Changes in Abundance of Oral Microbiota Associated with Oral Cancer
Publication Date
June 02, 2014
Journal
PLOS ONE
Authors
Brian L. Schmidt, Justin Kuczynski, Aditi Bhattacharya, Bing Huey, et al
Volume
9
Issue
6
Pages
e98741
DOI
https://dx.plos.org/10.1371/journal.pone.0098741
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0098741
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24887397
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041887
Europe PMC
http://europepmc.org/abstract/MED/24887397
Web of Science
000336956300102
Scopus
84902336218
Mendeley
http://www.mendeley.com/research/changes-abundance-oral-microbiota-associated-oral-cancer
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Mendeley | Further Information

{"title"=>"Changes in abundance of oral microbiota associated with oral cancer", "type"=>"journal", "authors"=>[{"first_name"=>"Brian L.", "last_name"=>"Schmidt", "scopus_author_id"=>"7402828720"}, {"first_name"=>"Justin", "last_name"=>"Kuczynski", "scopus_author_id"=>"36093149800"}, {"first_name"=>"Aditi", "last_name"=>"Bhattacharya", "scopus_author_id"=>"54583221700"}, {"first_name"=>"Bing", "last_name"=>"Huey", "scopus_author_id"=>"7003700119"}, {"first_name"=>"Patricia M.", "last_name"=>"Corby", "scopus_author_id"=>"6508121006"}, {"first_name"=>"Erica L.S.", "last_name"=>"Queiroz", "scopus_author_id"=>"55267749000"}, {"first_name"=>"Kira", "last_name"=>"Nightingale", "scopus_author_id"=>"56203426300"}, {"first_name"=>"A. Ross", "last_name"=>"Kerr", "scopus_author_id"=>"24477055900"}, {"first_name"=>"Mark D.", "last_name"=>"DeLacure", "scopus_author_id"=>"6701860411"}, {"first_name"=>"Ratna", "last_name"=>"Veeramachaneni", "scopus_author_id"=>"57191086331"}, {"first_name"=>"Adam B.", "last_name"=>"Olshen", "scopus_author_id"=>"6602777491"}, {"first_name"=>"Donna G.", "last_name"=>"Albertson", "scopus_author_id"=>"7101804288"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84902336218", "doi"=>"10.1371/journal.pone.0098741", "pui"=>"373302429", "pmid"=>"24887397", "scopus"=>"2-s2.0-84902336218", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)"}, "id"=>"5799a52f-a1bc-3d77-a5b2-d4ab1a5d0c40", "abstract"=>"Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer. To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal samples from the same patient. Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals. Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases. These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.", "link"=>"http://www.mendeley.com/research/changes-abundance-oral-microbiota-associated-oral-cancer", "reader_count"=>55, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>12, "Other"=>4, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>12, "Other"=>4, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Unspecified"=>6, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>19, "Medicine and Dentistry"=>13, "Immunology and Microbiology"=>4, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>13}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>6}}, "reader_count_by_country"=>{"Netherlands"=>1, "United Kingdom"=>1, "Spain"=>1}, "group_count"=>9}

CrossRef

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1516381"], "description"=>"<p>(a – e) Relative abundance of each of the five more abundant phyla in cancers compared to clinically normal samples from each of five patients. Note, that data are shown on different scales, reflecting the abundance of the phyla. The magnitudes of the changes in abundance are clearly greater than the statistical counting noise, as indicated by the error bar estimates, which are based on the square root of the actual number of reads. (f) Change in relative abundance shown as the difference in abundance of phyla associated with cancers compared to anatomically matched contralateral clinically normal samples. In cancers, decreases in the relative abundance of <i>Firmicutes</i> and <i>Actinobacteria</i> were seen in all patients, while the relative abundance of <i>Fusobacteria</i> was elevated in cancers from all patients.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "biotechnology", "Applied microbiology", "ecology", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Medical microbiology", "dermatology", "Skin neoplasms", "Skin tumors", "Oral mucosal cancers", "Diagnostic medicine", "oncology", "Cancers and neoplasms", "carcinomas", "Squamous cell carcinomas", "Head and neck squamous cell carcinoma", "Head and neck tumors", "Oral leukoplakia", "Basic cancer research", "Cancer detection and diagnosis", "otorhinolaryngology", "Head and neck cancers", "Pathology and laboratory medicine", "abundance", "phyla", "cancer", "compared", "anatomically", "matched", "contralateral", "clinically", "samples"], "article_id"=>1042225, "categories"=>["Biological Sciences"], "users"=>["Brian L. Schmidt", "Justin Kuczynski", "Aditi Bhattacharya", "Bing Huey", "Patricia M. Corby", "Erica L. S. Queiroz", "Kira Nightingale", "A. Ross Kerr", "Mark D. DeLacure", "Ratna Veeramachaneni", "Adam B. Olshen", "Donna G. Albertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098741.g002", "stats"=>{"downloads"=>4, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Change_in_relative_abundance_of_phyla_associated_with_cancer_compared_to_anatomically_matched_contralateral_clinically_normal_samples_in_Study_1_/1042225", "title"=>"Change in relative abundance of phyla associated with cancer compared to anatomically matched contralateral clinically normal samples in Study 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1516382"], "description"=>"<p>(a) Shown is the relative distribution of phyla (percent of sequences). For cancers, we included only patients for which both the cancer and contralateral clinically normal samples were available. (b) Change in relative abundance of phyla shown as the difference in abundance of phyla associated with cancers or pre-cancers compared to anatomically matched contralateral clinically normal samples. For healthy normal samples, we compared left and right sides of the lateral tongue or floor of mouth.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "biotechnology", "Applied microbiology", "ecology", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Medical microbiology", "dermatology", "Skin neoplasms", "Skin tumors", "Oral mucosal cancers", "Diagnostic medicine", "oncology", "Cancers and neoplasms", "carcinomas", "Squamous cell carcinomas", "Head and neck squamous cell carcinoma", "Head and neck tumors", "Oral leukoplakia", "Basic cancer research", "Cancer detection and diagnosis", "otorhinolaryngology", "Head and neck cancers", "Pathology and laboratory medicine", "phyla", "pre-cancer", "samples"], "article_id"=>1042226, "categories"=>["Biological Sciences"], "users"=>["Brian L. Schmidt", "Justin Kuczynski", "Aditi Bhattacharya", "Bing Huey", "Patricia M. Corby", "Erica L. S. Queiroz", "Kira Nightingale", "A. Ross Kerr", "Mark D. DeLacure", "Ratna Veeramachaneni", "Adam B. Olshen", "Donna G. Albertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098741.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_phyla_in_cancer_pre_cancer_and_healthy_normal_samples_in_Study_2_/1042226", "title"=>"Distribution of phyla in cancer, pre-cancer and healthy normal samples in Study 2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1516383"], "description"=>"<p>PCoA based on Weighted UniFrac distance between samples given abundance of 12 OTUs. Axis 1 (PCoA1): 54% of variation explained. Axis 2 (PCoA2): 24% of variation explained. N0 and N+ indicate the nodal status of the cancer patient, N0  =  node negative, N+  =  node positive. Cancer control and pre-cancer control are contralateral clinically normal patient samples. Other identifies samples from healthy normal individuals.