Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity.
Lactobacillus casei strains are lactic acid bacteria (LAB) that colonize diverse ecological niches, and have broad commercial applications. To probe their evolution and phylogeny, 40 L. casei strains were characterized; the strains included isolates from plant materials (n=9), human gastrointestinal tracts (n=7), human blood (n=1), cheeses from different geographical locations (n=22), and one strain of unknown origin. API biochemical testing identified niche-specific carbohydrate fermentation profiles. A multilocus sequence typing (MLST) scheme was developed for L. casei. Partial sequencing of six housekeeping genes (ftsZ, metRS, mutL, nrdD, pgm and polA) revealed between 11 (nrdD) and 20 (mutL) allelic types, as well as 36 sequence types. Phylogenetic analysis of MLST data by Reticulate and split decomposition analysis indicated frequent intra-species recombination. Purifying selection was detected, and is likely to have contributed to the evolution of certain L. casei genes. Pulsed-field gel electrophoresis (PFGE) using SfiI was able to discriminate all the isolates, even those not differentiated by MLST. Phylogenetic trees reconstructed based on the MLST data using minimum evolution algorithm, and the SfiI-PFGE restriction patterns using the unweighted-pair group method with arithmetic mean (UPGMA), revealed consensus clusters of strains specific to cheese and silage. Topological discrepancies between the MLST and PFGE trees were also observed, suggesting that intragenic point mutations have accumulated at a slower rate than indels and genome rearrangements in L. casei. The L. casei population analysed in this study demonstrated both a high level of phenotypic and genotypic diversity, as well as specificity to different ecological niches.
Cai
Hui
H
Department of Food Science, 1605 Linden Dr., University of Wisconsin, Madison, WI 53706, USA.
Rodríguez
Beatriz T
BT
Utah Veterinary Diagnostic Laboratory, 950 East 1400 North, Logan, UT 84322, USA.
Zhang
Wei
W
National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, IL 60501, USA.
Broadbent
Jeff R
JR
Utah Veterinary Diagnostic Laboratory, 950 East 1400 North, Logan, UT 84322, USA.
Steele
James L
JL
Department of Food Science, 1605 Linden Dr., University of Wisconsin, Madison, WI 53706, USA.
D001426:Bacterial Proteins / Q000235:genetics; D015373:Bacterial Typing Techniques; D001769:Blood / Q000382:microbiology; D050260:Carbohydrate Metabolism; D002611:Cheese / Q000382:microbiology; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field / Q000379:methods; D041981:Gastrointestinal Tract / Q000382:microbiology; D014644:Genetic Variation; D006801:Humans; D007780:Lacticaseibacillus casei / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010944:Plants / Q000382:microbiology; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012820:Silage / Q000382:microbiology
D001426:Bacterial Proteins; D004269:DNA, Bacterial