Name: Nocardioides vastitatis 21Sc5-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 164533

Type strain:

Species: Nocardioides vastitatis

Strain Designation: 21Sc5-5

Culture col. no.: JCM 33365, CGMCC 4.7608

Strain history: C.-H. Sun; Inst. of Med. Biotechnol., Chin. Acad. of Med. Sci., China; 21Sc5-5.

NCBI tax ID(s): 2568655 (species)

Section

Nocardioides vastitatis 21Sc5-5 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Soil at the rhizosphere of Inula salsoloides in the Taklamakan Desert in Xinjiang Uygur Autonomous Region.

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

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	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides vastitatis**
	Full Scientific Name (LPSN)	Nocardioides vastitatis Liu et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #69494]	Gram stain	positive

[Ref.: #69494]	Cell length	1.1-2.3 µm

[Ref.: #69494]	Cell width	0.4-0.7 µm

[Ref.: #69494]	Cell shape	rod-shaped

[Ref.: #69494]	Motility	no

[Ref.: #69494]	Colony color	creamy white
[Ref.: #69494]	Colony shape	circular
[Ref.: #69494]	Incubation period	5 days
[Ref.: #69494]	Cultivation medium used	ISP 2 agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP 2 agar

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Culture medium growth

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Culture medium

ISP 2, TSA, R2A

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Culture medium growth

		Temperature
[Ref.: #67770]	growth	28 °C
[Ref.: #69494]	growth	10.0-37.0 °C
[Ref.: #69494]	optimum	28.0-30.0 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #69494]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #69494]			optimum	7
[Ref.: #69494]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69494]		NaCl		growth	0.0-3.0	%(w/v)
[Ref.: #69494]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]	Observation	quinones: MK-8(H₄)
[Ref.: #69494]	Observation	The cell-wall peptidoglycan contains LL-diaminopimelic acid as the diagnostic diamino acid.
[Ref.: #69494]	Observation	The predominant menaquinone is MK-8(H4).

