Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome

Abstract

The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signaling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases are reviewed.Samples collected from the human gut contains microbiome and host proteins. These microbiome/host proteins directly represent the functional activity of the intestinal ecosystem and can be simultaneously measured by metaproteomics. Metaproteomics can also provide valuable information on the pathways and taxaspecific functions, which provides a more in-depth perspective for studying detailed mechanisms underlying host-microbiome

Bacterial Vaginosis: Current Diagnostic Avenues and Future Opportunities

“…Proteomics is the study of the collection of proteins produced by the host and microbiome that embody the functional activity of the entire bionetwork (Peters et al, 2019 ). Metabolomics is the study of low molecular weight compounds (<1,500 Da) that are produced as substrates or by-products of enzymatic reactions in response to stimuli in a biological system (Peters et al, 2019 ). Compared to other components in an ecosystem, the metabolome may be the component that best represent the phenotype of that ecosystem (Guijas et al, 2018 ).…”

“…Compared to other components in an ecosystem, the metabolome may be the component that best represent the phenotype of that ecosystem (Guijas et al, 2018 ). Nonetheless, both proteomics and metabolomics are useful in studying host-microbiome interactions on a functional level and could be used to elucidate the pathogenesis of disease (Peters et al, 2019 ). Newer, high-throughput technologies have created the opportunity to screen and study metabolites and proteins on a large scale.…”

Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR)

“…For example, in soils, where polar microbiomes have been extracted using methanol: water mixtures [ 41 ], methanol: water:chloroform mixtures [ 41 ], methanol for extracellular metabolomes [ 42 ] and/or water and ethyl acetate:water for non-polar metabolites [ 42 ]. In the human gut microbiome, solvent and solvent mixtures for polar compounds have included methanol:chloroform:acetonitrile (reviewed in [ 2 ]), acetonitrile: methanol: formic acid [ 5 ], methanol: water [ 2 , 5 ] and, pure methanol [ 5 ] for compounds of intermediate polarity and isopropanol for both polar- and non-polar metabolites [ 5 ]. Future systematic studies on understanding the influence of extraction solvents on metabolite scope and diversity in varying microbiome contexts are clearly warranted, along with increased public availability of these raw datasets.…”

“…Performing metabolomics on microbial community samples remains challenging [ 2 ], in part due to the fact that multiple member species could produce or utilise a given compound [ 3 ] and in part due to the high proportion of unannotated mass features that will be detected [ 4 ]. Solving these problems will require substantial efforts in the areas of data analysis and interpretation [ 5 , 6 ], new modelling methods [ 7 , 8 ] and large-scale compound annotation [ 4 , 9 ].…”

Biliary Tract Carcinogenesis Model Based on Bile Metaproteomics

“…The characterization of a single species protein profile is known as proteomics, while the characterization of a multi-species protein profile is known as metaproteomics (35). The metaproteomic concept has been studied in humans through the characterization of fecal microbiota and the proteins produced by the different local bacterial species, enabling a better comprehension of the local conditions in the gastrointestinal tract (36,37). In theory, the microenvironment within the biliary tract and the gallbladder will be more resistant to external variation and more accessible for bile retrieval in animal models.…”