New library catalogs the human intestine microbiome | Spectrum
Gut Guide: An online data set describes the metabolites produced by nearly 200 microorganisms in the human gut.
Steve Gschmeissner / Science Photo Library
A new online repository gathers information about the small molecules, or metabolites, produced by nearly 200 microorganisms that commonly live in the human gut. The resource, described in Nature in July, could help scientists characterize gut microbiota outcomes in autistic people and study how gut flora could contribute to autism.
Gut microbes produce myriad compounds that can affect various aspects of the physiology, brain, and behavior of their host. However, scientists have struggled to accurately measure these compounds and match them to the microbes that made them.
“This challenge motivated us to build this gut microbe-focused metabolomics pipeline,” said Shuo Han, Stanford University postdoctoral fellow and lead researcher on the study.
Han and her colleagues at Stanford and the Chan Zuckerberg Biohub in San Francisco developed a special analysis technique based on mass spectrometry to identify metabolites based on their mass and charge.
The team first created a reference set of mass spectral profiles for 833 known metabolites. They then measured these metabolites in laboratory-grown cultures of 178 strains of bacteria commonly found in the human intestine. They also measured the metabolites in blood, urine and faeces samples from mice colonized with defined communities of some of these bacteria.
Further analyzes showed how the evolutionary relationship of different microorganisms corresponds to their metabolite profiles. For example, two closely related Clostridium species have very different metabolite profiles, while two distant bacterial species have more similar profiles, as the analysis showed. Using machine learning, the researchers discovered a previously unknown metabolic process powered by a microorganism called Bacteroidetes.
The researchers made their data publicly available in an online explorer. They also published their custom Python code for the pipeline.
“We hope that our mass spectrometry-based methodology and data sets will enable users to construct their own pipelines and enable future functional studies of the microbial communities in the gut,” says Han.
Quote this article: https://doi.org/10.53053/TWRG5542