Proteomics Approaches to Uncover the Drug Resistance Mechanisms of Microbial Biofilms
Chaminda Jayampath Seneviratne in Microbial Biofilms, 2017
Most of the existing studies on microbial biofilms have been performed under in vitro conditions simulating in vivo biofilms. Notwithstanding the insight gained from in vitro studies, it is obvious that in vitro biofilms are not equivalent to their in vivo counterparts. Therefore, it is worth looking into the data derived from in vivo or clinical study samples. The introduction of metaproteomics has made such studies possible. Metaproteomics can be defined as the large-scale characterisation of the entire protein complement of environmental microbiota at a given point in time. It has been used to study complex samples derived from clinical settings, and natural ecosystems such as wastewaters, or acid mine drainage, among many other applications [82,162]. Metaproteomics tools have facilitated the study of microbial communities both at a functional biomolecular and a whole-community level [163,164].
Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics
Published in Expert Review of Proteomics, 2020
Patrick Lohmann, Stephanie Serena Schäpe, Sven-Bastiaan Haange, Kaitlyn Oliphant, Emma Allen-Vercoe, Nico Jehmlich, Martin Von Bergen
This review highlights the challenges of species and proteome coverage in metaproteomics for microbial communities of high complexity. We observed a severe reduction of assigned species to identified protein groups, from 45% for the complex intestinal community down to 19.4% for the highly complex environmental community. Furthermore, we identified a decrease of 85% for species richness and 96.5% for species evenness, by considering only species which are identified by at least two protein groups. In complex microbiomes, we observed that low abundance proteins are mostly undetected, and therefore potentially important cellular functions could be not identified. However, metaproteomics can analyze the functional traits of microbial communities as a whole. The functional assignment of protein groups was approximately 50% higher than the species coverage in complex microbiomes. Therefore, functional profiling of complex communities by metaproteomics is considered as a promising technique to investigate ecosystem functioning of environmental microbiomes.
Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications?
Published in Expert Review of Proteomics, 2018
Until recently, the properties of intestinal microbiome were largely unknown. Knowledge of the compositions of microbes in the microbiome is vital for understanding homeostasis and acquiring important information about the molecular insights of diseases. Cataloging the microbiome involves sequencing the DNA of the microorganisms present. Metagenomics provides a scan of the population of microorganisms present and the coverage of the individual genomes depends on the complexity of the community and the depth of the sequencing. It has been shown that the genetic predispositions of the host, together with abnormal composition of intestinal bacteria may be causing dysregulation of gut microbiome interactions and thus could be pathogenic factors in the development of Crohn’s disease [66]. Another study illustrated that gut microbiomes may play a critical role in the pathological process of type 1 diabetes [67]. Metagenomics provides a catalog of the organisms present, but does not provide any information about ongoing biochemical interactions among the community. Metaproteomics, the analysis of the expressed proteins, is being used to better understand the ongoing interactions of the microbial community [68].
An overview of technologies for MS-based proteomics-centric multi-omics
Published in Expert Review of Proteomics, 2022
Andrew T. Rajczewski, Pratik D. Jagtap, Timothy J. Griffin
Another emerging area that fits in the scope of MS-based proteomic-centered multi-omics is the field of metaproteomics [152]. Metaproteomics incorporates metagenome information on microbial communities from a wide-variety of settings – from human host samples to complex samples (e.g. wastewater, soil) relevant to environmental studies. These multi-omic data can be used to create large protein sequence databases of potential microbe-derived proteins within these samples, which are then used to search for MS/MS data generated from these samples. When analyzed with specialized multi-omic tools [153], the results provide a unique snapshot of the functional proteins expressed by microbial communities, which may drive host biology or regulate characteristics of complex ecological systems. These results can also help identify potential metabolic pathways and small molecules generated by the microbiota that play a role in interactions and regulatory mechanisms. Metaproteomics also expands the reach of proteomic-centered multi-omics to studying flora, fauna, and microbial communities responding to environmental factors (e.g. climate change, pollution [154], bioremediation [155]) in addition to biomedical applications [156].
Related Knowledge Centers
- Amplicon
- Gene Expression
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- Metagenomics
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