Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.
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 R/M 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.
Altermann
Eric
E
Department of Food Science, Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, NC 27695, USA.
Russell
W Michael
WM
Azcarate-Peril
M Andrea
MA
Barrangou
Rodolphe
R
Buck
B Logan
BL
McAuliffe
Olivia
O
Souther
Nicole
N
Dobson
Alleson
A
Duong
Tri
T
Callanan
Michael
M
Lick
Sonja
S
Hamrick
Alice
A
Cano
Raul
R
Klaenhammer
Todd R
TR
D001422:Bacterial Adhesion / Q000235:genetics; D001430:Bacteriocins / Q000235:genetics; D001435:Bacteriophages / Q000235:genetics / Q000472:pathogenicity; D050260:Carbohydrate Metabolism; D019295:Computational Biology; D016680:Genome, Bacterial; D007779:Lactobacillus acidophilus / Q000235:genetics* / Q000378:metabolism / Q000821:virology; D008969:Molecular Sequence Data; D010447:Peptide Hydrolases / Q000235:genetics; D039002:Prophages / Q000235:genetics; D017422:Sequence Analysis, DNA; D019895:Transposases / Q000235:genetics
D001430:Bacteriocins; D019895:Transposases; D010447:Peptide Hydrolases