16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment

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
Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W, Sidransky D
Journal
Oncotarget
Year
2016
Keywords:
16s rRNA, human papilloma virus (HPV), microbiome, oral cancer, oropharyngeal cancer
Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from Oropharyngeal (OPSCC), Oral Cavity Squamous Cell Carcinoma (OCSCC) patients and normal epithelium controls, to characterize the HNSCC saliva microbiota and examine their abundance before and after surgical resection.The analyses identified a predominance of Firmicutes, Proteobacteria and Bacteroidetes, with less frequent presence of Actinobacteria and Fusobacteria before surgery. At lower taxonomic levels, the most abundant genera were Streptococcus, Prevotella, Haemophilus, Lactobacillus and Veillonella, with lower numbers of Citrobacter and Neisseraceae genus Kingella. HNSCC patients had a significant loss in richness and diversity of microbiota species (p<0.05) compared to the controls. Overall, the Operational Taxonomic Units network shows that the relative abundance of OTU's within genus Streptococcus, Dialister, and Veillonella can be used to discriminate tumor from control samples (p<0.05). Tumor samples lost Neisseria, Aggregatibacter (Proteobacteria), Haemophillus (Firmicutes) and Leptotrichia (Fusobacteria). Paired taxa within family Enterobacteriaceae, together with genus Oribacterium, distinguish OCSCC samples from OPSCC and normal samples (p<0.05). Similarly, only HPV positive samples have an abundance of genus Gemellaceae and Leuconostoc (p<0.05). Longitudinal analyses of samples taken before and after surgery, revealed a reduction in the alpha diversity measure after surgery, together with an increase of this measure in patients that recurred (p<0.05). These results suggest that microbiota may be used as HNSCC diagnostic and prognostic biomonitors.

Experiment 1


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects
United States of America
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
Oral squamous cell carcinoma mouth scc,mouth squamous cell carcinoma,OCSC,oral cavity scc,oral cavity squamous cell cancer,oral cavity squamous cell carcinoma,oral squamous cell carcinoma,scc of mouth,scc of oral cavity,scc of the mouth,scc of the oral cavity,squamous cell carcinoma of mouth,squamous cell carcinoma of oral cavity,squamous cell carcinoma of the mouth,squamous cell carcinoma of the oral cavity,Oral 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
HNSCC
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample
Group 0 sample size Number of subjects in the control (unexposed) group
25
Group 1 sample size Number of subjects in the case (exposed) group
17

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V5
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).
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

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
decreased

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, Aiyshaaaa

Source: Figure 6, Sup Fig1

Description: Relative abundance of oral microbiome in HNSCC patients and controls

Abundance in Group 1: increased abundance in HNSCC

NCBI Quality ControlLinks
Lactobacillus
Parvimonas
Peptostreptococcus
Staphylococcus
Streptococcus
Tannerella
Veillonella

Revision editor(s): WikiWorks, Aiyshaaaa

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: Figure 6, Sup Fig1

Description: Relative abundance of oral microbiome in HNSCC patients and controls

Abundance in Group 1: decreased abundance in HNSCC

NCBI Quality ControlLinks
Aggregatibacter
Lautropia
Haemophilus
Neisseria
Leptotrichia

Revision editor(s): WikiWorks

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV -
Group 1 name Corresponds to the case (exposed) group for case-control studies
HPV +
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who are HPV+
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
7

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
decreased

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: Figure 6, Text

Description: Relative abundance of oral microbiome in HNSCC HPV + and HPV -

Abundance in Group 1: increased abundance in HPV +

NCBI Quality ControlLinks
Lactobacillus
Weeksella

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: Figure 6, Text

Description: Relative abundance of oral microbiome in HNSCC HPV + and HPV -

Abundance in Group 1: decreased abundance in HPV +

NCBI Quality ControlLinks
Eikenella
Neisseria
Leptotrichia

Revision editor(s): WikiWorks

Experiment 3


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
surgery
Group 1 name Corresponds to the case (exposed) group for case-control studies
chemotherapy-radiation and surgery
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) patients with at least one post-treatment salivary sample who received chemo/radiation and surgery
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
13

Lab analysis

Statistical Analysis

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: Figure 6, Text

Description: Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery

Abundance in Group 1: increased abundance in chemotherapy-radiation and surgery

NCBI Quality ControlLinks
Lactobacillaceae
Lactobacillus

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/19

Curated date: 2022/12/19

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 6, text

Description: Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery

Abundance in Group 1: decreased abundance in chemotherapy-radiation and surgery

NCBI Quality ControlLinks
Haemophilus
Aggregatibacter
Leptotrichia

Revision editor(s): Claregrieve1