Archive BacDiveID:10.13145/bacdive16902.20230509.8.1

Strain identifier

BacDive ID: 16902

Type strain:

Species: Caldanaerovirga acetigignens

Strain Designation: JW-Sb4, JW/SA-NV4

Strain history: <- J. Wiegel, Univ. of Georgia, Athens, USA; JW/SA-NV4 <- S. Ahmed and J. Wiegel {2005}

NCBI tax ID(s): 1121258 (strain), 447595 (species)

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

General

@ref: 7707

BacDive-ID: 16902

DSM-Number: 18802

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

description: Caldanaerovirga acetigignens JW-Sb4 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from soil sample.

NCBI tax id

NCBI tax id	Matching level
447595	species
1121258	strain

strain history

@ref: 7707
history: <- J. Wiegel, Univ. of Georgia, Athens, USA; JW/SA-NV4 <- S. Ahmed and J. Wiegel {2005}

doi: 10.13145/bacdive16902.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Thermosediminibacterales
family: Thermosediminibacteraceae
genus: Caldanaerovirga
species: Caldanaerovirga acetigignens
full scientific name: Caldanaerovirga acetigignens Wagner et al. 2009

@ref: 7707

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermosediminibacteraceae

genus: Caldanaerovirga

species: Caldanaerovirga acetigignens

full scientific name: Caldanaerovirga acetigignens Wagner et al. 2009

strain designation: JW-Sb4, JW/SA-NV4

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29060	negative	4.5 µm	0.6 µm	rod-shaped	no
69480					yes	94.389

Culture and growth conditions

culture medium

@ref: 7707
name: CALDANAEROVIRGA MEDIUM (DSMZ Medium 1206)
growth: yes
link: https://mediadive.dsmz.de/medium/1206
composition: Name: CALDANAEROVIRGA MEDIUM (DSMZ Medium 1206) Composition: D-Xylose 2.96736 g/l TAPS sodium salt 2.37389 g/l NaHCO3 1.48368 g/l Yeast extract 0.98912 g/l NH4Cl 0.49456 g/l (NH4)2SO4 0.49456 g/l KH2PO4 0.267062 g/l Na2S x 9 H2O 0.24728 g/l L-Cysteine HCl x H2O 0.24728 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l MgCl2 x 6 H2O 0.0098912 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l CaCl2 x 2 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 Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Biotin 1.97824e-05 g/l Folic acid 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
7707	positive	growth	62	thermophilic
29060	positive	growth	44-74	thermophilic
29060	positive	optimum	61	thermophilic
69480				thermophilic	100

culture pH

@ref	ability	type	pH	PH range
29060	positive	growth	6.8-8.8	alkaliphile
29060	positive	optimum	8.4

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
7707	anaerobe
29060	anaerobe
69480	anaerobe	99.999

spore formation

@ref: 29060
spore formation: no

halophily

@ref: 29060
salt: NaCl
growth: positive
tested relation: growth
concentration: 0-4 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29060	17057	cellobiose	+	carbon source
29060	28757	fructose	+	carbon source
29060	17234	glucose	+	carbon source
29060	29864	mannitol	+	carbon source
29060	37684	mannose	+	carbon source
29060	15361	pyruvate	+	carbon source
29060	33942	ribose	+	carbon source
29060	18222	xylose	+	carbon source

enzymes

@ref: 29060
value: acid phosphatase
activity: +
ec: 3.1.3.2

Isolation, sampling and environmental information

isolation

@ref: 7707
sample type: soil sample
geographic location: Nevada, Trego Hot Spring
country: USA
origin.country: USA
continent: North America

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_39375.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_499;96_18500;97_22870;98_28815;99_39375&stattab=map
Last taxonomy: Caldanaerovirga acetigignens subclade
16S sequence: EF530069
Sequence Identity:
Total samples: 12
aquatic counts: 12

Safety information

risk assessment

@ref: 7707
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7707
description: Caldanaerovirga acetigignens strain JW/SA-NV4 16S ribosomal RNA gene, partial sequence
accession: EF530069
length: 1418
database: ena
NCBI tax ID: 447595

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Caldanaerovirga acetigignens DSM 18802	GCA_900142995	scaffold	ncbi	447595
66792	Caldanaerovirga acetigignens strain DSM 18802	447595.3	wgs	patric	447595
66792	Caldanaerovirga acetigignens DSM 18802	2599185231	draft	img	447595

GC content

@ref	GC-content	method
7707	38.6	high performance liquid chromatography (HPLC)
29060	38.6

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	83	no
motile	yes	88.163	no
flagellated	no	92.099	yes
gram-positive	no	84.861	no
anaerobic	yes	99.529	yes
aerobic	no	96.838	yes
halophile	no	91.694	no
spore-forming	yes	56.935	no
thermophile	yes	100	yes
glucose-util	yes	87.031	yes
glucose-ferment	yes	50.866	no

External links

@ref: 7707

culture collection no.: DSM 18802, ATCC BAA 1454

straininfo link

@ref: 85908
straininfo: 397554

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19625440	Caldanaerovirga acetigignens gen. nov., sp. nov., an anaerobic xylanolytic, alkalithermophilic bacterium isolated from Trego Hot Spring, Nevada, USA.	Wagner ID, Ahmed S, Zhao W, Zhang CL, Romanek CS, Rohde M, Wiegel J	Int J Syst Evol Microbiol	10.1099/ijs.0.005207-0	2009	Alkalies/metabolism, Anaerobiosis, Bacteria/chemistry/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Hot Springs/microbiology, Hot Temperature, Molecular Sequence Data, Nevada, Phylogeny, RNA, Ribosomal, 16S/genetics, Xylose/*metabolism	Metabolism
Genetics	36425965	Draft genome sequence of Thermovorax subterraneus 70B(T), a thermophile isolated from a geothermally active underground mine that produces hydrogen.	Goh KM, Liew KJ, Shahar S, Zakaria II, Kahar UM	Data Brief	10.1016/j.dib.2022.108695	2022

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
7707	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18802)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-18802
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
29060	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	25490	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)
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)
85908	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID397554.1	StrainInfo: A central database for resolving microbial strain identifiers