Genome-Based Taxonomic Classification of Bacteroidetes
Abstract
The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to valuesmore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1421999
- Alternate Identifier(s):
- OSTI ID: 1378745
- Grant/Contract Number:
- AC02-05CH11231; 22016812
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Name: Frontiers in Microbiology Journal Volume: 7; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Media SA
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; G+C content; genome BLAST distance phylogeny; gliding motility; gut microbiome; marine microbiology; one thousand microbial genomes project; phylogenetic classification; Bacteroidaeota-Rhodothermaeota-Balneolaeota-Chlorobaeota superphylum
Citation Formats
Hahnke, Richard L., Meier-Kolthoff, Jan P., García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N., Woyke, Tanja, Kyrpides, Nikos C., Klenk, Hans-Peter, and Göker, Markus. Genome-Based Taxonomic Classification of Bacteroidetes. Switzerland: N. p., 2016.
Web. doi:10.3389/fmicb.2016.02003.
Hahnke, Richard L., Meier-Kolthoff, Jan P., García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N., Woyke, Tanja, Kyrpides, Nikos C., Klenk, Hans-Peter, & Göker, Markus. Genome-Based Taxonomic Classification of Bacteroidetes. Switzerland. https://doi.org/10.3389/fmicb.2016.02003
Hahnke, Richard L., Meier-Kolthoff, Jan P., García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N., Woyke, Tanja, Kyrpides, Nikos C., Klenk, Hans-Peter, and Göker, Markus. Tue .
"Genome-Based Taxonomic Classification of Bacteroidetes". Switzerland. https://doi.org/10.3389/fmicb.2016.02003.
@article{osti_1421999,
title = {Genome-Based Taxonomic Classification of Bacteroidetes},
author = {Hahnke, Richard L. and Meier-Kolthoff, Jan P. and García-López, Marina and Mukherjee, Supratim and Huntemann, Marcel and Ivanova, Natalia N. and Woyke, Tanja and Kyrpides, Nikos C. and Klenk, Hans-Peter and Göker, Markus},
abstractNote = {The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.},
doi = {10.3389/fmicb.2016.02003},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {Switzerland},
year = {Tue Dec 20 00:00:00 EST 2016},
month = {Tue Dec 20 00:00:00 EST 2016}
}
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https://doi.org/10.3389/fmicb.2016.02003
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Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea
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Porphyromonas somerae sp. nov., a Pathogen Isolated from Humans and Distinct from Porphyromonas levii
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Rhodothermus profundi sp. nov., a thermophilic bacterium isolated from a deep-sea hydrothermal vent in the Pacific Ocean
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Muricauda lutaonensis sp. nov., a moderate thermophile isolated from a coastal hot spring
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Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus
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Chryseobacterium defluvii sp. nov., isolated from wastewater
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Rubrivirga marina gen. nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater
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Bacteroides propionicifaciens sp. nov., isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms
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Carboxylicivirga gen. nov. in the family Marinilabiliaceae with two novel species, Carboxylicivirga mesophila sp. nov. and Carboxylicivirga taeanensis sp. nov., and reclassification of Cytophaga fermentans as Saccharicrinis fermentans gen. nov., comb. nov.
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Runella zeae sp. nov., a novel Gram-negative bacterium from the stems of surface-sterilized Zea mays
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Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense
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Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea
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Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland
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Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk
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Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton-waste composts for the cultivation of oyster mushroom
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