKey="Knox C" first="C. L." last="Knox">C. L. Knox</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>The Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology</institution>, Brisbane, 4059,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>In utero</italic> and upon delivery, neonates are exposed to a wide array of microorganisms from various sources, including maternal bacteria. Prior studies have proposed that the mode of feeding shapes the gut microbiota and, subsequently the child’s health. However, the effect of the mode of feeding and its influence on the development of the neonatal oral microbiota in early infancy has not yet been reported. The aim of this study was to compare the oral microbiota of healthy infants that were exclusively breast-fed or formula-fed using 16S-rRNA gene sequencing. We demonstrated that the oral bacterial communities were dominated by the phylum <italic>Firmicutes</italic>, in both groups. There was a higher prevalence of the phylum <italic>Bacteroidetes</italic> in the mouths of formula-fed infants than in breast-fed infants (<italic>p</italic> = 0.01), but in contrast <italic>Actinobacteria</italic> were more prevalent in breast-fed babies; <italic>Proteobacteria</italic> was more prevalent in saliva of breast-fed babies than in formula-fed neonates (<italic>p</italic> = 0.04). We also found evidence suggesting that the oral microbiota composition changed over time, particularly <italic>Streptococcus</italic> species, which had an increasing trend between 4–8 weeks in both groups. This study findings confirmed that the mode of feeding influences the development of oral microbiota, and this may have implications for long-term human health.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Aagaard, K" uniqKey="Aagaard K">K. Aagaard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gueimonde, M" uniqKey="Gueimonde M">M. Gueimonde</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vaishampayan, P A" uniqKey="Vaishampayan P">P. A. Vaishampayan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koenig, J E" uniqKey="Koenig J">J. E. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Sci Rep</journal-id><journal-id journal-id-type="iso-abbrev">Sci Rep</journal-id><journal-title-group><journal-title>Scientific Reports</journal-title></journal-title-group><issn pub-type="epub">2045-2322</issn><publisher><publisher-name>Nature Publishing Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27922070</article-id><article-id pub-id-type="pmc">5138828</article-id><article-id pub-id-type="pii">srep38309</article-id><article-id pub-id-type="doi">10.1038/srep38309</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Al-Shehri</surname><given-names>S. S.</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Sweeney</surname><given-names>E. L.</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Cowley</surname><given-names>D. M.</given-names></name><xref ref-type="aff" rid="a4">4</xref></contrib><contrib contrib-type="author"><name><surname>Liley</surname><given-names>H. G.</given-names></name><xref ref-type="aff" rid="a4">4</xref></contrib><contrib contrib-type="author"><name><surname>Ranasinghe</surname><given-names>P. D.</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Charles</surname><given-names>B. G.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Shaw</surname><given-names>P. N.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Vagenas</surname><given-names>D.</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Duley</surname><given-names>J. A.</given-names></name><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a4">4</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Knox</surname><given-names>C. L.</given-names></name><xref ref-type="aff" rid="a3">3</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><aff id="a1"><label>1</label><institution>School of Pharmacy, The University of Queensland</institution>, St Lucia, 4102,<country>Australia</country></aff><aff id="a2"><label>2</label><institution>School of Applied Medical Sciences, Taif University</institution>, Taif, 21974,<country>Saudi Arabia</country></aff><aff id="a3"><label>3</label><institution>The Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology</institution>, Brisbane, 4059,<country>Australia</country></aff><aff id="a4"><label>4</label><institution>Mater Research Institute, The University of Queensland</institution>, Woolloongabba, 4102,<country>Australia</country></aff><aff id="a5"><label>5</label><institution>Queensland University of Technology, Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences</institution>, 4001,<country>Australia</country></aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email>sa.alshehri@tu.edu.sa</email></corresp><fn