Archive BacDiveID:10.13145/bacdive17798.20250331.9.3

Strain identifier

BacDive ID: 17798

Type strain:

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.

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/bacdive17798.20250331.9.3

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	gram stain	cell length	cell width	motility	confidence
29275	negative	4.95 µm	0.3 µm	yes
125439	negative				98.5

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

@ref	growth	type	temperature
15992	positive	growth	65
29275	positive	growth	55-70
29275	positive	optimum	65

culture pH

@ref	ability	type	pH
29275	positive	growth	5.5-7.5
29275	positive	optimum	6.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
15992	anaerobe
29275	anaerobe

spore formation

@ref	spore formation	confidence
29275	no
125439	no	92.1

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

Cat1	Cat2	Cat3
#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

@ref	description	accession	length	database	NCBI tax ID
20218	Caldisericum exile culture DSM:21853 16S ribosomal RNA gene, partial sequence	JQ346734	1426	nuccore	693075
15992	Caldisericum exile AZM16c01 gene for 16S rRNA, partial sequence	AB428365	1481	nuccore	511051

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Caldisericum exile AZM16c01	GCA_000284335	complete	ncbi	511051
66792	Caldisericum exile AZM16c01	511051.3	complete	patric	511051
66792	Caldisericum exile AZM16c01, NBRC 104410	2513237181	complete	img	511051

GC content

@ref	GC-content	method
15992	34.6	high performance liquid chromatography (HPLC)
29275	34.6

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	no	54.34	yes
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	82.97	yes
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	89.745	yes
125438	spore-forming	spore-forming	Ability to form endo- or exospores	no	81.284	yes
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	yes	67.606	yes
125438	motile2+	flagellated	Ability to perform flagellated movement	no	86.542	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	no	92.1
125439	BacteriaNet	motility	Ability to perform movement	no	74.3
125439	BacteriaNet	gram_stain	Reaction to gram-staining	negative	98.5
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	obligate aerobe	84.3

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

@id	authors	catalogue	doi/url	title	journal	pubmed	ID_cross_reference
15992	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21853)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21853
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
29275	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information		28776041	25692
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
86790	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID407941.1	StrainInfo: A central database for resolving microbial strain identifiers
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann		10.1101/2024.08.12.607695	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy		https://github.com/GenomeNet/deepG	deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1