55284 |
Notification of changes in taxonomic opinion previously published outside the IJSEM. Int. J. Syst. Evol. Microbiol. (2017) 67:2081-2086.
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48660 |
Hahnke RL,
Meier-Kolthoff JP,
García-López M,
Mukherjee S,
Huntemann M,
Ivanova NN,
Woyke T,
Kyrpides NC,
Klenk HP,
Göker M,
( 2016 )
Genome-Based Taxonomic Classification of Bacteroidetes.
Frontiers in microbiology 7 (N/A)
PMID : 28066339
DOI : 10.3389/fmicb.2016.02003
PMC : PMC5167729
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 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.
Keyword | MeSH Terms |
Bacteroidaeota-Rhodothermaeota-Balneolaeota-Chlorobaeota superphylum
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
G+C content
genome BLAST distance phylogeny
gliding motility
gut microbiome
marine microbiology
one thousand microbial genomes project
phylogenetic classification
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15228 |
Weon HY,
Kim BY,
Kwon SW,
Park IC,
Cha IB,
Tindall BJ,
Stackebrandt E,
Trüper HG,
Go SJ,
( 2005 )
Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton-waste composts for the cultivation of oyster mushroom.
International journal of systematic and evolutionary microbiology 55 (Pt 6)
PMID : 16280486
DOI : 10.1099/ijs.0.63741-0
Abstract >>
A bacterial strain, designated 4M15T, was isolated from cotton-waste composts used as mushroom cultivation in South Korea. Properties of this isolate were studied on the basis of physiological and biochemical characteristics, fatty acid profile, isoprenoid quinone, DNA G+C content and phylogenetic position based on 16S rRNA gene sequence analysis. The strain was found to form a distinct phylogenetic lineage related to the family 'Flexibacteraceae' within the phylum 'Bacteroidetes'. No recognized species showed >85 % 16S rRNA gene sequence similarity to strain 4M15T. The fatty acid profile of strain 4M15(T) included C(16 : 1)omega7c/iso-C(15 : 0) 2-OH (30.5 %), iso-C(15 : 0) (24.2 %), iso-C(15 : 0) 2-OH/C(16 : 1)omega7c (15.9), iso-C(17 : 0) 3-OH (10.5 %) and C(16 : 0) (5.6 %). The major isoprenoid quinone was menaquinone MK-7. The DNA G+C content was 33.0 mol%. Cells were Gram-negative, strictly aerobic, rod-shaped, non-motile, catalase-positive, oxidase-positive and flexirubin-positive. The strain hydrolysed aesculin, gelatin, starch and tyrosine. Several phenotypic tests could be used to differentiate strain 4M15T from other members of the family 'Flexibacteraceae'. On the basis of the data presented, strain 4M15T should be assigned to the phylum 'Bacteroidetes' as a novel genus and species, for which the name Leadbetterella byssophila gen. nov., sp. nov. is proposed. The type strain is 4M15T (=KACC 11308T=DSM 17132T).
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