Lactic acid bacteria: from starter cultures to producers of chemicals

FEMS Microbiology Letters, 365, 2018, fny213 doi: 10.1093/femsle/fny213 Advance Access Publication Date: 30 August 2018 Review R E V I E W – Biotechnology & Synthetic Biology Rajni Hatti-Kaul1,∗ , Lu Chen1 , Tarek Dishisha2 and Hesham El Enshasy3,4 1 Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden, 2 Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, 62511 Beni-Suef, Egypt, 3 Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81 310 Skudai, Johor, Malaysia and 4 City of Scientific Research and Technology Applications, New Burg Al Arab, Alexandria, Egypt ∗ Corresponding author: Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, SE-221 00 Lund, Sweden. Tel: +46-46-222 4840 Fax: +46-46-222 4713; E-mail: One sentence summary: Lactic acid bacteria are among the most important group of industrial microorganisms, which besides being well established as starter cultures and probiotics, constitute promising biofactories for products for food and non-food sectors. Editor: Michael Sauer ABSTRACT Lactic acid bacteria constitute a diverse group of industrially significant, safe microorganisms that are primarily used as starter cultures and probiotics, and are also being developed as production systems in industrial biotechnology for biocatalysis and transformation of renewable feedstocks to commodity- and high-value chemicals, and health products. Development of strains, which was initially based mainly on natural approaches, is also achieved by metabolic engineering that has been facilitated by the availability of genome sequences and genetic tools for transformation of some of the bacterial strains. The aim of this paper is to provide a brief overview of the potential of lactic acid bacteria as biological catalysts for production of different organic compounds for food and non-food sectors based on their diversity, metabolicand stress tolerance features, as well as the use of genetic/metabolic engineering tools for enhancing their capabilities. Keywords: lactic acid bacteria; metabolic engineering; rerouting metabolism; biological catalysts; biobased chemicals INTRODUCTION Lactic acid bacteria (LAB) have been associated since time immemorial with fermentation of foods and their preservation, and today they are clearly the most important group of industrial microorganisms with a market in the range of multibillion dollars. LAB are used as starter cultures for fermentation of milk, vegetables, meat, fish and cereals, and also animal feed in the form of silage. The fermented dairy products are economically the most important with an estimated value of over 80 billion Euros (in 2011) (de Vos 2011). The well-known features of LAB that are utilized to formulate functional starter cultures are production of exopolysaccharides (EPS), organic acids, poly- ols, aromatic compounds, bacteriocins, among others, which are released into the food matrix giving improved characteristics in terms of texture, aroma, flavor, health effects and shelf life (Leroy and De Vuyst 2004). The application that has experienced growing global market is the use of LAB as probiotics—estimated at 20 billion Euros, a market that was predicted to grow 10% per year (de Vos 2011). Other important applications include their use as delivery vehicles for preventive and therapeutic drugs including proteins and DNA vaccines (Michon et al. 2016), and as biological catalysts for production of value added products for both food and non-food sectors from renewable feedstocks in a biobased economy. The efforts in the latter area have gathered Received: 6 July 2018; Accepted: 29 August 2018  C FEMS 2018. All rights reserved. For permissions, please e-mail: 1 Lactic acid bacteria: from starter cultures to producers of chemicals 2 FEMS Microbiology Letters, 2018, Vol. 365, No. 20 LAB GENERAL FEATURES LAB comprise a genetically and ecologically diverse group of non-motile, microaerophilic Gram-positive bacteria including several genera (Enterococcus, Lactobacillus, Pediococcus, Leuconostoc, Oenococcus, Lactococcus, Streptococcus, Weissella, etc. within the order Lactobacillales) belonging to the phylum Firmicutes, and anaerobic Bifidobacterium genus under the phylum Actinobacteria. The most commercially formulated starter cultures are represented by Lactobacillus, Lactococcus, Streptococcus species, while the most commonly reported probiotics belong to the genera Lactobacillus and Bifidobacterium (Corona-Hernandez et al. 2013), especially the former because of their known antimicrobial effects and other health benefits (Guandalini 2011). LAB genomes are characterized by small size ranging from 1.23 Mb (Lactobacillus sanfranciscensis) to 4.91 Mb (Lactobacillus parakefiri). Since the early 21st century, genomic data from more than 200 LAB strains has been collected in different public databases (Douillard and de Vos 2014; Sun et al. 2015). Comparative genomic analysis has revealed vast diversity among the LAB, which is attributed to their varying interactions with the environmental niches involving gene loss and -gain through horizontal gene transfer (Wu, Huang and Zhou 2017). This diversity is reflected in the large phenotypic variability observed among the species and even among strains. Noteworthy is the phenomenon of reductive evolution of the genomes involving loss of several metabolic genes and related biosynthetic limitations, presence of pseudogenes, and also fewer higher-level genetic control systems as compared to many other microbes, which is attributed to their adaptation to nutrient rich niches (Schroeter and Klaenhammer 2009; Wu, Huang and Zhou 2017). The sequenced genomes have revealed the presence of several families of glycoside hydrolases in the CAZy database, many of which remain uncharacterized (Sun et al. 2015). Several LAB have retained transporter genes for enabling the microbes to acquire nutrients from their environment, and also genes that allow them to tolerate environmental stresses like temperature, pH, salts, etc. and inhibit pathogens (Zhang and Cai 2014). With respect to their safety features, genome analysis of different LAB has shown the absence of virulence-related and toxin encoding genes (Wu, Huang and Zhou 2017). LAB possess a rich ensemble of genetic elements like plasmids, conjugative transposons and bacteriophages (de Vos 2011). Megaplasmids with sizes in the range of 110–490 kb have been found in several species of LAB (Zhang and Cai 2014; Sun et al. 2015). The plasmids and conjugative transposons encode variety of functions like lactose and citrate metabolism, bacteriophage resistance, bacteriocin production, proteolysis, etc. (Schroeter and Klaenhammer 2009). Also, CRISPRs and associated cas genes are widespread in the genomes of a number of LAB (Barrangou et al. 2007; Sun et al. 2015), which provide adaptiv (...truncated)