Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma

From BugSigDB
Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y, Zhou L
Journal
Applied and environmental microbiology
Year
2014
The compositions and abundances of the microbiota in the ecological niche of the human throat and the possible relationship between the microbiota and laryngeal cancer are poorly understood. To obtain insight into this, we enrolled 27 laryngeal carcinoma patients and 28 subjects with vocal cord polyps as controls. For each subject, we simultaneously collected swab samples from the upper throat near the epiglottis (site I) and tissue samples from the vestibulum laryngis to the subglottic region (site II). The microbiota of the throat were fully characterized by pyrosequencing of barcoded 16S rRNA genes. We found 14 phyla, 20 classes, 38 orders, 85 families, and 218 genera in the throats of enrolled subjects. The main phyla were Firmicutes (54.7%), Fusobacteria (14.8%), Bacteroidetes (12.7%), and Proteobacteria (10.6%). Streptococcus (37.3%), Fusobacterium (11.3%), and Prevotella (10.6%) were identified as the three most predominant genera in the throat. The relative abundances of 23 bacterial genera in site I were significantly different from those in site II (P < 0.05). The relative proportions of 12 genera largely varied between laryngeal cancer patients and control subjects (P < 0.05). Collectively, this study outlined the spatial structure of microbial communities in the human throat. The spatial structure of bacterial communities significantly varied in two anatomical sites of the throat. The bacterial profiles of the throat of laryngeal cancer patients were strongly different from those of control subjects, and several of these microorganisms may be related to laryngeal carcinoma.

Experiment 1


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, 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
Throat Gula,Throat,throat
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Squamous cell carcinoma carcinoma, squamous cell, malignant,epidermoid carcinoma,epidermoid cell cancer,malignant epidermoid cell neoplasm,malignant epidermoid cell tumor,malignant squamous cell neoplasm,malignant squamous cell tumor,squamous carcinoma,squamous cell cancer,squamous cell carcinoma,squamous cell carcinoma (morphologic abnormality),squamous cell carcinoma NOS (morphologic abnormality),squamous cell epithelioma,Squamous cell carcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
laryngeal squamous cell carcinoma (LSCC)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy
Group 0 sample size Number of subjects in the control (unexposed) group
28
Group 1 sample size Number of subjects in the case (exposed) group
27
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V2
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
T-Test
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)?
Yes


Signature 1

Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Table 2, Text, Supplementary Table S2

Description: Differences in bacterial communities in the throats of LSCC patients and control subjects

Abundance in Group 1: increased abundance in laryngeal squamous cell carcinoma (LSCC)

NCBI Quality ControlLinks
Fusobacterium
Prevotella
Parvimonas
Peptostreptococcus
Dialister
Catonella
Selenomonas
Treponema
Burkholderia
Peptostreptococcaceae

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Table 2, Text, Supplementary Table S2

Description: Differences in bacterial communities in the throats of LSCC patients and control subjects

Abundance in Group 1: decreased abundance in laryngeal squamous cell carcinoma (LSCC)

NCBI Quality ControlLinks
Streptococcus
Rothia

Revision editor(s): WikiWorks

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks

Differences from previous experiment shown

Subjects

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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Site 2 (site below the epiglottis in the throat)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Site 1 (upper portion of throat near the epiglottis)

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
Not specified


Signature 1

Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Table 2, Text, Supplementary Table S2

Description: Differences in bacterial communities in the throats of LSCC patients and control subjects

Abundance in Group 1: increased abundance in Site 1 (upper portion of throat near the epiglottis)

NCBI Quality ControlLinks
Veillonella
Leptotrichia
Actinomyces
Rothia
Granulicatella
Megasphaera
Oribacterium
Atopobium
Moryella
Candidatus Saccharibacteria

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Rimsha Azhar on 2021/02/09

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks

Source: Table 2, Text, Supplementary Table S2

Description: Differences in bacterial communities in the throats of LSCC patients and control subjects

Abundance in Group 1: decreased abundance in Site 1 (upper portion of throat near the epiglottis)

NCBI Quality ControlLinks
Fusobacterium
Prevotella
Parvimonas
Peptostreptococcus
Porphyromonas
Dialister
Mycoplasma
Filifactor
Catonella
Eikenella
Treponema
Aggregatibacter
Peptostreptococcaceae

Revision editor(s): WikiWorks