Complete genome sequence of the probiotic lactic acid bacteriumLactobacillus acidophilusNCFM

Abstract

Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R͞M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus-and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.adhesion ͉ stress response ͉ proteolytic system ͉ sugar metabolism ͉ in silico analysis

The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K

“…For instance, L. sakei lacks homologs of MUB proteins 31,32 for adherence to intestinal mucus. On the other hand, L. sakei may colonize the meat surface through aggregation and biofilm formation with a set of components having no homolog in other lactobacilli.…”

Multireplicon genome architecture of Lactobacillus salivarius

“…The application of genomic technologies recently has led to major advances in our understanding of lactobacilli (13,14), through genome sequence determination for Lactobacillus plantarum, Lactobacillus johnsonii, Lactobacillus acidophilus, and Lactobacillus sakei (15)(16)(17)(18). L. plantarum has the largest Lactobacillus genome sequenced to date (3.3 Mb) and has a commensurate biochemical complexity.…”

“…L. johnsonii and L. acidophilus are more related to each other than to L. plantarum (see also below) and have smaller genomes, reflected in nutritional fastidiousness. L. acidophilus appears to be auxotropic for 14 amino acids (17). L. johnsonii lacks the ability for de novo synthesis of purines and cofactors (16,19).…”

Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays

“…In particular, the versatile saccharolytic potential of L. acidophilus likely reflects its ability to efficiently use energy sources available in the intestinal environment. Although the L. acidophilus NCFM genome encodes numerous putative genes potentially involved in the uptake and metabolism of a variety of carbohydrates (16), little information is available regarding their biological functions and expression profiles.…”