Strain identifier

BacDive ID: 14324

Type strain: Yes

Species: Gracilinema caldarium

Strain Designation: H1

Strain history: <- M. Pohlschroeder, University of Massachusetts, Department of Microbiology, USA; H1 <- M. Pohlschroeder {1990}

NCBI tax ID(s): 215591 (species)

« back to strain detail view
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: 2903

BacDive-ID: 14324

DSM-Number: 7334

keywords: genome sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, spiral-shaped

description: Gracilinema caldarium H1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from cyanobacterial mat of freshwater hot spring.

NCBI tax id

  • NCBI tax id: 215591
  • Matching level: species

strain history

  • @ref: 2903
  • history: <- M. Pohlschroeder, University of Massachusetts, Department of Microbiology, USA; H1 <- M. Pohlschroeder {1990}

doi: 10.13145/bacdive14324.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Spirochaetales
  • family: Breznakiellaceae
  • genus: Gracilinema
  • species: Gracilinema caldarium
  • full scientific name: Gracilinema caldarium (Pohlschröder et al. 1995) Brune et al. 2022

  • synonyms

    @refsynonym
    20215Spirochaeta caldaria
    20215Treponema caldaria
    20215Spirochaeta caldarium
    20215Treponema caldarium

@ref: 2903

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Treponemataceae

genus: Treponema

species: Treponema caldarium

full scientific name: Treponema caldarium (Pohlschröder et al. 1995) Abt et al. 2013

strain designation: H1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43420negative15-25 µm0.2-0.3 µmspiral-shapedyes
69480yes92.412
69480negative99.974

colony morphology

@refincubation periodcolony colorcolony shape
29032-3 days
43420white, fluffy, cotton-ball likecircular

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_7334_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 2903
  • name: GRACILINEMA MEDIUM (DSMZ Medium 635)
  • growth: yes
  • link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium635.pdf

culture temp

@refgrowthtypetemperaturerange
2903positivegrowth50thermophilic
43420nogrowth25mesophilic
43420nogrowth60thermophilic
43420positiveoptimum48-52thermophilic

culture pH

@refabilitytypepHPH range
43420positivegrowth5.8-8.5alkaliphile
43420positiveoptimum7.2-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2903anaerobe
43420obligate anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
43420no
69481no100
69480no99.988

halophily

@refsaltgrowthtested relationconcentration
43420NaClpositivegrowth0.25 %(w/v)
43420NaClnogrowth0.4 %(w/v)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43420casein hydrolysate-assimilation
43420cellobiose+fermentation17057
43420cellotetraose+fermentation62974
43420cellotriose+fermentation3528
43420cellulose-assimilation62968
43420D-fructose+fermentation15824
43420D-galactose+fermentation12936
43420D-glucose+fermentation17634
43420D-mannose+fermentation16024
43420D-ribose-assimilation16988
43420D-xylose+fermentation65327
43420glucose+fermentation17234
43420glycerol-assimilation17754
43420L-arabinose+fermentation30849
43420lactose+fermentation17716
43420maltose+fermentation17306
43420mannitol-assimilation29864
43420peptone-assimilation
43420sodium acetate-assimilation32954
43420starch+fermentation28017
43420sucrose+fermentation17992
43420xylan-assimilation37166
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose-fermentation16024
68380raffinose-fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4342017698chloramphenicolyesyes10 µg/mL
434207507neomycinyesyes10 µg/mL
4342018208penicillin gyesyes10 µg/mL
4342027902tetracyclineyesyes10 µg/mL
4342028077rifampicinyesyes100 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
4342030089acetateyes
4342016526carbon dioxideyes
4342018276dihydrogenyes
4342024996DL-lactateyes
4342016236ethanolno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
2903--+------+-------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitude
2903cyanobacterial mat of freshwater hot springOregon, Lakeview, Hunter's hot springUSAUSANorth America
43420Hot SpringHunter'2 Hot Spring, OregonUSAUSANorth America1990-0842.222-120.368

isolation source categories

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

Safety information

risk assessment

  • @ref: 2903
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gracilinema caldarium DSM 7334GCA_000219725completencbi744872
66792Treponema caldaria DSM 7334744872.3completepatric744872
66792Treponema caldarium DSM 73342505679006completeimg744872

GC content

@refGC-contentmethod
290345.6sequence analysis
290345.0thermal denaturation, midpoint method (Tm)
4342046

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.927no
flagellatedno75.885no
gram-positiveno92.569no
anaerobicyes99.01no
aerobicno98.448yes
halophileno77.295no
spore-formingno87.582yes
thermophileyes70.187no
glucose-utilyes86.611no
glucose-fermentyes81.144yes

External links

@ref: 2903

culture collection no.: DSM 7334, ATCC 51460

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2903Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7334)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7334
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
43420Birte Abt, Markus Goeker, Carmen Scheuner, Cliff Han, Megan Lu, Monica Misra, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Lynne A. Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Marcel Huntemann, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Sabine Gronow, John C. Detter, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Tanja Woyke, Hans-Peter Klenk10.4056/sigs.3096473Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1 T ), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus TreponemaStand Genomic Sci 8: 88-105 201323961314
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
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
68380Automatically annotated from API rID32A
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