Strain identifier
BacDive ID: 3801
Type strain:
Species: Hymenobacter arizonensis
Strain Designation: OR362-8
Strain history: F. Garcia-Pichel OR362-8.
NCBI tax ID(s): 1227077 (species)
General
@ref: 7148
BacDive-ID: 3801
DSM-Number: 17870
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Hymenobacter arizonensis OR362-8 is a mesophilic, Gram-negative bacterium that was isolated from biological soil crusts.
NCBI tax id
- NCBI tax id: 1227077
- Matching level: species
strain history
@ref | history |
---|---|
7148 | <- G. S. N. Reddy; OR 362-8 |
67770 | F. Garcia-Pichel OR362-8. |
doi: 10.13145/bacdive3801.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Hymenobacteraceae
- genus: Hymenobacter
- species: Hymenobacter arizonensis
- full scientific name: Hymenobacter arizonensis Reddy and Garcia-Pichel 2013
synonyms
- @ref: 20215
- synonym: Siccationidurans arizonensis
@ref: 7148
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Hymenobacter
species: Hymenobacter arizonensis
full scientific name: Hymenobacter arizonensis Reddy and Garcia-Pichel 2013
strain designation: OR362-8
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.975
Culture and growth conditions
culture medium
- @ref: 7148
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7148 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.997 |
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
7148 | biological soil crusts | Colorado Plateau | USA | USA | North America | ||
67770 | Biological soil crusts sample from southwestern arid lands of the USA (42° 30' 716" N 118° 31' 993" W) | USA | USA | North America | 42.5 | -118.517 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_99044.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_263;96_1104;97_1293;98_1557;99_99044&stattab=map
- Last taxonomy: Siccationidurans arizonensis
- 16S sequence: JX294485
- Sequence Identity:
- Total samples: 18
- soil counts: 15
- aquatic counts: 2
- plant counts: 1
Safety information
risk assessment
- @ref: 7148
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7148
- description: Hymenobacter arizonensis strain OR362-8 16S ribosomal RNA gene, partial sequence
- accession: JX294485
- length: 1422
- database: ena
- NCBI tax ID: 1227077
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Hymenobacter arizonensis strain OR362-8,ATCC BAA-1266,JCM 13504 | 1227077.3 | wgs | patric | 1227077 |
66792 | Siccationidurans arizonensis DSM 17870 | 2636416085 | draft | img | 1227077 |
67770 | Hymenobacter arizonensis OR362-8,ATCC BAA-1266,JCM 13504 | GCA_900115775 | scaffold | ncbi | 1227077 |
GC content
@ref | GC-content | method |
---|---|---|
7148 | 70.0 | thermal denaturation, midpoint method (Tm) |
67770 | 67.5-72.5 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | no | 93.836 | no |
gram-positive | no | 96.98 | no |
anaerobic | no | 99.586 | no |
aerobic | yes | 93.52 | no |
halophile | no | 93.688 | no |
spore-forming | no | 93.954 | no |
glucose-util | yes | 82.155 | no |
flagellated | no | 96.403 | no |
thermophile | no | 98.224 | yes |
glucose-ferment | no | 90.191 | no |
External links
@ref: 7148
culture collection no.: DSM 17870, ATCC BAA 1266, JCM 13504
straininfo link
- @ref: 73313
- straininfo: 298288
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22987249 | Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America. | Reddy GS, Garcia-Pichel F | Antonie Van Leeuwenhoek | 10.1007/s10482-012-9812-1 | 2012 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desert Climate, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Quinones/immunology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Southwestern United States | Genetics |
Phylogeny | 25822157 | Hymenobacter humi sp. nov., a bacterium isolated from soil. | Srinivasan S, Joo ES, Lee JJ, Kim MK | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0436-0 | 2015 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Temperature | Genetics |
Phylogeny | 27033203 | Hymenobacter sedentarius sp. nov., isolated from a soil. | Lee JJ, Kang MS, Joo ES, Jung HY, Kim MK | J Microbiol | 10.1007/s12275-016-5386-3 | 2016 | Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, Gamma Rays, Genes, rRNA, Hydrogen-Ion Concentration, Lipids/analysis, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seoul, *Soil Microbiology, Temperature | Phenotype |
Phylogeny | 28629503 | Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica. | Sedlacek I, Kralova S, Kyrova K, Maslanova I, Busse HJ, Stankova E, Vrbovska V, Nemec M, Bartak M, Holochova P, Svec P, Pantucek R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001898 | 2017 | Antarctic Regions, Bacterial Typing Techniques, Base Composition, Cytophagaceae/classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 29767618 | Hymenobacter pedocola sp. nov., a novel bacterium isolated from soil. | Lim SJ, Ten LN, Kim BO, Kang IK, Jung HY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002818 | 2018 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 32697187 | Hymenobacter ginkgonis sp. nov., isolated from bark of Ginkgo biloba. | Cha I, Kang H, Kim H, Bae S, Joh K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004343 | 2020 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginkgo biloba/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
7148 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17870) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17870 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
73313 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID298288.1 | StrainInfo: A central database for resolving microbial strain identifiers |