Strain identifier

BacDive ID: 17798

Type strain: Yes

Species: Caldisericum exile

Strain Designation: AZM16c01

Strain history: <- K. Mori, NBRC; AZM16c01 <- K. Mori {2007}

NCBI tax ID(s): 693075 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 15992

BacDive-ID: 17798

DSM-Number: 21853

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

description: Caldisericum exile AZM16c01 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from hot spring.

NCBI tax id

  • NCBI tax id: 693075
  • Matching level: species

strain history

  • @ref: 15992
  • history: <- K. Mori, NBRC; AZM16c01 <- K. Mori {2007}

doi: 10.13145/bacdive17798.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/caldisericota
  • domain: Bacteria
  • phylum: Caldisericota
  • class: Caldisericia
  • order: Caldisericales
  • family: Caldisericaceae
  • genus: Caldisericum
  • species: Caldisericum exile
  • full scientific name: Caldisericum exile Mori et al. 2009

@ref: 15992

domain: Bacteria

phylum: Caldiserica

class: Caldisericia

order: Caldisericales

family: Caldisericaceae

genus: Caldisericum

species: Caldisericum exile

full scientific name: Caldisericum exile Mori et al. 2009

strain designation: AZM16c01

type strain: yes

Morphology

cell morphology

  • @ref: 29275
  • gram stain: negative
  • cell length: 4.95 µm
  • cell width: 0.3 µm
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 15992
  • name: CALDISERICUM MEDIUM (DSMZ Medium 1211)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1211
  • composition: Name: CALDISERICUM MEDIUM (DSMZ Medium 1211) Composition: Yeast extract 4.98504 g/l Na2S2O3 x 5 H2O 2.49252 g/l Na2S x 9 H2O 0.249252 g/l L-Cysteine HCl x H2O 0.249252 g/l NH4Cl 0.249252 g/l MgSO4 x 7 H2O 0.249252 g/l Na2CO3 0.249252 g/l KH2PO4 0.0897308 g/l K2HPO4 0.0498504 g/l Nitrilotriacetic acid 0.0127617 g/l FeCl2 x 4 H2O 0.000997009 g/l NaCl 0.000997009 g/l Sodium resazurin 0.000498504 g/l CaCl2 x 2 H2O 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 9.97009e-05 g/l NiCl2 x 6 H2O 9.97009e-05 g/l Na2WO4 x 2 H2O 3.98804e-05 g/l Na2SeO3 x 5 H2O 2.99103e-05 g/l CoCl2 x 6 H2O 2.99103e-05 g/l Na2MoO4 x 2 H2O 2.99103e-05 g/l CuCl2 1.99402e-05 g/l Pyridoxine hydrochloride 1.99402e-05 g/l p-Aminobenzoic acid 9.97009e-06 g/l Calcium D-(+)-pantothenate 9.97009e-06 g/l Nicotinic acid 9.97009e-06 g/l Riboflavin 9.97009e-06 g/l Thiamine HCl 9.97009e-06 g/l (DL)-alpha-Lipoic acid 9.97009e-06 g/l H3BO3 9.97009e-06 g/l Biotin 3.98804e-06 g/l Folic acid 3.98804e-06 g/l Vitamin B12 1.99402e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15992positivegrowth65thermophilic
29275positivegrowth55-70thermophilic
29275positiveoptimum65thermophilic

culture pH

@refabilitytypepH
29275positivegrowth5.5-7.5
29275positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15992anaerobe
29275anaerobe

spore formation

  • @ref: 29275
  • spore formation: no

halophily

  • @ref: 29275
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1 %

Isolation, sampling and environmental information

isolation

  • @ref: 15992
  • sample type: hot spring
  • geographic location: Nagano
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3466.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_407;96_1810;97_2169;98_2661;99_3466&stattab=map
  • Last taxonomy: Caldisericum exile subclade
  • 16S sequence: JQ346734
  • Sequence Identity:
  • Total samples: 457
  • soil counts: 11
  • aquatic counts: 367
  • animal counts: 74
  • plant counts: 5

Safety information

risk assessment

  • @ref: 15992
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Caldisericum exile strain AZM16c01 16S ribosomal RNA gene, partial sequenceJQ3467341426ena693075
15992Caldisericum exile AZM16c01 gene for 16S rRNA, partial sequenceAB4283651481ena511051

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caldisericum exile AZM16c01GCA_000284335completencbi511051
66792Caldisericum exile AZM16c01511051.3completepatric511051
66792Caldisericum exile AZM16c01, NBRC 1044102513237181completeimg511051

GC content

@refGC-contentmethod
1599234.6high performance liquid chromatography (HPLC)
2927534.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno84.082yes
flagellatedno98.784no
gram-positiveno91.702yes
anaerobicyes99.195yes
aerobicno98.753no
halophileno86.714yes
spore-formingno96.3yes
glucose-utilyes79.177no
thermophileyes99.598no
glucose-fermentno60.7no

External links

@ref: 15992

culture collection no.: DSM 21853, NBRC 104410

straininfo link

  • @ref: 86790
  • straininfo: 407941

literature

  • topic: Phylogeny
  • Pubmed-ID: 19628600
  • title: Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.
  • authors: Mori K, Yamaguchi K, Sakiyama Y, Urabe T, Suzuki K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010033-0
  • year: 2009
  • mesh: Anaerobiosis, Bacteria/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hot Springs/*microbiology, Hot Temperature, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15992Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21853)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21853
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
29275Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125692
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
86790Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407941.1StrainInfo: A central database for resolving microbial strain identifiers