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Special Issue Introduction:

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.