Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer

From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W, Huang Z
Journal
Frontiers in cellular and infection microbiology
Year
2019
Keywords:
16S rRNA gene, early diagnosis, microbiome, next-generation sequencing, oral health, throat cancer
In this study, a next-generation sequencing strategy on 16S ribosomal RNA (16S rRNA) gene was employed to analyze 70 oral samples from 32 patients with throat cancer, nine patients with vocal cord polyp, and 29 healthy individuals (normal controls). Using this strategy, we demonstrated, for the first time, that the salivary microbiota of cancer patients were significantly different from those of patients with a polyp and healthy individuals. We observed that the beta diversity of the cancer group was divergent from both the normal and polyp groups, while alpha-diversity indices such as the Chao1 estimator (P = 8.1e-05), Simpson (P = 0.0045), and Shannon (P = 0.0071) were significantly reduced in cancer patients compared with patients containing a polyp and normal healthy individuals. Linear discriminant analysis (LDA) and Kruskal-Wallis test analyses and real-time quantitative polymerase chain reaction (qPCR) verification test revealed that the genera Aggregatibacter, Pseudomonas, Bacteroides, and Ruminiclostridium were significantly enriched in the throat cancer group compared with the vocal cord polyp and normal control groups (score value >2). Finally, diagnostic models based on putatively important constituent bacteria were constructed with 87.5% accuracy [area under the curve (AUC) = 0.875, 95% confidence interval (CI): 0.695-1]. In summary, in this study we characterized, for the first time, the oral microbiota of throat cancer patients without smoking history. We speculate that these results will help in the pathogenic mechanism and early diagnosis of throat cancer.

Experiment 1


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Head and neck carcinoma carcinoma of craniocervical region,carcinoma of head and neck,carcinoma of neck,carcinoma of the head and neck,carcinoma of the neck,craniocervical region carcinoma,head and neck cancer,head and neck carcinoma,neck carcinoma,Head and neck carcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Throat cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx
Group 0 sample size Number of subjects in the control (unexposed) group
29
Group 1 sample size Number of subjects in the case (exposed) group
32
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
4

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 2, Figure 3, Text

Description: Variations in oral microbiota composition associated with a risk of Throat Cancer

Abundance in Group 1: increased abundance in Throat cancer

NCBI Quality ControlLinks
Pseudomonas
Aggregatibacter
Faecalibacterium
Ruminiclostridium
Lautropia
Phocaeicola
Bacteroides
Prevotellaceae
Azotobacter group
Bacteroidaceae
Burkholderiaceae
Burkholderiales
Alphaproteobacteria
Rickettsiales

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): Lwaldron, WikiWorks

Source: Figure 2, Figure 3, Text

Description: Variations in oral microbiota composition associated with a risk of Throat Cancer

Abundance in Group 1: decreased abundance in Throat cancer

NCBI Quality ControlLinks
Actinobacillus
Anaerovorax
Bergeyella
Campylobacter
Campylobacteraceae
Campylobacterales
Candidatus Gracilibacteria
Candidatus Saccharibacteria
Clostridia
Corynebacteriaceae
Mycobacteriales
Corynebacterium
Campylobacterota
Eubacteriales
Eubacterium
Fusobacteriota
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacterium
Haemophilus
Lachnoclostridium
Leptotrichia
Leptotrichiaceae
Moraxella
Moraxellaceae
Negativicutes
Neisseria
Parvimonas
Peptostreptococcaceae
Peptostreptococcus
Porphyromonas
Prevotella
Roseburia
Rothia
Selenomonadales
Selenomonas
Spirochaetaceae
Spirochaetales
Spirochaetia
Treponema
Veillonella
Veillonellaceae

Revision editor(s): Lwaldron, WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Vocal cord polyp
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cancer
Group 0 sample size Number of subjects in the control (unexposed) group
9

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 2, Figure 3, Text

Description: Variations in oral microbiota composition associated with a risk of Throat Cancer

Abundance in Group 1: increased abundance in Cancer

NCBI Quality ControlLinks
Enterobacter
Aggregatibacter
Pseudomonas
Azotobacter group

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Figure 2, Figure 3, Text

Description: Variations in oral microbiota composition associated with a risk of Throat Cancer

Abundance in Group 1: decreased abundance in Cancer

NCBI Quality ControlLinks
Fusobacterium
Prevotella
Filifactor
Actinobacillus
Helicobacter
Rikenellaceae
Eubacterium
Roseburia
Anaerovorax
Desulfovibrio
Johnsonella
Fusobacteriia
Fusobacteriota
Fusobacteriales
Fusobacteriaceae
Leptotrichiaceae
Peptostreptococcaceae
Candidatus Saccharibacteria
Sphingobacteriales
Sphingobacteriia
Lentimicrobiaceae
Helicobacteraceae
Candidatus Gracilibacteria
Caulobacteraceae
Caulobacterales
Defluviitaleaceae
Desulfovibrionaceae
Desulfovibrionales

Revision editor(s): WikiWorks