Microbiomes – Embracing complexity

Pratik Jagtap Tim Griffin Jean Armengaud Microbiomes have been traditionally studied using genomics methods to address questions about the taxonomic composition of the microbial samples under study. Their importance for human health, environmental key questions, and biotechnology, is such that metagenomics studies are flourishing. Despite their value, metagenomics methods fall short in terms of direct evidence for the functional state of microbiomes. To fill this gap, other “meta-omics” approaches, such as mass spectrometry-based metaproteomics and metabolomics have started shedding light on the functional dynamics of microbiomes, increasing our biological understanding of these complex systems. We, as editors of this issue, were keen to capture the progress, challenges and opportunities of these emerging methods for microbiomes research –through a diverse array of contributions for this special issue. This special issue of PROTEOMICS covers microbiome environments ranging from the oral cavity (Belda-Ferre et al.), gut (Kolmeder et al., Young et al., Xiong et al.), biocathode, (Leary et al.) to the Pacific Ocean (Saito et al.). Wilmes et al. cover how the field of metaproteomics has progressed in the last 10 years in various systems and describe the exciting developments in the analytical workflow for metaproteomics including mass spectrometry and bioinformatics that will help address more complex questions in the near future. In their viewpoint on meta-omics 2.0, Pible and Armengaud cover the need for improvement in search templates (genome, protein sequence and taxonomy databases) required for interpretation of metaproteomics data. Xiong et al. provide a comprehensive overview of gut microbiome research where most medical-oriented meta-omics efforts have been done till now. The publications in the special issue also reflect the multi-faceted nature of metaproteomics analysis. Sample preparation is the focus of several contributions to this special issue. Tanca et al. stress the importance of critical evaluation when selecting appropriate sample preparation protocols. Kohrs et al. and Deutsch et al. highlight the importance of pre-fractionation of extremely complex protein mixtures many times encountered in metaproteomics studies. Puttker et al. demonstrate the benefits of extended fractionation in their pilot study on activated sludge from a wastewater treatment plant. Metaproteomics also poses “big data” challenges, thus, not surprisingly, bioinformatics is a focus of a number of contributions. Muth et al. address the challenges of large databases encountered in metaproteomics, illustrating the caution required for data interpretation while also suggesting solutions. Kuhring et al. demonstrate the use of the LiDSiM (LImits of Detection SImulation for Microbes) approach to determine the suitability of protein sequence databases for detection of non-model microbial organisms. Saito et al. show the importance of estimating and selecting unique tryptic peptides for targeted proteomic analysis using METATRYP (a Python toolkit). Jagtap et al. provide flexible workflows that can be used on the Galaxy platform for reproducible metaproteomics analysis using customized ‘tandem’ databases. Finally, a number of contributions focus on application of approaches to investigate the functional state of a variety of microbiomes. These include study of both the microbial and human protein expression in a preterm infant's gut during its first month of development (Young et al.); a comparative study of the intestinal microbiome of obese and non-obese individuals (Kolmeder et al.); the protein repertoire of human dental plaque and comparative analysis of healthy and caries-affected individuals to identify candidate biomarkers (Belda-Ferre et al.); the use of metabolomics and metaproteomics to study petroleum polluted sites (Bargiela et al.); the study on exo-enzymes secreted by heterotrophs to hydrolyze biomaterials released by phototrophs from oceans (Christie-Oleza et al.); vertical metaproteomic profiling of the microbiome from a deep estuary (Colatriano et al.); metaproteomic profiling of anaerobic digestion within sewage sludge to identify key microbial players (Bize et al.); and a targeted metaproteomics workflow for nitrogen regulatory proteins from microorganisms from the Central Pacific Ocean (Saito et al.). We thank all the contributors for sharing their latest, valuable research works for this special issue. We are indebted to the many solicited experts for their time to assess the suitability of the contributions and their numerous, helpful suggestions at the reviewing stage. We would like to thank the editorial board at Proteomics Wiley, especially Professor Mike Dunn and Dr. Hans-Joachim Kraus, for giving us the opportunity to contribute and assemble this special issue. We greatly enjoyed this co-editing task and really appreciated the numerous exchanges of ideas and opinions we had throughout the whole editing process. We hope that this special issue will encourage others for further contributions to the growing field of meta-omic analysis for the study of microbiomes. Beyond promoting new and emerging meta-approaches for microbiome studies, we also hope this special issue may catalyze an open discussion on specific standards for data reporting, particularly in the area of metaproteomics. These studies offer many challenges – from large sequence databases which test the ability to confidently match tandem mass spectrometry data to proteins, to ambiguities in taxonomic assignment of identified proteins. Input from the community of researchers interested in these studies is necessary to help define standards and benchmarks for generating and reporting these data. While the field of meta-omics has made significant progress, continued breakthroughs addressing the current challenges are needed to deepen our knowledge of microbiomes. We are confident these will come. Are you ready for the next decade of meta-omics? Regards,