Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments
Publication Date
December 04, 2014
Journal
PLOS Neglected Tropical Diseases
Authors
Katrine L. Whiteson, Vladimir Lazarevic, Manuela Tangomo Bento, Myriam Girard, et al
Volume
8
Issue
12
Pages
e3240
DOI
https://dx.plos.org/10.1371/journal.pntd.0003240
Publisher URL
http://journals.plos.org/plosntds/article?id=10.1371%2Fjournal.pntd.0003240
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25474262
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256271
Europe PMC
http://europepmc.org/abstract/MED/25474262
Web of Science
000346701000001
Scopus
84928254308
Mendeley
http://www.mendeley.com/research/noma-affected-children-niger-distinct-oral-microbial-communities-based-highthroughput-sequencing-16s
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Mendeley | Further Information

{"title"=>"Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments", "type"=>"journal", "authors"=>[{"first_name"=>"Katrine L.", "last_name"=>"Whiteson", "scopus_author_id"=>"14049413300"}, {"first_name"=>"Vladimir", "last_name"=>"Lazarevic", "scopus_author_id"=>"35741110300"}, {"first_name"=>"Manuela", "last_name"=>"Tangomo-Bento", "scopus_author_id"=>"23978741400"}, {"first_name"=>"Myriam", "last_name"=>"Girard", "scopus_author_id"=>"35755912300"}, {"first_name"=>"Heather", "last_name"=>"Maughan", "scopus_author_id"=>"6506305951"}, {"first_name"=>"Didier", "last_name"=>"Pittet", "scopus_author_id"=>"7102541220"}, {"first_name"=>"Patrice", "last_name"=>"Francois", "scopus_author_id"=>"7201904519"}, {"first_name"=>"Jacques", "last_name"=>"Schrenzel", "scopus_author_id"=>"7004121246"}], "year"=>2014, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"scopus"=>"2-s2.0-84928254308", "isbn"=>"1935-2727", "doi"=>"10.1371/journal.pntd.0003240", "pui"=>"603940709", "sgr"=>"84928254308", "issn"=>"19352735", "pmid"=>"25474262"}, "id"=>"5f8a6f3d-c400-3d83-9139-92b9a8e9b22b", "abstract"=>"We aim to understand the microbial ecology of noma (cancrum oris), a devastating ancient illness which causes severe facial disfigurement in>140,000 malnourished children every year. The cause of noma is still elusive. A chaotic mix of microbial infection, oral hygiene and weakened immune system likely contribute to the development of oral lesions. These lesions are a plausible entry point for unidentified microorganisms that trigger gangrenous facial infections. To catalog bacteria present in noma lesions and identify candidate noma-triggering organisms, we performed a cross-sectional sequencing study of 16S rRNA gene amplicons from sixty samples of gingival fluid from twelve healthy children, twelve children suffering from noma (lesion and healthy sites), and twelve children suffering from Acute Necrotizing Gingivitis (ANG) (lesion and healthy sites). Relative to healthy individuals, samples taken from lesions in diseased mouths were enriched with Spirochaetes and depleted for Proteobacteria. Samples taken from healthy sites of diseased mouths had proportions of Spirochaetes and Proteobacteria that were similar to healthy control individuals. Samples from noma mouths did not have a higher abundance of Fusobacterium, casting doubt on its role as a causative agent of noma. Microbial communities sampled from noma and ANG lesions were dominated by the same Prevotella intermedia OTU, which was much less abundant in healthy sites sampled from the same mouths. Multivariate analysis confirmed that bacterial communities in healthy and lesion sites were significantly different. Several OTUs in the Orders Erysipelotrichales, Clostridiales, Bacteroidales, and Spirochaetales were identified as indicators of noma, suggesting that one or more microbes within these Orders is associated with the development of noma lesions. Future studies should include longitudinal sampling of viral and microbial components of this community, before and early in noma lesion development.", "link"=>"http://www.mendeley.com/research/noma-affected-children-niger-distinct-oral-microbial-communities-based-highthroughput-sequencing-16s", "reader_count"=>14, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Mathematics"=>1, "Medicine and Dentistry"=>5, "Agricultural and Biological Sciences"=>2, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Computer Science"=>{"Computer Science"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1821994"], "description"=>"<p>The network in (A) was created using the 99% OTUs whereas (B) was created using the top 35 OTUs from the 90% cutoff dataset. The data in (B) are also shown as a barplot in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003240#pntd.0003240.s002\" target=\"_blank\">Figure S1</a>, and as a Venn diagram in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003240#pntd.0003240.s003\" target=\"_blank\">Figure S2A</a>.</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260460, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.g005", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Network_analysis_of_bacterial_communities_/1260460", "title"=>"Network analysis of bacterial communities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821917"], "description"=>"<p>For each sample type, the median and range of abundances of the most abundant OTUs are plotted. Circles indicate outliers (i.e., data points that are 1.5-fold lower or higher than the 25% and 75% quartiles, respectively).