Extending colonic mucosal microbiome analysis-assessment of colonic lavage as a proxy for endoscopic colonic biopsies

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-12-10

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

27884202

DOI Digital object identifier for electronic documents.

10.1186/s40168-016-0207-9

URI

Authors

Watt E, Gemmell MR, Berry S, Glaire M, Farquharson F, Louis P, Murray GI, El-Omar E, Hold GL

Journal

Microbiome

Year

2016

Keywords:

Colonic biopsies, Colonic lavage, Microbiome analysis, Next-generation sequencing

BACKGROUND: Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy. RESULTS: Next-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types. CONCLUSIONS: We propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-10

Curated date: 2024/11/11

Curator: Ifeanyisam

Revision editor(s): Ifeanyisam

Subjects

Location of subjects: United Kingdom

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: Sigmoid colon Colon sigmoideum,Pelvic colon,Sigmoid colon,Sigmoid flexure,sigmoid colon

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Sampling site Sampling site,sampling site

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Colonic Biopsy sample

Group 1 name Corresponds to the case (exposed) group for case-control studies: Colonic Lavage Sample

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Colonic lavage samples from the sigmoid colon of 23 participants undergoing colorectal cancer screening colonoscopy

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 23

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: V1-V2

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2.0

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: increased

Signature 1

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Source: Table S2 and Figure 6A

Description: LefSe results showing differentially abundant OTUs between the two samples (Biopsy and Lavage)

Abundance in Group 1: increased abundance in Colonic Lavage Sample

NCBI	Quality Control	Links
Bifidobacterium
Holdemania
unclassified Lachnospiraceae

Revision editor(s): Ifeanyisam

Signature 2

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Curated date: 2024/11/12

Curator: Ifeanyisam

Revision editor(s): Ifeanyisam

Source: Table S2 and Figure 6A

Description: LefSe results showing differentially abundant OTUs between the two samples (Biopsy and Lavage)

Abundance in Group 1: decreased abundance in Colonic Lavage Sample

NCBI	Quality Control	Links
Acinetobacter
Blautia
Blautia sp.
Cloacibacterium
Comamonadaceae
Diaphorobacter
Lachnospiraceae incertae sedis
Peptostreptococcaceae incertae sedis
Propionibacterium
Staphylococcus
Streptococcus
unclassified Rhizobiaceae

Revision editor(s): Ifeanyisam