The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

Abstract

Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

“…These strategies must also assist in unraveling the molecular mechanisms underlying the interactions [ 201 ]. In this regard, the assistance of a vast array of state-of-the-art “omic” techniques is crucial [ 61 , 202 ]. For example, metagenomic surveys of the microbiota of cheeses [ 17 , 74 , 80 , 82 , 83 , 95 , 103 , 107 , 117 , 118 , 203 , 204 , 205 ] can help uncover patterns of community composition, while transcriptomic profiling [ 173 , 184 , 189 , 190 , 191 , 198 , 206 ] can be used to study microorganisms in a pairwise fashion and thus dissect interaction mechanisms.…”

An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents

“…In addition, the detection of dysregulation of a molecule, protein, or pathway by more than one omics method reinforces the observation that it is a key regulator or target for modulation. A variety of different integration methods are currently available, primarily for human studies (Lee et al, 2019;Misra et al, 2019), although similar approaches have been recently considered for lactic acid bacteria (O'Donnell et al, 2020).…”

Molecular Determinants of Antibiotic Resistance in the Costa Rican Pseudomonas aeruginosa AG1 by a Multi-omics Approach: A Review of 10 Years of Study

“…Biological systems rely on the DNA–RNA–protein information transfer paradigm that determines the phenotype of an organism (O’Donnell et al 2020 ). The comprehensive or global assessment of a set of molecules, which requires interpretation of molecular intricacy and variations at multiple levels, has been referred to as “-omics sciences” (Subramanian et al 2020 ).…”

“…The comprehensive or global assessment of a set of molecules, which requires interpretation of molecular intricacy and variations at multiple levels, has been referred to as “-omics sciences” (Subramanian et al 2020 ). The current high-throughput nature of these techniques, as well as their increased accessibility in terms of time and cost, has triggered the volume of information that can be gathered in individual studies including multiple-omics levels, which together are called “multi-omics” (O’Donnell et al 2020 ; Subramanian et al 2020 ).…”