Cite this strain

Lentzea nigeriaca (DSM 45680, JCM 31207, KCTC 29057)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24445

Type strain

Strain Designation NJ2035

Culture col. no. DSM 45680 JCM 31207 KCTC 29057 NRRL B-24881 NJ2035

NCBI tax ID(s) 1128665

Special Collections DSMZ JCM KCTC Literature strains

Links

Name and taxonomic classification

Lentzea nigeriaca NJ2035 is an aerobe, spore-forming, mesophilic bacterium that was isolated from arid soil.

spore-forming Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 403146

DSM 45680

Last LPSN update 2024-12-09 10:45:47

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Lentzea

Species Lentzea nigeriaca

Full scientific name Lentzea nigeriaca (Camas et al. 2013) Nouioui et al. 2018

Synonyms (1)

Lechevalieria nigeriaca

Morphology

Cell morphology

@ref	Gram stain	Cell shape
31106	positive	rod-shaped
67771	positive
125439	positive

Multimedia

@ref:	20625
manual_annotation:	1
multimedia content:	DSM_45680.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45680.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20625	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	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 (°C)	Range
20625	positive	growth	28	mesophilic
31106	positive	growth	20-45
31106	positive	optimum	29	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
31106	positive	optimum	7.2
31106	positive	growth	5.0-10.0

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31106	NaCl	positive	growth	1.0-5.0 %

Observation

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

Spore formation

31106

Spore formationyes

Enzymes

@ref	Value	Activity	Ec
31106	catalase	+	1.11.1.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31106	18240 ChEBI	4-hydroxy-L-proline	+	carbon source
31106	16449 ChEBI	alanine	+	carbon source
31106	22599 ChEBI	arabinose	+	carbon source
31106	29016 ChEBI	arginine	+	carbon source
31106	17057 ChEBI	cellobiose	+	carbon source
31106	23652 ChEBI	dextrin	+	carbon source
31106	4853 ChEBI	esculin	+	hydrolysis
31106	28260 ChEBI	galactose	+	carbon source
31106	17716 ChEBI	lactose	+	carbon source
31106	17306 ChEBI	maltose	+	carbon source
31106	29864 ChEBI	mannitol	+	carbon source
31106	37684 ChEBI	mannose	+	carbon source
31106	28044 ChEBI	phenylalanine	+	carbon source
31106	26271 ChEBI	proline	+	carbon source
31106	26546 ChEBI	rhamnose	+	carbon source
31106	17822 ChEBI	serine	+	carbon source
31106	17992 ChEBI	sucrose	+	carbon source
31106	26986 ChEBI	threonine	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
31106	aerobe
67771	aerobe
125439	obligate aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Condition	#Xerophilic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
20625	arid soil	Abuja	Nigeria	NGA	Africa
67770	Arid soil in Abuja		Nigeria	NGA	Africa
67771	From soil	Arid estate, Abuja city	Nigeria	NGA	Africa

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
20625	1	Risk group (German classification)

Sequence information

GC content

@ref	GC-content (mol%)	Method
20625	68.4	fluorimetric
31106	68.4
67770	68.4	thermal denaturation, midpoint method (Tm)

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20625	Lechevalieria nigeriaca strain NJ2035 16S ribosomal RNA gene, partial sequence	JN989291	1473		1128665

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Lentzea nigeriaca DSM 45680	GCA_016907955	contig		1128665
66792	Lentzea nigeriaca strain DSM 45680	1128665.3	wgs	PATRIC	1128665
66792	Lentzea nigeriaca DSM 45680	2901015569	draft	JGI IMG/M	1128665

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Lentzea nigeriaca DSM 45680
NCBI: GCA_016907955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	motility	BacteriaNetⓘ	no	84.30	no
125439	spore_formation	BacteriaNetⓘ	yes	63.50	no

Predictions from Diaspora project based on:
Lentzea nigeriaca strain DSM 45680
PATRIC: 1128665.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.62	yes
125438	anaerobic	anaerobicⓘ	no	97.42	no
125438	spore-forming	spore-formingⓘ	yes	82.95	no
125438	aerobic	aerobicⓘ	yes	89.42	yes
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	79.33	yes

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lechevalieria nigeriaca sp. nov., isolated from arid soil.	Camas M, Veyisoglu A, Tatar D, Saygin H, Cetin D, Sazak A, Guven K, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.052266-0	2013

Straininfo Link

@ref	Straininfo	Culture collections
88322	403146	DSM 45680

Culture collection no.

Culture collection no.
DSM 45680
JCM 31207
KCTC 29057
NRRL B-24881
NJ2035

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20625	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45680
#31106	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27435 (see below)
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#88322	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 . ( DOI 10.60712/SI-ID403146.1 )
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

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