Comparative genomics of the lactic acid bacteria

Abstract

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats. evolutionary genomics ͉ fermentation L actic acid bacteria (LAB) are historically defined as a group of microaerophilic, Gram-positive organisms that ferment hexose sugars to produce primarily lactic acid. This functional classification includes a variety of industrially important genera, including Lactococcus, Enterococcus, Oenococcus, Pediococcus, Streptococcus, Leuconostoc, and Lactobacillus species. The seemingly simplistic metabolism of LAB has been exploited throughout history for the preservation of foods and beverages in nearly all societies dating back to the origins of agriculture (1). Domestication of LAB strains passed down through various culinary traditions and continuous passage on food stuffs has resulted in modern-day cultures able to carry out these fermentations. Today, LAB play a prominent role in the world food supply, performing the main bioconversions in fermented dairy products, meats, and vegetables. LAB also are critical for the production of wine, coffee, silage, cocoa, sourdough, and numerous indigenous food fermentations (2).LAB species are indigenous to food-related habitats, including plant (fruits, vegetables, and cereal grains) and milk environments. In addition, LAB are naturally associated with the mucosal surfaces of animals, e.g., small intestine, colon, and vagina. Isolates of the same species often are obtained from plant, dairy, and animal habitats, implying wide distribution and specialized adaptation to these diverse environments. LAB species employ two pathways to metabolize hexose: a homofermentative pathway in which lactic acid is the primary product and a heterofermentative pathway in which lactic acid, CO 2 , acetic acid, and͞or ethanol are produced (3).Complete genome sequences have been published for eight fermentative and commensal LAB species: Lactococcus lactis, Lactobacillus plantarum, Lactobacillus johnsonii, Lactobacillus acidophilus, Lactobacillus sakei, Lactobacillus bulgaricus, Lactobacillus salivarius, and Streptococcus thermophilus (4-11). This study examines nine other LAB genomes representing the phylogenetic and functional diversity of lactic acid-producing microorganisms. The LAB have small genomes encoding a range of biosynthe...

Specific point mutations in Lactobacillus casei ATCC 27139 cause a phenotype switch from Lac− to Lac+

“…In order to characterize the Lac 2 phenotype of L. casei ATCC 27139, the lacTEGF and galKETRM operons of L. casei ATCC 27139 were sequenced. Unlike those of L. casei 64H and ATCC 334 strains (Bettenbrock & Alpert, 1998;Makarova et al, 2006), the two operons were found to be linked together and organized as a lacTEGF-galKETRM gene cluster, as reported previously for Lactobacillus rhamnosus TCELL-1 (Tsai & Lin, 2006) and L. casei BL23 (GenBank accession no. FM177140).…”

Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse forestomach

“…Complete genome sequences of many lactic acid bacteria have been determined and these show a prominence of genes associated with the metabolism of simple carbohydrates, including oligosaccharides, and energy conversion systems (Makarova et al, 2006). L. reuteri 100-23 and L. johnsonii 100-33 persist in the gut of mice following a single inoculation and have an equal capacity to inhabit the forestomach of the animals.…”

Multifactorial diversity sustains microbial community stability

“…lactis (Bolotin et al, 2001), SK11 L. lactis ssp. cremoris (Makarova et al, 2006) and KF147 L. lactis ssp. lactis (Siezen et al, 2010) were subjected to orthology prediction using the orthoMCL algorithm V2.0.2 (Li et al, 2003).…”