CoChat
Sign Up
Cited by 160

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

The Microbiome of Potentially Malignant Oral Leukoplakia Exhibits Enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia Species

Amer, Abdrazak, Galvin, Sheila, Healy, Claire M., Moran, Gary P.·2017·Frontiers in Microbiology
DOI 10.3389/fmicb.2017.02391PMC PMC5717034
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.3389/fmicb.2017.02391

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Figures

FIGURE 1 Overview of bacterial phyla distribution and Candida carriage patterns in patients with OLK and healthy controls. (A) Graph showing the abundance of the six most important phyla in healthy control subjects and sites of OLK and contralateral normal sites in patients. ∗ Indicates Metastats P < 0.05 and ∗∗P < 0.01. (B) Percentage of Candida positive samples recovered from patients (OLK and contralateral sites) and healthy controls, determined by qPCR.
FIGURE 1 Overview of bacterial phyla distribution and Candida carriage patterns in patients with OLK and healthy controls. (A) Graph showing the abundance of the six most important phyla in healthy control subjects and sites of OLK and contralateral normal sites in patients. ∗ Indicates Metastats P < 0.05 and ∗∗P < 0.01. (B) Percentage of Candida positive samples recovered from patients (OLK and contralateral sites) and healthy controls, determined by qPCR.CC BY · PubMed Central
FIGURE 2 Analysis community structure in samples from OLK and healthy mucosa. (A) Rarefaction curve showing analysis of OTUs identified in samples from healthy controls (green) and patients (red = OLK tissue, orange = contralateral normal tissue). (B) Non-metric multidimensional scaling (NMDS) plots generated from a matrix of Bray–Curtis dissimilarity values using Mothur (Schloss et al., 2009). Separation of OLK communities (red) from contralateral (orange; P = 0.007) and healthy control communities (green; P = 0.001) was determined using analysis of molecular variance (AMOVA).
FIGURE 2 Analysis community structure in samples from OLK and healthy mucosa. (A) Rarefaction curve showing analysis of OTUs identified in samples from healthy controls (green) and patients (red = OLK tissue, orange = contralateral normal tissue). (B) Non-metric multidimensional scaling (NMDS) plots generated from a matrix of Bray–Curtis dissimilarity values using Mothur (Schloss et al., 2009). Separation of OLK communities (red) from contralateral (orange; P = 0.007) and healthy control communities (green; P = 0.001) was determined using analysis of molecular variance (AMOVA).CC BY · PubMed Central
FIGURE 3 Results of LEfSe analysis to identify significantly enriched bacterial taxa in (A) communities from patients and healthy controls and (B) in communities from sites of OLK and contralateral tissue from patients.
FIGURE 3 Results of LEfSe analysis to identify significantly enriched bacterial taxa in (A) communities from patients and healthy controls and (B) in communities from sites of OLK and contralateral tissue from patients.CC BY · PubMed Central
FIGURE 4 Relative abundance of selected taxonomic groups identified by LEfSe analysis. The abundance of each organism (A–F) in OLK and contralateral healthy communities from each patient is plotted side by side. No healthy tissues were available from four patients (Supplementary Table S1) and these are plotted versus the average values for control tissue. P-values refer to Wilcoxon matched pairs test results.
FIGURE 4 Relative abundance of selected taxonomic groups identified by LEfSe analysis. The abundance of each organism (A–F) in OLK and contralateral healthy communities from each patient is plotted side by side. No healthy tissues were available from four patients (Supplementary Table S1) and these are plotted versus the average values for control tissue. P-values refer to Wilcoxon matched pairs test results.CC BY · PubMed Central
FIGURE 5 (A) Heatmap showing the abundance of taxa identified by LEfSe analysis. Heatmap and dendogram were generated in Vegan using a matrix of Bray–Curtis dissimilarity values. Separation of patient clusters marked 1 to 5 in the dendogram was highly significant (Unweighted UNIFRAC P < 0.001). The color-coded legend indicates whether each sample is from a buccal or lingual site and the degree of dysplasia following biopsy (mild, moderate, or severe). CON (light blue) correspond to the average values in healthy buccal (left) and healthy lingual (right) samples. (B) Co-occurrence map generated from Pearson correlation coefficients (r) generated in Prism (P < 0.01) and graphically presented using Cytoscape 3.2.1. Thickness of edges (connecting lines) are proportional to r-values (0.4–0.99). Clusters within the dotted line were identified in patients who were also colonized with Candida spp.
FIGURE 5 (A) Heatmap showing the abundance of taxa identified by LEfSe analysis. Heatmap and dendogram were generated in Vegan using a matrix of Bray–Curtis dissimilarity values. Separation of patient clusters marked 1 to 5 in the dendogram was highly significant (Unweighted UNIFRAC P < 0.001). The color-coded legend indicates whether each sample is from a buccal or lingual site and the degree of dysplasia following biopsy (mild, moderate, or severe). CON (light blue) correspond to the average values in healthy buccal (left) and healthy lingual (right) samples. (B) Co-occurrence map generated from Pearson correlation coefficients (r) generated in Prism (P < 0.01) and graphically presented using Cytoscape 3.2.1. Thickness of edges (connecting lines) are proportional to r-values (0.4–0.99). Clusters within the dotted line were identified in patients who were also colonized with Candida spp.CC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 37

  1. Abdulrahim, 2013, Genotyping Candida albicans from Candida leukoplakia and non-Candida leukoplakia shows no enrichment of multilocus sequence typing clades but enrichment of ABC genotype C in Candida leukoplakia., PLOS ONE, 8, 10.1371/journal.pone.0073738 · DOI
  2. Abed, 2016, Fap2 mediates Fusobacterium nucleatum colorectal adenocarcinoma enrichment by binding to tumor- expressed Gal-GalNAc., Cell Host Microbe, 20, 215, 10.1016/j.chom.2016.07.006 · DOI · Paper page
  3. Al-hebshi, 2017, Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma., Sci. Rep., 7, 10.1038/s41598-017-02079-3 · DOI
  4. Alnuaimi, 2015, Oral Candida colonization in oral cancer patients and its relationship with traditional risk factors of oral cancer: a matched case-control study., Oral Oncol., 51, 139, 10.1016/j.oraloncology.2014.11.008 · DOI
  5. Binder Gallimidi, 2015, Periodontal pathogens Porphyromonas gingivalis and Fusobacterium nucleatum promote tumor progression in an oral-specific chemical carcinogenesis model., Oncotarget, 6, 22613, 10.18632/oncotarget.4209 · DOI
  6. Castellarin, 2011, Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma., Genome Res., 22, 299, 10.1101/gr.126516.111 · DOI · Paper page
  7. Diaz, 2014, Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench., Front. Cell Infect. Microbiol., 4, 10.3389/fcimb.2014.00101 · DOI
  8. Edgar, 2011, UCHIME improves sensitivity and speed of chimera detection., Bioinformatics, 27, 2194, 10.1093/bioinformatics/btr381 · DOI · Paper page
  9. Frank, 2008, Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes., Appl. Environ. Microbiol., 74, 2461, 10.1128/AEM.02272-07 · DOI
  10. Gillison, 2000, Evidence for a causal association between human papillomavirus and a subset of head and neck cancers., J. Natl. Cancer Inst., 92, 709, 10.1093/jnci/92.9.709 · DOI
  11. Ho, 2012, The clinical determinants of malignant transformation in oral epithelial dysplasia., Oral Oncol., 48, 969, 10.1016/j.oraloncology.2012.04.002 · DOI
  12. Homann, 1997, High acetaldehyde levels in saliva after ethanol consumption: methodological aspects and pathogenetic implications., Carcinogenesis, 18, 1739, 10.1093/carcin/18.9.1739 · DOI
  13. Hu, 2016, Changes in the salivary microbiota of oral leukoplakia and oral cancer., Oral Oncol., 56, e6, 10.1016/j.oraloncology.2016.03.007 · DOI
  14. 2013, 16S Metagenomic Sequencing Library Preparation, 1
  15. Johnson, 2011, Squamous cell carcinoma and precursor lesions of the oral cavity: epidemiology and aetiology., Periodontol 2000, 57, 19, 10.1111/j.1600-0757.2011.00401.x · DOI
  16. Kobayashi, 2012, A selective medium for Rothia mucilaginosa and its distribution in oral cavities., J. Microbiol. Methods, 91, 364, 10.1016/j.mimet.2012.09.011 · DOI
  17. Kostic, 2011, Genomic analysis identifies association of Fusobacterium with colorectal carcinoma., Genome Res., 22, 292, 10.1101/gr.126573.111 · DOI · Paper page
  18. Kraneveld, 2012, The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults., PLOS ONE, 7, 10.1371/journal.pone.0042770.s008 · DOI
  19. Liu, 2012, Oral cancer development in patients with leukoplakia–clinicopathological factors affecting outcome., PLOS ONE, 7, 10.1371/journal.pone.0034773 · DOI
