Follow
International Journal of Current Microbiology and Applied Sciences (IJCMAS)
IJCMAS is now DOI (CrossRef) registered Research Journal. The DOIs are assigned to all published IJCMAS Articles.
Index Copernicus ICI Journals Master List 2023 - IJCMAS--ICV 2023: 95.56 For more details click here
National Academy of Agricultural Sciences (NAAS) : NAAS Score: *5.38 (2020) [Effective from January 1, 2020] For more details click here

Login as a Reviewer


See Guidelines to Authors
Current Issues
Download Publication Certificate

Original Research Articles                      Volume : 14, Issue:4, April, 2025

PRINT ISSN : 2319-7692
Online ISSN : 2319-7706
Issues : 12 per year
Publisher : Excellent Publishers
Email : editorijcmas@gmail.com /
submit@ijcmas.com
Editor-in-chief: Dr.M.Prakash
Index Copernicus ICV 2018: 95.39
NAAS RATING 2020: 5.38

Int.J.Curr.Microbiol.App.Sci.2025.14(4): 146-154
DOI: https://doi.org/10.20546/ijcmas.2025.1404.018


Decoding the Microbial World: An Introduction to Microbial Omics
Department of Biotechnology, Techno India University, EM-4, Salt Lake, Sector- V, Kolkata- 700091 (India)
*Corresponding author
Abstract:

The microbial world is one of the most crucial parts of the ecosystem on Earth. It has a significant contribution to our human health along with several other organisms and the functioning of our environment. Genomics, transcriptomics, proteomics, metabolomics, and metagenomics are all included in the new discipline of microbial omics, which provides strong instruments to decipher the intricate relationships between microbial populations and their physiological functions. Recent advances in multi-omics and integrated omics techniques revolutionized our understanding of microbial diversity. These techniques enable the investigation of uncultivable species' metabolic processes and interactions between species, thus having major ramifications for industrial biotechnology, customized medicine, disease modeling, and bioremediation. Notwithstanding the above developments, several problems related to data integration and standardization, together with the considerable cost of the omics technologies, persist as barriers to broader application. Their overcoming will result in further intensified research that makes it possible for the connection of microbial phenotype to genotype and opens new ways into environmental and health sciences research.


Keywords: Microbial omics, Microbial diversity, physiological functions,  Metabolic processes


References:
  1. Amer, B., & Baidoo, E. E. (2021). Omics-driven biotechnology for industrial applications. Frontiers in Bioengineering and Biotechnology, 9, 613307.
  2. Ar?kan, M., & Muth, T. (2023). Integrated multi-omics analyses of microbial communities: a review of the current state and future directions. Molecular omics.
  3. Aslam, B., Basit, M., Nisar, M. A., Khurshid, M., & Rasool, M. H. (2016). Proteomics: technologies and their applications. Journal of chromatographic science, 1-15.
  4. Aylward, F. O., Eppley, J. M., Smith, J. M., Chavez, F. P., Scholin, C. A., & DeLong, E. F. (2015). Microbial community transcriptional networks are conserved in three domains at ocean basin scales. Proceedings of the National Academy of Sciences, 112(17), 5443-5448.
  5. Baldrian, P., & López-Mondéjar, R. (2014). Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Applied microbiology and biotechnology, 98, 1531-1537.
  6. Biswas, R., & Sarkar, A. (2018). ‘Omics’ Tools in Soil Microbiology: The State of the Art.
  7. Buescher, J. M., & Driggers, E. M. (2016). Integration of omics: more than the sum of its parts. Cancer & metabolism, 4, 1-8.
  8. Castro-Nallar, E., Shen, Y., Freishtat, R. J., Pérez-Losada, M., Manimaran, S., Liu, G., ... & Crandall, K. A. (2015). Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities. BMC medical genomics, 8, 1-9.
  9. Chandran, H., Meena, M.K., & Sharma, K. (2020). Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches. Frontiers in Environmental Chemistry.) (Nathani, N.M., Rajyaguru, R.H., Prashanth, P., Mootapally, C., & Dave, B.P. (2020). Microbial Omics: Role in Ecological Studies and Environmental Control Measures. Environmental Biotechnology Vol. 2.)
  10. Chappell, L., Russell, A. J., & Voet, T. (2018). Single-cell (multi) omics technologies. Annual review of genomics and human genetics, 19(1), 15-41.
  11. Chernov, V. M., Chernova, O. A., Mouzykantov, A. A., Lopukhov, L. L., & Aminov, R. I. (2019). Omics of antimicrobials and antimicrobial resistance. Expert opinion on drug discovery, 14(5), 455-468.
  12. Cohen, O., Doron, S., Wurtzel, O., Dar, D., Edelheit, S., Karunker, I., ... & Sorek, R. (2016). Comparative transcriptomics across the prokaryotic tree of life. Nucleic Acids Research, 44(W1), W46-W53.
  13. Cozzolino, D. (2016). Metabolomics in grape and wine: Definition, current status and future prospects. Food Analytical Methods, 9(11), 2986-2997.
  14. De Sousa, C. S., Hassan, S. S., Pinto, A. C., Silva, W. M., De Almeida, S. S., Soares, S. D. C., ... & Azevedo, V. (2018). Microbial omics: applications in biotechnology. In Omics technologies and bio-engineering (pp. 3-20). Academic Press.
  15. Fondi, M., & Lio’, P. (2015). Multi –omics and metabolic modelling pipelines: challenges and tools for systems microbiology. bioRxiv.
  16. Franzosa, E.A., Hsu, T., Sirota-Madi, A., Shafquat, A., Abu-Ali, G.S., Morgan, X.C., & Huttenhower, C. (2015). Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nature Reviews Microbiology, 13, 360-372.
  17. Gayon J. (2016). From Mendel to epigenetics: History of genetics. Comptes rendus biologies, 339(7-8), 225–230. https://doi.org/10.1016/j.crvi.2016.05.009 
  18. 18.González-Plaza, J.J., Furlan, C., Rijavec, T., Lapanje, A., Barros, R., Tamayo-Ramos, J.A., & Suárez-Diez, M. (2022). Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels. Frontiers in Microbiology, 13.
  19. Gutleben, J., Chaib De Mares, M., Van Elsas, J. D., Smidt, H., Overmann, J., & Sipkema, D. (2018). The multi-omics promise in context: from sequence to microbial isolate. Critical reviews in microbiology, 44(2), 212-229.
  20. Hasin, Y., Seldin, M., & Lusis, A. (2017). Multi-omics approaches to disease. Genome biology, 18, 1-15.
  21. Hofker, M. H., Fu, J., & Wijmenga, C. (2014). The genome revolution and its role in understanding complex diseases. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 1842(10), 1889-1895.
  22. Horak, I., Engelbrecht, G., van Rensburg, P. J., & Claassens, S. (2019). Microbial metabolomics: essential definitions and the importance of cultivation conditions for utilizing Bacillus species as bionematicides. Journal of Applied Microbiology, 127(2), 326-343.
  23. Hu, L., Liu, J., Zhang, W., Wang, T., Zhang, N., Lee, Y. H., & Lu, H. (2020). Functional metabolomics decipher biochemical functions and associated mechanisms underlie small?molecule metabolism. Mass Spectrometry Reviews, 39(5-6), 417-433
  24. Ivashko, M., Burmei, S., Yusko, L., Chaikovska, T., & Boyko, N. (2023). Microbiological diagnostics: From traditional to molecular genetic methods: A literature review.
  25. Jiang, D., Armour, C. R., Hu, C., Mei, M., Tian, C., Sharpton, T. J., & Jiang, Y. (2019). Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities. Frontiers in genetics, 10, 995.
  26. Jiang, Y., Xiong, X., Danska, J., & Parkinson, J. (2016). Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. Microbiome, 4, 1-18.
  27. Kaster, A., & Sobol, M.S. (2020). Microbial single-cell omics: the crux of the matter. Applied Microbiology and Biotechnology, 104, 8209 – 8220.
  28. Kolisko, M., Boscaro, V., Burki, F., Lynn, D. H., & Keeling, P. J. (2014). Single-cell transcriptomics for microbial eukaryotes. Current Biology, 24(22), R1081-R1082.
  29. Kumar, V., Singh, K., Shah, M. P., Singh, A. K., Kumar, A., & Kumar, Y. (2021). Application of omics technologies for microbial community structure and function analysis in contaminated environment. In Wastewater treatment (pp. 1-40). Elsevier.
  30. Li, P. E., Lo, C. C., Anderson, J. J., Davenport, K. W., Bishop-Lilly, K. A., Xu, Y., ... & Chain, P. S. (2017). Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic acids research, 45(1), 67-80.
