Deep Metabotyping of the Murine Gastrointestinal Tract for the Visualization of Digestion and Microbial Metabolism

Abstract

Despite the gut's longitudinal specialization for digestion and microbiome organization, most studies focus on the analysis of its end product, feces. To determine the metabolic and physiological functions of different sections of the gut, we aimed to define a comprehensive list of characteristic metabolites for the physiological gut sections and to quantify the selected pathways. We investigated the metabolic composition of seven different gut sections from four C57Bl/6N mice with nontargeted metabolite profiling using high-resolution NMR spectroscopy, which returned a comprehensive metabolite overview with a single analytical measurement per sample. Here we deliver a list of characteristic metabolites, describe metabolite changes along the gut, and highlight the site specificity for selected metabolite pathways. We find that the largest metabolic changes happen in the cecum, where the microbiome produces microbial metabolites. Furthermore, we show the evolution of bile acids along the gut and describe their site-specific conversion. We establish a metabolic basis for future investigations of metabolic perturbations, which can be introduced by dietary challenges or gene knockouts and provide valuable information for tailored study design and targeted sample collection.

Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men

“…To gain a nontargeted overview of flaxseed‐induced fluctuations in dominant gut metabolites, including diet‐, host‐, and microbiome‐derived metabolites , we analyzed fecal extracts using NMR spectroscopy. When compared with bacterial phylogenetic makeups that were most similar for one given subject overtime, hierarchical clustering of NMR signals revealed metabolite profiles with intermingled subject‐time effects (Fig.…”

Non-invasive monitoring of microbiota and host metabolism using secondary electrospray ionization-mass spectrometry

“…First, fecal samples are not representative of active microbial metabolism, 57 which happens largely in the upper part of the large intestine. 58 , 59 , 60 Second, repeated fecal sampling, even though minimally invasive, will disturb an animal’s routine if conducted over longer time periods and will therefore affect its behavior and potentially the experimental outcomes. And third, sampling of fecal material is limited in its time resolution, which can lead to gaps in information when measuring the effects of experimental interventions that work with a time delay, which is true for most experimental interventions with an effect inside the host.…”

Non-invasive monitoring of microbiota and host metabolism using Secondary electrospray ionization-Mass spectrometry

“…This has, up to now, only been possible by collecting fecal samples, which comes with a set of limitations. First, fecal samples are not representative of active microbial metabolism [52], which happens largely in the upper part of the large intestine [53, 54, 55]. Second, repeated fecal sampling, even though minimally invasive, will disturb an animal’s routine if conducted over longer time periods and will therefore affect its behavior and potentially the experimental outcomes.…”