id="n1"><label>*</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="epub"><day>06</day><month>12</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>6</volume><elocation-id>38309</elocation-id><history><date date-type="received"><day>15</day><month>03</month><year>2016</year></date><date date-type="accepted"><day>08</day><month>11</month><year>2016</year></date></history><permissions><copyright-statement>Copyright © 2016, The Author(s)</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>The Author(s)</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><abstract><p><italic>In utero</italic> and upon delivery, neonates are exposed to a wide array of microorganisms from various sources, including maternal bacteria. Prior studies have proposed that the mode of feeding shapes the gut microbiota and, subsequently the child’s health. However, the effect of the mode of feeding and its influence on the development of the neonatal oral microbiota in early infancy has not yet been reported. The aim of this study was to compare the oral microbiota of healthy infants that were exclusively breast-fed or formula-fed using 16S-rRNA gene sequencing. We demonstrated that the oral bacterial communities were dominated by the phylum <italic>Firmicutes</italic>, in both groups. There was a higher prevalence of the phylum <italic>Bacteroidetes</italic> in the mouths of formula-fed infants than in breast-fed infants (<italic>p</italic> = 0.01), but in contrast <italic>Actinobacteria</italic> were more prevalent in breast-fed babies; <italic>Proteobacteria</italic> was more prevalent in saliva of breast-fed babies than in formula-fed neonates (<italic>p</italic> = 0.04). We also found evidence suggesting that the oral microbiota composition changed over time, particularly <italic>Streptococcus</italic> species, which had an increasing trend between 4–8 weeks in both groups. This study findings confirmed that the mode of feeding influences the development of oral microbiota, and this may have implications for long-term human health.</p></abstract></article-meta></front><floats-group><fig id="f1"><label>Figure 1</label><caption><title>Oral bacterial community richness analyses.</title><p>Alpha diversity measurements using a Shannon index analysis indicated samples with higher and lower Genus diversity in the mouths of breast-fed and formula-fed neonates. The depth of sequence reads was drawn against the richness of OTU clusters at different taxonomic assignments.</p></caption><graphic xlink:href="srep38309-f1"></graphic></fig><fig id="f2"><label>Figure 2</label><caption><title>Proportion of the relative abundance of the major oral bacterial phyla.</title><p>Taxa were detected by 16S rRNA analysis using Roche-454 GS FLX deep sequencing. Each column within the bar graph represents the percentages of the bacterial OTUs detected within each infant oral swab sample. (<bold>a</bold>) Bar graph showing the proportion of the relative abundance (%) of the major oral phyla operational taxonomic units (OTUs) for breast-fed samples (n = 26) and formula-fed samples (n = 12). (<bold>b</bold>) Bar graph showing the relative abundance (%) of oral phyla excluding the <italic>Firmicutes,</italic> of both breast-fed and formula-fed oral samples. There were key differences in the abundance of some phyla among breast-fed and formula-fed infants. (<bold>c</bold>) Relative abundance of the Phylum <italic>Bacteroidetes</italic> in oral swab samples from breast-fed and formula-fed infants (**<italic>p</italic> = 0.01).</p></caption><graphic xlink:href="srep38309-f2"></graphic></fig><fig id="f3"><label>Figure 3</label><caption><title>Relative abundance of 16S rRNA Genus-level sequences.</title><p>(<bold>a</bold>) Genus level sequences were detected in oral swabs from breast-fed (red) and formula-fed (blue) infants using deep sequencing. Values are expressed as box plot showing the mean, percentiles, and SD. (<bold>b</bold>) The relative abundance of sequences that were classified only to the Family level ‘<italic>Streptococcaceae</italic>_unclassified’, compared to known <italic>Streptococcus</italic> spp. sequences. (<bold>c</bold>) The relative abundance of the major Genera sequences detected in the oral samples: <italic>Lactobacillus</italic> spp. (Phylum <italic>Firmicutes</italic>), <italic>Rothia</italic> spp. (Phylum <italic>Actinobacteria</italic>) and <italic>Veillonella</italic> spp. (Phylum <italic>Firmicutes</italic>). (<bold>d</bold>) <italic>Prevotella</italic> spp. (Phylum <italic>Bacteroidetes</italic>) sequences were more abundant the oral samples from formula-fed compared to breast-fed infants (<italic>p</italic> = 0.02).