Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae
Identifieur interne : 000010 ( Pmc/Corpus ); précédent : 000009; suivant : 000011Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae
Auteurs : Ilias Lagkouvardos ; Thomas Weinmaier ; Federico M. Lauro ; Ricardo Cavicchioli ; Thomas Rattei ; Matthias HornSource :
- The ISME Journal [ 1751-7362 ] ; 2013.
Abstract
In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum
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DOI: 10.1038/ismej.2013.142
PubMed: 23949660
PubMed Central: 3869019
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PMC:3869019Le document en format XML
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<author><name sortKey="Lauro, Federico M" sort="Lauro, Federico M" uniqKey="Lauro F" first="Federico M" last="Lauro">Federico M. Lauro</name>
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<author><name sortKey="Rattei, Thomas" sort="Rattei, Thomas" uniqKey="Rattei T" first="Thomas" last="Rattei">Thomas Rattei</name>
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<author><name sortKey="Horn, Matthias" sort="Horn, Matthias" uniqKey="Horn M" first="Matthias" last="Horn">Matthias Horn</name>
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<series><title level="j">The ISME Journal</title>
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<front><div type="abstract" xml:lang="en"><p>In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum <italic>Chlamydiae</italic>
whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the <italic>Chlamydiae</italic>
, including 181 putative families. These <italic>in silico</italic>
findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel <italic>Chlamydiae</italic>
. In our analysis, the <italic>Rhabdochlamydiaceae</italic>
, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated <italic>Parachlamydiaceae</italic>
, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">ISME J</journal-id>
<journal-id journal-id-type="iso-abbrev">ISME J</journal-id>
<journal-title-group><journal-title>The ISME Journal</journal-title>
</journal-title-group>
<issn pub-type="ppub">1751-7362</issn>
<issn pub-type="epub">1751-7370</issn>
<publisher><publisher-name>Nature Publishing Group</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23949660</article-id>
<article-id pub-id-type="pmc">3869019</article-id>
<article-id pub-id-type="pii">ismej2013142</article-id>
<article-id pub-id-type="doi">10.1038/ismej.2013.142</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the <italic>Chlamydiae</italic>
</article-title>
<alt-title alt-title-type="running"><italic>Chlamydiae</italic>
in metagenomic and amplicon data sets</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Lagkouvardos</surname>
<given-names>Ilias</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Weinmaier</surname>
<given-names>Thomas</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lauro</surname>
<given-names>Federico M</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cavicchioli</surname>
<given-names>Ricardo</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rattei</surname>
<given-names>Thomas</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Horn</surname>
<given-names>Matthias</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="caf1">*</xref>
</contrib>
<aff id="aff1"><label>1</label>
<institution>Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna</institution>
, Vienna,<country>Austria</country>
</aff>
<aff id="aff2"><label>2</label>
<institution>Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna</institution>
, Vienna,<country>Austria</country>
</aff>
<aff id="aff3"><label>3</label>
<institution>School of Biotechnology and Biomolecular Sciences, The University of New South Wales</institution>
, Sydney, New South Wales,<country>Australia</country>
</aff>
</contrib-group>
<author-notes><corresp id="caf1"><label>*</label>
<institution>Division of Microbial Ecology, Department of Microbia, University of Vienna</institution>
, Althan Street 14, Vienna 1090, <country>Austria</country>
. E-mail: <email>horn@microbial-ecology.net</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>01</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>15</day>
<month>08</month>
<year>2013</year>
</pub-date>
<volume>8</volume>
<issue>1</issue>
<fpage>115</fpage>
<lpage>125</lpage>
<history><date date-type="received"><day>16</day>
<month>05</month>
<year>2013</year>
</date>
<date date-type="rev-recd"><day>12</day>
<month>07</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>16</day>
<month>07</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 International Society for Microbial Ecology</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>International Society for Microbial Ecology</copyright-holder>
</permissions>
<abstract><p>In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum <italic>Chlamydiae</italic>
whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the <italic>Chlamydiae</italic>
, including 181 putative families. These <italic>in silico</italic>
findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel <italic>Chlamydiae</italic>
. In our analysis, the <italic>Rhabdochlamydiaceae</italic>
, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated <italic>Parachlamydiaceae</italic>
, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.</p>
</abstract>
<kwd-group><kwd>16S rRNA</kwd>
<kwd>next-generation sequencing</kwd>
<kwd>amplicon sequencing</kwd>
<kwd>metagenomics</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
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