Comparison of partial tuf gene sequences for the identification of lactobacilli

Abstract

Comparative analysis of partial tuf sequences was evaluated for the identification and differentiation of lactobacilli. Comparison of the amino acid sequences allowed differentiation between species and also between the subspecies of Lactobacillus delbrueckii. The nucleotide sequence comparison allowed differentiation between other subspecies and between some strains. Lactobacilli from several collections and isolates from dairy samples were clearly identified by comparison of short tuf sequences with those of the type strains. In evaluating the taxonomy of the Lactobacillus casei-related taxa, different tuf amino acid signatures are in favour of a classification into three distinct species. The type strain designation for the L. casei species is discussed.

Analysis, Characterization, and Loci of the tuf Genes in Lactobacillus and Bifidobacterium Species and Their Direct Application for Species Identification

“…Consequently, 16S rDNA sequence analysis might not be an appropriate replacement for DNA reassociation to define closely related taxa. Our results and those of previous studies (4,18,19,26,27) suggested that tuf gene analysis also could be a valid tool for inferring relationships among closely related bacterial species. The use of the tuf gene, as well as the recA gene, as a phylogenetic marker for LAB has the advantage that the amino acid sequences from these genes can be used to infer bacterial phylogenies, avoiding the problems associated with rRNAs and the likely overestimation of the relatedness of taxa with similar nucleotide differences, nonindependence of substitution patterns at different sites, and bias derived from different GϩC contents of microorganisms (8).…”

“…It has been already applied to infer phylogeny in the genera Enterococcus (18), Mycoplasma (1), and Staphylococcus (28). In addition, in a very recent study, a comparative analysis of partial tuf sequences was evaluated for the differentiation of some Lactobacillus species (4). It fulfills all prerequisites to server as a suitable phylogenetic marker, such as very high genetic stability and a wide distribution (25).…”

“…Several new genetic approaches for the identification of Lactobacillus and Bifidobacterium species have been used in recent years, including the sequencing of rRNA genes (2,46,49,50,51,53), restriction endonuclease fingerprinting (51,52), analysis with oligonucleotide probes (13,33,35), analysis of plasmid content (41), analysis of sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis patterns of whole-cell proteins (13,33), and comparisons of tuf sequences (4,26,27). Now, with the advent of the genomics era, this rRNA-based view of bacterial phylogeny is being critically examined.…”

Similarity and Differences in the Lactobacillus acidophilus Group Identified by Polyphasic Analysis and Comparative Genomics

“…The 16S rRNA analysis can provide an overview of the phylogenetic relationships between the investigated lactobacilli that was largely confirmed by the other techniques applied. In multilocus sequence analysis of housekeeping genes, only three of the four genes allowed a clear separation of L. johnsonii from L. gasseri (rpoA and pheS, as suggested by Naser et al [38], and tuf, as suggested by Chavagnat et al [12], but not groEL, contrary to the report by Teng et al [52]). The two DNA-typing methods confirmed the close relationships within strains of the species L. johnsonii and allowed intraspecies strain differentiation, confirming earlier reports (59).…”

Comparative Sequence Analysis of the tuf and recA Genes and Restriction Fragment Length Polymorphism of the Internal Transcribed Spacer Region Sequences Supply Additional Tools for Discriminating Bifidobacterium lactis from Bifidobacterium animalis

“…The tuf and recA genes have been proposed as useful markers in inferring bacterial phylogeny (2,10,18) and have recently been successfully used to differentiate species and subspecies within various bacterial genera (3,7,8,17). Our results show that the sequence analysis of tuf and recA as well as restriction fragment length polymorphism (RFLP) analysis of the internal transcribed spacer (ITS) sequences are relatively simple and rapid methods by which B. lactis and B. animalis can be identified without resorting to the use of species-specific PCR primer sets.…”