Discovering lactic acid bacteria by genomics

Abstract

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 30 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.

Enhanced antiinflammatory capacity of a Lactobacillus plantarum mutant synthesizing modified teichoic acids

“…A mutant deficient in the D-alanylation of TAs was constructed by disrupting the dlt operon by single-step homologous recombination using a suicide knockout vector. To this end, an internal 596-bp fragment of dltB gene [lp 2018 (24)] was amplified by PCR from NCIMB8826 chromosomal DNA using primers NCIDLTB1 (5Ј-TTGGTAC-CGCTGTCGTTAAGATCACACC-3Ј) and NCIDLTBR2 (5Ј-TCGCCCGGGCAACCGCATGTAGATGAAATCACG-3Ј). The amplicon was cloned into pCR2.1 plasmid (Invitrogen and Life Technologies, Leek, The Netherlands), recovered as a BamHIXhoI fragment, and subcloned into the BamHI-SalI-digested pJDC9 suicide plasmid (eryR, ref.…”

Complete genome sequence of the probiotic lactic acid bacteriumLactobacillus acidophilusNCFM

“…Of these, Lactobacillus acidophilus remains to be the most widely recognized and commercially distributed probiotic culture. The organism was first isolated by Moro in 1900 from infant feces and is characterized as a homofermentative, short Gram-positive rod (2)(3)(4)(5)(6)(7)(8)(9)(10) m) that grows optimally from 37°C to 42°C (34).…”

“…NC 006347), and Lactobacillus plantarum (7). Others are nearing completion (8) and, collectively, these genomes will provide a solid platform for comparative genomic analysis of organisms that survive passage through and inhabit the gastrointestinal tract of humans.…”

Molecular analysis of the glucose-specific phosphoenolpyruvate : sugar phosphotransferase system from Lactobacillus casei and its links with the control of sugar metabolism

“…In order to identify the genes encoding the PTS Man in L. casei, a search for genes encoding putative IID proteins was performed in the draft genomic sequence of L. casei BL23 (Klaenhammer et al, 2002). In addition to IID Sor , IID Lev and IID Esu already described in L. casei, (Yebra et al, 2000(Yebra et al, , 2004Mazé et al, 2004) we found 11 ORFs encoding putative IID proteins.…”

“…L. casei has developed a great efficiency in the utilization of carbohydrates by the phosphoenolpyruvate (PEP) : sugar phosphotransferase system (PTS) (Viana et al, 2000), and this is supported by the large number of genes encoding PTS proteins that are present in its genome (Klaenhammer et al, 2002). The PTS consists of the general phosphotransferase proteins, enzyme I (EI) and HPr, and carbohydrate-specific transporters.…”