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "biotechnology", "Applied microbiology", "ecology", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Medical microbiology", "dermatology", "Skin neoplasms", "Skin tumors", "Oral mucosal cancers", "Diagnostic medicine", "oncology", "Cancers and neoplasms", "carcinomas", "Squamous cell carcinomas", "Head and neck squamous cell carcinoma", "Head and neck tumors", "Oral leukoplakia", "Basic cancer research", "Cancer detection and diagnosis", "otorhinolaryngology", "Head and neck cancers", "Pathology and laboratory medicine", "cancer"], "article_id"=>1042227, "categories"=>["Biological Sciences"], "users"=>["Brian L. Schmidt", "Justin Kuczynski", "Aditi Bhattacharya", "Bing Huey", "Patricia M. Corby", "Erica L. S. Queiroz", "Kira Nightingale", "A. Ross Kerr", "Mark D. DeLacure", "Ratna Veeramachaneni", "Adam B. Olshen", "Donna G. Albertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098741.g004", "stats"=>{"downloads"=>4, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distinguishing_cancer_and_normal_samples_/1042227", "title"=>"Distinguishing cancer and normal samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1516384"], "description"=>"1<p>Pathologic tumor stage according to the American Joint Committee on Cancer guidelines (T  =  tumor size, N  =  regional lymph node metastasis, M =  distant metastasis)</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "biotechnology", "Applied microbiology", "ecology", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Medical microbiology", "dermatology", "Skin neoplasms", "Skin tumors", "Oral mucosal cancers", "Diagnostic medicine", "oncology", "Cancers and neoplasms", "carcinomas", "Squamous cell carcinomas", "Head and neck squamous cell carcinoma", "Head and neck tumors", "Oral leukoplakia", "Basic cancer research", "Cancer detection and diagnosis", "otorhinolaryngology", "Head and neck cancers", "Pathology and laboratory medicine", "cohort", "cancer"], "article_id"=>1042228, "categories"=>["Biological Sciences"], "users"=>["Brian L. Schmidt", "Justin Kuczynski", "Aditi Bhattacharya", "Bing Huey", "Patricia M. Corby", "Erica L. S. Queiroz", "Kira Nightingale", "A. Ross Kerr", "Mark D. DeLacure", "Ratna Veeramachaneni", "Adam B. Olshen", "Donna G. Albertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098741.t001", "stats"=>{"downloads"=>5, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Discovery_Cohort_Cancer_Patient_Characteristics_/1042228", "title"=>"Discovery Cohort Cancer Patient Characteristics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1516385"], "description"=>"1<p>Pathologic tumor stage according to the American Joint Committee on Cancer guidelines (T  =  tumor size, N  =  regional lymph node metastasis, M  =  distant metastasis</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "biotechnology", "Applied microbiology", "ecology", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Medical microbiology", "dermatology", "Skin neoplasms", "Skin tumors", "Oral mucosal cancers", "Diagnostic medicine", "oncology", "Cancers and neoplasms", "carcinomas", "Squamous cell carcinomas", "Head and neck squamous cell carcinoma", "Head and neck tumors", "Oral leukoplakia", "Basic cancer research", "Cancer detection and diagnosis", "otorhinolaryngology", "Head and neck cancers", "Pathology and laboratory medicine", "cohort", "cancer"], "article_id"=>1042229, "categories"=>["Biological Sciences"], "users"=>["Brian L. Schmidt", "Justin Kuczynski", "Aditi Bhattacharya", "Bing Huey", "Patricia M. Corby", "Erica L. S. Queiroz", "Kira Nightingale", "A. Ross Kerr", "Mark D. DeLacure", "Ratna Veeramachaneni", "Adam B. Olshen", "Donna G. Albertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098741.t002", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conformation_Cohort_Cancer_Patient_Characteristics_/1042229", "title"=>"Conformation Cohort Cancer Patient Characteristics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1516387", "https://ndownloader.figshare.com/files/1516388", "https://ndownloader.figshare.com/files/1516389", "https://ndownloader.figshare.com/files/1516390", "https://ndownloader.figshare.com/files/1516391", "https://ndownloader.figshare.com/files/1516392", "https://ndownloader.figshare.com/files/1516393", "https://ndownloader.figshare.com/files/1516394", "https://ndownloader.figshare.com/files/1516395", "https://ndownloader.figshare.com/files/1516396", "https://ndownloader.figshare.com/files/1516397", "https://ndownloader.figshare.com/files/1516398", "