‘Multi-omics’ data integration: applications in probiotics studies

Abstract

The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several ‘omics’ technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one ‘omics’ level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a ‘single omics’ application to ignore the influence of other molecular processes justify the need for ‘multi-omics’ application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for ‘multi-omics’ and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.

Milk and Its Derivatives as Sources of Components and Microorganisms with Health-Promoting Properties: Probiotics and Bioactive Peptides

“…Due to the complexity of samples, no individual omic approach alone is able to unravel the complexity of the response and demonstrate a specific health claim of a potential probiotic formulation. To this aim, the multiomic approach and data integration are the novel frontiers for studying probiotics [260]. A system biology approach enables the integration of large datasets from experimental and theoretical models derived from genomics, metagenomics, transcriptomics and metatranscriptomics, proteomics, metabolomics, peptidomics and lipidomics, providing a comprehensive picture of the complex network of biological processes necessary to evaluate the beneficial effect of probiotic strains to the host in the treatment of specific diseases [261].…”

The roles and applications of short-chain fatty acids derived from microbial fermentation of dietary fibers in human cancer

“…Multi-omics analyses have emerged as novel approaches, integrating metagenomic, transcriptomic, proteomic, metabolomic, and lipidomic analysis. These comprehensive investigations shed further light on the host's response to probiotics at multiple levels ( 74 ). For instance, in a mouse model of HCC treated with probiotics, researchers utilized metagenomic analysis to identify altered pathways and corresponding biological functions ( 71 ).…”

The Vaginal Microbiome during Pregnancy in Health and Disease

“…have served to develop a multi-omics approach to genotyping and phenotyping that, besides having an impact on infectious diseases in pregnancy, is applied to many other areas such as aging mechanisms, cancer aetiology, cardio-metabolic diseases, organ transplantation, probiotics studies, etc. [50,51].…”

“…Conversely, the paucity of Lactobacillus spp. in this microbiome is a risk factor for several disease states such bacterial vaginosis [51], and adverse pregnancy outcomes such as miscarriage [64] and PTB [68,69]. Studies have showed that L. crispatus-dominated vaginal microbiomes are associated with a lower prevalence of bacterial vaginosis, vulvovaginal candidiasis, and sexually transmitted infections (STI) [70] such as infection with Chlamydia trachomatis [71], HIV [55], Neisseria gonorrhoeae [72], and HSV-2 [73].…”