Name: Pseudonocardia babensis VN05A0561
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13403

Type strain:

Species: Pseudonocardia babensis

Strain Designation: VN05A0561

Culture col. no.: DSM 45574, CIP 110219, NBRC 105793, VTCC A-1757

Strain history: CIP <- 2010, NBRC <- VTCC and NITE: strain VN05A0561

NCBI tax ID(s): 663386 (species)

SI-ID 371021

NBRC 105793, CIP 110219

Section

Pseudonocardia babensis VN05A0561 is an aerobe, spore-forming, mesophilic bacterium that was isolated from plant litter.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Pseudonocardia*
	Species	**Pseudonocardia babensis**
	Full Scientific Name (LPSN)	Pseudonocardia babensis Sakiyama et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29660]	Gram stain	positive
[Ref.: #116695]	Gram stain	positive

[Ref.: #29660]	Cell length	01-02 µm

[Ref.: #29660]	Cell width	0.3-0.5 µm

[Ref.: #29660]	Cell shape	rod-shaped
[Ref.: #116695]	Cell shape	rod-shaped

[Ref.: #29660]	Motility	no
[Ref.: #116695]	Motility	no

[Ref.: #29660]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17666]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #17666]

Culture medium growth

[Ref.: #17666]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17666]

Culture medium composition

expand / minimize

[Ref.: #40334]

Culture medium

MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum

[Ref.: #40334]

Culture medium growth

[Ref.: #40334]

Culture medium composition

expand / minimize

[Ref.: #116695]

Culture medium

CIP Medium 57

[Ref.: #116695]

Culture medium growth

[Ref.: #116695]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #17666]	growth	28 °C
[Ref.: #29660]	growth	10-45 °C
[Ref.: #29660]	optimum	28 °C
[Ref.: #40334]	growth	30 °C

[Ref.: #17666]	Temperature range	mesophilic
[Ref.: #29660]	Temperature range	mesophilic
[Ref.: #40334]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29660]			optimum	7
[Ref.: #29660]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29660]

Oxygen tolerance

aerobe

[Ref.: #29660]

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29660]		NaCl		growth	0-3	%
[Ref.: #29660]		NaCl		optimum	0-3	%

[Ref.: #29660]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29660]	arabinose ChEBI	+	carbon source
[Ref.: #29660]	cellobiose ChEBI	+	carbon source
[Ref.: #29660]	esculin ChEBI	+	hydrolysis
[Ref.: #29660]	fructose ChEBI	+	carbon source
[Ref.: #29660]	galactose ChEBI	+	carbon source
[Ref.: #29660]	glucose ChEBI	+	carbon source
[Ref.: #29660]	L-arabitol ChEBI	+	carbon source
[Ref.: #29660]	lactose ChEBI	+	carbon source
[Ref.: #29660]	maltose ChEBI	+	carbon source
[Ref.: #29660]	mannitol ChEBI	+	carbon source
[Ref.: #29660]	melibiose ChEBI	+	carbon source
[Ref.: #116695]	nitrate ChEBI	-	reduction
[Ref.: #116695]	nitrite ChEBI	-	reduction
[Ref.: #29660]	raffinose ChEBI	+	carbon source
[Ref.: #29660]	rhamnose ChEBI	+	carbon source
[Ref.: #29660]	salicin ChEBI	+	carbon source
[Ref.: #29660]	sorbitol ChEBI	+	carbon source
[Ref.: #29660]	sucrose ChEBI	+	carbon source
[Ref.: #29660]	trehalose ChEBI	+	carbon source
[Ref.: #29660]	xylitol ChEBI	+	carbon source
[Ref.: #29660]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116695]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116695]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #116695]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116695]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116695]	12446	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #17666]	Sample type/isolated from	plant litter
[Ref.: #17666]	Geographic location (country and/or sea, region)	Ba BE National Park, Back Kan
[Ref.: #17666]	Country	Vietnam
[Ref.: #17666]	Country ISO 3 Code	VNM
[Ref.: #17666]	Continent	Asia

[Ref.: #116695]	Sample type/isolated from	Plant, Litter
[Ref.: #116695]	Geographic location (country and/or sea, region)	Ba be National Park, Back Kan
[Ref.: #116695]	Country	Vietnam
[Ref.: #116695]	Country ISO 3 Code	VNM
[Ref.: #116695]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	-
#Host Body Product	#Plant	#Plant litter (Forest)
#Host Body Product	#Plant	#Plant litter (Forest)

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17666]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116695]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #17666]	Pseudonocardia babensis gene for 16S rRNA, partial sequence	AB514449	1454	ENA	663386 tax ID

[Ref.: #17666]

GC-content

73 mol%

Availability in culture collections External links

[Ref.: #17666]

Culture collection no.

DSM 45574, CIP 110219, NBRC 105793, VTCC A-1757

[Ref.: #82601]

SI-ID 371021

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudonocardia babensis sp. nov., isolated from plant litter.	Sakiyama Y, Thao NKN, Vinh HV, Giang NM, Miyadoh S, Hop DV, Ando K	Int J Syst Evol Microbiol	10.1099/ijs.0.018127-0	2009	*

References

#17666

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45574

#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 )

#29660

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 #26048 (see below)

#40334 ; Curators of the CIP;

#68382

Automatically annotated from API zym .

#82601

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-ID371021.1 )

#116695 Collection of Institut Pasteur ; Curators of the CIP; CIP 110219

#26048

IJSEM 2336 2010 ( DOI 10.1099/ijs.0.018127-0 , PubMed 19933589 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pseudonocardia babensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF