Identification of phenotypically and genotypically related Lactobacillus strains based on nucleotide sequence analysis of the groEL, rpoB, rplB, and 16S rRNA genes

Shevtsov, Alexandr; Kushugulova, Аlmagul; Tynybaeva, I K; Kozhakhmetov, Samat; Abzhalelov, Akhan; Momynaliev, K. Т.; Стоянова, Л.Г.

doi:10.1134/s0026261711050134

Cited by 15 publications

(12 citation statements)

References 18 publications

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“…Therefore, the necessity of identification and higher discrimination of LAB has led to the use of housekeeping gene sequence analysis [41,42]. Research by Shevtsov et al showed that the identification of the Lactobacillus genus using housekeeping gene sequences is superior and more sensitive than the 16S rRNA gene sequencing [43]. Previously, our group characterized different strains of Leu.…”

Section: Discussionmentioning

confidence: 99%

Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder

2019

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The present work aimed at tracking intentionally inoculated lactic acid bacteria (LAB) strains in yogurt and probiotic powder. Leuconostoc (Leu.) mesenteroides (11251), Lactobacillus (L.) brevis (B151), and Lactobacillus plantarum (LB41K) strains were tracked in yogurt, and L. plantarum (LB41P) was tracked in a commercial probiotic powder. The yogurt was intentionally inoculated with the selected bacterial strains. Two types of yogurt with known and unknown bacterial pools were utilized. The standard 16S rRNA gene sequencing was used to evaluate the initial screening. The molecular typing tools, random amplified polymorphic DNA (RAPD), repetitive element palindromic PCR (rep-PCR), and comparative gene sequence analysis of selected housekeeping loci were used to track the inoculated dubious strains. Out of 30 random selections for each inoculation, the developed method identified seven (11251), nine (B151), and five (LB41K) colonies in the yogurt. The validation was performed by identifying 7 colonies (LB41P) out of 30 in the probiotic powder. The DNA banding profiles and the gene sequence alignments led to the identification of the correct inoculated strains. Overall, the study summarizes the use of molecular tools to identify the deliberately inoculated LAB strains. In conclusion, the proposed polyphasic approach effectively tracked the intentionally inoculated strains: Leu. mesenteroides, L. brevis, and L. plantarum (LB41K) in yogurt and L. plantarum (LB41P) in probiotic powder. The study demonstrates how to track industrially relevant misused LAB strains in marketable food products.

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Section: Discussionmentioning

confidence: 99%

Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder

2019

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“…All orthologous proteins were aligned using MAFFT-7.313 software [45] and phylogenetic trees were constructed using the python script (https://github.com/jvollme/fasta2phylip) and the supertree was modified using Evolgenius (http:// www.evolgenius.info/evolview/). The house-keeping genes, pheS [46] and groEL [47], were extracted from the genomes using BLAST (Version 2.2.31+) [48], and the multiple alignments were carried out through Cluster-W (default parameters), and the single gene neighborjoining trees were built by MEGA 6.0 [49], with bootstrap by a self-test of 1000 resampling.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

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

et al. 2020

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Background: Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. Results: In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species. Conclusions: This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.

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“…The genomic DNA was extracted from cell pellets and the 16S rRNA gene of the hydrogen-producing bacterium was amplified by PCR as described in literature [22,23].The 16S rRNA gene sequence (1471 bp) of strain YA001 was obtained by PCR using a pair of universal primers, 27F (5 0 -AGA GTT TGA TCC TGG CTC AG-3 0 ) and 1492R (5 0 -TAC GGT TAC CTT GTT ACG ACT T-3 0 ). The PCR products were purified using DNA Fragment Purification Kit (Takara, Dalian, China) and then sent to sequence.…”

Section: Strain Identification and Phylogenetic Analysismentioning

confidence: 99%

Characterization on hydrogen production performance of a newly isolated Clostridium beijerinckii YA001 using xylose

An¹,

Li²,

Wang³

et al. 2014

International Journal of Hydrogen Energy

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Identification of phenotypically and genotypically related Lactobacillus strains based on nucleotide sequence analysis of the groEL, rpoB, rplB, and 16S rRNA genes

Cited by 15 publications

References 18 publications

Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder

Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder

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

Characterization on hydrogen production performance of a newly isolated Clostridium beijerinckii YA001 using xylose

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