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dc.contributor.authorWaite, David W.  Concept link
dc.contributor.authorVanwonterghem, Inka  Concept link
dc.contributor.authorRinke, Christian  Concept link
dc.contributor.authorParks, Donovan H.  Concept link
dc.contributor.authorZhang, Ying  Concept link
dc.contributor.authorTakai, Ken  Concept link
dc.contributor.authorSievert, Stefan M.  Concept link
dc.contributor.authorSimon, Jörg  Concept link
dc.contributor.authorCampbell, Barbara J.  Concept link
dc.contributor.authorHanson, Thomas E.  Concept link
dc.contributor.authorWoyke, Tanja  Concept link
dc.contributor.authorKlotz, Martin G.  Concept link
dc.contributor.authorHugenholtz, Philip  Concept link
dc.date.accessioned2017-06-01T18:30:24Z
dc.date.available2017-06-01T18:30:24Z
dc.date.issued2017-04-24
dc.identifier.citationFrontiers in Microbiology 8 (2017): 682en_US
dc.identifier.urihttps://hdl.handle.net/1912/9010
dc.description© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.en_US
dc.description.abstractThe Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.en_US
dc.description.sponsorshipThe study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.en_US
dc.language.isoen_USen_US
dc.publisherFrontiers Mediaen_US
dc.relation.requireshttps://hdl.handle.net/1912/10324
dc.relation.urihttps://doi.org/10.3389/fmicb.2017.00682
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectEpsilonproteobacteriaen_US
dc.subjectTaxonomyen_US
dc.subjectClassificationen_US
dc.subjectGenomeen_US
dc.subjectPhylogenomicsen_US
dc.subjectEpsilonbacteraeotaen_US
dc.subjectEvolutionen_US
dc.titleComparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)en_US
dc.typeArticleen_US
dc.identifier.doi10.3389/fmicb.2017.00682


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Attribution 4.0 International
Except where otherwise noted, this item's license is described as Attribution 4.0 International