title: Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.
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 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.
authors.affiliation: Department of Food Science, Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, NC 27695, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Altermann
authors.forename: W Michael
authors.initials: WM
authors.lastname: Russell
authors.forename: M Andrea
authors.initials: MA
authors.lastname: Azcarate-Peril
authors.forename: Rodolphe
authors.initials: R
authors.lastname: Barrangou
authors.forename: B Logan
authors.initials: BL
authors.lastname: Buck
authors.forename: Olivia
authors.initials: O
authors.lastname: McAuliffe
authors.forename: Nicole
authors.initials: N
authors.lastname: Souther
authors.forename: Alleson
authors.initials: A
authors.lastname: Dobson
authors.forename: Tri
authors.initials: T
authors.lastname: Duong
authors.forename: Michael
authors.initials: M
authors.lastname: Callanan
authors.forename: Sonja
authors.initials: S
authors.lastname: Lick
authors.forename: Alice
authors.initials: A
authors.lastname: Hamrick
authors.forename: Raul
authors.initials: R
authors.lastname: Cano
authors.forename: Todd R
authors.initials: TR
authors.lastname: Klaenhammer
mesh_terms: 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
chemical_list: D001430:Bacteriocins; D019895:Transposases; D010447:Peptide Hydrolases