Archive BacDiveID:10.13145/bacdive17108.20230509.8.1

Strain identifier

BacDive ID: 17108

Type strain:

Species: Tsukamurella pseudospumae

Strain Designation: SCNU5

Strain history: <- Chi Nam Seong, SCNU5

NCBI tax ID(s): 239498 (species)

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

General

@ref: 16297

BacDive-ID: 17108

DSM-Number: 45335

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Tsukamurella pseudospumae SCNU5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax id: 239498
Matching level: species

strain history

@ref	history
16297	<- D. P. Labeda, NRRL; NRRL B-24668 <- C. N. Seoung; SCNU5
67770	NRRL B-24668 <-- C. N. Seong et al. SCNU5.
67771	<- Chi Nam Seong, SCNU5

doi: 10.13145/bacdive17108.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Mycobacteriales
family: Tsukamurellaceae
genus: Tsukamurella
species: Tsukamurella pseudospumae
full scientific name: Tsukamurella pseudospumae Nam et al. 2004
synonyms
- @ref: 20215
- synonym: Tsukamurella sunchonensis

@ref: 16297

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella pseudospumae

full scientific name: Tsukamurella pseudospumae Nam et al. 2004 emend. Teng et al. 2016

strain designation: SCNU5

type strain: no

Morphology

cell morphology

@ref	gram stain	confidence
67771	positive
69480	positive	100

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
16297	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	yes	https://mediadive.dsmz.de/medium/535	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
16297	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes	https://mediadive.dsmz.de/medium/65	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16297	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 67771
oxygen tolerance: aerobe

spore formation

@ref: 69480
spore formation: no
confidence: 99.68

observation

@ref	observation
67770	quinones: MK-9
67771	quinones: MK-9(H_0_)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
16297	activated sludge	Suncheon	Republic of Korea	KOR	Asia
67770	Activated sludge plant in Sunchon		Republic of Korea	KOR	Asia
67771	From activated sludge		Republic of Korea	KOR	Asia

isolation source categories

Cat1: #Engineered
Cat2: #Waste
Cat3: #Activated sludge

taxonmaps

@ref: 69479
File name: preview.99_3845.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1974;97_2373;98_2929;99_3845&stattab=map
Last taxonomy: Tsukamurella
16S sequence: AF150494
Sequence Identity:
Total samples: 12359
soil counts: 3431
aquatic counts: 2978
animal counts: 5160
plant counts: 790

Safety information

risk assessment

@ref: 16297
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20218
description: Tsukamurella sp. SCNU5 16S ribosomal RNA gene, complete sequence
accession: AF150494
length: 1510
database: ena
NCBI tax ID: 105579

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Tsukamurella sunchonensis strain JCM 15929	105579.5	wgs	patric	239498
66792	Tsukamurella sunchonensis JCM 15929	2675903619	draft	img	239498
67770	Tsukamurella pseudospumae JCM 15929	GCA_001575195	contig	ncbi	239498

GC content

@ref	GC-content	method
16297	68.1
67770	68.1	thermal denaturation, midpoint method (Tm)
67770	70.5	genome sequence analysis
67770	70.1	genome sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	82	no
motile	no	92.991	no
flagellated	no	97.72	no
gram-positive	yes	90.224	yes
anaerobic	no	99.62	no
aerobic	yes	92.426	yes
halophile	no	93.886	no
spore-forming	no	80.757	no
thermophile	no	99.319	yes
glucose-util	yes	91.798	no
glucose-ferment	no	88.606	no

External links

@ref: 16297

culture collection no.: DSM 45335, KCTC 9827, NRRL B-24668, JCM 15929

straininfo link

@ref: 86108
straininfo: 107648

literature

topic: Phylogeny
Pubmed-ID: 26530900
title: Tsukamurella hongkongensis sp. nov. and Tsukamurella sinensis sp. nov., isolated from patients with keratitis, catheter-related bacteraemia and conjunctivitis.
authors: Teng JLL, Tang Y, Wong SSY, Ngan AHY, Huang Y, Tsang CC, Choi GKY, Lau SKP, Woo PCY
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijsem.0.000733
year: 2015
mesh: Actinomycetales/*classification/genetics/isolation & purification, Adult, Bacteremia/*microbiology, Bacterial Typing Techniques, Base Composition, Catheters, Indwelling/microbiology, Conjunctiva/microbiology, Conjunctivitis/*microbiology, Cornea/microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hong Kong, Humans, Keratitis/*microbiology, Male, Middle Aged, Molecular Sequence Data, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
topic2: Pathogenicity

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
16297	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45335)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-45335
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)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
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)
86108	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID107648.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

oxygen tolerance

spore formation

observation

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference