创作:mildbreeze 审核:mildbreeze 06月01日
  • 开发了一种可吞咽设备,能在正常消化过程中从人的特定肠道区域采样;
  • 收集15个健康人不同肠段240个肠道样本,多组学分析表明,肠道中的细菌、噬菌体、宿主蛋白和代谢物与粪便的有显著差异;
  • 相较于粪便,肠道样本中的菌群多样性较低,特定微生物被差异性富集(优势菌),且原噬菌体诱导更为普遍;
  • 宿主蛋白组和胆汁酸谱沿肠道变化,且与粪便很不同;
  • 分析胆汁酸浓度梯度与肠菌丰度间的关联,表明特定肠菌通过去结合作用改变胆汁酸池;
  • 肠菌介导生成的结合型胆汁酸的浓度变化模式呈现氨基酸特异性。
Nature [IF:69.504]

Profiling the human intestinal environment under physiological conditions



05-10, Article

Abstract & Authors:展开

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.

First Authors:
Dari Shalon,Rebecca Neal Culver,Jessica A Grembi,Jacob Folz

Correspondence Authors:
Rebecca Neal Culver,Oliver Fiehn,David A Relman,Kerwyn Casey Huang

All Authors:
Dari Shalon,Rebecca Neal Culver,Jessica A Grembi,Jacob Folz,Peter V Treit,Handuo Shi,Florian A Rosenberger,Les Dethlefsen,Xiandong Meng,Eitan Yaffe,Andrés Aranda-Díaz,Philipp E Geyer,Johannes B Mueller-Reif,Sean Spencer,Andrew D Patterson,George Triadafilopoulos,Susan P Holmes,Matthias Mann,Oliver Fiehn,David A Relman,Kerwyn Casey Huang

Nature Metabolism期刊

A multi-omic trip through the human gut


Nature Reviews Gastroenterology and Hepatology期刊

A sampling pill to swallow