Proteomics and metabolomics for analysis of the dynamics of microbiota

Infectious diseases and associated antibiotic resistance are two medical scourges in need of better laboratory diagnostics. Despite a current developmental focus on molecular testing including metagenomic nucleic acid sequencing, many alternative technologies need to be included in innovative diagnostic pipelines. An important issue is the quality comparison between genotypic and phenotypic methods. A wide variety of more classical phenotypic technologies exists and many of these will survive the current molecular and genomics boosts [1]. In addition, proteomic technologies have evolved significantly recently as did their use for the detection and (taxonomic) characterization of individual organisms and microbial communities. Some of the mass spectrometry (MS)-driven proteomic applications are targeted for specific organisms, while others have a wider field of use allowing for the dissection and characterization of complex mixtures of organisms including the direct analysis of clinical specimens obtained from patients or environmental sources. These diagnostic avenues still include classical, mostly culture-based methods, but the first applications of miniaturized lab-on-a-chip and nanopore-based protein biosensors have been presented as well. Beyond the strictly proteomic methods, analytical-chemical (metabolomics) analyses of small molecules (50–2000 Da) are also becoming more visible in microbiology. Metabolites are the building blocks of cellular function and involve enzymecatalyzed chemical reactions [2]. Metabolomics is particularly important for the comprehension of biological phenomena and mechanisms. It can associate phenotypes with various states of health, identify new biomarkers for disease, and assess correct from inadequate to even adverse drug use. As such, metabolomics approaches contribute significantly to personalized medicine. Of note, there is a strong overlap in the techniques used in proteomics and metabolomics, with advanced methods of MS being at their core. Proteomics and metabolomics are key technologies for the analysis of mixtures of microorganism (microbiota) of diverse origin and although the focus is usually on prokaryotes, viral diversity can also be examined [3]. Microbiota are widely varying and complex microbial communities occupying essentially all niches in the biological world within and around us. Their relevance to human health has become well-recognized over the past decade [4]. Microbiota play a role in intrinsic resistance against infectious diseases and a healthy microbial flora is even capable of combatting antibiotic-resistant pathogens [5]. There are many obvious but also more subtle interactions between host factors and resident microbiota. For instance, genetic defects on the host side may have profound effects on the composition of gastrointestinal microbiota and, hence, predispose to intestinal inflammatory diseases [6]. Additional and more detailed knowledge on the medical relevance of microbiome dynamics needs to be collected and proteomic and metabolomic technologies are at the center of such explorations. We will here highlight some examples of innovative translational applications of proteomic and metabolomic detection in their broadest sense, including immune assays, application of MS and next-generation nucleic acid sequencing (NGS, which is neither metabolomic nor proteomic in nature but hard to ignore to date . . .) for the analysis of microbiota diversity.