Profiling the human intestinal environment under physiological conditions.

The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.

Improved mouse models of the small intestine microbiota using region-specific sampling from humans.

Our understanding of region-specific microbial function within the gut is limited due to reliance on stool. Using a recently developed capsule device, we exploit regional sampling from the human intestines to develop models for interrogating small intestine (SI) microbiota composition and function. In vitro culturing of human intestinal contents produced stable, representative communities that robustly colonize the SI of germ-free mice. During mouse colonization, the combination of SI and stool microbes altered gut microbiota composition, functional capacity, and response to diet, resulting in increased diversity and reproducibility of SI colonization relative to stool microbes alone. Using a diverse strain library representative of the human SI microbiota, we constructed defined communities with taxa that largely exhibited the expected regional preferences. Response to a fiber-deficient diet was region-specific and reflected strain-specific fiber-processing and host mucus-degrading capabilities, suggesting that dietary fiber is critical for maintaining SI microbiota homeostasis. These tools should advance mechanistic modeling of the human SI microbiota and its role in disease and dietary responses.

Human metabolome variation along the upper intestinal tract.

Most processing of the human diet occurs in the small intestine. Metabolites in the small intestine originate from host secretions, plus the ingested exposome1 and microbial transformations. Here we probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy male and female participants. For this, we use a non-invasive, ingestible sampling device to collect and analyse 274 intestinal samples and 60 corresponding stool homogenates by combining five mass spectrometry assays2,3 and 16S rRNA sequencing. We identify 1,909 metabolites, including sulfonolipids and fatty acid esters of hydroxy fatty acids (FAHFA) lipids. We observe that stool and intestinal metabolomes differ dramatically. Food metabolites display trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites account for the largest inter-individual differences. Notably, two individuals who had taken antibiotics within 6 months before sampling show large variation in levels of bioactive FAHFAs and sulfonolipids and other microbially related metabolites. From inter-individual variation, we identify Blautia species as a candidate to be involved in FAHFA metabolism. In conclusion, non-invasive, in vivo sampling of the human small intestine and ascending colon under physiological conditions reveals links between diet, host and microbial metabolism.

Metabolomics analysis of time-series human small intestine lumen samples collected in vivo.

The human small intestine remains an elusive organ to study due to the difficulty of retrieving samples in a non-invasive manner. Stool samples as a surrogate do not reflect events in the upper gut intestinal tract. As proof of concept, this study investigates time-series samples collected from the upper gastrointestinal tract of a single healthy subject. Samples were retrieved using a small diameter tube that collected samples in the stomach and duodenum as the tube progressed to the jejunum, and then remained positioned in the jejunum during the final 8.5 hours of the testing period. Lipidomics and metabolomics liquid chromatography tandem mass spectrometry (LC-MS/MS) assays were employed to annotate 828 unique metabolites using accurate mass with retention time and/or tandem MS library matches. Annotated metabolites were clustered based on correlation to reveal sets of biologically related metabolites. Typical clusters included bile metabolites, food metabolites, protein breakdown products, and endogenous lipids. Acylcarnitines and phospholipids were clustered with known human bile components supporting their presence in human bile, in addition to novel human bile compounds 4-hydroxyhippuric acid, N-acetylglucosaminoasparagine and 3-methoxy-4-hydroxyphenylglycol sulfate. Food metabolites were observed passing through the small intestine after meals. Acetaminophen and its human phase II metabolism products appeared for hours after the initial drug treatment, due to excretion back into the gastrointestinal tract after initial absorption. This exploratory study revealed novel trends in timing and chemical composition of the human jejunum under standard living conditions.