Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both ofmore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1564534
- Alternate Identifier(s):
- OSTI ID: 1580865
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Name: Frontiers in Microbiology Journal Volume: 10; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Media SA
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; G+C content; genome size; genome BLAST distance phylogeny; chemotaxonomy; morphology; phylogenetic systematics; phylogenomics
Citation Formats
García-López, Marina, Meier-Kolthoff, Jan P., Tindall, Brian J., Gronow, Sabine, Woyke, Tanja, Kyrpides, Nikos C., Hahnke, Richard L., and Göker, Markus. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Switzerland: N. p., 2019.
Web. doi:10.3389/fmicb.2019.02083.
García-López, Marina, Meier-Kolthoff, Jan P., Tindall, Brian J., Gronow, Sabine, Woyke, Tanja, Kyrpides, Nikos C., Hahnke, Richard L., & Göker, Markus. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Switzerland. https://doi.org/10.3389/fmicb.2019.02083
García-López, Marina, Meier-Kolthoff, Jan P., Tindall, Brian J., Gronow, Sabine, Woyke, Tanja, Kyrpides, Nikos C., Hahnke, Richard L., and Göker, Markus. Mon .
"Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes". Switzerland. https://doi.org/10.3389/fmicb.2019.02083.
@article{osti_1564534,
title = {Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes},
author = {García-López, Marina and Meier-Kolthoff, Jan P. and Tindall, Brian J. and Gronow, Sabine and Woyke, Tanja and Kyrpides, Nikos C. and Hahnke, Richard L. and Göker, Markus},
abstractNote = {Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.},
doi = {10.3389/fmicb.2019.02083},
journal = {Frontiers in Microbiology},
number = ,
volume = 10,
place = {Switzerland},
year = {Mon Sep 23 00:00:00 EDT 2019},
month = {Mon Sep 23 00:00:00 EDT 2019}
}
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https://doi.org/10.3389/fmicb.2019.02083
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Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil
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Parapedobacter koreensis gen. nov., sp. nov.
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Moheibacter sediminis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from sediment, and emended descriptions of Empedobacter brevis, Wautersiella falsenii and Weeksella virosa
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Pedobacter luteus sp. nov., isolated from soil
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Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter
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Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil
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Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea
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Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana
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Muricauda olearia sp. nov., isolated from crude-oil-contaminated seawater, and emended description of the genus Muricauda
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Bacteroides luti sp. nov., an anaerobic, cellulolytic and xylanolytic bacterium isolated from methanogenic sludge
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Tenacibaculum jejuense sp. nov., isolated from coastal seawater
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Pibocella ponti gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi
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Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family 'Porphyromonadaceae' isolated from rat faeces
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Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats.
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Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter
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Fabibacter pacificus sp. nov., a moderately halophilic bacterium isolated from seawater
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Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm
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Chryseobacterium aahli sp. nov., isolated from lake trout (Salvelinus namaycush) and brown trout (Salmo trutta), and emended descriptions of Chryseobacterium ginsenosidimutans and Chryseobacterium gregarium
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Hymenobacter sedentarius sp. nov., isolated from a soil
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Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum
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1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
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Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss)
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Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent
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Flavobacterium cloacae sp. nov., isolated from waste water
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Prosthecobacter fusiformis gen. and sp. nov., nom. rev.
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Dyadobacter tibetensis sp. nov., isolated from glacial ice core
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Spongiibacterium flavum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine sponge Halichondria oshoro, and emended descriptions of the genera Croceitalea and Flagellimonas
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Oceanihabitans sediminis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Yellow Sea
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Flavisolibacter tropicus sp. nov., isolated from tropical soil
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Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment
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Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium
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Maribacter aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Maribacter
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Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003
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Verrucomicrobium spinosum gen. nov., sp. nov.: a Fimbriated Prosthecate Bacterium
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Cyclobacterium sediminis sp. nov. isolated from a sea cucumber aquaculture farm and emended description of the genus Cyclobacterium
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Pedobacter nutrimenti sp. nov., isolated from chilled food
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Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet
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Myroides marinus sp. nov., a member of the family Flavobacteriaceae, isolated from seawater
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Marinoscillum gen. nov., a member of the family 'Flexibacteraceae', with Marinoscillum pacificum sp. nov. from a marine sponge and Marinoscillum furvescens nom. rev., comb. nov.
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Myroides phaeus sp. nov., isolated from human saliva, and emended descriptions of the genus Myroides and the species Myroides profundi Zhang et al. 2009 and Myroides marinus Cho et al. 2011
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Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.
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Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants
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Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp
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Algibacter agarivorans sp. nov. and Algibacter agarilyticus sp. nov., isolated from seawater, reclassification of Marinivirga aestuarii as Algibacter aestuarii comb. nov. and emended description of the genus Algibacter
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Dysgonomonas hofstadii sp. nov., isolated from a human clinical source
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Hanstruepera neustonica gen. nov., sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from estuarine water, and emendation of Sediminibacter furfurosus Khan et al. 2007 emend. Kwon et al. 2014, Mangrovimonas yunxiaonensis Li et al. 2013, Antarcticimonas flava Yang et al. 2009 and Hoppeia youngheungensis Kwon et al. 2014
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Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris)
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Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana
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Reichenbachiella faecimaris sp. nov., isolated from a tidal flat, and emended descriptions of the genus Reichenbachiella and Reichenbachiella agariperforans
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Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum
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Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete
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Deinococcus phoenicis sp. nov., an extreme ionizing-radiation-resistant bacterium isolated from the Phoenix Lander assembly facility
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Halotolerant Thermus Strains from Marine and Terrestrial Hot Springs Belong to Thermus thermophilus (ex Oshima and Imahori, 1974) nom. rev. emend.
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Maripseudobacter aurantiacus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a sedimentation basin
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Transfer of Bacteroides splanchnicus to Odoribacter gen. nov. as Odoribacter splanchnicus comb. nov., and description of Odoribacter denticanis sp. nov., isolated from the crevicular spaces of canine periodontitis patients
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Diversity of Capnocytophaga species in children and description of Capnocytophaga leadbetteri sp. nov. and Capnocytophaga genospecies AHN8471
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Mucilaginibacter polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Mucilaginibacter
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Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov.
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Algoriphagus aquaeductus sp. nov., isolated from a freshwater pipe
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Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish
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Pseudarcicella hirudinis gen. nov., sp. nov., isolated from the skin of the medical leech Hirudo medicinalis
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Paludibacter propionicigenes gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil in Japan
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Algibacter mikhailovii sp. nov., a novel marine bacterium of the family Flavobacteriaceae, and emended description of the genus Algibacter
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Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae
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Parasegetibacter terrae sp. nov., isolated from paddy soil and emended description of the genus Parasegetibacter
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Olleya marilimosa gen. nov., sp. nov., an exopolysaccharide-producing marine bacterium from the family Flavobacteriaceae, isolated from the Southern Ocean
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Deinococcus mumbaiensis Shashidhar and Bandekar 2006 is a later heterotypic synonym of Deinococcus ficus Lai et al. 2006
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Schleiferia thermophila gen. nov., sp. nov., a slightly thermophilic bacterium of the phylum 'Bacteroidetes' and the proposal of Schleiferiaceae fam. nov.
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Lutibacter agarilyticus sp. nov., a marine bacterium isolated from shallow coastal seawater
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Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.
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Lacinutrix cladophorae sp. nov., a flavobacterium isolated from the green alga Cladophora stimpsonii, transfer of Flavirhabdus iliipiscaria Shakeela et al. 2015 to the genus Lacinutrix as Lacinutrix iliipiscaria comb. nov. and emended description of the genus Lacinutrix
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Soonwooa purpurea sp. nov., isolated from a fresh water river
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- Sirra, Mercy Rose Stella; Padakandla, Shalem Raj; Chae, Jong-Chan
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Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil
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Anaerophaga thermohalophila gen. nov., sp. nov., a moderately thermohalophilic, strictly anaerobic fermentative bacterium.
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Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus)
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Aequorivita capsosiphonis sp. nov., isolated from the green alga Capsosiphon fulvescens, and emended description of the genus Aequorivita
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Heliimonas saccharivorans gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a mineral water aquifer, and emended description of Filimonas lacunae
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Diversity and functional analysis of proteorhodopsin in marine Flavobacteria: Diversity and functional analysis of proteorhodopsin
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Mucilaginibacter auburnensis sp. nov., isolated from a plant stem
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Roseimaritima ulvae gen. nov., sp. nov. and Rubripirellula obstinata gen. nov., sp. nov. two novel planctomycetes isolated from the epiphytic community of macroalgae
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Pontibacter virosus sp. nov., isolated from a hexachlorocyclohexane-contaminated dumpsite
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Planobacterium taklimakanense gen. nov., sp. nov., a member of the family Flavobacteriaceae that exhibits swimming motility, isolated from desert soil
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Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium
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Novel Features of the Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as Revealed by Genome Sequence Analysis
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Description of Fabibacter halotolerans gen. nov., sp. nov. and Roseivirga spongicola sp. nov., and reclassification of [Marinicola] seohaensis as Roseivirga seohaensis comb. nov.
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Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater
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Mucilaginibacter frigoritolerans sp. nov., Mucilaginibacter lappiensis sp. nov. and Mucilaginibacter mallensis sp. nov., isolated from soil and lichen samples
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Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean
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Asinibacterium lactis gen. nov., sp. nov., a member of the family Chitinophagaceae, isolated from donkey (Equus asinus) milk
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Zunongwangia mangrovi sp. nov., isolated from mangrove (Avicennia marina) rhizosphere, and emended description of the genus Zunongwangia
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Confluentibacter citreus sp. nov., isolated from lake sediment, and emended description of the genus Confluentibacter
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Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer
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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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Mucilaginibacter gossypii sp. nov. and Mucilaginibacter gossypiicola sp. nov., plant-growth-promoting bacteria isolated from cotton rhizosphere soils
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Bizionia echini sp. nov., isolated from a sea urchin
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Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum
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Meiothermus rufus sp. nov., a new slightly thermophilic red-pigmented species and emended description of the genus Meiothermus
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Prevotella falsenii sp. nov., a Prevotella intermedia-like organism isolated from monkey dental plaque
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Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium
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Elizabethkingia endophytica sp. nov., isolated from Zea mays and emended description of Elizabethkingia anophelis Kämpfer et al. 2011
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Bizionia arctica sp. nov., isolated from Arctic fjord seawater, and emended description of the genus Bizionia
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Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov.
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Chryseobacterium arachidiradicis sp. nov., isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea)
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Bacteroides xylanolyticus sp. nov., a xylanolytic bacterium from methane producing cattle manure
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Flavirhabdus iliipiscaria gen. nov., sp. nov., isolated from intestine of flounder (Paralichthys olivaceus) and emended descriptions of the genera Flavivirga, Algibacter, Bizionia and Formosa
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Maribacter spongiicola sp. nov. and Maribacter vaceletii sp. nov., isolated from marine sponges, and emended description of the genus Maribacter
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Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena
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Williamwhitmania taraxaci gen. nov., sp. nov., a proteolytic anaerobe with a novel type of cytology from Lake Untersee in Antarctica, description of Williamwhitmaniaceae fam. nov., and emendation of the order Bacteroidales Krieg 2012
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Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans
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Maribacter thermophilus sp. nov., isolated from an algal bloom in an intertidal zone, and emended description of the genus Maribacter
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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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Sunxiuqinia elliptica gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment in a sea cucumber farm
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Thermus igniterrae sp. nov. and Thermus antranikianii sp. nov., two new species from Iceland
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Psychroserpens mesophilus sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae isolated from a young biofilm
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Psychroserpens damuponensis sp. nov., isolated from seawater
journal, April 2012
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota
journal, August 2016
- Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte
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Deinococcus aquatilis sp. nov., isolated from water
journal, December 2008
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 12
Aquimarina amphilecti sp. nov., isolated from the sponge Amphilectus fucorum
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
Alkalitalea saponilacus gen. nov., sp. nov., an obligately anaerobic, alkaliphilic, xylanolytic bacterium from a meromictic soda lake
journal, December 2011
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 11
Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil
journal, August 2012
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 5
Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces
journal, May 2010
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 4
Lacinutrix jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment and emended description of the genus Lacinutrix
journal, July 2014
- Lee, Yung Mi; Hwang, Chung Yeon; Lee, Inae
- Antonie van Leeuwenhoek, Vol. 106, Issue 3
Arcicella rigui sp. nov., isolated from water of a wetland, and emended descriptions of the genus Arcicella, Arcicella aquatica, Arcicella rosea and Arcicella aurantiaca
journal, February 2012
- Chen, W. -M.; Yang, S. -H.; Young, C. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 1
Base composition bias might result from competition for metabolic resources
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- Rocha, Eduardo P. C.; Danchin, Antoine
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Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 4
Rhodopirellula lusitana sp. nov. and Rhodopirellula rubra sp. nov., isolated from the surface of macroalgae
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- Systematic and Applied Microbiology, Vol. 37, Issue 3
Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences
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Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., New Species from Abscesses and Feces of Pigs
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- Benno, Yoshimi; Watabe, Junko; Mitsuoka, Tomotari
- Systematic and Applied Microbiology, Vol. 4, Issue 3
Flavobacterium croceum sp. nov., isolated from activated sludge
journal, October 2006
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 10
Deinococcus puniceus sp. nov., a Bacterium Isolated from Soil-Irradiated Gamma Radiation
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- Lee, Jae-Jin; Srinivasan, Sathiyaraj; Lim, Sangyong
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Bacterial genomic G+C composition-eliciting environmental adaptation
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- Mann, Scott; Chen, Yi-Ping Phoebe
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Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces
journal, December 2008
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 12
Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces
journal, June 2013
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 11
Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland
journal, April 2014
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 7
Bizionia psychrotolerans sp. nov., a psychrophilic bacterium isolated from the intestine of a sea cucumber (Apostichopus japonicus)
journal, August 2014
- Song, Eun-Ji; Lee, Mi-Hwa; Seo, Myung-Ji
- Antonie van Leeuwenhoek, Vol. 106, Issue 4
Analysis of the 16S rRNA gene of microorganism WSU 86-1044 from an aborted bovine foetus reveals that it is a member of the order Chlamydiales: proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov.
journal, April 1999
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- International Journal of Systematic Bacteriology, Vol. 49, Issue 2
Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog
journal, October 2007
- Pankratov, T. A.; Tindall, B. J.; Liesack, W.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 10
Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca
journal, August 2015
- Koblížek, Michal; Kaftan, David; Lukeš, Martin
- International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 8
Porphyromonas crevioricanis is an earlier heterotypic synonym of Porphyromonas cansulci and has priority
journal, March 2012
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
Bacteroides acidifaciens sp. nov., isolated from the caecum of mice
journal, January 2000
- Miyamoto, Y.; Itoh, K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 1
Croceivirga radicis gen. nov., sp. nov., isolated from a rotten tropical mangrove root
journal, October 2017
- Hu, Dong; Wang, Liping; Chen, Yanwu
- International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 10
Marinifilum fragile gen. nov., sp. nov., isolated from tidal flat sediment
journal, July 2009
- Na, H.; Kim, S.; Moon, E. Y.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 9
