Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Welham Z, Li J, Engel AF, Molloy MP
Journal
Cancers
Year
2023
Keywords:
16S rRNA sequencing, PacBio long-read sequencing, bowel polyps, gut microbiome
Numerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial taxonomy, and this has led, in part, to inconsistent findings between studies. Here, we examined mucosal microbiota from patients who presented with one or more polyps, compared to patients with no polyps, at the time of colonoscopy. We evaluated the results obtained using both short-read and PacBio long-read 16S rRNA sequencing. Neither sequencing technology identified significant differences in microbial diversity measures between patients with or without bowel polyps. Differential abundance measures showed that amplicon sequence variants (ASVs) associated with Ruminococcus gnavus and Escherichia coli were elevated in mucosa from polyp patients, while ASVs associated with Parabacteroides merdae, Veillonella nakazawae, and Sutterella wadsworthensis were relatively decreased. Only R. gnavus was consistently identified using both sequencing technologies as being altered between patients with polyps compared to patients without polyps, suggesting differences in technologies and bioinformatics processing impact study findings. Several of the differentially abundant bacteria identified using either sequencing technology are associated with inflammatory bowel diseases despite these patients being excluded from the current study, which suggests that early bowel neoplasia may be associated with a local inflammatory niche.
Experiment 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Subjects
- Location of subjects
- Australia
- 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
- Colonic mucosa Colon mucosa,Colon mucous membrane,Colonic mucosa,Colonic mucous membrane,Large bowel mucosa,Mucosa of colon,Mucosa of large bowel,colonic mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Intestinal polyp intestinal polyp,intestinal polyp (disease),Intestinal Polyps,Polyp, Intestinal,Polyps, Intestinal,Intestinal polyp
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polyp-free control patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with low-grade colorectal polyps cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- 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)
- Patients who had taken antibiotics up to four weeks before the colonoscopy.
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)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Source: Figure 7a , 7c
Description: LEfSe differential abundance plot for short-read samples
Abundance in Group 1: increased abundance in Patients with low-grade colorectal polyps cohort
Revision editor(s): Yjung24, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Source: Figure 7a , 7c
Description: LEfSe differential abundance plot for short read samples
Abundance in Group 1: decreased abundance in Patients with low-grade colorectal polyps cohort
Revision editor(s): Yjung24, Peace Sandy
Experiment 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Differences from previous experiment shown
Subjects
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V9
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- PacBio RS
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Source: Figure 7b, 7d
Description: Pacbio Long Read LefSe differential abundance plot between polyp and no polyp specimens.
Abundance in Group 1: increased abundance in Patients with low-grade colorectal polyps cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Mediterraneibacter gnavus | ||
| Bifidobacterium longum | ||
| Sutterella wadsworthensis | ||
| Alloprevotella | ||
| Phascolarctobacterium faecium |
Revision editor(s): Yjung24, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Source: 7b, 7d
Description: Pacbio Long Read LefSe differential abundance plot between polyp and no polyp specimens.
Abundance in Group 1: decreased abundance in Patients with low-grade colorectal polyps cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides merdae | ||
| Veillonella nakazawae |
Revision editor(s): Yjung24, Peace Sandy
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