Draft Genome Sequence of a New Homofermentative, Lactic AcidProducing Enterococcus faecalis Isolate, CBRD01

Lew P. Christopher, Vinayak Kapatral, Benjamin Vaisvil, Ginger Emel,b and Linda C. DeVeauxc

We report here the draft genome sequence of the novel homofermentative Enterococcus faecalis isolate CBRD01, which is capable of high lactic acid productivity and yields, with minimal nutritional requirements. The genome is 2.8 Mbp, with 37% G+C, and contains genes for two lactate dehydrogenase (LDH) enzymes found in related organisms.

Genome Announc. 2014 Mar-Apr; 2(2): e00147-14.
Published online 2014 Mar 27. doi:  10.1128/genomeA.00147-14

The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.

van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, Nicolas P, Robert C,
Oztas S, Mangenot S, Couloux A, Loux V, Dervyn R, Bossy R, Bolotin A, Batto JM,
Walunas T, Gibrat JF, Bessières P, Weissenbach J, Ehrlich SD, Maguin E.

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.

Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9274-9. Epub 2006 Jun 5.

Genome data mining of lactic acid bacteria: the impact of bioinformatics.

Siezen RJ, van Enckevort FH, Kleerebezem M, Teusink B.

Lactic acid bacteria (LAB) have been widely used in food fermentations and, more
recently, as probiotics in health-promoting food products. Genome sequencing and
functional genomics studies of a variety of LAB are now rapidly providing
insights into their diversity and evolution and revealing the molecular basis for
important traits such as flavor formation, sugar metabolism, stress response,
adaptation and interactions. Bioinformatics plays a key role in handling,
integrating and analyzing the flood of 'omics' data being generated.
Reconstruction of metabolic potential using bioinformatics tools and databases,
followed by targeted experimental verification and exploration of the metabolic
and regulatory network properties, are the present challenges that should lead to
improved exploitation of these versatile food bacteria.

Curr Opin Biotechnol. 2004 Apr;15(2):105-15.

Discovering lactic acid bacteria by genomics.

Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O'Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R.

This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics.