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

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2023-12-13

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

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

Keywords:

Fusobacterium nucleatum, colorectal cancer, gut microbiota, oral microbiota, quantitative polymerase chain reaction, taxonomic analysis

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

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-1-10

Curated date: 2022/01/04

Curator: Itslanapark

Revision editor(s): Itslanapark, WikiWorks, Atrayees, Peace Sandy

Subjects

Location of subjects: Italy

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: 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,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,Colorectal cancer

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: Colorectal Cancer 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

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)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-1-10

Curated date: 2022/01/12

Curator: Itslanapark

Revision editor(s): Itslanapark, Peace Sandy, Atrayees, Folakunmi

Source: Figure 7A

Description: Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and considering the three body sites sampled in this study, namely: biopsy (red), saliva (green), and stool (blue). (A) Different body sites showed a characteristic taxonomic composition with major clades strongly associated with a particular site. Proteobacteria were mostly associated with biopsy samples whereas Fusobacteria and Bacteroidetes were mainly associated with saliva and stool samples, respectively.

Abundance in Group 1: increased abundance in Colorectal Cancer Patients

NCBI	Quality Control	Links
Bacteroidaceae
Bacteroidales
Bacteroidia
Clostridia
Erysipelotrichaceae
Erysipelotrichales
Erysipelotrichia
Eubacteriales
Oscillospiraceae
Porphyromonadaceae
Rikenellaceae
unclassified Bacteria
unclassified Clostridiales Family XVII.

Revision editor(s): Itslanapark, Peace Sandy, Atrayees, Folakunmi

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-1-10

Curated date: 2022/01/19

Curator: Itslanapark

Revision editor(s): Itslanapark, WikiWorks, Peace Sandy

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 1 name Corresponds to the case (exposed) group for case-control studies: Colorectal cancer 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.

Lab analysis

Statistical Analysis

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-1-10

Curated date: 2022/01/25

Curator: Itslanapark

Revision editor(s): Itslanapark, Adanwa, Peace Sandy, Folakunmi

Source: Figure 7A

Description: Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and considering the three body sites sampled in this study, namely: biopsy (red), saliva (green), and stool (blue). (A) Different body sites showed a characteristic taxonomic composition with major clades strongly associated with a particular site. Proteobacteria were mostly associated with biopsy samples whereas Fusobacteria and Bacteroidetes were mainly associated with saliva and stool samples, respectively.

Abundance in Group 1: increased abundance in Colorectal cancer Patients

NCBI	Quality Control	Links
Actinomycetaceae
Actinomycetales
Actinomycetota
Bacillales
Bacilli
Betaproteobacteria
Flavobacteriaceae
Flavobacteriales
Fusobacteriia
Leptotrichiaceae
Micrococcaceae
Micrococcales
Negativicutes
Neisseriaceae
Neisseriales
Pasteurellaceae
Prevotellaceae
Selenomonadales
Streptococcaceae
Veillonellaceae
unclassified Candidatus Saccharibacteria
unclassified Lactobacillales

Revision editor(s): Itslanapark, Adanwa, Peace Sandy, Folakunmi

Experiment 3

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-1-10

Curated date: 2024/01/10

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Colorectum Colorectum,colorectum

Group 1 name Corresponds to the case (exposed) group for case-control studies: Biopsy samples of colorectal cancer patients

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-1-10

Curated date: 2024/01/10

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figure 7A

Description: Linear discriminant analysis of association between sampling sites and microbial taxa. A linear discriminant analysis was performed using Lefse and considering the three body sites sampled in this study, namely: biopsy, saliva, and stool.

Abundance in Group 1: increased abundance in Biopsy samples of colorectal cancer patients

NCBI	Quality Control	Links
Lachnospiraceae
Fusobacteriaceae
Hyphomicrobiales
Alphaproteobacteria
Deltaproteobacteria
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria

Revision editor(s): Folakunmi