Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae
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 th...
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ftpubmed:oai:pubmedcentral.nih.gov:3869019 2023-05-15T13:44:24+02:00 Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae Lagkouvardos, Ilias Weinmaier, Thomas Lauro, Federico M Cavicchioli, Ricardo Rattei, Thomas Horn, Matthias 2014-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869019 http://www.ncbi.nlm.nih.gov/pubmed/23949660 https://doi.org/10.1038/ismej.2013.142 en eng Nature Publishing Group http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/23949660 http://dx.doi.org/10.1038/ismej.2013.142 Copyright © 2014 International Society for Microbial Ecology Original Article Text 2014 ftpubmed https://doi.org/10.1038/ismej.2013.142 2015-01-04T00:55:31Z 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 Chlamydiae 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 Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, 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. Text Antarc* Antarctic PubMed Central (PMC) Antarctic The ISME Journal 8 1 115 125 |
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Original Article Lagkouvardos, Ilias Weinmaier, Thomas Lauro, Federico M Cavicchioli, Ricardo Rattei, Thomas Horn, Matthias Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae |
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Original Article |
description |
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 Chlamydiae 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 Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, 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. |
format |
Text |
author |
Lagkouvardos, Ilias Weinmaier, Thomas Lauro, Federico M Cavicchioli, Ricardo Rattei, Thomas Horn, Matthias |
author_facet |
Lagkouvardos, Ilias Weinmaier, Thomas Lauro, Federico M Cavicchioli, Ricardo Rattei, Thomas Horn, Matthias |
author_sort |
Lagkouvardos, Ilias |
title |
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae |
title_short |
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae |
title_full |
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae |
title_fullStr |
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae |
title_full_unstemmed |
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae |
title_sort |
integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the chlamydiae |
publisher |
Nature Publishing Group |
publishDate |
2014 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869019 http://www.ncbi.nlm.nih.gov/pubmed/23949660 https://doi.org/10.1038/ismej.2013.142 |
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Antarctic |
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Antarctic |
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Antarc* Antarctic |
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Antarc* Antarctic |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/23949660 http://dx.doi.org/10.1038/ismej.2013.142 |
op_rights |
Copyright © 2014 International Society for Microbial Ecology |
op_doi |
https://doi.org/10.1038/ismej.2013.142 |
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The ISME Journal |
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