Revised classification of native probiotic strains of Lactobacillus used in Russian Federation

Ботина, С. Г.; Klimina, Ksenia M.; Koroban, N. V.; Amerkhanova, A. M.; Зинченко, В.В.; Даниленко, В. Н.

doi:10.1134/s1022795410110050

Cited by 5 publications

(4 citation statements)

References 14 publications

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“…To validate that Lactobacillus and Bifidobacterium species were present in the microbiomes we plated feces suspension on nutrient media (K. Klimina and E. Poluektova, 2018, unpublished data). Lactobacilli was found in RM1 in much lesser quantities than in other metagenomes, which is the known feature of children microflora (Botina et al, 2010).…”

Section: Resultsmentioning

confidence: 99%

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes

Klimina

Kasianov

Полуэктова

et al. 2019

PeerJ

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Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.

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Section: Resultsmentioning

confidence: 99%

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes

Klimina

Kasianov

Полуэктова

et al. 2019

PeerJ

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“…Lactobacilli was found in RM1 in much lesser quantities than in other metagenomes, which is the known feature of children microflora [39].…”

Section: The Softwarementioning

confidence: 92%

Peer Review #2 of "Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes (v0.1)"

Gogleva¹

2019

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Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota, since it can contribute to health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota and not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human gut microbiota. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human gut microbiota we developed TAGMA software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strain of Lactobacillus and Bifidobacterium in metagenomes.

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“…The accurate identification of lactobacilli is achieved by applying well-established or novel molecular genetic methods, such as polymerase chain reaction, matrix-activated laser desorption/ionization (mass spectrometer MALDI-TOF MS), gas chromatography-mass spectrometry, and metagenomic studies [23,24]. Methods based on the analysis and comparison of the 16S rDNA sequence have become a reference in identification, as the 16S rDNA sequence is sufficiently conserved in the evolution of microorganisms; therefore, it is used for the species identification of prokaryotic microorganisms, including lactobacilli [25,26]. Such methods include the ribosomal DNA (rDNA) restriction analysis method ARDRA [22,[27][28][29][30][31] or the partial or complete sequencing of the 16S rRNA gene (16S rDNA) and comparison with reference sequences in DNA databases such as GenBank.…”

Section: Introductionmentioning

confidence: 99%

“…RAPD involves the random amplification of fragments from the target bacterial genome using single primers under less stringent conditions. In this way, a complex profile is created out of the large number of amplification products from random loci scattered throughout the genome [25,35,36].…”

Section: Introductionmentioning

confidence: 99%

Identification of Lactic Acid Bacteria Strains Isolated from Sourdoughs Prepared with Different Flour Types

Urshev,

Doynova,

Prasev

et al. 2024

Applied Sciences

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Species identification is the first step in the examination of newly isolated microorganism strains, including the cases when they are intended for application in the development of probiotic preparations or starters for different food products. The thorough identification process of newly isolated strains combines the application of different physiological, biochemical, and molecular genetic methods. The aim of the present study was to identify the species-level lactic acid bacteria (LAB) strains isolated from spontaneously fermented sourdoughs prepared from different flour types: Khorosan wheat, wheat, barley, buckwheat, spelled, spelt, and corn. Both classical phenotypic (cellular morphology characterization, and API 50 CHL) and molecular genetic methods (RAPD, ARDRA-analysis, 16S rDNA sequencing, and species-specific PCR) were applied. It was found that cultures with a short-rod morphology predominated among the 30 sourdough isolates. According to the RAPD profiles obtained, the isolates were divided into nine genotypes corresponding to nine genetically distinct strains. It was determined that individual sourdoughs made with different flour types shared cultures with a common genotype. The analysis of the physiological and biochemical profiles of the LAB isolates performed with the API 50 CHL system divided them into two groups according to their identification: Lactiplantibacillus plantarum (Lp. plantarum) 1 and Levilactobacillus brevis (Lv. brevis) 3. According to the 16S rDNA restriction profile, the LAB isolates showed two profiles corresponding to the Lp. plantarum and Lv. brevis groups. 16S rDNA sequencing and a comparison of the partially read 16S rDNA sequences of the studied isolates confirmed that some of them belonged to the Lv. Brevis species, but did not provide sufficient evidence that the rest of the cultures belonged to the Lp. Plantarum species. The species-specific PCR clearly separated the isolates from the Lp. plantarum group into two groups: isolates of the Lp. plantarum species and isolates of the Lp. paraplantarum species. The summary of the results of the conducted polyphasic taxonomic study determined the investigated LAB strains isolated from spontaneously fermented sourdoughs as representatives of the Lv. brevis, Lp. plantarum ssp. paraplantarum, and Lp. paraplantarum species.

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Revised classification of native probiotic strains of Lactobacillus used in Russian Federation

Cited by 5 publications

References 14 publications

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes

Peer Review #2 of "Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes (v0.1)"

Identification of Lactic Acid Bacteria Strains Isolated from Sourdoughs Prepared with Different Flour Types

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