Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling.
Identifieur interne : 000253 ( PubMed/Corpus ); précédent : 000252; suivant : 000254Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling.
Auteurs : Valery V. Panyukov ; Sergey S. Kiselev ; Olga N. OzolineSource :
- 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 k-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 k-mers to distinguish eight phylogroups of Escherichia coli (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 E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.
DOI: 10.3390/ijms21030944
PubMed: 32023871
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Unique <i>k</i>-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:affiliation>Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia.</nlm:affiliation></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:affiliation>Structural and Functional Genomics Group, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia.</nlm:affiliation></affiliation></author><author><name sortKey="Ozoline, Olga N" sort="Ozoline, Olga N" uniqKey="Ozoline O" first="Olga N" last="Ozoline">Olga N. 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Panyukov</name><affiliation><nlm:affiliation>Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia.</nlm:affiliation></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:affiliation>Structural and Functional Genomics Group, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia.</nlm:affiliation></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:affiliation>Structural and Functional Genomics Group, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia.</nlm:affiliation></affiliation></author></analytic><series><title level="j">International journal of molecular sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 <i>k</i>-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 <i>k</i>-mers to distinguish eight phylogroups of <i>Escherichia coli</i> (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 <i>E. coli</i> in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32023871</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>3</Issue><PubDate><Year>2020</Year><Month>Jan</Month><Day>31</Day></PubDate></JournalIssue><Title>International journal of molecular sciences</Title><ISOAbbreviation>Int J Mol Sci</ISOAbbreviation></Journal><ArticleTitle>Unique <i>k</i>-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E944</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms21030944</ELocationID><Abstract><AbstractText>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 <i>k</i>-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 <i>k</i>-mers to distinguish eight phylogroups of <i>Escherichia coli</i> (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 <i>E. coli</i> in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Panyukov</LastName><ForeName>Valery V</ForeName><Initials>VV</Initials><AffiliationInfo><Affiliation>Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Structural and Functional Genomics Group, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kiselev</LastName><ForeName>Sergey S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Structural and Functional Genomics Group, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ozoline</LastName><ForeName>Olga N</ForeName><Initials>ON</Initials><AffiliationInfo><Affiliation>Structural and Functional Genomics Group, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>18-14-00348</GrantID><Agency>Russian Science 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| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |