Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity

Microbiology (Reading). 2007 Aug;153(Pt 8):2655-2665. doi: 10.1099/mic.0.2007/006452-0.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Typing Techniques
  • Blood / microbiology
  • Carbohydrate Metabolism
  • Cheese / microbiology
  • Cluster Analysis
  • DNA Fingerprinting
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Electrophoresis, Gel, Pulsed-Field / methods
  • Gastrointestinal Tract / microbiology
  • Genetic Variation*
  • Humans
  • Lactobacillus casei / classification
  • Lactobacillus casei / genetics*
  • Lactobacillus casei / isolation & purification
  • Lactobacillus casei / physiology
  • Molecular Sequence Data
  • Phylogeny
  • Plants / microbiology
  • Recombination, Genetic*
  • Sequence Analysis, DNA
  • Sequence Homology
  • Silage / microbiology

Substances

  • Bacterial Proteins
  • DNA, Bacterial

Associated data

  • GENBANK/EF538428
  • GENBANK/EF538429
  • GENBANK/EF538430
  • GENBANK/EF538431
  • GENBANK/EF538432
  • GENBANK/EF538433
  • GENBANK/EF538434
  • GENBANK/EF538435
  • GENBANK/EF538436
  • GENBANK/EF538437
  • GENBANK/EF538438
  • GENBANK/EF538439
  • GENBANK/EF538440
  • GENBANK/EF538441
  • GENBANK/EF538442
  • GENBANK/EF538443
  • GENBANK/EF538444
  • GENBANK/EF538445
  • GENBANK/EF538446
  • GENBANK/EF538447
  • GENBANK/EF538448
  • GENBANK/EF538449
  • GENBANK/EF538450
  • GENBANK/EF538451
  • GENBANK/EF538452
  • GENBANK/EF538453
  • GENBANK/EF538454
  • GENBANK/EF538455
  • GENBANK/EF538456
  • GENBANK/EF538457
  • GENBANK/EF538458
  • GENBANK/EF538459
  • GENBANK/EF538460
  • GENBANK/EF538461
  • GENBANK/EF538462
  • GENBANK/EF538463
  • GENBANK/EF538464
  • GENBANK/EF538465
  • GENBANK/EF538466
  • GENBANK/EF538467
  • GENBANK/EF538468
  • GENBANK/EF538469
  • GENBANK/EF538470
  • GENBANK/EF538471
  • GENBANK/EF538472
  • GENBANK/EF538473
  • GENBANK/EF538474
  • GENBANK/EF538475
  • GENBANK/EF538476
  • GENBANK/EF538477
  • GENBANK/EF538478
  • GENBANK/EF538479
  • GENBANK/EF538480
  • GENBANK/EF538481
  • GENBANK/EF538482
  • GENBANK/EF538483
  • GENBANK/EF538484
  • GENBANK/EF538485
  • GENBANK/EF538486
  • GENBANK/EF538487
  • GENBANK/EF538488
  • GENBANK/EF538489
  • GENBANK/EF538490
  • GENBANK/EF538491
  • GENBANK/EF538492
  • GENBANK/EF538493
  • GENBANK/EF538494
  • GENBANK/EF538495
  • GENBANK/EF538496
  • GENBANK/EF538497
  • GENBANK/EF538498
  • GENBANK/EF538499
  • GENBANK/EF538500
  • GENBANK/EF538501
  • GENBANK/EF538502
  • GENBANK/EF538503
  • GENBANK/EF538504
  • GENBANK/EF538505
  • GENBANK/EF538506
  • GENBANK/EF538507
  • GENBANK/EF538508
  • GENBANK/EF538509
  • GENBANK/EF538510
  • GENBANK/EF538511
  • GENBANK/EF538512
  • GENBANK/EF538513
  • GENBANK/EF538514
  • GENBANK/EF538515
  • GENBANK/EF538516
  • GENBANK/EF538517
  • GENBANK/EF538518
  • GENBANK/EF538519
  • GENBANK/EF538520
  • GENBANK/EF538521
  • GENBANK/EF538522
  • GENBANK/EF538523
  • GENBANK/EF538524
  • GENBANK/EF538525
