The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533

Abstract

Lactobacillus johnsonii NCC 533 is a member of the acidophilus group of intestinal lactobacilli that has been extensively studied for their "probiotic" activities that include, pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into its physiology and identify genes potentially involved in interactions with the host, we sequenced and analyzed the 1.99-Mb genome of L. johnsonii NCC 533. Strikingly, the organism completely lacked genes encoding biosynthetic pathways for amino acids, purine nucleotides, and most cofactors. In apparent compensation, a remarkable number of uncommon and often duplicated amino acid permeases, peptidases, and phosphotransferase-type transporters were discovered, suggesting a strong dependency of NCC 533 on the host or other intestinal microbes to provide simple monomeric nutrients. Genome analysis also predicted an abundance (>12) of large and unusual cell-surface proteins, including fimbrial subunits, which may be involved in adhesion to glycoproteins or other components of mucin, a characteristic expected to affect persistence in the gastrointestinal tract (GIT). Three bile salt hydrolases and two bile acid transporters, proteins apparently critical for GIT survival, were also detected. In silico genome comparisons with the >95% complete genome sequence of the closely related Lactobacillus gasseri revealed extensive synteny punctuated by clear-cut insertions or deletions of single genes or operons. Many of these regions of difference appear to encode metabolic or structural components that could affect the organisms competitiveness or interactions with the GIT ecosystem.

Fig. 1.

Schematic of the L. johnsonii NCC 533 genome. The outer ring shows results of blastp analysis of L. johnsonii ORFs against L. gasseri ORFs; the darkness of the ORF lines is inversely proportional to the observed E value (i.e., darker denotes lower E value, more conserved; white, no homologs detected). The next ring shows results of a similar analysis of L. johnsonii ORFs against the nonredundant protein database. Ring 3 shows the position of the predicted genes on the leading strand (outer circle) and lagging strands (inner circle). Ring 4 shows positions of rRNA operons (squares), the 14 complete IS elements (lines), and the predicted replication terminus (T). Positions of peptidases (circles) and other genes discussed in the text (mub, mucus-binding protein; prtP, cell-wall protease; prtM, maturase; fim, fimbrae-like operon; IgAse, IgA protease; Lj928 and Lj965, prophages; bsh, bile salt hydrolase; ftf, fructosyltransferase) are indicated on the outside. The map was created by using gamola (58) and genewiz (59).

Fig. 2.

Comparison of the S. gordoni gspB fimbrial operon (GenBank accession no. AY028381) to the homologous segment of L. johnsonii NCC 533. LJ1708 and LJ0394, which are located elsewhere in the NCC 533 genome, are also homologous counterparts in the S. gordoni gspB fimbrial operon. Numbers adjacent to dotted lines show amino acid sequence identity between homologs.

Fig. 3.

Alignment of genomic regions of L. gasseri and L. johnsonii NCC 533 containing the galactose utilization genes. Hatched arrows represent lactose catabolism genes of NCC 533 that were apparently inserted into the common L. gasseri–L. johnsonii backbone. Homologous and syntenic genes flanking the insertion are indicated by gray circles and black arrows (gal genes). reg denotes a lacI-type regulator gene. The minimum percentage identity between the group of proteins are indicated on the dotted line.