Trajectories of microbiome-derived bile acids in early life - insights into the progression to islet autoimmunity.

Recent studies reveal that gut microbes produce diverse bile acid conjugates, termed microbially conjugated bile acids (MCBAs). However, their regulation and health effects remain unclear. Here, we analyzed early-life MCBA patterns and their link to islet autoimmunity.

A guide to reverse metabolomics-a framework for big data discovery strategy.

Untargeted metabolomics is evolving into a field of big data science. There is a growing interest within the metabolomics community in mining tandem mass spectrometry (MS/MS)-based data from public repositories. In traditional untargeted metabolomics, samples to address a predefined question are collected and liquid chromatography with MS/MS data are generated.

The microbiome diversifies -acyl lipid pools - including short-chain fatty acid-derived compounds.

-acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of -acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving -acyl lipid patterns from 2,700 public datasets, identifying 851 -acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs.

Ordering molecular diversity in untargeted metabolomics via molecular community networking.

Nature's molecular diversity is not random but displays intricate organization stemming from biological necessity. Molecular networking connects metabolites with structural similarity, enabling molecular discoveries from mass spectrometry data using arbitrary similarity thresholds that can fracture natural metabolite families. We present molecular community networking (MCN), that optimizes connectivity for each metabolite, rescuing lost relationships and capturing otherwise "hidden" metabolite connections.