Profiling the human intestinal environment under physiological conditions

Abstract

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.

Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target

“…Also, we should note that our enzyme activity workflow can only measure the overall activity of each isozyme at a single substrate concentration, and the source of the isozyme, its gene, and its kinetic analysis deserve further attention. Moreover, our workflow was mainly based on stool samples; however, it has been reported that fecal microbiota composition does not accurately reflect the intestinal environments such as the colon ( 55 , 56 ). Therefore, our microbial-host isozyme system only simulates the activity of fecal microbiota, and the activity of different enzymes in diverse intestinal segments still needs to be further evaluated.…”

Electrostatic Interactions Dictate Bile Salt Hydrolase Substrate Preference

“…Gut microbial BA deconjugation, catalyzed by BSHs, is critical for secondary BA metabolism in the intestines. Recent studies identified BA conjugation, which was previously thought to only occur via host-encoded enzymes, as a widespread transformation mediated by the gut microbiota to produce MCBAs. − To understand the role of BSH in the deconjugation of MCBAs, we biochemically characterized the substrate preference of two representative BSHs, L. plantarum BSH1 and C.…”

“…Gut microbial enzymes can then further metabolize unconjugated BAs through epimerization and redox modifications to produce secondary BAs . Recent work demonstrated that unconjugated BAs can also be reconjugated to a wide variety of many amino acids, including tyrosine, phenylalanine, and leucine, by microbial enzymes to produce microbially conjugated bile acids (MCBAs, Figure a). − As BSH activity is thought to precede all subsequent BA transformations, this enzyme has been termed the “gatekeeper” enzyme of secondary BA metabolism. , …”

Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

“…Despite these limitations, in situ studies like ours are necessary for investigating how colonization is shaped by uniquely human aspects of lifestyle and gastrointestinal anatomy, factors that are difficult to replicate in mouse models 42,80 or in vitro communities 81 . Future work that combines our approaches with barcoded strain libraries 82 or spatially resolved sampling devices 83 can further illuminate the ecological and evolutionary forces that shape colonization in the human gut.…”