</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260410, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.g002", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_box_plot_of_the_top_10_97_OTUs_by_group_/1260410", "title"=>"A box plot of the top 10 97% OTUs by group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821945"], "description"=>"<p>(A) The relative abundance of the top 4 97% OTUs that indicate the noma lesion samples are shown across the sample types (B) The relative abundances of several taxonomic groups of interest.</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260424, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.g004", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Box_plots_of_abundances_proportion_of_total_reads_for_several_bacterial_taxa_of_interest_/1260424", "title"=>"Box plots of abundances (proportion of total reads) for several bacterial taxa of interest.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821911"], "description"=>"<p>The abundances of seven major bacterial phyla averaged across all samples of a given type (furthest panel on left), or for each individual sampled (five panels to the right). The y-axis indicates the proportion of each phylum.</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260404, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Abundance_of_Phyla_across_samples_/1260404", "title"=>"Abundance of Phyla across samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821997"], "description"=>"<p>Tests were performed with PERMANOVA using Bray-Curtis dissimilarity measures of OTU abundances (results from the 97% identity cutoff are shown here). The Pseudo-F statistic comparing all five groups is 3.56 with a permutation test P value of 0.001. The groups are defined as ANGH: Acute Necrotizing Gingivitis healthy site, ANG: Acute Necrotizing Gingivitis lesion site, C: Control, NH: Noma Healthy site, N: Noma lesion site. *P-values corrected for multiple comparisons using the False Discovery Rate. <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003240#pntd.0003240-Benjamini1\" target=\"_blank\">[42]</a>.</p><p>Comparisons of microbial community composition between the five health status groups.</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260464, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparisons_of_microbial_community_composition_between_the_five_health_status_groups_/1260464", "title"=>"Comparisons of microbial community composition between the five health status groups.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821996"], "description"=>"<p>Averages from individual samples (and standard deviations) are shown for each category. *Only includes sites from affected individuals, not healthy controls.</p><p>Diversity comparisons between lesion and healthy sites*.</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260462, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.t001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_comparisons_between_lesion_and_healthy_sites_/1260462", "title"=>"Diversity comparisons between lesion and healthy sites*.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1822010", "https://ndownloader.figshare.com/files/1822011", "https://ndownloader.figshare.com/files/1822012", "https://ndownloader.figshare.com/files/1822013", "https://ndownloader.figshare.com/files/1822014", "https://ndownloader.figshare.com/files/1822015", "https://ndownloader.figshare.com/files/1822016", "https://ndownloader.figshare.com/files/1822018", "https://ndownloader.figshare.com/files/1822019"], "description"=>"<div><p>We aim to understand the microbial ecology of noma (cancrum oris), a devastating ancient illness which causes severe facial disfigurement in>140,000 malnourished children every year. The cause of noma is still elusive. A chaotic mix of microbial infection, oral hygiene and weakened immune system likely contribute to the development of oral lesions. These lesions are a plausible entry point for unidentified microorganisms that trigger gangrenous facial infections. To catalog bacteria present in noma lesions and identify candidate noma-triggering organisms, we performed a cross-sectional sequencing study of 16S rRNA gene amplicons from sixty samples of gingival fluid from twelve healthy children, twelve children suffering from noma (lesion and healthy sites), and twelve children suffering from Acute Necrotizing Gingivitis (ANG) (lesion and healthy sites). Relative to healthy individuals, samples taken from lesions in diseased mouths were enriched with <i>Spirochaetes</i> and depleted for <i>Proteobacteria</i>. Samples taken from healthy sites of diseased mouths had proportions of <i>Spirochaetes</i> and <i>Proteobacteria</i> that were similar to healthy control individuals. Samples from noma mouths did not have a higher abundance of <i>Fusobacterium</i>, casting doubt on its role as a causative agent of noma. Microbial communities sampled from noma and ANG lesions were dominated by the same <i>Prevotella intermedia</i> OTU, which was much less abundant in healthy sites sampled from the same mouths. Multivariate analysis confirmed that bacterial communities in healthy and lesion sites were significantly different. Several OTUs in the Orders Erysipelotrichales, Clostridiales, Bacteroidales, and Spirochaetales were identified as indicators of noma, suggesting that one or more microbes within these Orders is associated with the development of noma lesions. Future studies should include longitudinal sampling of viral and microbial components of this community, before and early in noma lesion development.</p></div>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260476, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0003240.s001", "https://dx.doi.org/10.1371/journal.pntd.0003240.s002", "https://dx.doi.org/10.1371/journal.pntd.0003240.s003", "https://dx.doi.org/10.1371/journal.pntd.0003240.s004", "https://dx.doi.org/10.1371/journal.pntd.0003240.s005", "https://dx.doi.org/10.1371/journal.pntd.0003240.s006", "https://dx.doi.org/10.1371/journal.pntd.0003240.s007", "https://dx.doi.org/10.1371/journal.pntd.0003240.s008", "https://dx.doi.org/10.1371/journal.pntd.0003240.s009"], "stats"=>{"downloads"=>67, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Noma_Affected_Children_from_Niger_Have_Distinct_Oral_Microbial_Communities_Based_on_High_Throughput_Sequencing_of_16S_rRNA_Gene_Fragments_/1260476", "title"=>"Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1822001"], "description"=>"<p>Indicator values were calculated using the abundance distribution of OTUs at the 97% identity cutoff. Boldface highlights the taxa that are indicators for noma. The abundance ranges for taxa with high indicator species values are shown in box plots in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003240#pntd-0003240-g004\" target=\"_blank\">Figure 4A</a>. Results with all groups in “Other” being treated separately are shown in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003240#pntd.0003240.s009\" target=\"_blank\">Table S6</a>.</p><p>Indicator species analysis comparing the noma lesion site samples (“Noma” in “Indicator of” column) with the other four health status groups (control, noma healthy site, ANG healthy site, and ANG lesion site; “Other” in “Indicator of” column).</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260467, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.t004", "stats"=>{"downloads"=>3, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Indicator_species_analysis_comparing_the_noma_lesion_site_samples_8220_Noma_8221_in_8220_Indicator_of_8221_column_with_the_other_four_health_status_groups_control_noma_healthy_site_ANG_healthy_site_and_ANG_lesion_site_8220_Other_8221_in_8220_Indicator_of/1260467", "title"=>"Indicator species analysis comparing the noma lesion site samples (“Noma” in “Indicator of” column) with the other four health status groups (control, noma healthy site, ANG healthy site, and ANG lesion site; “Other” in “Indicator of” column).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1822000"], "description"=>"<p>Taxa indicated in bold are more abundant in noma or both noma and ANG samples compared to the control. Abbreviations are identical to those used in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003240#pntd-0003240-t002\" target=\"_blank\">Table 2</a>. <b>*</b>indicates 1 read obtained, which equals a percentage of <10<sup>−3</sup>.</p><p>Percentage of reads that correspond to bacterial groups suspected of triggering noma in the different sample groups, as determined by OTUs from the 97% cutoff.</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260466, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.t003", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_reads_that_correspond_to_bacterial_groups_suspected_of_triggering_noma_in_the_different_sample_groups_as_determined_by_OTUs_from_the_97_cutoff_/1260466", "title"=>"Percentage of reads that correspond to bacterial groups suspected of triggering noma in the different sample groups, as determined by OTUs from the 97% cutoff.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821922"], "description"=>"<p>Numbers correspond to individuals sampled, as reported in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003240#pntd-0003240-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["16 S rRNA Gene Fragments", "16 S rRNA gene amplicons", "Prevotella intermedia OTU", "ang", "noma lesions", "Acute Necrotizing Gingivitis", "Distinct Oral Microbial Communities", "noma lesion development", "site"], "article_id"=>1260415, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Katrine L. Whiteson", "Vladimir Lazarevic", "Manuela Tangomo-Bento", "Myriam Girard", "Heather Maughan", "Didier Pittet", "Patrice François", "Jacques Schrenzel"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0003240.g003", "stats"=>{"downloads"=>2, "page_views"=>160, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multidimensional_scaling_MDS_plot_of_Bray_Curtis_dissimilarities_using_multi_dimensional_scaling_/1260415", "title"=>"Multidimensional scaling (MDS) plot of Bray-Curtis dissimilarities using multi-dimensional scaling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:13:29"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
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Relative Metric

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