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

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...

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Autores principales:	Maria Frolova, Sergey Yudin, Valentin Makarov, Olga Glazunova, Olga Alikina, Natalia Markelova, Nikolay Kolzhetsov, Timur Dzhelyadin, Viktoria Shcherbakova, Vladimir Trubitsyn, Valery Panyukov, Alexandr Zaitsev, Sergey Kiselev, Konstantin Shavkunov, Olga Ozoline
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Lacticaseibacillus paracasei</i> <i>k</i>-mer-based phylogeny human gut metagenomes Crohn’s disease autism obesity Science Q
Acceso en línea:	https://doaj.org/article/baddb1ee57c147ee8ffdcbf98caf4277
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spelling	oai:doaj.org-article:baddb1ee57c147ee8ffdcbf98caf42772021-11-25T18:11:33Z<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity10.3390/life111112462075-1729https://doaj.org/article/baddb1ee57c147ee8ffdcbf98caf42772021-11-01T00:00:00Zhttps://www.mdpi.com/2075-1729/11/11/1246https://doaj.org/toc/2075-1729Alignment-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.Maria FrolovaSergey YudinValentin MakarovOlga GlazunovaOlga AlikinaNatalia MarkelovaNikolay KolzhetsovTimur DzhelyadinViktoria ShcherbakovaVladimir TrubitsynValery PanyukovAlexandr ZaitsevSergey KiselevKonstantin ShavkunovOlga OzolineMDPI AGarticle<i>Lacticaseibacillus paracasei</i><i>k</i>-mer-based phylogenyhuman gut metagenomesCrohn’s diseaseautismobesityScienceQENLife, Vol 11, Iss 1246, p 1246 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Lacticaseibacillus paracasei</i> <i>k</i>-mer-based phylogeny human gut metagenomes Crohn’s disease autism obesity Science Q
spellingShingle	<i>Lacticaseibacillus paracasei</i> <i>k</i>-mer-based phylogeny human gut metagenomes Crohn’s disease autism obesity Science Q Maria Frolova Sergey Yudin Valentin Makarov Olga Glazunova Olga Alikina Natalia Markelova Nikolay Kolzhetsov Timur Dzhelyadin Viktoria Shcherbakova Vladimir Trubitsyn Valery Panyukov Alexandr Zaitsev Sergey Kiselev Konstantin Shavkunov Olga Ozoline <i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity
description	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.
format	article
author	Maria Frolova Sergey Yudin Valentin Makarov Olga Glazunova Olga Alikina Natalia Markelova Nikolay Kolzhetsov Timur Dzhelyadin Viktoria Shcherbakova Vladimir Trubitsyn Valery Panyukov Alexandr Zaitsev Sergey Kiselev Konstantin Shavkunov Olga Ozoline
author_facet	Maria Frolova Sergey Yudin Valentin Makarov Olga Glazunova Olga Alikina Natalia Markelova Nikolay Kolzhetsov Timur Dzhelyadin Viktoria Shcherbakova Vladimir Trubitsyn Valery Panyukov Alexandr Zaitsev Sergey Kiselev Konstantin Shavkunov Olga Ozoline
author_sort	Maria Frolova
title	<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity
title_short	<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity
title_full	<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity
title_fullStr	<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity
title_full_unstemmed	<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity
title_sort	<i>lacticaseibacillus paracasei</i>: occurrence in the human gut microbiota and <i>k</i>-mer-based assessment of intraspecies diversity
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/baddb1ee57c147ee8ffdcbf98caf4277
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<i>Lacticaseibacillus paracasei</i>: Occurrence in the Human Gut Microbiota and <i>K</i>-Mer-Based Assessment of Intraspecies Diversity

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