Differential clustering of fecal and mucosa-associated microbiota in 'healthy' individuals.
Author(s): Carstens A, Roos A, Andreasson A, Magnuson A, Agréus L, Halfvarson J, Engstrand L
Publication: J Dig Dis, 2018, Vol. 19, Page 745-752
PubMed ID: 30467977 PubMed Review Paper? No
Purpose of Paper
This paper compared microbial profiles in fecal specimens to those in mucosal colon biopsy tissue specimens using next-generation sequencing and investigated the effects of patient body mass index (BMI) and number of days between the fecal specimen collection and biopsy on the agreement between fecal and mucosal biopsy specimens.
Conclusion of Paper
The mean number of sequencing reads was higher and microbial diversity richer in the biopsy than in matched fecal specimens. Intra-individual agreement between the fecal and biopsy tissue microbial profiles was not correlated with body mass index or the number of days from the collection of fecal specimens until endoscopy.
Studies
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Study Purpose
This study compared microbial profiles in fecal specimens to those in mucosal colon biopsy tissue specimens using next-generation sequencing and investigated the effects of patient body mass index (BMI) and number of days between the fecal specimen collection and biopsy on the agreement between the microbial profiles. Fecal specimens were collected from 30 healthy individuals (aged 24-70 y) at home in a sterile collection tube, mailed at ambient temperature, and frozen at −70°C upon arrival at the laboratory. Mucosal biopsy specimens were collected 2-90 days later (median 16 days) from the colon during endoscopy (no details provided) with no macroscopic inflammation, no colorectal carcinoma, and no exposure to antibiotics in the previous three months and stored at −70°C in a freezing medium for sensitive bacteria. Bacterial DNA was extracted from fecal samples with the UltraClean Fecal DNA Isolation Kit and from biopsies using the DNeasy Blood and Tissue Kit. Bacterial 16S rRNA gene was amplified by PCR, resolved by gel electrophoresis to remove human DNA, and the corresponding band was excised and purified using a MinElute Gel Extraction Kit. PCR products were quantified using the Qubit system and sequenced on the 454-FLX GS-100 using the standard amplicon kit for biopsies and the FLX Titanium Kit for fecal specimens. All reads were truncated at 260 bp and clustered into operational taxonomic units (OTU) with a 3% distance threshold.
Summary of Findings:
The mean number of sequencing reads was higher in the biopsy than fecal specimens (n=2131 versus n=1457, P<0.0001). Analyses of OTUs showed a lower degree of richness and microbial diversity in the fecal specimens than in the biopsies (P<0.0001 and P=0.016, respectively). Analyses of individual phyla showed a lower relative abundance of Proteobacteria and Verrucomicrobia in the fecal specimens than in the biopsies (P<0.0001 and P=0.008, respectively) but no significant difference in relative abundance of Firmicutes, Bacteroidetes, or Actinobacteria (P=0.93, P=0.06, and P=0.23; respectively). Intra-individual agreement between the fecal and mucosa-associated microbial profiles was not correlated with body mass index (r = 0.15, P=0.41) or the number of days between the collection of fecal specimens and endoscopy (r = −0.19, P=0.32).
Biospecimens
Preservative Types
- Frozen
Diagnoses:
- Normal
Platform:
Analyte Technology Platform DNA PCR DNA Next generation sequencing DNA Spectrophotometry DNA Electrophoresis Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Biospecimen location Feces
Mucosal colon biopsy tissue
Preaquisition Patient body mass index 19.1-28.7
Biospecimen Acquisition Time of biospecimen collection 2-90 days prior to endoscopy
Endoscopy