Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling
Identifieur interne : 000031 ( Main/Exploration ); précédent : 000030; suivant : 000032Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling
Auteurs : Valery V. Panyukov ; Sergey S. Kiselev [Russie] ; Olga N. Ozoline [Russie]Source :
- International Journal of Molecular Sciences [ 1422-0067 ] ; 2020.
Abstract
The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker
Url:
DOI: 10.3390/ijms21030944
PubMed: 32023871
PubMed Central: 7037511
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Unique <italic>k</italic>-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling</title><author><name sortKey="Panyukov, Valery V" sort="Panyukov, Valery V" uniqKey="Panyukov V" first="Valery V." last="Panyukov">Valery V. Panyukov</name><affiliation><nlm:aff id="af1-ijms-21-00944">Institute of Mathematical Problems of Biology RAS—the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia;<email>panyukov@itaec.ru</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-ijms-21-00944">Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;<email>anthyllium@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Kiselev, Sergey S" sort="Kiselev, Sergey S" uniqKey="Kiselev S" first="Sergey S." last="Kiselev">Sergey S. Kiselev</name><affiliation><nlm:aff id="af2-ijms-21-00944">Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;<email>anthyllium@gmail.com</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-21-00944">Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino</wicri:regionArea><wicri:noRegion>142290 Pushchino</wicri:noRegion></affiliation></author><author><name sortKey="Ozoline, Olga N" sort="Ozoline, Olga N" uniqKey="Ozoline O" first="Olga N." last="Ozoline">Olga N. Ozoline</name><affiliation><nlm:aff id="af2-ijms-21-00944">Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;<email>anthyllium@gmail.com</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-21-00944">Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino</wicri:regionArea><wicri:noRegion>142290 Pushchino</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32023871</idno><idno type="pmc">7037511</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7037511</idno><idno type="RBID">PMC:7037511</idno><idno type="doi">10.3390/ijms21030944</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000D71</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000D71</idno><idno type="wicri:Area/Pmc/Curation">000D71</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000D71</idno><idno type="wicri:Area/Pmc/Checkpoint">000005</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000005</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:32023871</idno><idno type="wicri:Area/PubMed/Corpus">000253</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000253</idno><idno type="wicri:Area/PubMed/Curation">000253</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000253</idno><idno type="wicri:Area/PubMed/Checkpoint">000032</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000032</idno><idno type="wicri:Area/Ncbi/Merge">002516</idno><idno type="wicri:Area/Ncbi/Curation">002516</idno><idno type="wicri:Area/Ncbi/Checkpoint">002516</idno><idno type="wicri:Area/Main/Merge">000034</idno><idno type="wicri:Area/Main/Curation">000031</idno><idno type="wicri:Area/Main/Exploration">000031</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Unique <italic>k</italic>-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling</title><author><name sortKey="Panyukov, Valery V" sort="Panyukov, Valery V" uniqKey="Panyukov V" first="Valery V." last="Panyukov">Valery V. Panyukov</name><affiliation><nlm:aff id="af1-ijms-21-00944">Institute of Mathematical Problems of Biology RAS—the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia;<email>panyukov@itaec.ru</email></nlm:aff></affiliation><affiliation><nlm:aff id="af2-ijms-21-00944">Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;<email>anthyllium@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Kiselev, Sergey S" sort="Kiselev, Sergey S" uniqKey="Kiselev S" first="Sergey S." last="Kiselev">Sergey S. Kiselev</name><affiliation><nlm:aff id="af2-ijms-21-00944">Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;<email>anthyllium@gmail.com</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-21-00944">Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino</wicri:regionArea><wicri:noRegion>142290 Pushchino</wicri:noRegion></affiliation></author><author><name sortKey="Ozoline, Olga N" sort="Ozoline, Olga N" uniqKey="Ozoline O" first="Olga N." last="Ozoline">Olga N. Ozoline</name><affiliation><nlm:aff id="af2-ijms-21-00944">Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;<email>anthyllium@gmail.com</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-21-00944">Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino</wicri:regionArea><wicri:noRegion>142290 Pushchino</wicri:noRegion></affiliation></author></analytic><series><title level="j">International Journal of Molecular Sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker <italic>k</italic>-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific <italic>k</italic>-mers to distinguish eight phylogroups of <italic>Escherichia coli</italic> (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn’s disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific “barcodes” for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of <italic>E. coli</italic> in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Woese, C R" uniqKey="Woese C">C.R. Woese</name></author><author><name sortKey="Fox, G E" uniqKey="Fox G">G.E. Fox</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q. Wang</name></author><author><name sortKey="Garrity, G M" uniqKey="Garrity G">G.M. Garrity</name></author><author><name sortKey="Tiedje, J M" uniqKey="Tiedje J">J.M. Tiedje</name></author><author><name sortKey="Cole, J R" uniqKey="Cole J">J.R. 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Afgan</name></author><author><name sortKey="Baker, D" uniqKey="Baker D">D. Baker</name></author><author><name sortKey="Batut, B" uniqKey="Batut B">B. Batut</name></author><author><name sortKey="Van Den Beek, M" uniqKey="Van Den Beek M">M. van den Beek</name></author><author><name sortKey="Bouvier, D" uniqKey="Bouvier D">D. Bouvier</name></author><author><name sortKey="Cech, M" uniqKey="Cech M">M. Cech</name></author><author><name sortKey="Chilton, J" uniqKey="Chilton J">J. Chilton</name></author><author><name sortKey="Clements, D" uniqKey="Clements D">D. Clements</name></author><author><name sortKey="Coraor, N" uniqKey="Coraor N">N. Coraor</name></author><author><name sortKey="Gruning, B A" uniqKey="Gruning B">B.A. Gruning</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Russie</li></country></list><tree><noCountry><name sortKey="Panyukov, Valery V" sort="Panyukov, Valery V" uniqKey="Panyukov V" first="Valery V." last="Panyukov">Valery V. Panyukov</name></noCountry><country name="Russie"><noRegion><name sortKey="Kiselev, Sergey S" sort="Kiselev, Sergey S" uniqKey="Kiselev S" first="Sergey S." last="Kiselev">Sergey S. Kiselev</name></noRegion><name sortKey="Ozoline, Olga N" sort="Ozoline, Olga N" uniqKey="Ozoline O" first="Olga N." last="Ozoline">Olga N. Ozoline</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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