Archive BacDiveID:10.13145/bacdive132828.20230509.8.1

Strain identifier

BacDive ID: 132828

Type strain:

Species: Thermosipho africanus

Strain Designation: TCF52B

Strain history: <- H. Dahle, Univ. Bergen, Norway; TCF52B <- H. Dahle {2003}

NCBI tax ID(s): 2421 (species)

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

General

@ref: 24616

BacDive-ID: 132828

DSM-Number: 24758

keywords: genome sequence, 16S sequence, Bacteria, thermophilic

description: Thermosipho africanus TCF52B is a thermophilic bacterium that was isolated from produced water from oil well.

NCBI tax id

NCBI tax id: 2421
Matching level: species

strain history

@ref: 24616
history: <- H. Dahle, Univ. Bergen, Norway; TCF52B <- H. Dahle {2003}

doi: 10.13145/bacdive132828.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/thermotogota
domain: Bacteria
phylum: Thermotogota
class: Thermotogae
order: Thermotogales
family: Fervidobacteriaceae
genus: Thermosipho
species: Thermosipho africanus
full scientific name: Thermosipho africanus Huber et al. 1989

@ref: 24616

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Fervidobacteriaceae

genus: Thermosipho

species: Thermosipho africanus

full scientific name: Thermosipho africanus Huber et al. 1989 emend. Ravot et al. 1996

strain designation: TCF52B

type strain: no

Culture and growth conditions

culture medium

@ref: 24616
name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c)
growth: yes
link: https://mediadive.dsmz.de/medium/141c
composition: Name: METHANOCOCCOIDES MEDIUM (DSMZ Medium 141c; with strain-specific modifications) Composition: NaHCO3 4.89237 g/l MgCl2 x 6 H2O 3.91389 g/l Yeast extract 1.95695 g/l Trypticase peptone 1.95695 g/l Na-acetate 0.978474 g/l Na2S x 9 H2O 0.489237 g/l L-Cysteine HCl x H2O 0.489237 g/l KCl 0.332681 g/l NH4Cl 0.244618 g/l K2HPO4 0.136986 g/l MgSO4 x 7 H2O 0.0293542 g/l Nitrilotriacetic acid 0.0146771 g/l NaCl 0.00978474 g/l MnSO4 x H2O 0.00489237 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00195695 g/l CoSO4 x 7 H2O 0.00176125 g/l ZnSO4 x 7 H2O 0.00176125 g/l CaCl2 x 2 H2O 0.000978474 g/l FeSO4 x 7 H2O 0.000978474 g/l Sodium resazurin 0.000489237 g/l NiCl2 x 6 H2O 0.000293542 g/l AlK(SO4)2 x 12 H2O 0.000195695 g/l CuSO4 x 5 H2O 9.78474e-05 g/l Pyridoxine hydrochloride 9.78474e-05 g/l Na2MoO4 x 2 H2O 9.78474e-05 g/l H3BO3 9.78474e-05 g/l (DL)-alpha-Lipoic acid 4.89237e-05 g/l Thiamine HCl 4.89237e-05 g/l Riboflavin 4.89237e-05 g/l Nicotinic acid 4.89237e-05 g/l Calcium D-(+)-pantothenate 4.89237e-05 g/l p-Aminobenzoic acid 4.89237e-05 g/l Biotin 1.95695e-05 g/l Folic acid 1.95695e-05 g/l Na2WO4 x 2 H2O 3.91389e-06 g/l Na2SeO3 x 5 H2O 2.93542e-06 g/l Vitamin B12 9.78474e-07 g/l Distilled water

culture temp

@ref: 24616
growth: positive
type: growth
temperature: 75
range: thermophilic

Isolation, sampling and environmental information

isolation

@ref: 24616
sample type: produced water from oil well
geographic location: North Sea
country: Norway
origin.country: NOR
continent: Europe