  31. Maghembe, R.S., Damian, D., Makaranga, A., Nyandoro, S.S., Lyantagaye, S.L., Kusari, S., & Hatti-Kaul, R. (2020). Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae. Antibiotics, 9.
  32. Mallik, B., Mishra, T., Dubey, P., Kesheri, M., & Kanchan, S. (2024). Exploring the Secrets of Microbes: Unveiling the Hidden World Through Microbial Omics in Environment and Health. In Microbial Omics in Environment and Health (pp. 269-294). Singapore: Springer Nature Singapore.
  33. Malla, M.A., Dubey, A., Yadav, S., Kumar, A., Hashem, A., & Abd_Allah, E.F. (2018). Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches. Frontiers in Microbiology, 9.
  34. Mincarelli, L., Lister, A., Lipscombe, J., & Macaulay, I. C. (2018). Defining cell identity with single?cell omics. Proteomics, 18(18), 1700312.
  35. Misra, B. B., Langefeld, C., Olivier, M., & Cox, L. A. (2019). Integrated omics: tools, advances and future approaches. Journal of molecular endocrinology, 62(1), R21-R45.
  36. Munguía-Fragozo, P.V., Alatorre-Jacome, O., Rico-García, E., Torres-Pacheco, I., Cruz-Hernández, A., Ocampo-Velázquez, R.V., García-Trejo, J.F., & Guevara-González, R.G. (2015). Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis. BioMed Research International, 2015.
  37. Nam, N.N., Do, H.D., Loan Trinh, K.T., & Lee, N.Y. (2023). Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods, 12.
  38. Nathani, N.M., Rajyaguru, R.H., Prashanth, P., Mootapally, C., & Dave, B.P. (2020). Microbial Omics: Role in Ecological Studies and Environmental Control Measures. Environmental Biotechnology Vol. 2.
  39. Otto, A., Becher, D., & Schmidt, F. (2014). Quantitative proteomics in the field of microbiology. Proteomics, 14(4-5), 547-565.
  40. Pagare, S., Bhatia, M., Tripathi, N., Pagare, S., & Bansal, Y. K. (2015). Secondary metabolites of plants and their role: Overview. Current trends in biotechnology and pharmacy, 9(3), 293-304.
  41. 41.Pal, S., Jana, A., Mondal, K. C., & Halder, S. K. (2022). Omics Approach to Understanding Microbial Diversity. In Biotechnological Advances for Microbiology, Molecular Biology, and Nanotechnology (pp. 25-38). Apple Academic Press.
  42. Parmar, K.M., Gaikwad, S., Dhakephalkar, P.K., Kothari, R.K., & Singh, R.P. (2017). Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Frontiers in Microbiology, 8.
  43. Pérez-Llarena, F. J., & Bou, G. (2016). Proteomics as a tool for studying bacterial virulence and antimicrobial resistance. Frontiers in microbiology, 7, 410.
  44. Piras, C., Roncada, P., Rodrigues, P. M., Bonizzi, L., & Soggiu, A. (2016). Proteomics in food: quality, safety, microbes, and allergens. Proteomics, 16(5), 799-815.
  45. Preidis, G. A., & Hotez, P. J. (2015). The newest “omics”—metagenomics and metabolomics—enter the battle against the neglected tropical diseases. PLoS Neglected Tropical Diseases, 9(2), e0003382.
  46. 46.Prosser, J. I. (2015). Dispersing misconceptions and identifying opportunities for the use of’omics’ in soil microbial ecology. Nature Reviews Microbiology, 13(7), 439-446.
  47. Satya, S., Sharma, S., Choudhary, G., & Kaushik, G. (2024). Advances in Environmental Microbiology: A Multi-omic Perspective. In Microbial Omics in Environment and Health (pp. 175-204). Singapore: Springer Nature Singapore.
  48. Sauer, U. G., Deferme, L., Gribaldo, L., Hackermüller, J., Tralau, T., van Ravenzwaay, B., ... & Gant, T. W. (2017). The challenge of the application of’omics technologies in chemicals risk assessment: background and outlook. Regulatory Toxicology and Pharmacology, 91, S14-S26.
  49. 49.Singh, D., Geat, N., Mehriya, M., Rajawat, M. V. S., Prasanna, R., Kumar, A., ... & Jha, M. N. (2020). Omics (genomics, proteomics, metabolomics, etc.) tools to study the environmental microbiome and bioremediation. Waste to Energy: Prospects and Applications, 235-260.
  50. Starr, A. E., Deeke, S. A., Li, L., Zhang, X., Daoud, R., Ryan, J., ... & Figeys, D. (2018). Proteomic and metaproteomic approaches to understand host–microbe interactions. Analytical chemistry, 90(1), 86-109.
  51. 51.Stoeva, M. K., Aris-Brosou, S., Chételat, J., Hintelmann, H., Pelletier, P., & Poulain, A. J. (2014). Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics. PLoS One, 9(3), e89531.
  52. Subramanian, I., Verma, S., Kumar, S., Jere, A., & Anamika, K. (2020). Multi-omics data integration, interpretation, and its application. Bioinformatics and biology insights, 14, 1177932219899051.
  53. 53.Temperton, B., & Giovannoni, S. J. (2012). Metagenomics: microbial diversity through a scratched lens. Current opinion in microbiology, 15(5), 605-612.
  54. Ventosa, A., de la Haba, R. R., Sanchez-Porro, C., & Papke, R. T. (2015). Microbial diversity of hypersaline environments: a metagenomic approach. Current Opinion in Microbiology, 25, 80-87.
  55. Wissenbach, D. K., Oliphant, K., Rolle-Kampczyk, U., Yen, S., Hoeke, H., Baumann, S., ... & von Bergen, M. (2016). Optimization of metabolomics of defined in vitro gut microbial ecosystems. International Journal of Medical Microbiology, 306(5), 280-289.
  56. 56.  Xu, X., Wang, J., Wu, L., Guo, J., Song, Y., Tian, T., ... & Yang, C. (2020). Microfluidic single?cell omics analysis. Small, 16(9), 1903905.

Download this article as Download

How to cite this article:

Ankita Banerjee, Rojina Khatun, Sudeshna Sengupta and Malavika Bhattacharya. 2025. Decoding the Microbial World: An Introduction to Microbial Omics.Int.J.Curr.Microbiol.App.Sci. 14(4): 146-154. doi: https://doi.org/10.20546/ijcmas.2025.1404.018
Copyright: This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

Citations