Archive BacDiveID:10.13145/bacdive17051.20230509.8.1

Strain identifier

BacDive ID: 17051

Type strain:

Species: Petrotoga halophila

Strain Designation: MET-B

Strain history: <- M.-L. Fardeau, IRD, Marseille; MET-B <- E. Miranda-Tello {2003}

NCBI tax ID(s): 1122953 (strain), 301141 (species)

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

General

@ref: 6645

BacDive-ID: 17051

DSM-Number: 16923

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

description: Petrotoga halophila MET-B is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from oil well TBM.

NCBI tax id

NCBI tax id	Matching level
301141	species
1122953	strain

strain history

@ref: 6645
history: <- M.-L. Fardeau, IRD, Marseille; MET-B <- E. Miranda-Tello {2003}

doi: 10.13145/bacdive17051.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/thermotogota
domain: Bacteria
phylum: Thermotogota
class: Thermotogae
order: Petrotogales
family: Petrotogaceae
genus: Petrotoga
species: Petrotoga halophila
full scientific name: Petrotoga halophila Miranda-Tello et al. 2007

@ref: 6645

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Petrotogaceae

genus: Petrotoga

species: Petrotoga halophila

full scientific name: Petrotoga halophila Miranda-Tello et al. 2007

strain designation: MET-B

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31847	negative	23.5 µm	0.6 µm	rod-shaped	no
69480	negative					99.932

colony morphology

@ref: 58792
incubation period: 4 days

pigmentation

@ref: 31847
production: yes

Culture and growth conditions

culture medium

@ref: 6645
name: PETROTOGA HALOPHILA MEDIUM (DSMZ Medium 718a)
growth: yes
link: https://mediadive.dsmz.de/medium/718a
composition: Name: PETROTOGA HALOPHILA MEDIUM (DSMZ Medium 718a) Composition: D-Glucose 4.93583 g/l MgCl2 x 6 H2O 3.94867 g/l Yeast extract 1.97433 g/l NaHCO3 0.987167 g/l Na2S x 9 H2O 0.493583 g/l KCl 0.335637 g/l NH4Cl 0.246792 g/l K2HPO4 0.138203 g/l MgSO4 x 7 H2O 0.029615 g/l Nitrilotriacetic acid 0.0148075 g/l NaCl 0.00987167 g/l MnSO4 x H2O 0.00493583 g/l Fe(NH4)2(SO4)2 x 7 H2O 0.00197433 g/l CoSO4 x 7 H2O 0.0017769 g/l ZnSO4 x 7 H2O 0.0017769 g/l CaCl2 x 2 H2O 0.000987167 g/l FeSO4 x 7 H2O 0.000987167 g/l Sodium resazurin 0.000493583 g/l NiCl2 x 6 H2O 0.00029615 g/l AlK(SO4)2 x 12 H2O 0.000197433 g/l Na2MoO4 x 2 H2O 9.87167e-05 g/l Pyridoxine hydrochloride 9.87167e-05 g/l CuSO4 x 5 H2O 9.87167e-05 g/l H3BO3 9.87167e-05 g/l p-Aminobenzoic acid 4.93583e-05 g/l Nicotinic acid 4.93583e-05 g/l Riboflavin 4.93583e-05 g/l Thiamine HCl 4.93583e-05 g/l Calcium D-(+)-pantothenate 4.93583e-05 g/l (DL)-alpha-Lipoic acid 4.93583e-05 g/l Biotin 1.97433e-05 g/l Folic acid 1.97433e-05 g/l Na2WO4 x 2 H2O 3.94867e-06 g/l Na2SeO3 x 5 H2O 2.9615e-06 g/l Vitamin B12 9.87167e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
6645	positive	growth	60	thermophilic
31847	positive	growth	35-65
31847	positive	optimum	55	thermophilic
58792	positive	growth	56	thermophilic
69480				thermophilic	99.999

culture pH

@ref	ability	type	pH	PH range
31847	positive	growth	5.5-9	alkaliphile
31847	positive	optimum	6.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6645	anaerobe
31847	anaerobe
58792	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
31847	no
69480	no	99.954

halophily

@ref	salt	growth	tested relation	concentration
31847	NaCl	positive	growth	0.5-10 %
31847	NaCl	positive	optimum	2 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31847	22599	arabinose	+	carbon source
31847	17057	cellobiose	+	carbon source
31847	28757	fructose	+	carbon source
31847	28260	galactose	+	carbon source
31847	17234	glucose	+	carbon source
31847	17716	lactose	+	carbon source
31847	17306	maltose	+	carbon source
31847	15361	pyruvate	+	carbon source
31847	26546	rhamnose	+	carbon source
31847	33942	ribose	+	carbon source
31847	17992	sucrose	+	carbon source
31847	18222	xylose	+	carbon source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	sampling date
6645	oil well TBM	Tchibouella oilfield	Republic of the Congo	COG	Africa
58792	Oil well TBM					1993

isolation source categories

Cat1: #Engineered
Cat2: #Industrial
Cat3: #Oil reservoir

taxonmaps

@ref: 69479
File name: preview.99_114848.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_617;96_3283;97_4027;98_23459;99_114848&stattab=map
Last taxonomy: Petrotoga
16S sequence: AY800102
Sequence Identity:
Total samples: 104
soil counts: 7
aquatic counts: 87
animal counts: 10

Safety information

risk assessment

@ref: 6645
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6645
description: Petrotoga halophila strain MET-B 16S ribosomal RNA gene, partial sequence
accession: AY800102
length: 1477
database: ena
NCBI tax ID: 301141

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Petrotoga halophila DSM 16923	GCA_002924615	scaffold	ncbi	1122953
66792	Petrotoga halophila DSM 16923	1122953.3	wgs	patric	1122953
66792	Petrotoga halophila DSM 16923	2556793017	draft	img	1122953

GC content

@ref: 31847
GC-content: 34.6

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	74	no
flagellated	no	91.251	yes
gram-positive	no	93.835	yes
anaerobic	yes	99.176	yes
aerobic	no	98.287	yes
halophile	no	90.966	no
spore-forming	no	89.71	yes
glucose-util	yes	89.328	no
thermophile	yes	100	yes
motile	yes	74.192	yes
glucose-ferment	yes	55.728	no

External links

@ref: 6645

culture collection no.: DSM 16923, CCUG 50214

straininfo link

@ref: 86051
straininfo: 297272

literature

topic: Phylogeny
Pubmed-ID: 17220438
title: Petrotoga halophila sp. nov., a thermophilic, moderately halophilic, fermentative bacterium isolated from an offshore oil well in Congo.
authors: Miranda-Tello E, Fardeau ML, Joulian C, Magot M, Thomas P, Tholozan JL, Ollivier B
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.64516-0
year: 2007
mesh: Bacterial Typing Techniques, Congo, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/*isolation & purification/physiology, *Hot Temperature, Molecular Sequence Data, *Petroleum, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride
topic2: Stress

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
6645	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16923)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16923
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
31847	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	28111	28776041
58792	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 50214)	https://www.ccug.se/strain?id=50214
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)
86051	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID297272.1	StrainInfo: A central database for resolving microbial strain identifiers