Topic: Metabolomics and Proteomic Approaches Applied to Microbiomes

Microbiome research is currently undergoing a transition from descriptive and association studies towards more functional and translational investigations. While next-generation sequencing (NGS)-based metagenomics has greatly contributed to our understanding of microbiomes, recent advancements in metabolomics, proteomics or metaproteomics, both in terms of technology and bioinformatics, have opened up new avenues for functional studies of microbial communities at the protein and metabolite levels with decent sensitivity, throughput and depth. High-resolution mass spectrometry (HRMS)-based proteomic and metabolomic approaches, in particular, are increasingly being utilized to characterize microbiomes of various origins. The application of these functional-omic approaches has shed light on important microbiome functionalities and the mechanisms underlying host-microbiome interactions.

In this Special Issue, we invite submissions on all topics related to metabolomics and proteomics applied to microbiomes. This includes, but is not limited to, method development such as sample preparation methods, optimization of instrumental set-up, establishment of bioinformatic workflows, and integrative multi-omics approaches. The aim is to further enhance the applicability of proteomics and metabolomics in microbiome research. We especially encourage submissions that employ proteomics, metabolomics and beyond to address specific biological questions in in vitro, in vivo, ex vivo and clinical studies. These questions may involve exploring the role of microbiomes in health and diseases, drug-microbiome interactions, as well as the assessment of therapeutics targeting or derived from microbiomes. 

We welcome original research articles, reviews, perspectives, opinions, and commentaries for this Special Issue.