Croceitalea marina sp. nov., isolated from marine particles of Yellow Sea, and emended description of the genera Croceitalea
journal, October 2017
- Su, Ying; Yu, Min; Ren, Qiaomeng
- International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 10
Lishizhenia tianjinensis sp. nov., isolated from coastal seawater
journal, July 2009
- Chen, L. -P.; Xu, H. -Y.; Fu, S. -Z.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 10
Sediminitomix flava gen. nov., sp. nov., of the phylum Bacteroidetes, isolated from marine sediment
journal, August 2007
- Khan, S. T.; Nakagawa, Y.; Harayama, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 8
Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat
journal, April 2012
- Jeong, S. H.; Jin, H. M.; Kim, J. M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
Dysgonomonas gen. nov. to accommodate Dysgonomonas gadei sp. nov., an organism isolated from a human gall bladder, and Dysgonomonas capnocytophagoides (formerly CDC group DF-3)
journal, November 2000
- Hofstad, T.; Olsen, I.; Eribe, E. R.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 6
Polaribacter sejongensis sp. nov., isolated from Antarctic soil, and emended descriptions of the genus Polaribacter, Polaribacter butkevichii and Polaribacter irgensii
journal, May 2013
- Kim, B. -C.; Oh, H. W.; Kim, H.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 11
Lutibacter flavus sp. nov., a marine bacterium isolated from a tidal flat sediment
journal, June 2012
- Choi, A.; Yang, S. -J.; Cho, J. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 3
Thermophagus xiamenensis gen. nov., sp. nov., a moderately thermophilic and strictly anaerobic bacterium isolated from hot spring sediment
journal, February 2012
- Gao, Z. -M.; Liu, X.; Zhang, X. -Y.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 1
Emendation of the family Chlamydiaceae: Proposal of a single genus, Chlamydia, to include all currently recognized species
journal, March 2015
- Sachse, Konrad; Bavoil, Patrik M.; Kaltenboeck, Bernhard
- Systematic and Applied Microbiology, Vol. 38, Issue 2
Bizionia argentinensis sp. nov., isolated from surface marine water in Antarctica
journal, October 2008
- Bercovich, A.; Vazquez, S. C.; Yankilevich, P.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 10
Gillisia mitskevichiae sp. nov., a novel bacterium of the family Flavobacteriaceae, isolated from sea water
journal, January 2005
- Nedashkovskaya, O. I.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 1
Phenotypic Diversity among Ruminal Isolates of Prevotella ruminicola: Proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and Redefinition of Prevotella ruminicola
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- International Journal of Systematic Bacteriology, Vol. 47, Issue 2
Algibacter lectus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from green algae
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- Nedashkovskaya, O. I.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 4
Bacteroides faecis sp. nov., isolated from human faeces
journal, December 2009
- Kim, M. -S.; Roh, S. W.; Bae, J. -W.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 11
Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water
journal, June 2012
- Albert, R. A.; Waas, N. E.; Pavlons, S. C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 3
A Classification of Flexibacteria
journal, October 1969
- Lewin, R. A.
- Journal of General Microbiology, Vol. 58, Issue 2
Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov.
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- Gosink, J. J.; Woese, C. R.; Staley, J. T.
- International Journal of Systematic Bacteriology, Vol. 48, Issue 1
Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces
journal, July 2011
- Kitahara, M.; Sakamoto, M.; Tsuchida, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 5
Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class 'Spartobacteria' in the phylum Verrucomicrobia, isolated from a rice paddy field
journal, February 2014
- Qiu, Y. -L.; Kuang, X. -z.; Shi, X. -s.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5
Gelidibacter sediminis sp. nov., isolated from a sediment sample of the Yellow Sea
journal, July 2015
- Margesin, Rosa; Zhang, De-Chao
- International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 7
Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants
journal, February 2006
- Park, M. S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 2
Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.
journal, January 2014
- Gerritsen, J.; Fuentes, S.; Grievink, W.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5
Chryseobacterium culicis sp. nov., isolated from the midgut of the mosquito Culex quinquefasciatus
journal, November 2009
- Kampfer, P.; Chandel, K.; Prasad, G. B. K. S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 10
Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000
journal, May 2005
- Reddy, G. S. N.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 3
Dokdonia pacifica sp. nov., isolated from seawater
journal, July 2015
- Gao, Xin; Zhang, Zenghu; Zhang, Xiao-Hua
- International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 7
Description of Croceitalea gen. nov. in the family Flavobacteriaceae with two species, Croceitalea eckloniae sp. nov. and Croceitalea dokdonensis sp. nov., isolated from the rhizosphere of the marine alga Ecklonia kurome
journal, November 2008
- Lee, H. -S.; Kwon, K. K.; Yang, S. -H.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 11
Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont
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- McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A.
