Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
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

Curated date: 2023/11/29

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

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

Curated date: 2023/11/29

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

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

NCBI Quality ControlLinks
Acidaminococcus intestini
Alistipes inops
Anaerotignum faecicola
Bacteroides
Bacteroides ovatus
Bacteroides uniformis
Collinsella aerofaciens
Escherichia/Shigella sp.
Flintibacter butyricus
Mediterraneibacter gnavus
Parabacteroides distasonis
Ruminococcus

Revision editor(s): Yjung24, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3

Curated date: 2023/11/29

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

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

NCBI Quality ControlLinks
Anaerostipes hadrus
Bacteroides uniformis
Blautia
Christensenellaceae
Faecalibacterium prausnitzii
Mediterraneibacter faecis
Sutterella wadsworthensis
Schaedlerella
Anaerosacchariphilus

Revision editor(s): Yjung24, Peace Sandy

Experiment 2


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3

Curated date: 2024/02/03

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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

Curated date: 2023/11/29

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

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 ControlLinks
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

Curated date: 2023/11/29

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

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 ControlLinks
Parabacteroides merdae
Veillonella nakazawae

Revision editor(s): Yjung24, Peace Sandy