Archive BacDiveID:10.13145/bacdive17776.20230509.8.1

Strain identifier

BacDive ID: 17776

Type strain:

Species: Thermovirga lienii

Strain Designation: Cas60314

Strain history: <- H. Dahle, University of Bergen, Department of Biology, Bergen, Norway; Cas60314 <- H. Dahle

NCBI tax ID(s): 580340 (strain), 336261 (species)

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

General

@ref: 6876

BacDive-ID: 17776

DSM-Number: 17291

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

description: Thermovirga lienii Cas60314 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from production water from an oil well .

NCBI tax id

NCBI tax id	Matching level
336261	species
580340	strain

strain history

@ref: 6876
history: <- H. Dahle, University of Bergen, Department of Biology, Bergen, Norway; Cas60314 <- H. Dahle

doi: 10.13145/bacdive17776.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/synergistota
domain: Bacteria
phylum: Synergistota
class: Synergistia
order: Synergistales
family: Synergistaceae
genus: Thermovirga
species: Thermovirga lienii
full scientific name: Thermovirga lienii Dahle and Birkeland 2006

@ref: 6876

domain: Bacteria

phylum: Synergistetes

class: Synergistia

order: Synergistales

family: Synergistaceae

genus: Thermovirga

species: Thermovirga lienii

full scientific name: Thermovirga lienii Dahle and Birkeland 2006

strain designation: Cas60314

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31610	negative	02-03 µm	0.4-0.8 µm	rod-shaped	yes
69480	negative					97.627

pigmentation

@ref: 31610
production: yes

multimedia

@ref: 66793
multimedia content: EM_DSM_17291_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 6876
name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383)
growth: yes
link: https://mediadive.dsmz.de/medium/383
composition: Name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383; with strain-specific modifications) Composition: NaCl 20.9372 g/l Casamino acids 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na2SO4 2.99103 g/l Na2CO3 0.997009 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
6876	positive	growth	55	thermophilic
31610	positive	growth	37-68
31610	positive	optimum	58	thermophilic
69480				thermophilic	99.638

culture pH

@ref	ability	type	pH
31610	positive	growth	6.2-8
31610	positive	optimum	6.5-7

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6876	anaerobe
31610	anaerobe
69480	anaerobe	99.666

spore formation

@ref	spore formation	confidence
31610	no
69480	no	99.996

observation

@ref: 31610
observation: aggregates in chains

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31610	16449	alanine	+	carbon source
31610	29016	arginine	+	carbon source
31610	29987	glutamate	+	carbon source
31610	25017	leucine	+	carbon source

Isolation, sampling and environmental information

isolation

@ref: 6876
sample type: production water from an oil well (the Troll C oil well)
geographic location: North Sea
country: Norway
origin.country: NOR
continent: Europe

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Oil reservoir
#Environmental	#Aquatic

taxonmaps

@ref: 69479
File name: preview.99_7591.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_655;96_3536;97_4342;98_5559;99_7591&stattab=map
Last taxonomy: Thermovirga lienii subclade
16S sequence: DQ071273
Sequence Identity:
Total samples: 1628
soil counts: 141
aquatic counts: 694
animal counts: 727
plant counts: 66

Safety information

risk assessment

@ref: 6876
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6876
description: Thermovirga lienii strain Cas60314 16S ribosomal RNA gene, partial sequence
accession: DQ071273
length: 1427
database: ena
NCBI tax ID: 580340

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermovirga lienii DSM 17291	GCA_000233775	complete	ncbi	580340
66792	Thermovirga lienii DSM 17291	580340.6	complete	patric	580340
66792	Thermovirga lienii DSM 17291	580340.17	plasmid	patric	580340
66792	Thermovirga lienii Cas60314, DSM 17291	2505119043	complete	img	580340

GC content

@ref	GC-content	method
6876	47.1	sequence analysis
31610	46.6

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	62	no
motile	yes	88.075	no
flagellated	no	87.108	no
gram-positive	no	99.253	yes
anaerobic	yes	99.999	no
aerobic	no	99.323	no
halophile	no	88.602	no
spore-forming	no	89.744	no
thermophile	yes	100	yes
glucose-util	yes	60.843	no
glucose-ferment	no	60.729	no

External links

@ref: 6876

culture collection no.: DSM 17291, ATCC BAA 1197

straininfo link

@ref: 86767
straininfo: 297362

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	16825627	Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well.	Dahle H, Birkeland NK	Int J Syst Evol Microbiol	10.1099/ijs.0.63894-0	2006	Alcohols/metabolism, Amino Acids/metabolism, Base Composition, Carbohydrate Metabolism, Carboxylic Acids/metabolism, Cysteine/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/metabolism, Fermentation, Genes, rRNA, Gentian Violet, Gram-Positive Bacteria/classification/cytology/isolation & purification/physiology, Growth Inhibitors/pharmacology, Hydrogen-Ion Concentration, Molecular Sequence Data, Movement, North Sea, Oxidation-Reduction, Petroleum, Phenazines, Phylogeny, Proteins/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Sulfur/metabolism, Temperature	Phylogeny
Genetics	22768366	Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)).	Goker M, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.2726028	2012

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
6876	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17291)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17291
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
31610	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	27898	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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life		28604660	35: 676-683 2017
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates		33211880	Nucleic Acids Res. 49: D498-D508 2020
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)
86767	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID297362.1	StrainInfo: A central database for resolving microbial strain identifiers