Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination
Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination
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DOI：
10.1128/aem.01095-07
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发表时间：
2007-10-01
影响因子：
4.4
通讯作者：
Brisse, Sylvain
中科院分区：
文献类型：
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作者：
Diancourt, Laure;Passet, Virginie;Brisse, Sylvain
干酪乳杆菌的强大的基因分型方法需要菌株跟踪和收集管理，以及群体生物学研究。收集了52株最初标记为L.干酪乳杆菌或副干酪乳杆菌首先与玉米乳杆菌、鼠李糖乳杆菌和其它物种的参考菌株一起进行rpIB基因测序。系统发育分析表明，52株菌均属于同一紧凑型L.干酪湖paracasei序列簇，与菌株CIP 107868（= ATCC 334）一起，但明显不同于L. rhamnosus和L. zeae和CIP 103137（T）（= ATCC 393 T）。使用扩增片段长度多态性、基于七个管家基因fusA、ileS、lepA、leuS、pyrG、recA和recG的内部部分的多位点序列分型以及串联重复变异（多位点可变数量串联重复分析[MLVA]使用九个基因座）对菌株进行基因分型。三种方法之间的一致性非常高。虽然7个基因的核苷酸变异量低（pi范围从0.0038到0.0109），3至12个等位基因被区分，导致31个序列类型。一个序列类型（ST 1）是常见的（17株），但大多数其他的是由一个单一的菌株。试图分型ST1菌株MLVA，核糖分型，成簇的定期间隔短回文重复特征，和单核苷酸重复变异是不成功的。我们发现了在L. casei克隆，包括推定的基因内导入DNA到一个菌株中。据估计，核苷酸的变化频率的四倍以上的重组比突变。然而，个体基因树之间的统计一致性被保留，表明重组的频率不足以破坏系统发育信号。本研究所建立的多位点基因分型方法对今后的研究具有一定的参考价值。干酪菌株多样性和进化。
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.