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Oil reservoir
#Engineered	#Waste	#Wastewater

taxonmaps

@ref: 69479
File name: preview.99_547.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_93;96_347;97_387;98_444;99_547&stattab=map
Last taxonomy: Thermosipho
16S sequence: DQ647058
Sequence Identity:
Total samples: 46
aquatic counts: 33
animal counts: 12
plant counts: 1

Safety information

risk assessment

@ref: 24616
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 24616
description: Thermosipho africanus strain TCF52B 16S ribosomal RNA gene, partial sequence
accession: DQ647058
length: 1492
database: ena
NCBI tax ID: 484019

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermosipho africanus TCF52B	GCA_000021285	complete	ncbi	484019
66792	Thermosipho africanus TCF52B	484019.4	complete	patric	484019
66792	Thermosipho africanus TCF52B	643348583	complete	img	484019

GC content

@ref: 24616
GC-content: 30.8
method: sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	89.758	no
flagellated	no	88.982	no
gram-positive	no	94.52	no
anaerobic	yes	99.448	no
halophile	no	91.768	no
spore-forming	no	88.054	no
glucose-util	yes	89.233	no
aerobic	no	98.704	no
thermophile	yes	100	yes
glucose-ferment	yes	51.245	no

External links

@ref: 24616

culture collection no.: DSM 24758

straininfo link

@ref: 91120
straininfo: 397232

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19124572	The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.	Nesbo CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, Doolittle WF	J Bacteriol	10.1128/JB.01448-08	2009	Archaea/classification/genetics, Bacteria/classification/genetics/isolation & purification, Gene Transfer, Horizontal, Genome, Bacterial, Molecular Sequence Data, Phylogeny	Genetics
Metabolism	27303896	Putative thioredoxin Trx1 from Thermosipho africanus strain TCF52B: expression, purification and structural determination using S-SAD.	Sahtout N, Kuttiyatveetil JR, Fodje M, Sanders DA	Acta Crystallogr F Struct Biol Commun	10.1107/S2053230X16007214	2016	Bacteria/metabolism, Bacterial Proteins/chemistry/genetics/metabolism, Protein Conformation, Thioredoxins/chemistry/genetics/*metabolism	Enzymology
Metabolism	28687766	Biochemical properties of GH94 cellodextrin phosphorylase THA_1941 from a thermophilic eubacterium Thermosipho africanus TCF52B with cellobiose phosphorylase activity.	Wu Y, Mao G, Fan H, Song A, Zhang YP, Chen H	Sci Rep	10.1038/s41598-017-05289-x	2017	Bacteria/enzymology/genetics, Cellobiose/metabolism, Cellulose/analogs & derivatives/metabolism, Cloning, Molecular, Dextrins/metabolism, Gene Expression, Glucose/metabolism, Glucosyltransferases/genetics/*metabolism, Hydrogen-Ion Concentration, Kinetics, Oligosaccharides/metabolism, Recombinant Proteins/genetics/metabolism, Substrate Specificity, Temperature, Tetroses/metabolism	Enzymology
Stress	30716506	Structure and function of the putative thioredoxin 1 from the thermophilic eubacterium Thermosipho africanus strain TCF52B.	Sahtout N, Kuttiyatveetil JRA, Sanders DAR	Biochim Biophys Acta Proteins Proteom	10.1016/j.bbapap.2019.01.011	2019	Amino Acid Sequence, Bacterial Proteins/chemistry, Eubacterium, Insulin/chemistry, Protein Conformation, Protein Stability, Thioredoxins/*chemistry

Reference

@id	authors	title	doi/url	catalogue
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ	10.1099/ijsem.0.004332
24616	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-24758	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24758)
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)	https://diaspora-project.de/progress.html#genomes
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.	MicrobeAtlas 1.0 beta	https://microbeatlas.org/
91120	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.	StrainInfo: A central database for resolving microbial strain identifiers	10.60712/SI-ID397232.1