Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study

Study information

Needs review Marked as Needs review by Chloe on 2022/03/28

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29375539

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2017.02699

URI Uniform resource identifier for web resources.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/

Authors

Russo E, Bacci G, Chiellini C, Fagorzi C, Niccolai E, Taddei A, Ricci F, Ringressi MN, Borrelli R, Melli F, Miloeva M, Bechi P, Mengoni A, Fani R, Amedei A

Journal

Frontiers in microbiology

Year

2017

In this study Next-Generation Sequencing (NGS) was used to analyze and compare human microbiota from three different compartments, i.e., saliva, feces, and cancer tissue (CT), of a selected cohort of 10 Italian patients with colorectal cancer (CRC) vs. 10 healthy controls (saliva and feces). Furthermore, the Fusobacterium nucleatum abundance in the same body site was investigated through real-time quantitative polymerase chain reaction (qPCR) to assess the association with CRC. Differences in bacterial composition, F. nucleatum abundance in healthy controls vs. CRC patients, and the association of F. nucleatum with clinical parameters were observed. Taxonomic analysis based on 16S rRNA gene, revealed the presence of three main bacterial phyla, which includes about 80% of reads: Firmicutes (39.18%), Bacteroidetes (30.36%), and Proteobacteria (10.65%). The results highlighted the presence of different bacterial compositions; in particular, the fecal samples of CRC patients seemed to be enriched with Bacteroidetes, whereas in the fecal samples of healthy controls Firmicutes were one of the major phyla detected though these differences were not statistically significant. The CT samples showed the highest alpha diversity values. These results emphasize a different taxonomic composition of feces from CRC compared to healthy controls. Despite the low number of samples included in the study, these results suggest the importance of microbiota in the CRC progression and could pave the way to the development of therapeutic interventions and novel microbial-related diagnostic tools in CRC patients.

Experiment 1

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Curated date: 2022/01/04

Curator: Itslanapark

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Subjects

Location of subjects: Italy

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine

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: CRC Patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections
Group 0 sample size Number of subjects in the control (unexposed) group: 10
Group 1 sample size Number of subjects in the case (exposed) group: 10
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: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: ANOSIM; T-Test

Alpha Diversity

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

Signature 1

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Curated date: 2022/01/12

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Source: Figure 1, Discussion Text

Description: Linear discriminant analysis performed with the “lefse“ pipeline to identify distinctive taxa of saliva, feces, and biopsy was used to reveal body site-specific microbial distributions.

Abundance in Group 1: increased abundance in CRC Patients

NCBI	Links
Bacillota
Fusobacteriota

Revision editor(s): Itslanapark

Experiment 2

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Curated date: 2022/01/19

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Subjects

Location of subjects: Italy

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine

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: CRC Patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections.
Group 0 sample size Number of subjects in the control (unexposed) group: 10
Group 1 sample size Number of subjects in the case (exposed) group: 10
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: ANOSIM

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased
Chao1 Abundance-based estimator of species richness: decreased
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: decreased

Signature 1

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Mark reviewed

Your review change was submitted

Needs review

Curated date: 2022/01/25

Curator: Itslanapark

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Source: Figure 1, Results Text

Description: Linear discriminant analysis performed with the “lefse“ pipeline to identify distinctive taxa of saliva, feces, and biopsy was used to reveal body site-specific microbial distributions.

Abundance in Group 1: increased abundance in CRC Patients

NCBI	Links
Actinomycetota
Betaproteobacteria
Bacillota
Flavobacteriia
Fusobacteriota
Prevotellaceae
Candidatus Saccharibacteria

Revision editor(s): Itslanapark