https://ndownloader.figshare.com/files/1516399", "https://ndownloader.figshare.com/files/1516400", "https://ndownloader.figshare.com/files/1516401", "https://ndownloader.figshare.com/files/1516402", "https://ndownloader.figshare.com/files/1516403", "https://ndownloader.figshare.com/files/1516404", "https://ndownloader.figshare.com/files/1516405", "https://ndownloader.figshare.com/files/1516406", "https://ndownloader.figshare.com/files/1516407", "https://ndownloader.figshare.com/files/1516408", "https://ndownloader.figshare.com/files/1516409", "https://ndownloader.figshare.com/files/1516410", "https://ndownloader.figshare.com/files/1516411", "https://ndownloader.figshare.com/files/1516412", "https://ndownloader.figshare.com/files/1516413"], "description"=>"<div><p>Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer. To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of <i>Firmicutes</i> (especially <i>Streptococcus</i>) and <i>Actinobacteria</i> (especially <i>Rothia</i>) was significantly decreased relative to contralateral normal samples from the same patient. Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals. Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases. These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.</p></div>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "biotechnology", "Applied microbiology", "ecology", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Medical microbiology", "dermatology", "Skin neoplasms", "Skin tumors", "Oral mucosal cancers", "Diagnostic medicine", "oncology", "Cancers and neoplasms", "carcinomas", "Squamous cell carcinomas", "Head and neck squamous cell carcinoma", "Head and neck tumors", "Oral leukoplakia", "Basic cancer research", "Cancer detection and diagnosis", "otorhinolaryngology", "Head and neck cancers", "Pathology and laboratory medicine", "abundance", "microbiota"], "article_id"=>1042231, "categories"=>["Biological Sciences"], "users"=>["Brian L. Schmidt", "Justin Kuczynski", "Aditi Bhattacharya", "Bing Huey", "Patricia M. Corby", "Erica L. S. Queiroz", "Kira Nightingale", "A. Ross Kerr", "Mark D. DeLacure", "Ratna Veeramachaneni", "Adam B. Olshen", "Donna G. Albertson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0098741.s001", "https://dx.doi.org/10.1371/journal.pone.0098741.s002", "https://dx.doi.org/10.1371/journal.pone.0098741.s003", "https://dx.doi.org/10.1371/journal.pone.0098741.s004", "https://dx.doi.org/10.1371/journal.pone.0098741.s005", "https://dx.doi.org/10.1371/journal.pone.0098741.s006", "https://dx.doi.org/10.1371/journal.pone.0098741.s007", "https://dx.doi.org/10.1371/journal.pone.0098741.s008", "https://dx.doi.org/10.1371/journal.pone.0098741.s009", "https://dx.doi.org/10.1371/journal.pone.0098741.s010", "https://dx.doi.org/10.1371/journal.pone.0098741.s011", "https://dx.doi.org/10.1371/journal.pone.0098741.s012", "https://dx.doi.org/10.1371/journal.pone.0098741.s013", "https://dx.doi.org/10.1371/journal.pone.0098741.s014", "https://dx.doi.org/10.1371/journal.pone.0098741.s015", "https://dx.doi.org/10.1371/journal.pone.0098741.s016", "https://dx.doi.org/10.1371/journal.pone.0098741.s017", "https://dx.doi.org/10.1371/journal.pone.0098741.s018", "https://dx.doi.org/10.1371/journal.pone.0098741.s019", "https://dx.doi.org/10.1371/journal.pone.0098741.s020", "https://dx.doi.org/10.1371/journal.pone.0098741.s021", "https://dx.doi.org/10.1371/journal.pone.0098741.s022", "https://dx.doi.org/10.1371/journal.pone.0098741.s023", "https://dx.doi.org/10.1371/journal.pone.0098741.s024", "https://dx.doi.org/10.1371/journal.pone.0098741.s025", "https://dx.doi.org/10.1371/journal.pone.0098741.s026", "https://dx.doi.org/10.1371/journal.pone.0098741.s027"], "stats"=>{"downloads"=>63, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Changes_in_Abundance_of_Oral_Microbiota_Associated_with_Oral_Cancer_/1042231", "title"=>"Changes in Abundance of Oral Microbiota Associated with Oral Cancer", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-02 03:31:01"}

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Relative Metric

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