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Life, volume 11, issue 11, pages 1246

Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity

Yudin Sergey 2
Makarov Valentin 2
Glazunova Olga 1
Alikina Olga 1
Markelova Natalia 1
Kolzhetsov Nikolay 1
Dzhelyadin Timur 1
Shcherbakova Viktoria 3
Panyukov Valery 1, 4
Zaitsev Alexandr 4
Kiselev Sergey 1
Shavkunov Konstantin 1
Ozoline Olga 1
Publication typeJournal Article
Publication date2021-11-17
Journal: Life
Quartile SCImago
Q2
Quartile WOS
Q2
Impact factor3.2
ISSN20751729
PubMed ID:  34833122
General Biochemistry, Genetics and Molecular Biology
Ecology, Evolution, Behavior and Systematics
Paleontology
Space and Planetary Science
Abstract
Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this “rare” strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.

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Frolova M. E. et al. Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity // Life. 2021. Vol. 11. No. 11. p. 1246.
GOST all authors (up to 50) Copy
Frolova M. E., Yudin S., Makarov V., Glazunova O., Alikina O., Markelova N., Kolzhetsov N., Dzhelyadin T., Shcherbakova V., Trubitsyn V., Panyukov V., Zaitsev A., Kiselev S., Shavkunov K., Ozoline O. Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity // Life. 2021. Vol. 11. No. 11. p. 1246.
RIS |
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RIS Copy
TY - JOUR
DO - 10.3390/life11111246
UR - https://doi.org/10.3390%2Flife11111246
TI - Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity
T2 - Life
AU - Yudin, Sergey
AU - Makarov, Valentin
AU - Glazunova, Olga
AU - Alikina, Olga
AU - Kolzhetsov, Nikolay
AU - Dzhelyadin, Timur
AU - Shcherbakova, Viktoria
AU - Panyukov, Valery
AU - Zaitsev, Alexandr
AU - Kiselev, Sergey
AU - Shavkunov, Konstantin
AU - Ozoline, Olga
AU - Markelova, Natalia
AU - Frolova, Maria E
AU - Trubitsyn, Vladimir
PY - 2021
DA - 2021/11/17 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 1246
IS - 11
VL - 11
PMID - 34833122
SN - 2075-1729
ER -
BibTex |
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BibTex Copy
@article{2021_Frolova
author = {Sergey Yudin and Valentin Makarov and Olga Glazunova and Olga Alikina and Nikolay Kolzhetsov and Timur Dzhelyadin and Viktoria Shcherbakova and Valery Panyukov and Alexandr Zaitsev and Sergey Kiselev and Konstantin Shavkunov and Olga Ozoline and Natalia Markelova and Maria E Frolova and Vladimir Trubitsyn},
title = {Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity},
journal = {Life},
year = {2021},
volume = {11},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {nov},
url = {https://doi.org/10.3390%2Flife11111246},
number = {11},
pages = {1246},
doi = {10.3390/life11111246}
}
MLA
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MLA Copy
Frolova, Maria E., et al. “Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity.” Life, vol. 11, no. 11, Nov. 2021, p. 1246. https://doi.org/10.3390%2Flife11111246.
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