Systems Biology - A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria.

Peter Ruhdal Jensen,Christian Solem,Siu Hung Joshua Chan,Jun Chen,Jianming Liu

doi:10.3389/fmicb.2019.00876

Abstract

Lactic Acid Bacteria (LAB) are extensively employed in the production of various fermented foods, due to their safe status, ability to affect texture and flavor and finally due to the beneficial effect they have on shelf-life. More recently, LAB have also gained interest as production hosts for various useful compounds, particularly compounds with sensitive applications, such as food ingredients and therapeutics. As for all industrial microorganisms, it is important to have a good understanding of the physiology and metabolism of LAB in order to fully exploit their potential, and for this purpose, many systems biology approaches are available. Systems metabolic engineering, an approach that combines optimization of metabolic enzymes/pathways at the systems level, synthetic biology as well as in silico model simulation, has been used to build microbial cell factories for production of biofuels, food ingredients and biochemicals. When developing LAB for use in foods, genetic engineering is in general not an accepted approach. An alternative is to screen mutant libraries for candidates with desirable traits using high-throughput screening technologies or to use adaptive laboratory evolution to select for mutants with special properties. In both cases, by using omics data and data-driven technologies to scrutinize these, it is possible to find the underlying cause for the desired attributes of such mutants. This review aims to describe how systems biology tools can be used for obtaining both engineered as well as non-engineered LAB with novel and desired properties.

Highlights

Lactic acid bacteria (LAB) are traditionally used as starters in fermented food production
LAB are capable of producing various aromatic compounds, the formation of which are initiated by lipolysis and proteolysis, and these contribute to the pleasant organoleptic characteristics of different fermented products such as yogurt, cheese, and butter (Song et al, 2017)
In many single strain omics and systems biology studies, cells are scrutinized under steady-state conditions, which is useful for the purpose of exploring and understanding the regulation of cellular metabolism of LAB, e.g., glycolysis

Summary

Introduction

Lactic acid bacteria (LAB) are traditionally used as starters in fermented food production. Traditional non-GMO (genetically modified organism) strain modification approaches such as random mutagenesis and screening, selection using toxic analogs and adaptive evolution, have a long history of successful use for improving properties of LAB. The use of mutagenesis for improving LAB is only constrained by the genetic repertoire of the bacteria, but a large screening input is usually required to identify desired mutants. The latter two methods are specific and very selective, but their implementation is largely condition-dependent. Rational strain modification methods, such as metabolic engineering and synthetic biology, have demonstrated their effectiveness to endow LAB with new/improved characteristics useful for food applications beyond what traditional approaches are capable of delivering. Since LAB are often present in the final product destined for human consumption, there are still hurdles that have to be overcome before recombinant DNA technologies can be widely implemented, e.g., regulatory issues and skepticism of consumers

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Conclusion