Altered diversity and composition of the gut microbiome in patients with cervical cancer

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/11
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X, Yuan Z
Journal
AMB Express
Year
2019
Keywords:
16S rRNA, Cervical cancer, Deep sequencing, Gut microbiota
Gut microbiota have been implicated in the development of many human diseases, including both digestive diseases and non-digestive diseases. In this study, we investigated whether the gut bacteria differed in cervical cancer (CCa) patients compared with healthy controls by 16S rRNA sequencing analysis. Subjects including eight CCa and five healthy controls were included. Microbiota profiles in fecal DNA were characterized by PCR amplification of the 16S rRNA V4 variable region and deep sequencing using the Illumina HiSeq platform. The CCa-associated gut microbiota had an increasing trend in alpha diversity, although statistical significance was not reached. Inter-group variability in community structure by beta diversity analysis showed a clear separation between cancer patients and healthy controls. Gut microbiota profiles were different between patients and controls; namely, the proportions of Proteobacteria phylum was notably higher in patients with CCa (ρ = 0.012). Seven genera differentiated significantly in relative abundance between CCa and controls (all ρ < 0.05), including Escherichia-Shigella, Roseburia, Pseudomonas, Lachnoclostridium, Lachnospiraceae_UCG-004, Dorea and Succinivibrio. The characteristic microbiome in CCa patients was also identified by linear discriminant analysis effect size (LEfSe). The phylum Proteobacteria, and the genus Parabacteroides, Escherichia_Shigells and Roseburia may provide novel potential biomarkers for CCa. Taken together, this is the first study on gut microbiota in patients with CCa, and demonstrated the significantly altered diversity and composition.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/11

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, Victoria

Subjects

Location of subjects
Finland
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
Cervical cancer cancer of uterine cervix,cervical neoplasm,cervix cancer,cervix uteri cancer,malignant cervical neoplasm,malignant cervical tumor,malignant cervix neoplasm,malignant cervix tumor,malignant cervix uteri neoplasm,malignant cervix uteri tumor,malignant neoplasm of cervix,malignant neoplasm of cervix uteri,malignant neoplasm of the cervix,malignant neoplasm of the cervix uteri,malignant neoplasm of the uterine cervix,malignant neoplasm of uterine cervix,malignant tumor of cervix,malignant tumor of cervix uteri,malignant tumor of the cervix,malignant tumor of the cervix uteri,malignant tumor of the uterine cervix,malignant tumor of uterine cervix,malignant uterine cervix neoplasm,malignant uterine cervix tumor,tumor of the cervix uteri,uterine cervical neoplasm,uterine cervix cancer,Cervical cancer,cervical 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
cervical cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
pathology confirmed cervical cancer patients
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
8
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
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).
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)?
No
Matched on Factors on which subjects have been matched on in a case-control study
age

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/11

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

Source: Table 3

Description: Differential microbial abundance between patients with cervical cancer and healthy controls

Abundance in Group 1: increased abundance in cervical cancer

NCBI Quality ControlLinks
Dorea
Morganella
Proteus
Ruminococcus
Shewanella
Succinivibrio

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/11

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

Source: Table 3

Description: Differential microbial abundance between patients with cervical cancer and healthy controls

Abundance in Group 1: decreased abundance in cervical cancer

NCBI Quality ControlLinks
Halomonas
Phascolarctobacterium

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/11

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
cervical cancer patients

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
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
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/11

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 4, Table 3, Figure 5

Description: Differential microbial abundance between patients with cervical cancer and healthy controls

Abundance in Group 1: increased abundance in cervical cancer patients

NCBI Quality ControlLinks
Bacteroides stercoris
Enterobacterales
Enterobacteriaceae
Escherichia coli
Gammaproteobacteria
Parabacteroides
Parabacteroides distasonis
Phocaeicola plebeius
Pseudomonadota
Roseburia
Roseburia inulinivorans

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/11

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 4, Table 3, Figure 5

Description: Differential microbial abundance between patients with cervical cancer and healthy controls

Abundance in Group 1: decreased abundance in cervical cancer patients

NCBI Quality ControlLinks
Acidaminococcaceae
Negativicutes
Phascolarctobacterium
Selenomonadales

Revision editor(s): Claregrieve1, WikiWorks