Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination.
Robust genotyping methods for Lactobacillus casei are needed for strain tracking and collection management, as well as for population biology research. A collection of 52 strains initially labeled L. casei or Lactobacillus paracasei was first subjected to rplB gene sequencing together with reference strains of Lactobacillus zeae, Lactobacillus rhamnosus, and other species. Phylogenetic analysis showed that all 52 strains belonged to a single compact L. casei-L. paracasei sequence cluster, together with strain CIP107868 (= ATCC 334) but clearly distinct from L. rhamnosus and from a cluster with L. zeae and CIP103137(T) (= ATCC 393(T)). The strains were genotyped using amplified fragment length polymorphism, multilocus sequence typing based on internal portions of the seven housekeeping genes fusA, ileS, lepA, leuS, pyrG, recA, and recG, and tandem repeat variation (multilocus variable-number tandem repeats analysis [MLVA] using nine loci). Very high concordance was found between the three methods. Although amounts of nucleotide variation were low for the seven genes (pi ranging from 0.0038 to 0.0109), 3 to 12 alleles were distinguished, resulting in 31 sequence types. One sequence type (ST1) was frequent (17 strains), but most others were represented by a single strain. Attempts to subtype ST1 strains by MLVA, ribotyping, clustered regularly interspaced short palindromic repeat characterization, and single nucleotide repeat variation were unsuccessful. We found clear evidence for homologous recombination during the diversification of L. casei clones, including a putative intragenic import of DNA into one strain. Nucleotides were estimated to change four times more frequently by recombination than by mutation. However, statistical congruence between individual gene trees was retained, indicating that recombination is not frequent enough to disrupt the phylogenetic signal. The developed multilocus sequence typing scheme should be useful for future studies of L. casei strain diversity and evolution.
Diancourt
Laure
L
Institut Pasteur, Unité Biodiversité des Bactéries Pathogènes Emergentes, 25-28 rue du Dr Roux, 75724 Paris, France.
Passet
Virginie
V
Chervaux
Christian
C
Garault
Peggy
P
Smokvina
Tamara
T
Brisse
Sylvain
S
D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D004269:DNA, Bacterial / Q000032:analysis; D007780:Lacticaseibacillus casei / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D012269:Ribosomal Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012269:Ribosomal Proteins
Annu Rev Microbiol. 2001;55:561-90
11544367
Mol Microbiol. 2002 Mar;43(6):1565-75
11952905
Curr Pharm Des. 2003;9(2):175-91
12570667
Mol Biol Evol. 1999 Nov;16(11):1496-502
10555280
Int J Syst Evol Microbiol. 2001 Nov;51(Pt 6):2113-7
11760954
Bioinformatics. 1999 Feb;15(2):174-5
10089204
J Bacteriol. 2006 Apr;188(7):2364-74
16547022
Bioinformatics. 2005 Jan 15;21(2):260-2
15377507
J Microbiol Methods. 2004 Nov;59(2):163-72
15369852
Microbiology. 2006 Jan;152(Pt 1):85-93
16385118
Ann Clin Microbiol Antimicrob. 2003 Dec 10;2:12
14664722
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
9862982
PLoS Pathog. 2005 Sep;1(1):e5
16201017
Int J Clin Pract. 1999 Apr-May;53(3):179-84
10665128
Microbiology. 2005 Aug;151(Pt 8):2551-61
16079334
FEMS Microbiol Lett. 2002 Dec 17;217(2):177-83
12480101
Appl Environ Microbiol. 2003 Nov;69(11):6908-22
14602655
J Food Prot. 2005 Jan;68(1):111-9
15690811
Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3140-5
9501229
Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):182-7
11136255
J Clin Microbiol. 1997 Apr;35(4):907-14
9157152
BMC Microbiol. 2006;6:23
16519816
J Clin Microbiol. 2006 Mar;44(3):777-82
16517854
FEMS Microbiol Lett. 2006 Feb;255(1):1-10
16436055
Nat Rev Microbiol. 2004 Jun;2(6):483-95
15152204
Int J Clin Pract. 2000 Nov;54(9):568-71
11220983
Am J Physiol Gastrointest Liver Physiol. 2007 Jan;292(1):G358-68
16990449
Folia Microbiol (Praha). 2005;50(3):223-8
16295661
Appl Environ Microbiol. 2004 Dec;70(12):7210-9
15574919
Environ Microbiol. 2004 Jul;6(7):754-9
15186354
Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15611-6
17030793
J Bacteriol. 2004 Mar;186(5):1518-30
14973027
Electrophoresis. 2005 Jun;26(13):2567-82
15937984
Int J Syst Bacteriol. 1996 Jan;46(1):337-40
8573516
Genome Res. 2000 Jan;10(1):62-71
10645951
Antonie Van Leeuwenhoek. 2002 Aug;82(1-4):279-89
12369194
Science. 2006 Nov 24;314(5803):1301-4
17124322
Mol Microbiol. 2006 Jun;60(5):1136-51
16689791
Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1917-27
17062411
Bioinformatics. 2001 Dec;17(12):1244-5
11751241
Microbiology. 2005 Mar;151(Pt 3):653-63
15758212
Int J Syst Evol Microbiol. 2002 Jan;52(Pt 1):285-7
11837314
Microbiol Mol Biol Rev. 1998 Jun;62(2):275-93
9618442
Int J Syst Evol Microbiol. 2003 Jan;53(Pt 1):67-75
12656154
Science. 1994 Nov 25;266(5189):1380-3
7973728
Bioinformatics. 1998;14(1):68-73
9520503
J Clin Microbiol. 2004 Oct;42(10):4503-11
15472301
Mol Biol Evol. 2006 Feb;23(2):254-67
16221896
Can J Microbiol. 2004 Jul;50(7):482-8
15381972
J Bacteriol. 2000 May;182(10):2928-36
10781564
J Clin Microbiol. 2003 Jan;41(1):15-26
12517820
Appl Environ Microbiol. 1999 Sep;65(9):3908-14
10473394
J Bacteriol. 2004 Aug;186(16):5496-505
15292152