- PLoS Genetics, Vol. 5, Issue 7
Bacterial Gliding Motility: Rolling Out a Consensus Model
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- Nan, Beiyan
- Current Biology, Vol. 27, Issue 4
Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004
journal, September 2004
- Nedashkovskaya, O. I.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 5
Evidence, Content and Corroboration and the Tree of Life
journal, November 2008
- Kurt Lienau, E.; DeSalle, Rob
- Acta Biotheoretica, Vol. 57, Issue 1-2
Roseivirga ehrenbergii gen. nov., sp. nov., a novel marine bacterium of the phylum 'Bacteroidetes', isolated from the green alga Ulva fenestrata
journal, January 2005
- Nedashkovskaya, O. I.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 1
Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum
journal, March 2016
- Hahnke, Sarah; Langer, Thomas; Koeck, Daniela E.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 3
Cloacibacterium normanense gen. nov., sp. nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater
journal, June 2006
- Allen, T. D.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 6
Spongiibacterium pacificum sp. nov., isolated from seawater of South Pacific Gyre and emended description of the genus Spongiibacterium
journal, October 2014
- Gao, X.; Zhang, Z.; Dai, X.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 65, Issue Pt 1
Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water
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- Shiratori, H.; Tagami, Y.; Morishita, T.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 5
Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris)
journal, March 2007
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 3
Environmental and Gut Bacteroidetes: The Food Connection
journal, January 2011
- Thomas, François; Hehemann, Jan-Hendrik; Rebuffet, Etienne
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Marivirga atlantica sp. nov., isolated from seawater and emended description of the genus Marivirga
journal, February 2015
- Lin, C. -Y.; Zhang, X. -Y.; Liu, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 65, Issue Pt 5
Longimonas halophila gen. nov., sp. nov., isolated from a marine solar saltern
journal, July 2015
- Zhao, Li-Hua; Xia, Jun; Chen, Guan-Jun
- International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 7
Pedobacter insulae sp. nov., isolated from soil
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- Yoon, J. -H.; Kang, S. -J.; Oh, H. W.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 9
Robiginitalea myxolifaciens sp. nov., a novel myxol-producing bacterium isolated from marine sediment, and emended description of the genus Robiginitalea
journal, July 2008
- Manh, H. D.; Matsuo, Y.; Katsuta, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 7
Aureibacter tunicatorum gen. nov., sp. nov., a marine bacterium isolated from a coral reef sea squirt, and description of Flammeovirgaceae fam. nov.
journal, October 2010
- Yoon, J.; Adachi, K.; Park, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 10
Wenyingzhuangia marina gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a recirculating mariculture system
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- Liu, Y.; Liu, L. -Z.; Liu, H. -C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces
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- Kitahara, M.; Sakamoto, M.; Tsuchida, S.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 9
Cutting a Gordian Knot: Emended Classification and Description of the Genus Flavobacterium, Emended Description of the Family Flavobacteriaceae, and Proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978)
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- International Journal of Systematic Bacteriology, Vol. 46, Issue 1
Flavobacterium sinopsychrotolerans sp. nov., isolated from a glacier
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 1
Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., Anaerobic Gram-Negative Bacilli from the Human Gingival Crevice
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- Moore, L. V. H.; Moore, W. E. C.
- International Journal of Systematic Bacteriology, Vol. 44, Issue 2
Mesonia phycicola sp. nov., isolated from seaweed, and emended description of the genus Mesonia
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 3
Pedobacter agri sp. nov., from soil
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- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 7
Mesoflavibacter sabulilitoris sp. nov., isolated from seashore sand
journal, August 2014
- Park, S.; Park, J. -M.; Jung, Y. -T.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 11
Flavobacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond, and emended descriptions of Flavobacterium haoranii, Flavobacterium cauense, Flavobacterium terrae and Flavobacterium aquatile
journal, November 2012
- Sheu, S. -Y.; Lin, Y. -S.; Chen, W. -M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 6