Archive BacDiveID:10.13145/bacdive17061.20230509.8.1

Strain identifier

BacDive ID: 17061

Type strain:

Species: Thermotoga neapolitana

Strain Designation: NS-E

Strain history: <- K.O. Stetter <- H.W. Jannasch, NS-E

NCBI tax ID(s): 309803 (strain), 2337 (species)

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

General

@ref: 1545

BacDive-ID: 17061

DSM-Number: 4359

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, hyperthermophilic, Gram-negative

description: Thermotoga neapolitana NS-E is an anaerobe, hyperthermophilic, Gram-negative bacterium that was isolated from submarine hot spring.

NCBI tax id

NCBI tax id	Matching level
309803	strain
2337	species

strain history

@ref: 1545
history: <- K.O. Stetter <- H.W. Jannasch, NS-E

doi: 10.13145/bacdive17061.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/thermotogota
domain: Bacteria
phylum: Thermotogota
class: Thermotogae
order: Thermotogales
family: Thermotogaceae
genus: Thermotoga
species: Thermotoga neapolitana
full scientific name: Thermotoga neapolitana Jannasch et al. 1989

@ref: 1545

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Thermotogaceae

genus: Thermotoga

species: Thermotoga neapolitana

full scientific name: Thermotoga neapolitana Jannasch et al. 1989

strain designation: NS-E

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.811

Culture and growth conditions

culture medium

@ref: 1545
name: THERMOTOGA TF(C) MEDIUM (DSMZ Medium 613)
growth: yes
link: https://mediadive.dsmz.de/medium/613
composition: Name: THERMOTOGA TF(C) MEDIUM (DSMZ Medium 613; with strain-specific modifications) Composition: Yeast extract 1.97824 g/l Trypticase peptone 1.97824 g/l K2HPO4 1.58259 g/l MgCl2 x 6 H2O 1.38477 g/l Na2HPO4 x H2O 0.98912 g/l Starch 0.49456 g/l NH4Cl 0.49456 g/l Na2S x 9 H2O 0.296736 g/l L-Cysteine HCl x H2O 0.296736 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 H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Thiamine HCl 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
1545	positive	growth	85	hyperthermophilic
69480				thermophilic	100

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
1545	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.715

Isolation, sampling and environmental information

isolation

@ref: 1545
sample type: submarine hot spring
geographic location: Bay of Naples
country: Italy
origin.country: ITA
continent: Europe

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_1632.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_177;96_929;97_1081;98_1290;99_1632&stattab=map
Last taxonomy: Thermotoga
16S sequence: AB039768
Sequence Identity:
Total samples: 777
soil counts: 93
aquatic counts: 246
animal counts: 428
plant counts: 10

Safety information

risk assessment

@ref: 1545
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20218
description: Thermotoga neapolitana gene for 16S rRNA
accession: AB039768
length: 1482
database: ena
NCBI tax ID: 309803

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermotoga neapolitana DSM 4359	GCA_000018945	complete	ncbi	309803
66792	Thermotoga neapolitana DSM 4359	309803.4	complete	patric	309803
66792	Thermotoga neapolitana DSM 4359	643348584	complete	img	309803

GC content

@ref: 1545
GC-content: 46
method: sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	85.885	no
flagellated	no	89.114	no
gram-positive	no	93.689	no
anaerobic	yes	99.481	yes
aerobic	no	98.207	yes
halophile	no	92.408	no
spore-forming	no	91.277	no
thermophile	yes	100	yes
glucose-util	yes	88.949	no
glucose-ferment	yes	54.185	no