  20. Mager, 2005, The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects., J. Transl. Med., 3, 10.1186/1479-5876-3-27 · DOI
  21. Marttila, 2013, Acetaldehyde production and microbial colonization in oral squamous cell carcinoma and oral lichenoid disease., Oral Surg. Oral Med. Oral Pathol. Oral Radiol., 116, 61, 10.1016/j.oooo.2013.02.009 · DOI
  22. McCullough, 2002, Oral yeast carriage correlates with presence of oral epithelial dysplasia., Oral Oncol., 38, 391, 10.1016/S1368-8375(01)00079-3 · DOI
  23. Mills, 1976, N-Nitrosamine formation by cultures of several microorganisms., Appl. Environ. Microbiol., 31, 892, 10.1128/AEM.31.6.892-895.1976 · DOI
  24. Moritani, 2015, Acetaldehyde production by major oral microbes., Oral Dis., 21, 748, 10.1111/odi.12341 · DOI
  25. Nagy, 1998, The microflora associated with human oral carcinomas., Oral Oncol., 34, 304, 10.1016/S1368-8375(98)80012-2 · DOI
  26. Perera, 2016, Emerging role of bacteria in oral carcinogenesis: a review with special reference to perio-pathogenic bacteria., J. Oral Microbiol., 8, 10.3402/jom.v8.32762 · DOI
  27. Pushalkar, 2011, Microbial diversity in saliva of oral squamous cell carcinoma., FEMS Immunol. Med. Microbiol., 61, 269, 10.1111/j.1574-695X.2010.00773.x · DOI
  28. Rubinstein, 2013, Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/b-catenin signaling via its FadA adhesin., Cell Host Microbe, 14, 195, 10.1016/j.chom.2013.07.012 · DOI · Paper page
  29. Schloss, 2008, Evaluating different approaches that test whether microbial communities have the same structure., ISME J., 2, 265, 10.1111/j.1365-294X.2007.03326.x · DOI
  30. Schloss, 2009, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities., Appl. Environ. Microbiol., 75, 7537, 10.1128/AEM.01541-09 · DOI · Paper page
  31. Schmidt, 2014, Changes in abundance of oral microbiota associated with oral cancer., PLOS ONE, 9, 10.1371/journal.pone.0098741.s027 · DOI
  32. Scully, 2009, Oral squamous cell carcinoma: overview of current understanding of aetiopathogenesis and clinical implications., Oral Dis., 15, 388, 10.1111/j.1601-0825.2009.01563.x · DOI
  33. Segata, 2011, Metagenomic biomarker discovery and explanation., Genome Biol., 12, 10.1186/gb-2011-12-6-r60 · DOI · Paper page
  34. Silverman, 1984, Oral leukoplakia and malignant transformation. A follow-up study of 257 patients., Cancer, 53, 563, 10.1002/1097-0142(19840201)53:3<563::AID-CNCR2820530332>3.0.CO;2-F · DOI
  35. Storey, 2003, Statistical significance for genomewide studies., Proc. Natl. Acad. Sci. U.S.A., 100, 9440, 10.1073/pnas.1530509100 · DOI · Paper page
  36. White, 2009, Statistical methods for detecting differentially abundant features in clinical metagenomic samples., PLOS Comput. Biol., 5, 10.1371/journal.pcbi.1000352 · DOI
  37. Yanik, 2015, Leukoplakia, oral cavity cancer risk, and cancer survival in the U.S. elderly., Cancer Prev. Res., 8, 857, 10.1158/1940-6207.CAPR-15-0091 · DOI

Cited by

Sorted by citations

See all 160

Metadata

Authors
Amer, A., Galvin, S., Healy, C. M., & Moran, G. P.
Venue
Frontiers in Microbiology
Publisher
Frontiers Media SA
Published
2017-12-01
Volume
8
ISSN
1664-302X
DOI
10.3389/fmicb.2017.02391
PMC
PMC5717034
Cited by
160
References
3
Funders
Ministry of Education

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review