The progress of multi-omics technologies: determining function in lactic acid bacteria using a systems level approach

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fmicb-10-03084.pdf(3.08 MB)
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Date
2020
Authors
O'Donnell, Shane
Ross, R. Paul
Stanton, Catherine
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Frontiers Media S.A.
Published Version
10.3389/fmicb.2019.03084
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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.
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Keywords
Lactic acid bacteria , Multi-omics , Microbiome , Genomics , Transcriptomics , Proteomics , Metabolomics , Meta-omics
Citation
O’Donnell, S.T., Ross, R.P. and Stanton, C. (2020) ‘The progress of multi-omics technologies: determining function in lactic acid bacteria using a systems level approach’, Frontiers in Microbiology, 10, 3084 (17pp). doi: 10.3389/fmicb.2019.03084
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https://hdl.handle.net/10468/15696
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APC Microbiome Ireland - Journal Articles
Microbiology - Journal Articles
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© 2020 O’Donnell, Ross and Stanton. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.