By MEHREEN ANJUM & ARTHUR C. OUWEHAND – Global Health & Nutrition Sciences – International Flavors & Fragrances
Consumers and scientists wish to better understand the gut microbiota, and innovation is driving the research in the field of probiotics towards discovering new and better strains. Utilizing high-throughput methods, encompassing genomics, transcriptomics, proteomics, and metabolomics, collectively referred to as the ‘omics’ approach, can enhance the process of identifying novel strains (Kwoji et al., 2023). This advantage of harnessing data generated by these ‘omics’ technologies may lead to the selection of a promising strain, facilitating a comprehensive and expedited exploration of its potential mechanisms of action, physiological and functional activities, and beneficial biochemical pathways relevant to human health. Omics tools are continually becoming powerful methods for obtaining an impartial and integrated view of complex biological processes such as the role of microbiota in maintenance of gut health.
‘Genomics’ includes whole genome sequencing and analysis of the entire DNA, including its structure, function, and regulators of expression in an organism. Using this approach researchers have been able to study probiotic properties and identify elements that regulate gene expression for e.g., promoters or terminators. It has been possible to study gene evolution for conserved functional traits or study adaptation of bacteria to certain hosts and environments. The combination of new sequencing technologies and advanced data analytics has allowed improved identification and characterization of different strains (Idrees et al., 2022).
Enzymes engaged in the transcription process convert the genome from DNA to RNA, and these transcribed sequences, forming the transcriptome, are subsequently translated into proteins. The study of genome expression to transcripts is referred to as ‘transcriptomics’ and researchers use it to determine when and where genes are turned on or off in a biological system by studying the structure, expression, and regulation of genes. Transcriptomics analysis will allow studying molecular mechanisms employed by the potential strain for interaction with host and other microbes.
‘Proteomics’ involves studying the entire protein content that is expressed by a genome of an organism in defined conditions in a specified growth phase and physiological condition. The total proteins are complex and dynamic because of the changes that occur in protein maturation phase; post-transcriptional modification. During post-transcriptional modification a protein structure can undergo addition of molecules such as phosphate groups, methyl groups or it can undergo oxidation etc. Thus, the techniques used for proteomics need to be robust enough to capture the total protein content (Papadimitriou et al., 2015).
‘Metabolomics’ quantitively and qualitatively determines the collection of secreted and endogenous compounds/metabolites that define the phenotypic behavior of the microbe. Metabolomic analysis, like proteomics, is situational depending on the sampling time and growth conditions of the microbe. There can be two approaches to determine the metabolite composition from biological systems: targeted metabolomics which focuses on detection and quantification of a known, defined metabolite panel and untargeted metabolomics that encompasses profiling all the metabolites that can possibly be measured and identified. Through the metabolomics techniques it has been possible to map and identify novel substrates and metabolic pathways and select compounds affecting human health (Kwoji et al., 2023).
The extensive information generated using the above mentioned “omics” approach can serve as a basis for identifying new potential strains with better understood functionalities. These prospective strains should then undergo thorough validation through carefully designed preclinical studies utilizing suitable animal models, and ultimately, appropriately structured human intervention trials. The integrated “omics” combine the dry and wet lab work together to generate validated information with speed and accuracy regarding a probiotic strain that would be selected not only based on its properties but also from an immense pool of potential strains. Using traditional methods, a strain selection with similar amount of data would require years of work. The integration of “omics” with in vivo studies may lead to selection of probiotics whose mode of action is well known, and which can then be administered for the appropriate health benefit.
References
Kwoji ID, Aiyegoro OA, Okpeku M, Adeleke MA. ‘Multi-omics’ data integration: applications in probiotics studies. NPJ Sci Food. 2023 Jun 5;7(1):25. doi: 10.1038/s41538-023-00199-x.
Idrees M, Imran M, Atiq N, Zahra R, Abid R, Alreshidi M, Roberts T, Abdelgadir A, Tipu MK, Farid A, Olawale OA, Ghazanfar S. Probiotics, their action modality and the use of multi-omics in metamorphosis of commensal microbiota into target-based probiotics. Front Nutr. 2022 Sep 16;9:959941. doi: 10.3389/fnut.2022.959941.
Papadimitriou K, Zoumpopoulou G, Foligné B, Alexandraki V, Kazou M, Pot B, Tsakalidou E. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches. Frontiers in microbiology. 2015 Feb 17;6:58.
