Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics
Identifieur interne : 000213 ( Main/Exploration ); précédent : 000212; suivant : 000214Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics
Auteurs : Gemma L. Kay ; Martin J. Sergeant ; Valentina Giuffra ; Pasquale Bandiera ; Marco Milanese ; Barbara Bramanti ; Raffaella Bianucci ; Mark J. PallenSource :
- mBio [ 2150-7511 ] ; 2014.
Abstract
Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a
Url:
DOI: 10.1128/mBio.01337-14
PubMed: 25028426
PubMed Central: 4161259
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Recovery of a Medieval <italic>Brucella melitensis</italic> Genome Using Shotgun Metagenomics</title><author><name sortKey="Kay, Gemma L" sort="Kay, Gemma L" uniqKey="Kay G" first="Gemma L." last="Kay">Gemma L. Kay</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sergeant, Martin J" sort="Sergeant, Martin J" uniqKey="Sergeant M" first="Martin J." last="Sergeant">Martin J. Sergeant</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Giuffra, Valentina" sort="Giuffra, Valentina" uniqKey="Giuffra V" first="Valentina" last="Giuffra">Valentina Giuffra</name></author><author><name sortKey="Bandiera, Pasquale" sort="Bandiera, Pasquale" uniqKey="Bandiera P" first="Pasquale" last="Bandiera">Pasquale Bandiera</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Milanese, Marco" sort="Milanese, Marco" uniqKey="Milanese M" first="Marco" last="Milanese">Marco Milanese</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Bramanti, Barbara" sort="Bramanti, Barbara" uniqKey="Bramanti B" first="Barbara" last="Bramanti">Barbara Bramanti</name><affiliation><nlm:aff id="aff5"></nlm:aff></affiliation></author><author><name sortKey="Bianucci, Raffaella" sort="Bianucci, Raffaella" uniqKey="Bianucci R" first="Raffaella" last="Bianucci">Raffaella Bianucci</name></author><author><name sortKey="Pallen, Mark J" sort="Pallen, Mark J" uniqKey="Pallen M" first="Mark J." last="Pallen">Mark J. Pallen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25028426</idno><idno type="pmc">4161259</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161259</idno><idno type="RBID">PMC:4161259</idno><idno type="doi">10.1128/mBio.01337-14</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000400</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000400</idno><idno type="wicri:Area/Pmc/Curation">000400</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000400</idno><idno type="wicri:Area/Pmc/Checkpoint">000080</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000080</idno><idno type="wicri:Area/Ncbi/Merge">000D61</idno><idno type="wicri:Area/Ncbi/Curation">000D61</idno><idno type="wicri:Area/Ncbi/Checkpoint">000D61</idno><idno type="wicri:Area/Main/Merge">000214</idno><idno type="wicri:Area/Main/Curation">000213</idno><idno type="wicri:Area/Main/Exploration">000213</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Recovery of a Medieval <italic>Brucella melitensis</italic> Genome Using Shotgun Metagenomics</title><author><name sortKey="Kay, Gemma L" sort="Kay, Gemma L" uniqKey="Kay G" first="Gemma L." last="Kay">Gemma L. Kay</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sergeant, Martin J" sort="Sergeant, Martin J" uniqKey="Sergeant M" first="Martin J." last="Sergeant">Martin J. Sergeant</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Giuffra, Valentina" sort="Giuffra, Valentina" uniqKey="Giuffra V" first="Valentina" last="Giuffra">Valentina Giuffra</name></author><author><name sortKey="Bandiera, Pasquale" sort="Bandiera, Pasquale" uniqKey="Bandiera P" first="Pasquale" last="Bandiera">Pasquale Bandiera</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Milanese, Marco" sort="Milanese, Marco" uniqKey="Milanese M" first="Marco" last="Milanese">Marco Milanese</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Bramanti, Barbara" sort="Bramanti, Barbara" uniqKey="Bramanti B" first="Barbara" last="Bramanti">Barbara Bramanti</name><affiliation><nlm:aff id="aff5"></nlm:aff></affiliation></author><author><name sortKey="Bianucci, Raffaella" sort="Bianucci, Raffaella" uniqKey="Bianucci R" first="Raffaella" last="Bianucci">Raffaella Bianucci</name></author><author><name sortKey="Pallen, Mark J" sort="Pallen, Mark J" uniqKey="Pallen M" first="Mark J." last="Pallen">Mark J. Pallen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a <italic>Brucella melitensis</italic> genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of <italic>B. melitensis</italic> strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS<italic>711</italic> insertions. 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Perna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Handsaker, B" uniqKey="Handsaker B">B Handsaker</name></author><author><name sortKey="Wysoker, A" uniqKey="Wysoker A">A Wysoker</name></author><author><name sortKey="Fennell, T" uniqKey="Fennell T">T Fennell</name></author><author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name></author><author><name sortKey="Homer, N" uniqKey="Homer N">N Homer</name></author><author><name sortKey="Marth, G" uniqKey="Marth G">G Marth</name></author><author><name sortKey="Abecasis, G" uniqKey="Abecasis G">G Abecasis</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Bandiera, Pasquale" sort="Bandiera, Pasquale" uniqKey="Bandiera P" first="Pasquale" last="Bandiera">Pasquale Bandiera</name><name sortKey="Bianucci, Raffaella" sort="Bianucci, Raffaella" uniqKey="Bianucci R" first="Raffaella" last="Bianucci">Raffaella Bianucci</name><name sortKey="Bramanti, Barbara" sort="Bramanti, Barbara" uniqKey="Bramanti B" first="Barbara" last="Bramanti">Barbara Bramanti</name><name sortKey="Giuffra, Valentina" sort="Giuffra, Valentina" uniqKey="Giuffra V" first="Valentina" last="Giuffra">Valentina Giuffra</name><name sortKey="Kay, Gemma L" sort="Kay, Gemma L" uniqKey="Kay G" first="Gemma L." last="Kay">Gemma L. Kay</name><name sortKey="Milanese, Marco" sort="Milanese, Marco" uniqKey="Milanese M" first="Marco" last="Milanese">Marco Milanese</name><name sortKey="Pallen, Mark J" sort="Pallen, Mark J" uniqKey="Pallen M" first="Mark J." last="Pallen">Mark J. Pallen</name><name sortKey="Sergeant, Martin J" sort="Sergeant, Martin J" uniqKey="Sergeant M" first="Martin J." last="Sergeant">Martin J. Sergeant</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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