External links

@ref: 1545

culture collection no.: DSM 4359, ATCC 49049, NBRC 107923

straininfo link

@ref: 86061
straininfo: 42266

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	8085828	Growth requirements of hyperthermophilic sulfur-dependent heterotrophic archaea isolated from a shallow submarine geothermal system with reference to their essential amino acids.	Hoaki T, Nishijima M, Kato M, Adachi K, Mizobuchi S, Hanzawa N, Maruyama T	Appl Environ Microbiol	10.1128/aem.60.8.2898-2904.1994	1994	Amino Acids, Essential/metabolism, Anaerobiosis, Archaea/genetics/growth & development/physiology/ultrastructure, Base Composition, Base Sequence, Culture Media, DNA, Ribosomal/analysis, Hot Temperature, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, *Soil Microbiology	Cultivation
Genetics	16547022	Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences.	DeBoy RT, Mongodin EF, Emerson JB, Nelson KE	J Bacteriol	10.1128/JB.188.7.2364-2374.2006	2006	Base Sequence, Chromosome Inversion/genetics, Chromosomes, Bacterial/genetics, DNA, Bacterial/genetics, DNA, Intergenic/genetics, Evolution, Molecular, Molecular Sequence Data, Open Reading Frames, Repetitive Sequences, Nucleic Acid/genetics, Thermotoga maritima/classification/genetics, Thermotoga neapolitana/classification/*genetics	Phylogeny
Enzymology	19125220	Purification and biochemical characterization of a native invertase from the hydrogen-producing Thermotoga neapolitana (DSM 4359).	Dipasquale L, Gambacorta A, Siciliano RA, Mazzeo MF, Lama L	Extremophiles	10.1007/s00792-008-0222-2	2009	Hydrogen-Ion Concentration, Hydrolysis, Inulin/chemistry, Ions, Kinetics, Metals/chemistry, Models, Chemical, Polymers/chemistry, Substrate Specificity, Temperature, Thermotoga neapolitana/enzymology, beta-Fructofuranosidase/chemistry
Enzymology	21795792	Expression, crystallization and preliminary X-ray diffraction studies of thermostable beta-1,3-xylanase from Thermotoga neapolitana strain DSM 4359.	Okazaki F, Ogino C, Kondo A, Mikami B, Kurebayashi Y, Tsuruta H	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309111017222	2011	Crystallization, Crystallography, X-Ray, Enzyme Stability, Gene Expression, Thermotoga neapolitana/enzymology, Xylan Endo-1,3-beta-Xylosidase/chemistry
Enzymology	22914897	Cloning and biochemical characterization of a glucosidase from a marine bacterium Aeromonas sp. HC11e-3.	Huang X, Zhao Y, Dai Y, Wu G, Shao Z, Zeng Q, Liu Z	World J Microbiol Biotechnol	10.1007/s11274-012-1145-8	2012	Aeromonas/enzymology/genetics/isolation & purification, Amino Acid Sequence, Cations, Divalent/metabolism, Chromatography, Affinity, Cloning, Molecular, Enzyme Activators/metabolism, Enzyme Inhibitors/metabolism, Enzyme Stability, Escherichia coli/genetics, Gene Expression, Glucosidases/chemistry/genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, Metals/metabolism, Models, Molecular, Molecular Sequence Data, Protein Conformation, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Seawater/microbiology, Sequence Homology, Amino Acid, Temperature, Thermotoga neapolitana/enzymology/genetics	Metabolism
Enzymology	23149756	Biochemical characterization of a thermostable beta-1,3-xylanase from the hyperthermophilic eubacterium, Thermotoga neapolitana strain DSM 4359.	Okazaki F, Nakashima N, Ogino C, Tamaru Y, Kondo A	Appl Microbiol Biotechnol	10.1007/s00253-012-4555-5	2012	Amino Acid Sequence, Base Sequence, Biocatalysis, DNA Primers, Enzyme Stability, Hydrolysis, Kinetics, Mutagenesis, Site-Directed, Sequence Homology, Amino Acid, Substrate Specificity, Thermotoga neapolitana/enzymology, Xylan Endo-1,3-beta-Xylosidase/chemistry/metabolism	Metabolism
Metabolism	25467925	Introducing capnophilic lactic fermentation in a combined dark-photo fermentation process: a route to unparalleled H2 yields.	Dipasquale L, Adessi A, d'Ippolito G, Rossi F, Fontana A, De Philippis R	Appl Microbiol Biotechnol	10.1007/s00253-014-6231-4	2014	Culture Media, Fermentation, Glucose/metabolism, Hydrogen/metabolism, Lactic Acid/metabolism, Models, Molecular, Rhodopseudomonas/metabolism, Thermotoga neapolitana/metabolism	Biotechnology
Metabolism	30968346	Enzymatic transformation of ginsenosides Re, Rg1, and Rf to ginsenosides Rg2 and aglycon PPT by using beta-glucosidase from Thermotoga neapolitana.	Bi YF, Wang XZ, Jiang S, Liu JS, Zheng MZ, Chen P	Biotechnol Lett	10.1007/s10529-019-02665-7	2019	Biotransformation, Ginsenosides/metabolism, Hydrogen-Ion Concentration, Sapogenins/metabolism, Temperature, Thermotoga neapolitana/enzymology, beta-Glucosidase/metabolism	Enzymology

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
1545	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4359)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-4359
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
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)
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
86061	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID42266.1	StrainInfo: A central database for resolving microbial strain identifiers