Strain identifier

BacDive ID: 5881

Type strain: Yes

Species: Halorhabdus utahensis

Strain Designation: AX-2

Strain history: DSM 12940 <-- M. Wainø AX-2.

NCBI tax ID(s): 519442 (strain), 146826 (species)

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General

@ref: 4867

BacDive-ID: 5881

DSM-Number: 12940

keywords: genome sequence, 16S sequence, Archaea

description: Halorhabdus utahensis AX-2 is an archaeon that was isolated from sediment.

NCBI tax id

NCBI tax idMatching level
519442strain
146826species

strain history

@refhistory
4867<- M. Wainö; AX-2
67770DSM 12940 <-- M. Wainø AX-2.

doi: 10.13145/bacdive5881.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Halobacteriales
  • family: Haloarculaceae
  • genus: Halorhabdus
  • species: Halorhabdus utahensis
  • full scientific name: Halorhabdus utahensis Wainø et al. 2000

@ref: 4867

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Haloarculaceae

genus: Halorhabdus

species: Halorhabdus utahensis

full scientific name: Halorhabdus utahensis Wainø et al. 2000

strain designation: AX-2

type strain: yes

Morphology

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_12940_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 4867
  • name: HALORHABDUS UTAHENSIS MEDIUM (DSMZ Medium 927)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/927
  • composition: Name: HALORHABDUS UTAHENSIS MEDIUM (DSMZ Medium 927) Composition: NaCl 270.0 g/l MgSO4 x 7 H2O 20.0 g/l Tris-HCl 12.0 g/l KCl 5.0 g/l NH4Cl 2.0 g/l Glucose 2.0 g/l Yeast extract 1.0 g/l KH2PO4 0.125 g/l NaBr 0.1 g/l CaCl2 x 6 H2O 0.05 g/l FeCl2 x 4 H2O 0.005 g/l MnCl2 x 4 H2O 0.005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
4867positivegrowth37-45
67770positivegrowth37mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-8(H2)

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4867sedimentUtah, Great Salt LakeUSAUSANorth America
67770Sediment of Great Salt LakeUTUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_187217.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17660;96_68870;97_89517;98_121798;99_187217&stattab=map
  • Last taxonomy: Halorhabdus
  • 16S sequence: AF071880
  • Sequence Identity:
  • Total samples: 33
  • soil counts: 10
  • aquatic counts: 23

Safety information

risk assessment

  • @ref: 4867
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halorhabdus utahensis gene for 16S rRNA, complete sequence, strain: JCM 11049AB6634001472ena146826
67770Halobacter utahensis 16S ribosomal RNA gene, partial sequenceAF0718801422ena519442

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorhabdus utahensis DSM 12940GCA_000023945completencbi519442
66792Halorhabdus utahensis AX-2, DSM 12940644736373completeimg519442
66792Halorhabdus utahensis DSM 12940519442.20completepatric519442

GC content

@refGC-contentmethod
486764
6777064high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno74.078no
flagellatedno96.14no
gram-positiveno96.337no
anaerobicno79.961no
aerobicyes60.294no
halophileyes56.608no
spore-formingno95.235no
thermophileno78.109yes
glucose-utilyes87.202no
glucose-fermentno73.074no

External links

@ref: 4867

culture collection no.: DSM 12940, JCM 11049

straininfo link

  • @ref: 75360
  • straininfo: 100678

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10826803Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah.Waino M, Tindall BJ, Ingvorsen KInt J Syst Evol Microbiol10.1099/00207713-50-1-1832000Base Composition, Culture Media, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Halobacteriaceae/*classification/isolation & purification/physiology/ultrastructure, Lipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Utah, *Water MicrobiologyCultivation
Genetics21304660Complete genome sequence of Halorhabdus utahensis type strain (AX-2).Anderson I, Tindall BJ, Pomrenke H, Goker M, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Chen F, Tice H, Cheng JF, Lucas S, Chertkov O, Bruce D, Brettin T, Detter JC, Han C, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Pitluck S, Pati A, Mavromatis K, Ivanova N, Ovchinnikova G, Chen A, Palaniappan K, Chain P, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HPStand Genomic Sci10.4056/sigs.318642009
Phylogeny21828022Halovenus aranensis gen. nov., sp. nov., an extremely halophilic archaeon from Aran-Bidgol salt lake.Makhdoumi-Kakhki A, Amoozegar MA, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.031419-02011Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Iran, Lakes/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolismMetabolism
Genetics24428220Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glockner FO, Golyshina OV, Golyshin PN, Teeling HEnviron Microbiol10.1111/1462-2920.123932014Adaptation, Physiological, Anaerobiosis/physiology, Biological Evolution, Ecosystem, Enzyme Assays, *Genome, Archaeal, Glycoside Hydrolases/genetics/metabolism, Halobacteriaceae/classification/enzymology/*genetics, Indian Ocean, Lakes/microbiology, *Metagenomics, Oxygen/metabolism/pharmacology, Phylogeny, Polysaccharides/*metabolism, Salt Tolerance/*genetics, Sodium Chloride, Utah, *Water MicrobiologyMetabolism
Phylogeny26749115Halorhabdus rudnickae sp. nov., a halophilic archaeon isolated from a salt mine borehole in Poland.Albuquerque L, Kowalewicz-Kulbat M, Drzewiecka D, Staczek P, d'Auria G, Rossello-Mora R, da Costa MSSyst Appl Microbiol10.1016/j.syapm.2015.12.0042015Bacterial Typing Techniques, Geologic Sediments/*microbiology, Halobacteriaceae/*classification/isolation & purification, PolandEnzymology
Phylogeny35482509Halorhabdus amylolytica sp. nov. and Halorhabdus salina sp. nov., isolated from hypersaline environments.Wang R, Chen F, Wang J, Liu A, Ke L, Wan F, Chen SInt J Syst Evol Microbiol10.1099/ijsem.0.0053462022Animals, *Arthropods, Bacterial Typing Techniques, Base Composition, DNA, Archaeal/genetics, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Halobacteriaceae, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4867Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12940)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12940
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
75360Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100678.1StrainInfo: A central database for resolving microbial strain identifiers