Metaproteome and metabolome of oral microbial communities

Abstract

Protein function is representative of active biologic processes, and the proteome describes the entire protein makeup of a cell, tissue, or bodily fluid at a given point in time. The composition and modular organization of the proteome governs the phenotype. The term proteomics was coined in 1994 1 and over the last 25 years the field has advanced with the rapid changes in mass spectrometry instrumentation and innovations in quantitative chemistries and bioinformatic tools. Although two-dimensional gel electrophoresis, accompanied by mass spectrometry detection, was extensively used as the proteomics method of choice in earlier days, 2,3 it is time-consuming, labor-intensive, and limited by the number of resolved proteins. 4 Currently, liquid chromatography coupled to tandem mass spectrometry is the most valuable tool for the systematic identification and quantification of proteins on a large scale. 5 Most of the proteomics workflows seek to identify a set of proteins (discovery proteomics) or to quantify a relative or absolute amount of identified proteins (quantitative proteomics) between conditions or to study the protein interactions within larger protein complexes (interactomes) or in the context of broader biologic networks (systems biology). 6 The spectrum fragmentation method includes two approaches, namely, "untargeted shotgun proteomics", which help achieve a deep coverage of the proteome, and "targeted proteomics" for quantitatively comparing large numbers of samples (hundreds to thousands) based on a defined set of proteins (eg, selected reaction monitoring) (Figure 1). Most high-throughput proteomic strategies utilize "bottom-up" workflows that rely on mass spectrometry analysis of digested peptides from proteins with the help of specific enzymes (eg, trypsin), but a "top-down" approach for analysis of intact proteins is also possible. This allows not only identification of a protein by name, but also of its intact molecular form, the presence of isoforms, and potential modifications. 7 The large-scale characterization of any given proteome is accomplished by comparing measured protein or peptide data with predicted protein or peptide data derived from genomic information.

Microbiological Aspects of Root Canal Infections and Disinfection Strategies: An Update Review on the Current Knowledge and Challenges

“…One element of answer may stem from shotgun metagenomics, that can re-assemble complete metagenomes to identify strain-level changes and predict the functional genetic potential of microbial communities [ 92 ]. Besides, to better grasp the metabolic processes and functional networks that underlie pathogenicity, assessment of the microbial genes that are actively transcribed (metatranscriptomics) and/or translated (metaproteomics) is also necessary [ 93 , 94 ].…”

“…Omics-approaches have considerably enhanced our appreciation of the taxonomic diversity within root canal communities, and to a lesser extent, of the functional and metabolic pathways of bacterial survival within root canals. These aspects can be further addressed by metatranscriptomic, metaproteomic, and metabolomic approaches [ 93 ] that may well reveal altered functional profiles in disease-associated communities that underpin pathogenicity.…”

Functional Biomarkers of Ex-vivo Dental Caries Onset

“…Thus, metabolomic profiling reveals what is actually happening as opposed to the potential for something to happen. Furthermore, the metabolome is the closest link to the phenotype that reflects all the information expressed and modulated by all other Omic-layers along the biological hierarchy (62).…”

Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era

“…Collectively, the difficulties involved in performing metaproteomics, such as inconsistent reproducibly and expense, have been an issue compared to what can be more easily achieved via metatranscriptomics at the same level of coverage and quantitative reliability (Kuboniwa et al, 2009;Kuboniwa et al, 2012). Although metaproteomics is a powerful tool for studying the composition, abundance, and modular organization of proteins in oral microbial communities that govern the phenotype, the aforementioned difficulties and concerns may explain why there are only a handful of studies published in dental caries research (Table 1) (Bostanci et al, 2021). Still, proteomics is uniquely positioned to analyze the interplay between microbial protein expression and the host response which will be addressed under the host-microbe interaction section.…”