</p></caption><graphic xlink:href="srep38309-f3"></graphic></fig><fig id="f4"><label>Figure 4</label><caption><title>Heat map of oral bacterial community compositions within breast-fed and formula-fed infants and their hierarchical clustering.</title><p>The 16S rRNA gene sequencing revealed differences in the abundance of oral bacterial communities. The bacterial genera are represented as heat maps corresponding to a phylogenetic tree. The heat map demonstrates the higher abundance of <italic>Prevotella</italic> spp. within the oral samples from breast-fed compared to formula-fed infants.</p></caption><graphic xlink:href="srep38309-f4"></graphic></fig><fig id="f5"><label>Figure 5</label><caption><title>Temporal changes in streptococcal relative abundance in oral samples from breast-fed and formula-fed infants.</title><p>The relative abundance of oral <italic>Streptococcus</italic> Genus-level sequences increased from weeks 4 to 8, for both breast-fed and formula-fed infants. Paralleling this increase, there was a decrease in the number of Genus-level sequences that could not be classified (‘<italic>Streptococcaceae</italic>_unclassified’) from 4, 6 and 8 weeks of life. Each box plot corresponds to a sample time point and the mode of infant feeding versus the abundance of the OTUs. Box plots showing the mean, percentiles and SD.</p></caption><graphic xlink:href="srep38309-f5"></graphic></fig><fig id="f6"><label>Figure 6</label><caption><title>Heat map of sequences identified as ‘Bacteria_others’ within oral samples from infants.</title><p>The heat map demonstrates the abundance of ‘Bacteria_others’ sequences and the taxonomic identities (phylogeny). The identities were explored using an RDP naïve Bayesian classifier and are shown at the Class level. The percentage values (taxonomic assignment) indicate the homology to bacteria classified to the Class level that have been isolated/identified previously, and the accession isolation source indicates the sites from which these closely-related bacterial DNA sequences have been previously isolated.</p></caption><graphic xlink:href="srep38309-f6"></graphic></fig><table-wrap position="float" id="t1"><label>Table 1</label><caption><title>A comparison of the gestational age, birth weight, and age at the time of oral specimen collection, for breast-fed and formula-fed infants.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="bottom"><tr><th rowspan="2" align="left" valign="top" charoff="50"> </th><th colspan="3" align="center" valign="top" charoff="50">Breast-fed<hr></hr></th><th colspan="3" align="center" valign="top" charoff="50">Formula-fed<hr></hr></th><th rowspan="2" align="center" valign="top" charoff="50"><italic>p</italic> value</th></tr><tr><th align="center" valign="top" charoff="50">Male</th><th align="center" valign="top" charoff="50">Female</th><th align="center" valign="top" charoff="50">Total</th><th align="center" valign="top" charoff="50">Male</th><th align="center" valign="top" charoff="50">Female</th><th align="center" valign="top" charoff="50">Total</th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50"> </td><td align="center" valign="top" charoff="50">12</td><td align="center" valign="top" charoff="50">14</td><td align="center" valign="top" charoff="50">26</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">12</td><td align="center" valign="top" charoff="50"> </td></tr><tr><td colspan="8" align="left" valign="top" charoff="50">Gestational age (w)<xref ref-type="fn" rid="t1-fn1">1</xref></td></tr><tr><td align="left" valign="top" charoff="50"> Mean ± SD</td><td align="center" valign="top" charoff="50">40 ± 0.5</td><td align="center" valign="top" charoff="50">40 ± 1</td><td rowspan="2" align="center" valign="top" charoff="50">40 ± 1</td><td align="center" valign="top" charoff="50">40 ± 2</td><td align="center" valign="top" charoff="50">39 ± 2</td><td rowspan="2" align="center" valign="top" charoff="50">40 ± 2</td><td rowspan="2" align="center" valign="top" charoff="50">0.3</td></tr><tr><td align="left" valign="top" charoff="50"> Range</td><td align="center" valign="top" charoff="50">39–41</td><td align="center" valign="top" charoff="50">38–42</td><td align="center" valign="top" charoff="50">38–41</td><td align="center" valign="top" charoff="50">37–41</td></tr><tr><td colspan="8" align="left" valign="top" charoff="50">Birth weight (g)</td></tr><tr><td align="left" valign="top" charoff="50"> Mean ± SD</td><td align="center" valign="top" charoff="50">3488 ± 316</td><td align="center" valign="top" charoff="50">3584 ± 570</td><td rowspan="2" align="center" valign="top" charoff="50">3539 ± 464</td><td align="center" valign="top" charoff="50">3916 ± 599</td><td align="center" valign="top" charoff="50">3664 ± 227</td><td rowspan="2" align="center" valign="top" charoff="50">3779 ± 432</td><td