Archive BacDiveID:10.13145/bacdive17038.20230509.8.1

Strain identifier

BacDive ID: 17038

Type strain:

Species: Fervidobacterium changbaicum

Strain Designation: CBS-1

Strain history: Y. Feng; Jilin Univ., China; CBS-1.

NCBI tax ID(s): 1121882 (strain), 310769 (species)

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

General

@ref: 7216

BacDive-ID: 17038

DSM-Number: 17883

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

description: Fervidobacterium changbaicum CBS-1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from hot spring mixture of water and mud.

NCBI tax id

NCBI tax id	Matching level
1121882	strain
310769	species

strain history

@ref	history
7216	<- Y. Feng, Key Laboratory for Molecular Enzymology and Engineering, Jilin University, Changchun, China; CBS-1 <- J. Cai {2004}
67770	Y. Feng; Jilin Univ., China; CBS-1.

doi: 10.13145/bacdive17038.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/thermotogota
domain: Bacteria
phylum: Thermotogota
class: Thermotogae
order: Thermotogales
family: Fervidobacteriaceae
genus: Fervidobacterium
species: Fervidobacterium changbaicum
full scientific name: Fervidobacterium changbaicum Cai et al. 2007

@ref: 7216

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Fervidobacteriaceae

genus: Fervidobacterium

species: Fervidobacterium changbaicum

full scientific name: Fervidobacterium changbaicum Cai et al. 2007

strain designation: CBS-1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	confidence
31983	negative	4.5 µm	0.55 µm	rod-shaped
69480	negative				99.811

pigmentation

@ref: 31983
production: yes

Culture and growth conditions

culture medium

@ref: 7216
name: FERVIDOBACTERIUM TF(A) MEDIUM (DSMZ Medium 740)
growth: yes
link: https://mediadive.dsmz.de/medium/740
composition: Name: FERVIDOBACTERIUM TF(A) MEDIUM (DSMZ Medium 740; with strain-specific modifications) Composition: D-Glucose 2.96736 g/l Trypticase peptone 1.97824 g/l Yeast extract 1.97824 g/l K2HPO4 1.58259 g/l Na2HPO4 x H2O 0.98912 g/l NH4Cl 0.49456 g/l Na2S x 9 H2O 0.296736 g/l L-Cysteine HCl x H2O 0.296736 g/l Elemental sulfur 0.197824 g/l CaCl2 x 2 H2O 0.0593472 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
7216	positive	growth	75	thermophilic
31983	positive	growth	55-90	hyperthermophilic
31983	positive	optimum	75-80	hyperthermophilic
67770	positive	growth	75	thermophilic
69480				thermophilic	100

culture pH

@ref	ability	type	pH	PH range
31983	positive	growth	6.4-8.5	alkaliphile
31983	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
7216	anaerobe
31983	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
31983	no
69481	no	100
69480	no	99.087

halophily

@ref: 31983
salt: NaCl
growth: positive
tested relation: growth
concentration: 0-1 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31983	17057	cellobiose	+	carbon source
31983	23652	dextrin	+	carbon source
31983	28757	fructose	+	carbon source
31983	28260	galactose	+	carbon source
31983	17234	glucose	+	carbon source
31983	17716	lactose	+	carbon source
31983	17306	maltose	+	carbon source
31983	28053	melibiose	+	carbon source
31983	15361	pyruvate	+	carbon source
31983	30911	sorbitol	+	carbon source
31983	17992	sucrose	+	carbon source
31983	27082	trehalose	+	carbon source

metabolite production

@ref: 31983
Chebi-ID: 16136
metabolite: hydrogen sulfide
production: yes

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
7216	hot spring mixture of water and mud	Changbai Mountains	China	CHN	Asia
67770	Hot spring mixture of water and mud of the Changbai Mountains		China	CHN	Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_1893.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_134;96_1065;97_1243;98_1492;99_1893&stattab=map
Last taxonomy: Fervidobacterium changbaicum
16S sequence: AY878719
Sequence Identity:
Total samples: 161
soil counts: 14
aquatic counts: 109
animal counts: 30
plant counts: 8

Safety information

risk assessment

@ref: 7216
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7216
description: Fervidobacterium changbaicum strain CBS-1 16S ribosomal RNA gene, partial sequence
accession: AY878719
length: 1502
database: ena
NCBI tax ID: 310769

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Fervidobacterium changbaicum CBS-1	GCA_004117075	chromosome	ncbi	310769
66792	Fervidobacterium changbaicum strain DSM 17883	310769.5	wgs	patric	310769
66792	Fervidobacterium changbaicum DSM 17883	2619619036	draft	img	1121882
66792	Fervidobacterium changbaicum CBS-1	2848342349	complete	img	310769
67770	Fervidobacterium changbaicum DSM 17883	GCA_900100515	scaffold	ncbi	310769

GC content

@ref	GC-content	method
7216	31.9±0.3
31983	31.9
67770	31.9	thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait: spore-forming
prediction: no
confidence: 100
training_data: no

External links

@ref: 7216

culture collection no.: DSM 17883, JCM 13353

straininfo link

@ref: 86038
straininfo: 311052

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	17911306	Fervidobacterium changbaicum sp. nov., a novel thermophilic anaerobic bacterium isolated from a hot spring of the Changbai Mountains, China.	Cai J, Wang Y, Liu D, Zeng Y, Xue Y, Ma Y, Feng Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64758-0	2007	Bacteria, Anaerobic/classification/cytology/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbon/metabolism, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hot Springs/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial/cytology, Temperature	Genetics
Enzymology	21046373	Fervidobacterium changbaicum Lip1: identification, cloning, and characterization of the thermophilic lipase as a new member of bacterial lipase family V.	Cai J, Xie Y, Song B, Wang Y, Zhang Z, Feng Y	Appl Microbiol Biotechnol	10.1007/s00253-010-2971-y	2010	Amino Acid Sequence, Bacteria/enzymology/genetics, Cloning, Molecular, Enzyme Stability, Hot Temperature, Hydrogen-Ion Concentration, Kinetics, Lipase/chemistry/genetics/*metabolism, Molecular Sequence Data, Phylogeny, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Substrate Specificity	Phylogeny

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
7216	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17883)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17883
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
31983	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	28237	28776041
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)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
86038	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID311052.1	StrainInfo: A central database for resolving microbial strain identifiers