Strain identifier

BacDive ID: 4239

Type strain: Yes

Species: Dictyoglomus thermophilum

Strain Designation: H-6-12

Strain history: <- R. Koch <- ATCC <- T. Saiki, H-6-12

NCBI tax ID(s): 14 (species)

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General

@ref: 1531

BacDive-ID: 4239

DSM-Number: 3960

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, rod-shaped

description: Dictyoglomus thermophilum H-6-12 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from tsuetate Hot Spring.

NCBI tax id

  • NCBI tax id: 14
  • Matching level: species

strain history

  • @ref: 1531
  • history: <- R. Koch <- ATCC <- T. Saiki, H-6-12

doi: 10.13145/bacdive4239.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/dictyoglomerota
  • domain: Bacteria
  • phylum: Dictyoglomerota
  • class: Dictyoglomeria
  • order: Dictyoglomerales
  • family: Dictyoglomeraceae
  • genus: Dictyoglomus
  • species: Dictyoglomus thermophilum
  • full scientific name: Dictyoglomus thermophilum Saiki et al. 1985

@ref: 1531

domain: Bacteria

phylum: Dictyoglomi

class: Dictyoglomia

order: Dictyoglomales

family: Dictyoglomaceae

genus: Dictyoglomus

species: Dictyoglomus thermophilum

full scientific name: Dictyoglomus thermophilum Saiki et al. 1985

strain designation: H-6-12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23230negative5.0-20.0 µm0.4-0.6 µmrod-shapedno
69480negative99.972

colony morphology

  • @ref: 23230
  • colony size: 2-4 mm
  • colony color: light pink
  • incubation period: 3-5 days

pigmentation

  • @ref: 23230
  • production: no
  • name: no pigments

Culture and growth conditions

culture medium

  • @ref: 1531
  • name: DICTYOGLOMUS MEDIUM (DSMZ Medium 388)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/388
  • composition: Name: DICTYOGLOMUS MEDIUM (DSMZ Medium 388) Composition: Starch 4.93583 g/l Na2HPO4 x 12 H2O 4.1461 g/l Yeast extract 1.97433 g/l Polypeptone 1.97433 g/l KH2PO4 1.48075 g/l Na2CO3 0.987167 g/l L-Cysteine HCl x H2O 0.987167 g/l NH4Cl 0.493583 g/l MgCl2 x 6 H2O 0.375123 g/l CaCl2 x 2 H2O 0.05923 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.0394867 g/l CoCl2 x 6 H2O 0.00286278 g/l ZnSO4 0.00276407 g/l Na2MoO4 x 2 H2O 0.0023692 g/l MnCl2 x 4 H2O 0.00197433 g/l Sodium resazurin 0.000493583 g/l Na2SeO3 x 5 H2O 0.000167818 g/l Pyridoxine hydrochloride 9.87167e-05 g/l (DL)-alpha-Lipoic acid 4.93583e-05 g/l p-Aminobenzoic acid 4.93583e-05 g/l Thiamine HCl 4.93583e-05 g/l Riboflavin 4.93583e-05 g/l Nicotinic acid 4.93583e-05 g/l Calcium D-(+)-pantothenate 4.93583e-05 g/l Biotin 1.97433e-05 g/l Folic acid 1.97433e-05 g/l Vitamin B12 9.87167e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
1531positivegrowth70thermophilic
23230positivemaximum80hyperthermophilic
23230positiveminimum51thermophilic
23230positiveoptimum73-78thermophilic
69480thermophilic100

culture pH

@refabilitytypepHPH range
23230positiveminimum5.4
23230positivemaximum8.9alkaliphile
23230positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1531anaerobe
23230anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
23230no
69480no99.924

