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Review
. 2024 Sep 28;25(19):10467.
doi: 10.3390/ijms251910467.

A Proteogenomic Approach to Unveiling the Complex Biology of the Microbiome

Luciana Alexandra Pavelescu  1 , Monica Profir  1   2 , Robert Mihai Enache  3 , Oana Alexandra Roşu  1   2 , Sanda Maria Creţoiu  1 , Bogdan Severus Gaspar  4   5
Affiliations
Review

A Proteogenomic Approach to Unveiling the Complex Biology of the Microbiome

Luciana Alexandra Pavelescu et al. Int J Mol Sci. .

Abstract

The complex biology of the microbiome was elucidated once the genomics era began. The proteogenomic approach analyzes and integrates genetic makeup (genomics) and microbial communities' expressed proteins (proteomics). Therefore, researchers gained insights into gene expression, protein functions, and metabolic pathways, understanding microbial dynamics and behavior, interactions with host cells, and responses to environmental stimuli. In this context, our work aims to bring together data regarding the application of genomics, proteomics, and bioinformatics in microbiome research and to provide new perspectives for applying microbiota modulation in clinical practice with maximum efficiency. This review also synthesizes data from the literature, shedding light on the potential biomarkers and therapeutic targets for various diseases influenced by the microbiome.

Keywords: genomics; metabolomics; microbiota; proteomics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The relationship between gut microbiota, dysbiosis, bacterial species/genes, and metagenomic studies in human health. The gut microbiota undergoes significant development during the first 2–3 years of life, eventually establishing the mature adult microbiota. Metagenomic studies can identify the genes and bacterial composition of the gut microbiota, potentially playing a crucial role in early detection of genes involved in dysbiosis and related diseases. Black arrow represent the normal evolution and characterization of the intestinal microbiome during life. Red arrows represent the importance of metagenomic studies in dysbiotic circumstances. Created with BioRender.com (accessed on 3 September 2024).
Figure 2
Figure 2
The development of the proteome and metaproteome and their use in analyzing proteins and associated microbial species from feces, colon biopsies, or colonic lavage samples, along with their applications in discovering various diseases. The blue arrow indicates the complexity of the improved analytical techniques, which led to the discovery of a multitude of peptides following the post-translational process. The red arrow indicates the importance of functional proteomics in identifying the roles proteins play in carrying out cellular processes at the molecular level. Created with BioRender.com (accessed on 3 September 2024).
Figure 3
Figure 3
A proteogenomic approach to sample analysis can help identify new potential biomarkers for prevention, diagnosis, prognosis, and surveillance, while also determining the most effective therapeutic plan for a patient through the lens of precision medicine. Created with BioRender.com (accessed on 22 September 2024).
See this image and copyright information in PMC

References

    1. Pan S., Chen R. Metaproteomic analysis of human gut microbiome in digestive and metabolic diseases. Adv. Clin. Chem. 2020;97:1–12. doi: 10.1016/bs.acc.2019.12.002. - DOI - PMC - PubMed
    1. Xiong W., Giannone R.J., Morowitz M.J., Banfield J.F., Hettich R.L. Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J. Proteome Res. 2015;14:133–141. doi: 10.1021/pr500936p. - DOI - PMC - PubMed
    1. Zhang W., Sun J., Cao H., Tian R., Cai L., Ding W., Qian P.Y. Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment. Microbiome. 2016;4:49. doi: 10.1186/s40168-016-0194-x. - DOI - PMC - PubMed
    1. Zhang X., Ning Z., Mayne J., Moore J.I., Li J., Butcher J., Deeke S.A., Chen R., Chiang C.K., Wen M., et al. MetaPro-IQ: A universal metaproteomic approach to studying human and mouse gut microbiota. Microbiome. 2016;4:31. doi: 10.1186/s40168-016-0176-z. - DOI - PMC - PubMed
    1. Heyer R., Schallert K., Zoun R., Becher B., Saake G., Benndorf D. Challenges and perspectives of metaproteomic data analysis. J. Biotechnol. 2017;261:24–36. doi: 10.1016/j.jbiotec.2017.06.1201. - DOI - PubMed

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