The complete genome sequence ofLactobacillus bulgaricusreveals extensive and ongoing reductive evolution

Abstract

Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.bulgaricus) is one of the economically most important representatives of the heterogeneous group of lactic acid bacteria, with a worldwide application in yogurt production. Yogurt has long been recognized as a nutritious, natural, and safe component of a healthy diet and is at the basis of the concept of probiotics (1, 2). A well documented health benefit of the consumption of yogurt containing live L. bulgaricus and Streptococcus thermophilus is an attenuation of lactose intolerance (3). In addition, immune modulation and diarrhea-alleviating effects have been reported (4), and both L. bulgaricus and S. thermophilus have been implicated in these effects (3,5). During yogurt fermentations protocooperation between these two bacteria results in an accelerated acidification, but the mechanisms involved are not completely understood (6).Among the lactic acid bacteria, L. bulgaricus belongs to the acidophilus complex, a group of lactobacilli related to Lactobacillus acidophilus, Lactobacillus johnsonii, and Lactobacillus gasseri, which have been used as probiotic cultures. Although within this group L. bulgaricus is considered unique because of its atypical GC content, until recently the lack of tools for genetic manipulation has severely hampered a more detailed analysis of this organism (7, 8, † †).Here we present the genome sequence of L. bulgaricus strain ATCC11842, originally isolated from bulgarian yogurt by S. OrlaJensen in 1919 (unpublished work). The analysis of this genome and comparison to other members of the acidophilus complex and S. thermophilus (9) have contributed to a more complete understanding of its p...

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

“…These carbon sources are particularly abundant in plant-associated niches, and their loss or down-regulation is expected and consistent with earlier descriptions of genomic and phenotypic traits of dairy lactococci (Siezen et al 2008). Notably, also dairy adapted strains of Streptococcus thermophilus and Lactobacillus bulgaricus show high proportions of pseudogenes related to carbohydrate metabolism (Bolotin et al 2004;van de Guchte et al 2006).…”

At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1

“…As observed previously (18), L. bulgaricus had approximately one-half the number of carbohydrate transport and metabolism (COG category G) genes as the mean of the remaining three lactobacilli (excluding L. iners), creating an unusually high variance in this category. The severely reduced number of genes in L. bulgaricus is because of its long use as a milk starter culture and its adaptation to this specific nutrient-rich but carbohydratelimited environment.…”

Transcriptional and functional analysis of galactooligosaccharide uptake bylacSinLactobacillus acidophilus

“…4A) compared with the overall phylogenetic similarity of lactobacilli based on 16S rRNA homologies (38) demonstrates, first, how most lacS positive strains are associated with GIT colonization; and second, that the diversity of gene sequences and locus structure follow the evolutionary direction in all but Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 (39).…”