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2323027897tryptophan-energy source
2323017234glucose-fermentation
2323062968cellulose-fermentation
2323017113erythritol-fermentation
2323017754glycerol-fermentation
2323029864mannitol-fermentation
2323017268myo-inositol-fermentation
2323015361pyruvate-fermentation
2323026546rhamnose-fermentation
2323030911sorbitol-fermentation
2323017151xylitol-fermentation
2323017632nitrate-reduction
2323027613amygdalin+energy source
2323022599arabinose+energy source
2323017057cellobiose+energy source
2323028757fructose+energy source
2323033984fucose+energy source
2323028260galactose+energy source
2323017234glucose+energy source
2323017716lactose+energy source
2323017306maltose+energy source
2323037684mannose+energy source
232306731melezitose+energy source
2323028053melibiose+energy source
2323017309pectin+energy source
2323016634raffinose+energy source
2323033942ribose+energy source
2323017992sucrose+energy source
2323027082trehalose+energy source
2323018222xylose+energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
232307507neomycinyesyes10 µg/mL
2323017076streptomycinyesyes10 µg/mL
2323027902tetracyclineyesyes10 µg/mL
2323029699tunicamycinyesyes10 µg/mL
2323027666actinomycin dyesyes100 µg/mL
2323017698chloramphenicolyesyes100 µg/mL
232308984sodium dodecyl sulfateyesyes100 µg/mL
2323028001vancomycinyesyes100 µg/mL
2323026710sodium chlorideyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2323035581indoleno
2323015688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
2323015688acetoin+
2323017234glucose-
2323035581indole-

enzymes

@refvalueactivityec
23230catalase-1.11.1.6
23230tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
1531tsuetate Hot SpringJapanJPNAsia
23230slightly alkaline hot springs (Tsuetate Hot Spring)JapanJPNAsiaKumamoto Prefecture

isolation source categories

Cat1Cat2Cat3
#Condition#Alkaline
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6707.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_379;96_1669;97_1998;98_2458;99_6707&stattab=map
  • Last taxonomy: Dictyoglomus thermophilum
  • 16S sequence: JQ346741
  • Sequence Identity:
  • Total samples: 270
  • soil counts: 16
  • aquatic counts: 226
  • animal counts: 28

Safety information

risk assessment

  • @ref: 1531
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dictyoglomus thermophilum H-6-12 16S ribosomal RNA gene, partial sequenceJQ3467411415ena309799
20218D.thermophilum gene for 16S rRNAX691941540ena309799

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dictyoglomus thermophilum H-6-12 H-6-12; ATCC 35947GCA_000020965completencbi309799
66792Dictyoglomus thermophilum H-6-12309799.4completepatric309799
66792Dictyoglomus thermophilum H-6-12, ATCC 35947643348542completeimg309799

GC content

@refGC-contentmethod
2323029.0
153133sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno59no
motileno82.705no
flagellatedno98.19yes
gram-positiveno94.752yes
anaerobicyes99.07no
aerobicno98.184yes
halophileno88.383no
spore-formingno93.188yes
thermophileyes100no
glucose-utilyes89.763no
glucose-fermentno70.909yes

External links

@ref: 1531

culture collection no.: DSM 3960, ATCC 35947

straininfo link

  • @ref: 73736
  • straininfo: 41384

literature

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Enzymology22824581Structure-functional analysis of the Dictyoglomus cell envelope.Hoppert M, Valdez M, Enseleit M, Theilmann W, Valerius O, Braus GH, Fost C, Liebl WSyst Appl Microbiol10.1016/j.syapm.2012.06.0042012Bacteria/*cytology/enzymology/genetics/ultrastructure, *Bacterial Physiological Phenomena, Cell Wall/*physiology/*ultrastructure, Cytoplasm/physiology, Fimbriae, Bacterial/physiology, Microscopy, Electron, Periplasm/physiology
Genetics24558247Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12.Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JAGenome Announc10.1128/genomeA.00109-142014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1531Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3960)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3960
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
23230TAKASHI SAIKI, YASUHIKO KOBAYASHI, KIYOTAKA KAWAGOE, TERUHIKO BEPPU10.1099/00207713-35-3-253Dictyoglomus thermophilum gen. nov., sp. nov., a Chemoorganotrophic, Anaerobic, Thermophilic BacteriumIJSEM 35: 253-259 1985
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)
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)
73736Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41384.1StrainInfo: A central database for resolving microbial strain identifiers