Genomics of lactic acid bacteria: Current status and potential applications

Abstract

Lactic acid bacteria (LAB) are widely used for the production of a variety of foods and feed raw materials where they contribute to flavor and texture of the fermented products. In addition, specific LAB strains are considered as probiotic due to their health-promoting effects in consumers. Recently, the genome sequencing of LAB is booming and the increased amount of published genomics data brings unprecedented opportunity for us to reveal the important traits of LAB. This review describes the recent progress on LAB genomics and special emphasis is placed on understanding the industry-related physiological features based on genomics analysis. Moreover, strategies to engineer metabolic capacity and stress tolerance of LAB with improved industrial performance are also discussed.

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

“…The mitis group of streptococci (MGS) consists of 20 different species, all gram positive cocci arranged as pairs or in chains (Spellerberg and Brandt, 2008). MGS is a part of the lactic acid bacteria, which along with the human pathogenic genera Streptococcus, Enterococcus, and Aerococcus is composed of a wide variety of bacteria important for the food industry (Wu et al, 2017).…”

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

“…Indeed, these emerging technologies unlocked the potential for microbial genome-wide association studies (GWAS), aiming at dissecting the genetic basis of known phenotypic traits (e.g., carbohydrate metabolism) (Dutilh et al 2013 ). Understanding certain genotype-phenotype associations brings unprecedented opportunities for better utilization/exploration of technologically useful microorganisms, such as starter cultures in food technology (Wu et al 2017 ), but also for the engineering of novel microbial organisms and consortia in synthetic biology applications (Freddolino et al 2014 ). Bacterial evolution, epidemiology, pathogens’ traceability during disease outbreaks, pathogenesis, antibiotic resistance, rapid detection, and food safety (Chen and Shapiro 2015 ; Brbić et al 2016 ; Klemm and Dougan 2016 ; Deurenberg et al 2017 ; Ruppé et al 2017 ), exemplify areas where sequencing and GWAS revolutionized modern microbiology.…”

“…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 ).…”

Metabolic cross-feeding allows a gut microbial community to overcome detrimental diets and alter host behaviour

“…Although lactate has been proposed to play a role in these interactions (Sommer and Newell, 2019) the mechanisms that promote and sustain bacterial growth in co-cultures and how they modify the host remain largely unexplored. Lactobacilli lack many key genes required for the synthesis of different essential nutrients such as AAs and vitamins Wu et al, 2017). Conversely their genome encodes an unusually large repertoire of transporters highlighting their ability if not requirement to take up nutrients from their environment (Kim et al, 2013;Martino et al, 2016).…”