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Questions Addressed by Metaproteomics
Metaproteomics allows for scientists to better understand organisms' gene functions, as genes in DNA are transcribed to mRNA which is then translated to protein. Gene expression changes can therefore be monitored through this method. Furthermore, proteins represent cellular activity and structure, so using metaproteomics in research can lead to functional information at the molecular level. Metaproteomics may also be more reliable in community analysis as opposed to 16S rRNA gene or metagenome sequencing.

Metaproteomics and the Human Intestinal Microbiome
Aside from the oral and vaginal microbiomes, several intestinal microbiome studies have used metaproteomic approaches. A 2020 study done by Long et. al. has shown, using metaproteomic approaches, that colorectal cancer pathogenesis may be due to changes in the intestinal microbiome. Several proteins examined in this study were associated with iron intake and transport as well as oxidative stress, as high intestinal iron content and oxidative stress are indicative of colorectal cancer.

Another study done in 2017 by Xiong et. al. used metaproteomics along with metagenomics in analyzing gut microbiome changes during human development. Xiong et. al. found that the infant gut microbiome may be initially populated with facultative anaerobes like Enterococcus and Klebsiella, and then later populated by obligate anaerobes like Clostridium, Bifidobacterium, and Bacteroides. While the human gut microbiome shifted over time, microbial metabolic functions remained consistent, including carbohydrate, amino acid and nucleotide metabolism.

A similar study done in 2017 by Maier et. al. combined metaproteomics with metagenomics and metabolomics to show the effects of resistant starch on the human intestinal microbiome. After subjects consumed diets high in resistant starch, it was discovered that several microbial proteins were altered such as butyrate kinase, enoyl coenzyme A (enoyl-CoA) hydratase, phosphotransacetylase, adenylosuccinate synthase, adenine phosphoribosyltransferases, and guanine phosphoribosyltransferases. The human subjects experienced increases in colipase, pancreatic triglyceride lipase, bile salt-stimulated lipase abundance while also experiencing a decrease in α-amylase.

Overall, metaproteomics has gained immense popularity in human intestinal microbiome studies as it has led to important discoveries in the health field.

Metaproteomics in Environmental Microbiome Studies
Metaproteomics has been especially useful in the identification of microbes involved in various biodegradation processes. A 2017 study done by Jia et. al. has shown the application of metaproteomics in examining protein expression profiles of biofuel-producing microorganisms. According to this study, bacterial and archaeal proteins are involved in producing hydrogen and methane-derived biofuels. Bacterial proteins involved are ferredoxin-NADP reductase, acetate kinase, and NADH-quinone oxidoreductase found in the Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes taxa. These particular proteins are involved in carbohydrate, lipid, and amino acid metabolism. The archaeal proteins involved are acetyl-CoA decarboxylase and methyl-coenzyme M reductase found in Methanosarcina. These proteins participate in biochemical pathways involving acetic acid utilization, CO2 reduction, and methyl nutrient usage.

A 2019 study by Li et. al. has demonstrated the use of metaproteomics in observing protein expression of polycyclic aromatic hydrocarbon (PAH) degradation genes. The authors of this study specifically focused on identifying the degradable microbial communities in activated sludge during wastewater treatment, as PAHs are highly prevalent wastewater pollutants. They showed that Burkholderiales bacteria are heavily involved in PAH degradation, and that the bacterial proteins are involved in DNA replication, fatty acid and glucose metabolism, stress response, protein synthesis, and aromatic hydrocarbon metabolism.

A similar study done in 2020 by Zhang et. al. involved metaproteomic profiling of azo dye-degrading microorganisms. As azo dyes are hazardous industrial pollutants, metaproteomics was used to observe the overall biodegradation mechanism. Pseudomonas Burkholderia, Enterobacter, Lactococcus and Clostridium strains were identified using metagenomic shotgun sequencing, and many bacterial proteins were found to show degradative activity. These proteins identified using metaproteomics include those involved in the TCA cycle, glycolysis, and aldehyde dehydrogenation. Identification of these proteins therefore led the scientists into proposing potential azo dye degradation pathways in Pseudomonas and Burkholderia.

All in all, metaproteomics is applicable not only to human health studies, but also to environmental studies involving potentially harmful contaminants.