rowspan="2" align="center" valign="top" charoff="50">0.2</td></tr><tr><td align="left" valign="top" charoff="50"> Range</td><td align="center" valign="top" charoff="50">3054–4110</td><td align="center" valign="top" charoff="50">2700–4492</td><td align="center" valign="top" charoff="50">3182–4720</td><td align="center" valign="top" charoff="50">3490–4092</td></tr><tr><td colspan="8" align="left" valign="top" charoff="50">Age (w) at collection<xref ref-type="fn" rid="t1-fn2">2</xref></td></tr><tr><td align="left" valign="top" charoff="50"> Mean ± SD</td><td align="center" valign="top" charoff="50">6 ± 1</td><td align="center" valign="top" charoff="50">6 ± 2</td><td rowspan="2" align="center" valign="top" charoff="50">6 ± 2</td><td align="center" valign="top" charoff="50">7 ± 1</td><td align="center" valign="top" charoff="50">6 ± 2</td><td rowspan="2" align="center" valign="top" charoff="50">6 ± 1</td><td rowspan="2" align="center" valign="top" charoff="50">0.2</td></tr><tr><td align="left" valign="top" charoff="50"> Range</td><td align="center" valign="top" charoff="50">4–8</td><td align="center" valign="top" charoff="50">4–8</td><td align="center" valign="top" charoff="50">6–8</td><td align="center" valign="top" charoff="50">4–8</td></tr></tbody></table><table-wrap-foot><fn id="t1-fn1"><p><sup>1</sup>w = weeks, at the time of delivery; term >37 weeks gestation.</p></fn><fn id="t1-fn2"><p><sup>2</sup>w = weeks, at the time of collection of oral specimen.</p></fn></table-wrap-foot></table-wrap><table-wrap position="float" id="t2"><label>Table 2</label><caption><title>The fusion primers design for 16S rRNA amplification, the fusion primer sequences contained [Adapter]-[Key]-[MID barcode]-[Target primers].</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="left"></col><col align="left"></col></colgroup><thead valign="bottom"><tr><th align="left" valign="top" charoff="50"> </th><th align="left" valign="top" charoff="50">Forward fusion primer sequence</th><th align="left" valign="top" charoff="50">Reverse fusion primer sequence</th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50">Adaptor</td><td align="left" valign="top" charoff="50">5′CCATCTCATCCCTGCGTGTCTCCGACC</td><td align="left" valign="top" charoff="50">5′CCTATCCCCTGTGTGCCTTGGCAGTC</td></tr><tr><td align="left" valign="top" charoff="50">Key</td><td align="left" valign="top" charoff="50">TCAG</td><td align="left" valign="top" charoff="50">TCAG</td></tr><tr><td align="left" valign="top" charoff="50">MID</td><td align="left" valign="top" charoff="50">Barcode sample specific</td><td align="left" valign="top" charoff="50">—</td></tr><tr><td align="left" valign="top" charoff="50">Target primer<xref ref-type="fn" rid="t2-fn1">*</xref></td><td align="left" valign="top" charoff="50">AGAGTTTGATCMTGGCTCAG</td><td align="left" valign="top" charoff="50">GWATTACCGCGGCKGCTG</td></tr></tbody></table><table-wrap-foot><fn id="t2-fn1"><p><sup>*</sup>Base redundancies were included within the target primers (W = A + T, K = T + G, M = A + C).</p></fn></table-wrap-foot></table-wrap></floats-group></pmc><affiliations><list><country><li>Arabie saoudite</li><li>Australie</li></country></list><tree><country name="Australie"><noRegion><name sortKey="Al Shehri, S S" sort="Al Shehri, S S" uniqKey="Al Shehri S" first="S. S." last="Al-Shehri">S. S. Al-Shehri</name></noRegion><name sortKey="Charles, B G" sort="Charles, B G" uniqKey="Charles B" first="B. G." last="Charles">B. G. Charles</name><name sortKey="Cowley, D M" sort="Cowley, D M" uniqKey="Cowley D" first="D. M." last="Cowley">D. M. Cowley</name><name sortKey="Duley, J A" sort="Duley, J A" uniqKey="Duley J" first="J. A." last="Duley">J. A. Duley</name><name sortKey="Duley, J A" sort="Duley, J A" uniqKey="Duley J" first="J. A." last="Duley">J. A. Duley</name><name sortKey="Knox, C L" sort="Knox, C L" uniqKey="Knox C" first="C. L." last="Knox">C. L. Knox</name><name sortKey="Liley, H G" sort="Liley, H G" uniqKey="Liley H" first="H. G." last="Liley">H. G. Liley</name><name sortKey="Ranasinghe, P D" sort="Ranasinghe, P D" uniqKey="Ranasinghe P" first="P. D." last="Ranasinghe">P. D. Ranasinghe</name><name sortKey="Shaw, P N" sort="Shaw, P N" uniqKey="Shaw P" first="P. N." last="Shaw">P. N. Shaw</name><name sortKey="Sweeney, E L" sort="Sweeney, E L" uniqKey="Sweeney E" first="E. L." last="Sweeney">E. L. Sweeney</name><name sortKey="Vagenas, D" sort="Vagenas, D" uniqKey="Vagenas D" first="D." last="Vagenas">D. Vagenas</name></country><country name="Arabie saoudite"><noRegion><name sortKey="Al Shehri, S S" sort="Al Shehri, S S" uniqKey="Al Shehri S" first="S. S." last="Al-Shehri">S. S. Al-Shehri</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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