  • GENBANK/EF538526
  • GENBANK/EF538527
  • GENBANK/EF538528
  • GENBANK/EF538529
  • GENBANK/EF538530
  • GENBANK/EF538531
  • GENBANK/EF538532
  • GENBANK/EF538533
  • GENBANK/EF538534
  • GENBANK/EF538535
  • GENBANK/EF538536
  • GENBANK/EF538537
  • GENBANK/EF538538
  • GENBANK/EF538539
  • GENBANK/EF538540
  • GENBANK/EF538541
  • GENBANK/EF538542
  • GENBANK/EF538543
  • GENBANK/EF538544
  • GENBANK/EF538545
  • GENBANK/EF538546
  • GENBANK/EF538547
  • GENBANK/EF538548
  • GENBANK/EF538549
  • GENBANK/EF538550
  • GENBANK/EF538551
  • GENBANK/EF538552
  • GENBANK/EF538553
  • GENBANK/EF538554
  • GENBANK/EF538555
  • GENBANK/EF538556
  • GENBANK/EF538557
  • GENBANK/EF538558
  • GENBANK/EF538559
  • GENBANK/EF538560
  • GENBANK/EF538561
  • GENBANK/EF538562
  • GENBANK/EF538563
  • GENBANK/EF538564
  • GENBANK/EF538565
  • GENBANK/EF538566
  • GENBANK/EF538567
  • GENBANK/EF538568
  • GENBANK/EF538569
  • GENBANK/EF538570
  • GENBANK/EF538571
  • GENBANK/EF538572
  • GENBANK/EF538573
  • GENBANK/EF538574
  • GENBANK/EF538575
  • GENBANK/EF538576
  • GENBANK/EF538577
  • GENBANK/EF538578
  • GENBANK/EF538579
  • GENBANK/EF538580
  • GENBANK/EF538581
  • GENBANK/EF538582
  • GENBANK/EF538583
  • GENBANK/EF538584
  • GENBANK/EF538585
  • GENBANK/EF538586
  • GENBANK/EF538587
  • GENBANK/EF538588
  • GENBANK/EF538589
  • GENBANK/EF538590
  • GENBANK/EF538591
  • GENBANK/EF538592
  • GENBANK/EF538593
  • GENBANK/EF538594
  • GENBANK/EF538595
  • GENBANK/EF538596
  • GENBANK/EF538597
  • GENBANK/EF538598
  • GENBANK/EF538599
  • GENBANK/EF538600
  • GENBANK/EF538601
  • GENBANK/EF538602
  • GENBANK/EF538603
  • GENBANK/EF538604
  • GENBANK/EF538605
  • GENBANK/EF538606
  • GENBANK/EF538607
  • GENBANK/EF538608
  • GENBANK/EF538609
  • GENBANK/EF538610
  • GENBANK/EF538611
  • GENBANK/EF538612
  • GENBANK/EF538613
  • GENBANK/EF538614
  • GENBANK/EF538615
  • GENBANK/EF538616
  • GENBANK/EF538617
  • GENBANK/EF538618
  • GENBANK/EF538619
  • GENBANK/EF538620
  • GENBANK/EF538621
  • GENBANK/EF538622
  • GENBANK/EF538623
  • GENBANK/EF538624
  • GENBANK/EF538625
  • GENBANK/EF538626
  • GENBANK/EF538627
  • GENBANK/EF538628
  • GENBANK/EF538629
  • GENBANK/EF538630
  • GENBANK/EF538631
  • GENBANK/EF538632
  • GENBANK/EF538633
  • GENBANK/EF538634
  • GENBANK/EF538635
  • GENBANK/EF538636
  • GENBANK/EF538637
  • GENBANK/EF538638
  • GENBANK/EF538639
  • GENBANK/EF538640
  • GENBANK/EF538641
  • GENBANK/EF538642
  • GENBANK/EF538643
  • GENBANK/EF538644
  • GENBANK/EF538645
  • GENBANK/EF538646
  • GENBANK/EF538647
  • GENBANK/EF538648
  • GENBANK/EF538649
  • GENBANK/EF538650
  • GENBANK/EF538651
  • GENBANK/EF538652
  • GENBANK/EF538653
  • GENBANK/EF538654
  • GENBANK/EF538655
  • GENBANK/EF538656
  • GENBANK/EF538657
  • GENBANK/EF538658
  • GENBANK/EF538659
  • GENBANK/EF538660
  • GENBANK/EF538661
  • GENBANK/EF538662
  • GENBANK/EF538663
  • GENBANK/EF538664
  • GENBANK/EF538665
  • GENBANK/EF538666
  • GENBANK/EF538667