A toolbox for the comprehensive analysis of small volume human intestinal samples that can be used with gastrointestinal sampling capsules

Melany Rios-Morales,Dirk-Jan Reijngoud,Albert Gerding,Theo Boer,Ran An,Mara P H Van Trijp,Christiane Rösch,Henk A Schols,M Rebecca Heiner-Fokkema,Naomi De Ruiter,Martijn Koehorst,Barbara M Bakker,Guido J E J Hooiveld

doi:10.1038/s41598-021-86980-y

Abstract

Detailed knowledge on the fate of dietary components inside the human intestinal tract is lacking. Access to this inner world of digestion is now possible through novel human gastrointestinal sampling capsules. Due to the novelty of such devices, no methodology has been published to stabilise and analyse the resulting samples. A complicating factor is that excretion of such capsules in faeces may take days, while degradation of the dietary components continues. Therefore a stabilising reagent should be pre-loaded in the capsule to ensure the measurement of a representative sample. Considering the small volume of recovered samples, analytical methods must be optimized to collect as many data as possible from little material. We present a complete workflow for stabilising and analysing the fermentation status of dietary fibres in such samples, including microbiota, fibre degradation, and short chain fatty acids. The final quenching reagent was designed based on safety and effectiveness to inhibit fructo- and galacto-oligosaccharides degradation and short chain fatty acids production by human ileostomy microbiota, and subsequently validated in faecal samples. The final composition of the stock quenching reagent is 175 mM Tris, 525 mM NaCl, 35 mM EDTA, 12% SDS, and 8 M urea at pH 8.5.

Highlights

Detailed knowledge on the fate of dietary components inside the human intestinal tract is lacking
After several unsuccessful attempts to develop a quenching fluid based on their potential to inhibit fibre degrading enzymes (Supplementary Table S1), a commonly used bacterial lysis buffer was adopted as quenching reagent (NaCl, Ethylenediaminetetraacetic acid (EDTA), Tris, sodium laurylsulfate (SDS), pH 8.5)[33], to which urea was added as general protein d enaturant[34]
This quenching reagent was first tested for its effectiveness to inhibit the degradation of GOS and chicory FOS/ inulin by commercially available β-galactosidase and endo-inulinase, respectively (Supplementary Table S2 and Supplementary Fig. S2)

Summary

Introduction

Detailed knowledge on the fate of dietary components inside the human intestinal tract is lacking. Non-invasive access to this inner world of gut microbiota and fermentation products has become possible with the development of novel human gastrointestinal capsules, some of which allow sampling of the luminal content[11,12,13,14,15,16,17]. Such devices allow a deeper understanding of diet–microbiota–host interactions.

Methods

Results

Discussion

Conclusion