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69494]	adipate ChEBI	-	assimilation
[Ref.: #69494]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #69494]	casein	-	hydrolysis
[Ref.: #69494]	citrate ChEBI	-	assimilation
[Ref.: #69494]	D-fructose ChEBI	+	builds acid from
[Ref.: #69494]	D-glucose ChEBI	-	assimilation
[Ref.: #69494]	D-glucose ChEBI	+	builds acid from
[Ref.: #69494]	D-mannitol ChEBI	+	assimilation
[Ref.: #69494]	D-mannose ChEBI	-	assimilation
[Ref.: #69494]	D-xylose ChEBI	+/-	builds acid from
[Ref.: #69494]	decanoate ChEBI	-	assimilation
[Ref.: #69494]	esculin ChEBI	-	hydrolysis
[Ref.: #69494]	esculin ChEBI	+	builds acid from
[Ref.: #69494]	gelatin ChEBI	-	hydrolysis
[Ref.: #69494]	glucose ChEBI	-	fermentation
[Ref.: #69494]	inulin ChEBI	+/-	builds acid from
[Ref.: #69494]	L-arabinose ChEBI	-	assimilation
[Ref.: #69494]	L-arabinose ChEBI	+	builds acid from
[Ref.: #69494]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #69494]	malate ChEBI	+	assimilation
[Ref.: #69494]	maltose ChEBI	-	assimilation
[Ref.: #69494]	mannitol ChEBI	+	builds acid from
[Ref.: #69494]	myo-inositol ChEBI	+	builds acid from
[Ref.: #69494]	N-acetyl-D-glucosamine ChEBI	-	assimilation
[Ref.: #69494]	nitrate ChEBI	-	reduction
[Ref.: #69494]	phenylacetate ChEBI	-	assimilation
[Ref.: #69494]	potassium gluconate ChEBI	-	assimilation
[Ref.: #69494]	raffinose ChEBI	+/-	builds acid from
[Ref.: #69494]	skimmed milk	-	hydrolysis
[Ref.: #69494]	starch ChEBI	-	hydrolysis
[Ref.: #69494]	sucrose ChEBI	+/-	builds acid from
[Ref.: #69494]	tween 20 ChEBI	+	hydrolysis
[Ref.: #69494]	tween 40 ChEBI	+	hydrolysis
[Ref.: #69494]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #69494]		hydrogen sulfide ChEBI	no
[Ref.: #69494]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #69494]	acid phosphatase	+	3.1.3.2
[Ref.: #69494]	alkaline phosphatase	+	3.1.3.1
[Ref.: #69494]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #69494]	alpha-fucosidase	-	3.2.1.51
[Ref.: #69494]	alpha-galactosidase	-	3.2.1.22
[Ref.: #69494]	alpha-glucosidase	+	3.2.1.20
[Ref.: #69494]	alpha-mannosidase	-	3.2.1.24
[Ref.: #69494]	arginine dihydrolase	-	3.5.3.6
[Ref.: #69494]	beta-galactosidase	+	3.2.1.23
[Ref.: #69494]	beta-glucosidase	+	3.2.1.21
[Ref.: #69494]	beta-glucuronidase	-	3.2.1.31
[Ref.: #69494]	catalase	+	1.11.1.6
[Ref.: #69494]	cystine arylamidase	-	3.4.11.3
[Ref.: #69494]	cytochrome oxidase	-	1.9.3.1
[Ref.: #69494]	esterase (C 4)	+
[Ref.: #69494]	esterase Lipase (C 8)	+
[Ref.: #69494]	leucine arylamidase	+	3.4.11.1
[Ref.: #69494]	lipase (C 14)	-
[Ref.: #69494]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #69494]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #69494]	trypsin	-	3.4.21.4
[Ref.: #69494]	urease	-	3.5.1.5
[Ref.: #69494]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67770]	Sample type/isolated from	Soil at the rhizosphere of Inula salsoloides in the Taklamakan Desert in Xinjiang Uygur Autonomous Region
[Ref.: #67770]	Host species	Inula salsoloides
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #69494]	Sample type/isolated from	soil sample from rhizosphere of Inula salsoloides
[Ref.: #69494]	Geographic location (country and/or sea, region)	Taklamakan desert, Xinjiang Uygur
[Ref.: #69494]	Country	China
[Ref.: #69494]	Country ISO 3 Code	CHN
[Ref.: #69494]	Continent	Asia
[Ref.: #69494]	Geographic location	38.6944°/80.9797°
[Ref.: #69494]	Enrichment culture	R2A
[Ref.: #69494]	Enrichment culture composition	R2A with cycloheximide (45 mg/l), nalidixic acid (25 mg/l), potassium dichromate (45 mg/l)
[Ref.: #69494]	Enrichment culture duration	56 days
[Ref.: #69494]	Enrichment culture temperature	28 ̊C
[Ref.: #69494]	Isolation/enrichment procedure	serial streaking technique
* marker position based on {}

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.: #67770]	Nocardioides vastitatis 16S ribosomal RNA gene, partial sequence	MK787305	1480	ENA	2568655 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardioides sp. 21Sc5-5	GCA_004803405	scaffold	GenBank	35761 tax ID
[Ref.: #69494]	genome sequence	SSXI00000000		GenBank	35761 tax ID

[Ref.: #67770]

GC-content

70.4 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides sp. 21Sc5-5 NCBI: GCA_004803405.1
[Ref.: #69480]	motile	no	96.624	no
[Ref.: #69480]	flagellated	no	98.536	no
[Ref.: #69480]	gram-positive	yes	91.441	no
[Ref.: #69480]	anaerobic	no	97.672	no
[Ref.: #69480]	aerobic	yes	86.111	no
[Ref.: #69480]	halophile	no	94.188	no
[Ref.: #69480]	spore-forming	no	77.316	no
[Ref.: #69480]	thermophile	no	91.989	yes
[Ref.: #69480]	glucose-util	yes	87.903	no
[Ref.: #69480]	glucose-ferment	no	87.527	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33365, CGMCC 4.7608

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil.	Liu SW, Xue CM, Li FN, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003718	2020	*

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69494

Panagiotis Ballas, Christian Rückert, Karen Wagener, Marc Drillich, Peter Kämpfer, Hans-Jürgen Busse, Monika Ehling-Schulz: Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil. IJSEM 70: 2019 ( DOI 10.1099/ijsem.0.003718 )

* These data were automatically processed and therefore are not curated

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Nocardioides sp. 21Sc5-5

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