Strain identifier

BacDive ID: 6958

Type strain: Yes

Species: Methanobrevibacter arboriphilus

Strain Designation: DH-1, DH1

Strain history: DSM 1125 <-- J. G. Zeikus DH1.

NCBI tax ID(s): 1300164 (strain), 39441 (species)

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General

@ref: 569

BacDive-ID: 6958

DSM-Number: 1125

keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic

description: Methanobrevibacter arboriphilus DH-1 is an anaerobe, mesophilic archaeon that was isolated from eastern Cotton Wood tree, wetwood.

NCBI tax id

NCBI tax idMatching level
39441species
1300164strain

strain history

@refhistory
569<- J.G. Zeikus, DH1 (Methanobacterium arbophilicum)
67770DSM 1125 <-- J. G. Zeikus DH1.

doi: 10.13145/bacdive6958.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Methanobacteria
  • order: Methanobacteriales
  • family: Methanobacteriaceae
  • genus: Methanobrevibacter
  • species: Methanobrevibacter arboriphilus
  • full scientific name: Methanobrevibacter arboriphilus corrig. (Zeikus and Henning 1975) Balch and Wolfe 1981

  • synonyms

    @refsynonym
    20215Methanobacterium arbophilicum
    20215Methanobrevibacter arboriphilicus

@ref: 569

domain: Archaea

phylum: Euryarchaeota

class: Methanobacteria

order: Methanobacteriales

family: Methanobacteriaceae

genus: Methanobrevibacter

species: Methanobrevibacter arboriphilus

full scientific name: Methanobrevibacter arboriphilus (Zeikus and Henning 1975) Balch and Wolfe 1981

strain designation: DH-1, DH1

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
569MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523)yeshttps://mediadive.dsmz.de/medium/1523Name: MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523) Composition: Brain heart infusion 5.98802 g/l Proteose peptone 5.98802 g/l NaHCO3 3.99202 g/l Yeast extract 1.99601 g/l Na-formate 1.99601 g/l Na-acetate 0.998004 g/l Na2S x 9 H2O 0.499002 g/l KH2PO4 0.499002 g/l L-Cysteine HCl x H2O 0.499002 g/l MgSO4 x 7 H2O 0.399202 g/l NH4Cl 0.399202 g/l NaCl 0.399202 g/l CaCl2 x 2 H2O 0.0499002 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l Pyridoxine hydrochloride 0.000299401 g/l Thiamine-HCl x 2 H2O 0.000199601 g/l Nicotinic acid 0.000199601 g/l CoCl2 x 6 H2O 0.000189621 g/l Calcium pantothenate 9.98004e-05 g/l Vitamin B12 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l p-Aminobenzoic acid 7.98403e-05 g/l ZnCl2 6.98603e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l D-(+)-biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Distilled water
569METHANOBACTERIUM MEDIUM (DSMZ Medium 119)yeshttps://mediadive.dsmz.de/medium/119Name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119) Composition: NaHCO3 3.98804 g/l Na-formate 1.99402 g/l Na-acetate 0.997009 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l KH2PO4 0.498504 g/l NH4Cl 0.398804 g/l NaCl 0.398804 g/l MgSO4 x 7 H2O 0.398804 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.0498504 g/l HCl 0.00249252 g/l FeSO4 x 7 H2O 0.00199402 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid H2SO4 Sludge Distilled water

culture temp

@refgrowthtypetemperaturerange
569positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 569
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
569eastern Cotton Wood tree, wetwoodMadisonUSAUSANorth America
67770Wetwood core from a western cottonwood tree in the University of Wisconsin ArboretumUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body Product#Plant#Timber

Safety information

risk assessment

  • @ref: 569
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 569
  • description: Methanobrevibacter arboriphilus strain DH-1 16S ribosomal RNA gene, partial sequence
  • accession: AY196665
  • length: 1268
  • database: ena
  • NCBI tax ID: 39441

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methanobrevibacter arboriphilus JCM 13429 = DSM 1125 DH1GCA_002072215contigncbi1300164
66792Methanobrevibacter arboriphilus JCM 13429 = DSM 1125GCA_001316345contigncbi1300164
66792Methanobrevibacter arboriphilus JCM 134292684622505draftimg1300164
66792Methanobrevibacter arboriphilus JCM 13429 = DSM 1125 strain DH11300164.4wgspatric1300164
66792Methanobrevibacter arboriphilus JCM 13429 = DSM 11251300164.3wgspatric1300164

GC content

  • @ref: 569
  • GC-content: 27.5

External links

@ref: 569

culture collection no.: DSM 1125, ATCC 33747, JCM 13429, OCM 147

straininfo link

  • @ref: 76420
  • straininfo: 40667

literature

  • topic: Phylogeny
  • Pubmed-ID: 14529955
  • title: Improved strategy for presumptive identification of methanogens using 16S riboprinting.
  • authors: Wright AD, Pimm C
  • journal: J Microbiol Methods
  • DOI: 10.1016/s0167-7012(03)00169-6
  • year: 2003
  • mesh: Base Sequence, DNA, Archaeal/chemistry/genetics, Methanobacteriales/classification/*genetics, Molecular Sequence Data, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/chemistry/*genetics, Ribotyping/*methods, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
569Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1125)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1125
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
76420Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40667.1StrainInfo: A central database for resolving microbial strain identifiers