Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses

Abstract

Three strains, JCM 5343, JCM 5344 and JCM 1130, currently identified as Lactobacillus gasseri, were investigated using a polyphasic taxonomic approach. Although these strains shared high 16S rRNA gene sequence similarities with L. gasseri ATCC 33323 (99.9 %), they formed a clade clearly distinct from ATCC 33323 based on whole-genome relatedness. The average nucleotide identity and in silico DNA-DNA hybridization values of these three strains compared to L. gasseri ATCC 33323 were 93.4-93.7 and 53.1-54.1 %, respectively, and both were less than the widely accepted threshold to distinguish two species (95 and 70 %, respectively). The three strains were Gram-stain positive, non-motile, non-spore-forming, catalase-negative and rod-shaped bacteria. They grew at 25-45 °C and in the presence of 2.0 % (w/v) NaCl. The major fatty acids of the three strains were C16 : 0 and C18 : 1 ω9c. Based on phylogenetic analyses of the phenylalanyl-tRNA synthase alpha subunit and RNA polymerase alpha subunit genes, and on phenotypic and chemotaxonomic characteristics, strains JCM 5343, JCM 5344 and JCM 1130 represent a novel species distinct from L. gasseri, for which we propose the name Lactobacillusparagasseri sp. nov. In addition, a large portion of genomes currently labelled as L. gasseri in the public sequence database should be reclassified as L. paragasseri based on whole-genome relatedness.

Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa

“…Seventy-nine strains were determined as L. paragasseri, and the remained 13 (14%) strains were L. gasseri, revealing that the most (86%) of isolates initially identified as L. gasseri by 16S rDNA sequencing were L. paragasseri. The current results were highly in line with previous publication by Tanizawa and colleagues [16], in which they reported that a large portion of genomes currently labelled as L. gasseri in the public database should be re-classified as L. paragasseri based on whole-genome sequence analyses as well. All those results indicated that L. gasseri and L. paragesseri are sister taxon with high similarity but not the same species, and the cultivable "L. gasseri" isolated from environment actually contained both L. gasseri and L. paragasseri species, which might be the reason for the high intraspecies diversity among "L. gasseri" exhibited.…”

“…All of the 94 strains were classified into two groups, with 80 strains including L. paragasseri K7 (as type L. paragasseri strain) showing an ANI value range 97-99%, and the other group consisted of 14 strains including the type strain L. gasseri ATCC 33323 (as type L. gasseri strain) with an ANI range 93-94% compared with L. paragasseri. According to a previous report, L. gasseri K7 was reclassified as L. paragasseri based on whole-genome analyses [16], therefore, other 79 strains on the same group with L. paragasseri K7 were preliminarily identified as L. paragasseri, while the remained 13 strains on the other branch with L. gasseri ATCC33323 were identified as L. gasseri.…”

“…The sequence length of L. paragasseri ranged from 1.87 to 2.14 Mb, with a mean size of 1.97 Mb, and all 14 L. gasseri genomes had an average Similarly, approximately 85% of L. gasseri ORFs were identified, while 15% were predicted to encode hypothetical proteins. The preference of the two species codons for the start codon were predicted, and the results showed that ATG, TTG and CTG in L. paragasseri with a calculated frequency percentage of 82.6, 10.3 and 7.1%, respectively, and 81.0, 11.7 and 7.4% in L. gasseri, respectively, suggesting that L. paragasseri and L. gasseri had a preference of using ATG as start codon [16]. To further analyse the genome-encoded functional proteins, the COG classification was performed for each draft genome.…”

“…The ANI values were higher than 62% within a genus, while more than 95% of ANI values was recommended as the delimitation criterion for same species [14]. Seventyfive L. gasseri strains with publically available genomes were divided into two intraspecific groups by ANI at the threshold of 94% [15], subsequently some strains were reclassified as a new group, L. paragasseri, based on wholegenome analysis [16].…”

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

“…In samples that had both a 16S and GTDB taxonomic classification, there was disagreement in 154 out of 1,467 samples. Of these, 47% were accounted for by the recently described L. paragasseri (95) (n=72). This possibly highlights a lag in the reclassification of assemblies in the NCBI Assembly database.…”