Archive BacDiveID:10.13145/bacdive13313.20240916.9.1

Strain identifier

BacDive ID: 13313

Type strain:

Species: Lentzea albidocapillata subsp. violacea

Strain Designation: LM 036

Strain history: <- J. Chun, SNU

NCBI tax ID(s): 128104 (subspecies)

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

General

@ref: 11983

BacDive-ID: 13313

DSM-Number: 44796

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

description: Lentzea albidocapillata subsp. violacea LM 036 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil from gold mine cave.

NCBI tax id

NCBI tax id: 128104
Matching level: subspecies

strain history

@ref	history
11983	<- KCTC <- J. S. Lee <- J. Chun
67770	S.-O. Kang LM 036.
67771	<- J. Chun, SNU

doi: 10.13145/bacdive13313.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Pseudonocardiales
family: Pseudonocardiaceae
genus: Lentzea
species: Lentzea albidocapillata subsp. violacea
full scientific name: Lentzea albidocapillata subsp. violacea (Lee et al. 2000) Nouioui et al. 2018
synonyms
@ref synonym
20215 Lentzea violacea
20215 Saccharothrix violacea

@ref	synonym
20215	Lentzea violacea
20215	Saccharothrix violacea

@ref: 11983

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Lentzea

species: Lentzea albidocapillata subsp. violacea

full scientific name: Lentzea albidocapillata subsp. violacea (Lee et al. 2000) Nouioui et al. 2018

strain designation: LM 036

type strain: yes

Morphology

cell morphology

@ref	gram stain	motility	confidence
67771	positive
69480		no	92.1

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
11983	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
11983	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	yes	https://mediadive.dsmz.de/medium/84	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@ref	growth	type	temperature
11983	positive	growth	28
67770	positive	growth	28
67771	positive	growth	30

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
67771	aerobe
69480	aerobe	92.16

spore formation

@ref: 69481
spore formation: yes
confidence: 97

observation

@ref	observation
67770	quinones: MK-9(H₄), MK-9(H₂), MK-9(H₆)
67771	quinones: MK-9(H4)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
11983	soil from gold mine cave	Korea, Kongju	Republic of Korea	KOR	Asia
67770	Soil at a gold mine cave	Kongju	Republic of Korea	KOR	Asia
67771	From soil from gold mine cave	Kongju	Republic of Korea	KOR	Asia

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil

taxonmaps

@ref: 69479
File name: preview.99_32369.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_982;98_3756;99_32369&stattab=map
Last taxonomy: Lentzea
16S sequence: AJ242633
Sequence Identity:
Total samples: 289
soil counts: 231
aquatic counts: 15
animal counts: 10
plant counts: 33

Safety information

risk assessment

@ref: 11983
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 11983
description: Saccharothrix violacea 16S rRNA gene (strain LM 036T)
accession: AJ242633
length: 1508
database: nuccore
NCBI tax ID: 128104

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Lentzea violacea strain DSM 44796	128104.3	wgs	patric	128104
66792	Lentzea albidocapillata DSM 44796	2619619033	draft	img	128104
67770	Lentzea albidocapillata subsp. violacea DSM 44796	GCA_900100275	scaffold	ncbi	128104

GC content

@ref	GC-content	method
11983	69.6
67770	69.6	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69481	spore-forming	spore-forming	Ability to form endo- or exospores	yes	97	no
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	yes	87.75	yes
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	97.932	yes
69480	spore-forming	spore-forming	Ability to form endo- or exospores	yes	87.414	no
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	92.16	no
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	97.5	no
69480	flagellated	motile2+	Ability to perform flagellated movement	no	92.1	no

External links

@ref: 11983

culture collection no.: DSM 44796, IMSNU 50388, KCTC 9948, JCM 10975, BCRC 16959, CGMCC 4.1702, CGMCC 4.2093

straininfo link

@ref	straininfo
82513	88654
82514	317403

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	10843077	Saccharothrix violacea sp. nov., isolated from a gold mine cave, and Saccharothrix albidocapillata comb. nov.	Lee SD, Kim ES, Roe JH, Kim J, Kang SO, Hah YC	Int J Syst Evol Microbiol	10.1099/00207713-50-3-1315	2000	Actinomycetales/classification/cytology/isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gold, Microscopy, Electron, Scanning, Mining, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology	Genetics
Phylogeny	29537362	Lentzea soli sp. nov., an actinomycete isolated from soil.	Li D, Zheng W, Zhao J, Han L, Zhao X, Jiang H, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002698	2018	Actinomycetales/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology	Transcriptome
Phylogeny	32699968	Lentzea indica sp. nov., a novel actinobacteria isolated from Indian Himalayan-soil.	Maiti PK, Mandal S	Antonie Van Leeuwenhoek	10.1007/s10482-020-01449-8	2020	Actinobacteria/classification/growth & development/isolation & purification, Bacterial Typing Techniques, Genotyping Techniques, India, Mycelium, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology	Phenotype

Reference

@id	authors	catalogue	doi/url	title
11983	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44796)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-44796
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
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)
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
82513	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID88654.1	StrainInfo: A central database for resolving microbial strain identifiers
82514	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID317403.1	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