Genomics of Lactic Acid Bacteria

Abstract

Lactic acid bacteria (LAB) are 'generally recognised as safe' microorganisms, and some of them were given the 'Qualified Presumption of Safety' status by the European Food Safety Authority. Due to their significant contribution to various industrial applications, many of these organisms were subjected to full genome sequencing projects. Together with the increased amount of published transcriptomics and proteomics data across the entire genome, we have unprecedented opportunities to revisit the important traits of LAB. More importantly, this increased amount of data will aid our understanding of the mechanisms underlying the interaction between LAB and human beings. In this chapter, we focus on the current research progress on LAB genomics and pay particular attention to those species that have played major roles in lactic fermentations. The key features of the genomes and the mechanisms that have been correlated to the beneficial actions of LAB are also discussed. We aim to provide some basic information to our colleagues within the scientific community.

Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

“…Plasmids are most commonly present in different LAB species, involved in 11 genera, including Bifidobacterium , Brevibacterium , Enterococcus , Lactobacillus , Lactococcus , Leuconostoc , Oenococcus , Pediococcus , Streptococcus , Tetragenococcus , and Weissella . LAB plasmids are extremely diverse in terms of size (0.87 kb to more than 250 kb), copy number (from 1 to more than 100 plasmids per cell), and phenotypes conferred to their hosts [ 5 , 6 , 8 , 9 , 10 , 11 , 12 ].…”

“…A large number of plasmids were isolated and characterized from different sources of LAB as self-replicating extrachromosomal genetic materials [ 4 ]. Although most plasmids remain cryptic, some plasmids have been found that are associated with many important functions of LAB species, including (1) hydrolysis of proteins; (2) amino acid, citrate, and carbohydrate metabolism (e.g., lactose/galactose utilization, and oligopeptide transport); (3) production of bacteriocin, exopolysaccharide, and pigments; (4) resistance to antibiotic, bacteriophage, heavy metal, and other stress responses; and (5) DNA restriction-modification systems [ 4 , 5 , 6 , 7 , 8 ]. A variety of industrially relevant characteristics are encoded on the LAB plasmids, including the degradation of casein, acidification by lactic acid, and production of flavor compounds, which contribute to the desired flavor and texture of the fermentation product and to optimal growth of strains in milk [ 6 , 7 , 8 , 9 , 10 ].…”

“…Identification, classification, construction, and application of LAB plasmids have attracted considerable scientific and technological attention. At present, there are over 400 LAB plasmids which have been isolated and studied [ 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ]. This review presents information concerning the diversity of LAB plasmids, their replication mechanisms, structures, functions, and applications.…”

Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes

“…Lactic acid bacteria (LAB) is a naturally biodiverse, well-established group of microorganisms widely used in food industry and of well-documented impact on human health (Wu et al 2017 ). LABs are “generally recognized as safe” (GRAS) in the USA and given the “Qualified Presumption of Safety” (QPS) status by the European Food Safety Authority (EFSA) (Zhang and Zhang 2014 ). They were isolated from various ecological niches, starting from the gastrointestinal tracts of humans, animals, and insects, through plant- and meat-based materials, to soil and water (Hammes and Hertel 2009 ).…”

“…The industrial and technological relevance of LAB strains motivated extensive genomic studies, which have provided significant insight into their metabolism, physiology, and potential for new applications (Zhang and Zhang 2014 ; Bosma et al 2017 ). Since 2001, when the first LAB genome was published (Bolotin et al 2001 ), hundreds of LAB genomes have been sequenced and are publicly available at different assembly levels (Sun et al 2015 ; Zheng et al 2015 ; Wu et al 2017 ; Salvetti et al 2018 ).…”