<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity
Alignment-free approaches employing short <i>k</i>-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 <i>Lacticaseibacillus paracasei</i> species as...
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| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
MDPI AG
2021
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| Materias: | |
| Acceso en línea: | https://doaj.org/article/baddb1ee57c147ee8ffdcbf98caf4277 |
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| Sumario: | Alignment-free approaches employing short <i>k</i>-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 <i>Lacticaseibacillus paracasei</i> species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of <i>L. paracasei</i> VKM B-1144 at the genus level, we identified four <i>L. paracasei</i> phylogroups and found that <i>L. casei</i> 12A belongs to one of them, rather than to the <i>L. casei</i> clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of <i>L. paracasei</i> 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 <i>L. paracasei</i> 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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