Strain identifier

BacDive ID: 3801

Type strain: Yes

Species: Hymenobacter arizonensis

Strain Designation: OR362-8

Strain history: F. Garcia-Pichel OR362-8.

NCBI tax ID(s): 1227077 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

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

@refhistory
7148<- G. S. N. Reddy; OR 362-8
67770F. 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

@refgrowthtypetemperaturerange
7148positivegrowth30mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.997

observation

  • @ref: 67770
  • observation: quinones: MK-7

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7148biological soil crustsColorado PlateauUSAUSANorth America
67770Biological soil crusts sample from southwestern arid lands of the USA (42° 30' 716" N 118° 31' 993" W)USAUSANorth America42.5-118.517

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter arizonensis strain OR362-8,ATCC BAA-1266,JCM 135041227077.3wgspatric1227077
66792Siccationidurans arizonensis DSM 178702636416085draftimg1227077
67770Hymenobacter arizonensis OR362-8,ATCC BAA-1266,JCM 13504GCA_900115775scaffoldncbi1227077

GC content

@refGC-contentmethod
714870.0thermal denaturation, midpoint method (Tm)
6777067.5-72.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno93.836no
gram-positiveno96.98no
anaerobicno99.586no
aerobicyes93.52no
halophileno93.688no
spore-formingno93.954no
glucose-utilyes82.155no
flagellatedno96.403no
thermophileno98.224yes
glucose-fermentno90.191no

External links

@ref: 7148

culture collection no.: DSM 17870, ATCC BAA 1266, JCM 13504

straininfo link

  • @ref: 73313
  • straininfo: 298288

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22987249Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America.Reddy GS, Garcia-Pichel FAntonie Van Leeuwenhoek10.1007/s10482-012-9812-12012Bacterial 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 StatesGenetics
Phylogeny25822157Hymenobacter humi sp. nov., a bacterium isolated from soil.Srinivasan S, Joo ES, Lee JJ, Kim MKAntonie Van Leeuwenhoek10.1007/s10482-015-0436-02015Bacterial 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, TemperatureGenetics
Phylogeny27033203Hymenobacter sedentarius sp. nov., isolated from a soil.Lee JJ, Kang MS, Joo ES, Jung HY, Kim MKJ Microbiol10.1007/s12275-016-5386-32016Bacteroidetes/*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, TemperaturePhenotype
Phylogeny28629503Red-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 RInt J Syst Evol Microbiol10.1099/ijsem.0.0018982017Antarctic 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/chemistryTranscriptome
Phylogeny29767618Hymenobacter pedocola sp. nov., a novel bacterium isolated from soil.Lim SJ, Ten LN, Kim BO, Kang IK, Jung HYInt J Syst Evol Microbiol10.1099/ijsem.0.0028182018Bacterial 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/chemistryTranscriptome
Phylogeny32697187Hymenobacter ginkgonis sp. nov., isolated from bark of Ginkgo biloba.Cha I, Kang H, Kim H, Bae S, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0043432020Bacterial 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7148Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17870)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17870
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73313Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID298288.1StrainInfo: A central database for resolving microbial strain identifiers