Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

Panyukov, V.V.; Kiselev, S. S.; Ozoline, Olga N.

doi:10.3390/ijms21030944

Cited by 8 publications

(16 citation statements)

References 87 publications

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“…The proportion of species-specific RNAs and oligonucleotides common to co-habiting bacteria in the fraction of secreted RNAs was estimated using k-mers present in the genome of E. coli and either absent or present in the genomes of the competing bacteria. Sets of E. coli-specific k-mers (k = 16, 18, 20, 22) were obtained with UniSeq software (Panyukov et al, 2017(Panyukov et al, , 2020. Sets of common k-mers of the same length were collected using a simpler program that sorted all k-mers in lexicographic order and searched for those that have copies in the genome of comparison.…”

Section: Bioinformatic Analysismentioning

confidence: 99%

Suppression of Escherichia coli Growth Dynamics via RNAs Secreted by Competing Bacteria

Markelova

Glazunova

Alikina

et al. 2021

Front. Mol. Biosci.

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With the discovery of secreted RNAs, it has become apparent that the biological role of regulatory oligonucleotides likely goes beyond the borders of individual cells. However, the mechanisms of their action are still comprehended only in general terms and mainly for eukaryotic microRNAs, which can interfere with mRNAs even in distant recipient cells. It has recently become clear that bacterial cells lacking interference systems can also respond to eukaryotic microRNAs that have targets in their genomes. However, the question of whether bacteria can perceive information transmitted by oligonucleotides secreted by other prokaryotes remained open. Here we evaluated the fraction of short RNAs secreted by Escherichia coli during individual and mixed growth with Rhodospirillum rubrum or Prevotella copri, and found that in the presence of other bacteria E. coli tends to excrete oligonucleotides homologous to alien genomes. Based on this observation, we selected four RNAs secreted by either R. rubrum or P. copri, together with one E. coli-specific oligonucleotide. Both fragments of R. rubrum 23S-RNA suppressed the growth of E. coli. Of the two fragments secreted by P. copri, one abolished the stimulatory effect of E. coli RNA derived from the 3′-UTR of ProA mRNA, while the other inhibited bacterial growth only in the double-stranded state with complementary RNA. The ability of two RNAs secreted by cohabiting bacteria to enter E. coli cells was demonstrated using confocal microscopy. Since selected E. coli-specific RNA also affected the growth of this bacterium, we conclude that bacterial RNAs can participate in inter- and intraspecies signaling.

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Section: Bioinformatic Analysismentioning

confidence: 99%

Suppression of Escherichia coli Growth Dynamics via RNAs Secreted by Competing Bacteria

Markelova

Glazunova

Alikina

et al. 2021

Front. Mol. Biosci.

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“…For taxonomic analysis of the human intestinal microflora, all 18-mers present in the genome of Homo sapiens were also removed from the obtained sets. All the procedures were carried out in the virtual machine with a 64-bit version of UniSeq software on a high-performance server (configuration: 2 Xeon Gold 5218, 64 Gb RAM) [5,26].…”

Section: Barcodingmentioning

confidence: 99%

“…The metagenomes were transcoded the same way as described in [5], i.e., (A), (C), (G), and (T) were substituted with the numerals (0), ( 1), ( 2) and (3), respectively, while line breaks were replaced with the numeral (4). As a result, metagenomes were digitized in one numeric string, which allowed use of the UniTestExpress software [5] to operate them in the same way as the genomes.…”

Section: Phylogroup-specific Taxonomic Analysis Of Human Metagenomesmentioning

confidence: 99%

“…Our previous study [5] showed that k-mer-based phylogenetic analysis, operating with thousands of marker sequences without any limitation from the level of genome functional annotation, could be efficiently used for intraspecific systematics. Such a taxonomy is of obvious importance for species containing pathogenic strains/phylogroups and, vice versa, for potential probiotics.…”

Section: Introductionmentioning

confidence: 99%

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

Frolova

Yudin

Makarov

et al. 2021

Life

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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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“…Valery Panyukov and co-authors [ 12 ] discussed the bioinformatics application to use k-mers in phylogenetic analysis and microbiome profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species but also strains of microorganisms with known genomes.…”

mentioning

confidence: 99%

Bioinformatics Methods in Medical Genetics and Genomics

Orlov

Baranova

Tatarinova

2020

IJMS

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Medical genomics relies on next-gen sequencing methods to decipher underlying molecular mechanisms of gene expression. This special issue collects materials originally presented at the “Centenary of Human Population Genetics” Conference-2019, in Moscow. Here we present some recent developments in computational methods tested on actual medical genetics problems dissected through genomics, transcriptomics and proteomics data analysis, gene networks, protein–protein interactions and biomedical literature mining. We have selected materials based on systems biology approaches, database mining. These methods and algorithms were discussed at the Digital Medical Forum-2019, organized by I.M. Sechenov First Moscow State Medical University presenting bioinformatics approaches for the drug targets discovery in cancer, its computational support, and digitalization of medical research, as well as at “Systems Biology and Bioinformatics”-2019 (SBB-2019) Young Scientists School in Novosibirsk, Russia. Selected recent advancements discussed at these events in the medical genomics and genetics areas are based on novel bioinformatics tools.

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Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

Cited by 8 publications

References 87 publications

Suppression of Escherichia coli Growth Dynamics via RNAs Secreted by Competing Bacteria

Suppression of Escherichia coli Growth Dynamics via RNAs Secreted by Competing Bacteria

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

Bioinformatics Methods in Medical Genetics and Genomics

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