Dataset Information

Profiling the human intestinal environment under physiological conditions.

ABSTRACT: The spatiotemporal structure of the human microbiome^1,2, proteome³ and metabolome^4,5 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.

SUBMITTER: Shalon D

PROVIDER: S-EPMC10191855 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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Profiling the human intestinal environment under physiological conditions.

Shalon Dari D Culver Rebecca Neal RN Grembi Jessica A JA Folz Jacob J Treit Peter V PV Shi Handuo H Rosenberger Florian A FA Dethlefsen Les L Meng Xiandong X Yaffe Eitan E Aranda-Díaz Andrés A Geyer Philipp E PE Mueller-Reif Johannes B JB Spencer Sean S Patterson Andrew D AD Triadafilopoulos George G Holmes Susan P SP Mann Matthias M Fiehn Oliver O Relman David A DA Huang Kerwyn Casey KC

Nature 20230510 7961

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 ...[more]

PMID: 37165188

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Dataset Information

Profiling the human intestinal environment under physiological conditions.

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Profiling the human intestinal environment under physiological conditions.

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