Cite this strain

Caldisericum exile (DSM 21853, NBRC 104410, AZM16c01)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17798

Type strain

Strain Designation AZM16c01

Culture col. no. DSM 21853 NBRC 104410 AZM16c01

NCBI tax ID(s) 693075

Special Collections DSMZ Literature strains

Links

Name and taxonomic classification

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

Gram-negative motile anaerobe thermophilic genome sequence 16S sequence Bacteria

SI-ID 407941

DSM 21853

Last LPSN update 2024-12-09 10:45:04

Domain Bacteria

Phylum Caldisericota

Class Caldisericia

Order Caldisericales

Family Caldisericaceae

Genus Caldisericum

Species Caldisericum exile

Full scientific name Caldisericum exile Mori et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Motility
29275	negative	4.95 µm	0.3 µm
125439	negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15992	CALDISERICUM MEDIUM (DSMZ Medium 1211)		Medium recipe at MediaDive	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

@ref	Growth	Type	Temperature (°C)	Range
15992	positive	growth	65	thermophilic
29275	positive	growth	55-70	thermophilic
29275	positive	optimum	65	thermophilic

Culture pH

@ref	Ability	Type	PH
29275	positive	optimum	6.5
29275	positive	growth	5.5-7.5

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29275	NaCl	positive	growth	<1 %

Spore formation

@ref	Spore formation
29275
125439

Oxygen tolerance

@ref	Oxygen tolerance
15992	anaerobe
29275	anaerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15992	hot spring	Nagano	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JQ346734 (>99% sequence identity) for Caldisericum exile subclade from Microbeatlas

Aquatic Samples	367
Soil Samples	11
Animal Samples	74
Plant Samples	5
Total Samples	457

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
15992	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
15992	34.6	high performance liquid chromatography (HPLC)
29275	34.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Caldisericum exile culture DSM:21853 16S ribosomal RNA gene, partial sequence	JQ346734	1426		693075
15992	Caldisericum exile AZM16c01 gene for 16S rRNA, partial sequence	AB428365	1481		511051

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Caldisericum exile AZM16c01	GCA_000284335	complete		511051
66792	Caldisericum exile AZM16c01	511051.3	complete	PATRIC	511051
66792	Caldisericum exile AZM16c01, NBRC 104410	2513237181	complete	JGI IMG/M	511051

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Caldisericum exile AZM16c01
PATRIC: 511051.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.10	no
125439	motility	BacteriaNetⓘ	no	74.30	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	84.30	no

Predictions from Diaspora project based on:
Caldisericum exile AZM16c01 AZM16c01
NCBI: GCA_000284335.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	54.34	yes
125438	anaerobic	anaerobicⓘ	yes	82.97	yes
125438	aerobic	aerobicⓘ	no	89.75	yes
125438	spore-forming	spore-formingⓘ	no	81.28	yes
125438	thermophilic	thermophileⓘ	yes	67.61	yes
125438	flagellated	motile2+ⓘ	no	86.54	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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.	Mori K, Yamaguchi K, Sakiyama Y, Urabe T, Suzuki K	Int J Syst Evol Microbiol	10.1099/ijs.0.010033-0	2009

Straininfo Link

@ref	Straininfo	Culture collections
86790	407941	DSM 21853

Culture collection no.

Culture collection no.
DSM 21853
NBRC 104410
AZM16c01

References

#15992	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21853
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#29275	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25692 (see below)
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#69479	João 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.: MicrobeAtlas 1.0 beta .
#86790	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID407941.1 )
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

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