Special Issue on “Metaproteomics and meta-omics perspectives to decrypt Microbiome Functionality”

Proteomics is inviting submissions to a special issue dedicated to microbiome research, emphasizing the integration of omics to uncover the functionality of microbiomes. This special issue is tentatively scheduled for publication for mid-2025. It provides an ideal platform for showcasing cutting-edge research on microbiomes, proposing new strategies to make the most of acquired molecular data, and fostering discussions on the future prospects of metaproteomics in the field and the synergies with other omics. The objective of this special issue is to cover the full spectrum of technologies aimed at enhancing our understanding of microbiome and holobionts' function and illustrate their practical applications. We encourage submissions from all areas of microbiome research focusing on functionality. We are open to considering different types of papers, including research articles, review articles, technical briefs, dataset briefs, and viewpoint articles.

Microorganisms contribute to crucial biological processes within vast and intricate ecosystems like soils and oceans [1]. Typically operating within complex communities known as microbiota, microorganisms employ an ingenious mixture of task specialization, cooperation, and competition as a winning strategy to navigate environmental conditions [2] and ensure the stability of ecosystems [3]. Establishing symbiotic relationships with their hosts if any, they often provide mutual benefits, although in some instances, they may contribute to host diseases. The significance of ecosystem services rendered by microbiota is increasingly recognized, underscoring the growing importance of characterizing these ecosystems. Enhanced understanding holds promise for diverse fields, including medicine, well-being, food industry, agriculture, animal breeding and fish farming, biotechnology, remediation and protection of the environment.

It's time to face the music and admit that exploring microbial communities will entail an extra layer of challenging hurdles due to their extensive taxonomic diversity, genomic heterogeneity, dynamic nature, and our limited understanding of their components, which primarily focuses on cultivable species [4]. Beyond mere taxonomic catalogue of microorganisms within a microbiota and their enumeration to determine their abundance, it is crucial to discern who the active contributors are and what the ongoing molecular processes are to grasp these biological systems fully. The functionality of microbiomes involves a complex interplay of numerous interconnected variables, ranging from genetic makeup and mRNA transcripts to proteins and their potential post-translational modifications, inherent protein catalytic properties, subcellular localization, and the resultant enzymatic products that can retroact on catalysis levels. Omics technologies have become indispensable in unravelling the intricacies of these molecular processes. Among these, metaproteomics emerges as a particularly suitable tool for understanding the protein composition of microbiomes [5]. Elevating the sophistication of computational and modelling methodologies is of paramount interest for exploiting the wealth of data collected on microbiomes with today's omics technologies and transitioning from mere statistical associations to causal relationships [6]. Thus, this special issue endeavors to gather contributions across all directions aiming to advance our understanding of microbiome functionality.

We have already received a substantial number of exciting papers and are pleased to continue accepting submissions until early December, 2024. Late submissions will still receive full consideration, but there is a risk that accepted papers may not meet the production schedule for inclusion in the special issue. While the special issue is scheduled for release in Spring/Summer 2025, all accepted papers can be published online upon acceptance and will be fully citable with a digital object identifier (DOI). This special issue aims to provide a platform to highlight the latest advancements in microbiome research and the diverse applications of metaproteomics and other meta-omics in the fields of medicine, the environment, agriculture, and biotechnology.

Lucia Grenga

Magnus Øverlie Arntzen

Jean Armengaud

The authors declare no conflicts of interest.