The gut microbiome-Does stool represent right?

Orly Levitan; Lanying Ma; Donato Giovannelli; Dawn B Burleson; Peter McCaffrey; Ayin Vala; David A Johnson

doi:10.1016/j.heliyon.2023.e13602

The gut microbiome-Does stool represent right?

Heliyon. 2023 Feb 10;9(3):e13602. doi: 10.1016/j.heliyon.2023.e13602. eCollection 2023 Mar.

Authors

Orly Levitan^{1

2}, Lanying Ma³, Donato Giovannelli^{4

5}, Dawn B Burleson¹, Peter McCaffrey³, Ayin Vala³, David A Johnson⁶

Affiliations

¹ Hygieacare Inc., Norfolk, VA, USA.
² Department of Biochemistry and Microbiology, Rutgers University, NJ, USA.
³ Pragma Bio, South San Francisco, CA, USA.
⁴ Department of Biology, University of Naples Federico II, Naples, Italy.
⁵ National Research Council - Institute of Marine Biological Resources and Biotechnologies (CNR-IRBIM), Ancona, Italy.
⁶ Eastern VA Medical School, Norfolk VA, USA.

Abstract

Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner-colonic microbiome. To test this hypothesis, we conducted prospective clinical studies with up to 20 patients undergoing an FDA-cleared gravity-fed colonic lavage without oral purgative pre-consumption. The objective of this study was to present the analysis of inner-colonic microbiota obtained non-invasively during the lavage and how these results differ from stool samples. The inner-colonic samples represented the descending, transverse, and ascending colon. All samples were analyzed for 16S rRNA and shotgun metagenomic sequences. The taxonomic, phylogenetic, and biosynthetic gene cluster analyses showed a distinctive biogeographic gradient and revealed differences between the sample types, especially in the proximal colon. The high percentage of unique information found only in the inner-colonic effluent highlights the importance of these samples and likewise the importance of collecting them using a method that can preserve these distinctive signatures. We proposed that these samples are imperative for developing future biomarkers, targeted therapeutics, and personalized medicine.

Keywords: 16S rRNA; Biogeography; Bowel Prep; Bowel prep; Colonoscopy; Drug design; Gut microbiome; Innovation; Microbiome; NGS; Personalized medicine; Prep; Stratification; WGS.