Name: Nocardioides phosphati WYH11-7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133104

Type strain:

Species: Nocardioides phosphati

Strain Designation: WYH11-7

Culture col. no.: DSM 104026, CGMCC 4.7371

Strain history: <- F. Xie, Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou, China; WYH11-7

NCBI tax ID(s): 1867775 (species)

SI-ID 406119

DSM 104026

Section

Nocardioides phosphati WYH11-7 is a Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from phosphate rock powder samples collected at a phosphate mining field in Kunming.

colony-forming
Gram-positive
rod-shaped
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 phosphati**
	Full Scientific Name (LPSN)	Nocardioides phosphati Xie et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25299]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25299]	Cell length	0.7-2.0 µm

[Ref.: #25299]	Cell width	0.4-0.6 µm

[Ref.: #25299]	Cell shape	rod-shaped
[Ref.: #25299]	Cell shape	coccus-shaped

[Ref.: #25299]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.028

[Ref.: #25299]	Colony color	creamy white
[Ref.: #25299]	Colony shape	circular
[Ref.: #25299]	Incubation period	2 days
[Ref.: #25299]	Cultivation medium used	R2A agar

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Multicellular complex forming ability

yes

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

PDA (potato-dextrose agar)

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Culture medium growth

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Culture medium

LB media

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Culture medium growth

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

		Temperature
[Ref.: #25299]	growth	4-38 °C
[Ref.: #25299]	optimum	30 °C
[Ref.: #64132]	growth	28 °C

[Ref.: #25299]	Temperature range	mesophilic
[Ref.: #64132]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25299]			optimum	7
[Ref.: #25299]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25299]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.841

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25299]		NaCl		growth	0-1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25299]	4-nitrophenyl beta-D-galactopyranoside ChEBI	-	hydrolysis
[Ref.: #25299]	adipate ChEBI	+	assimilation
[Ref.: #25299]	amygdalin ChEBI	-	builds acid from
[Ref.: #25299]	butyrate ChEBI	-	assimilation
[Ref.: #25299]	citrate ChEBI	+	assimilation
[Ref.: #25299]	D-fructose ChEBI	-	assimilation
[Ref.: #25299]	D-galactose ChEBI	-	assimilation
[Ref.: #25299]	D-glucose ChEBI	+	builds acid from
[Ref.: #25299]	D-glucose ChEBI	+	assimilation
[Ref.: #25299]	D-mannitol ChEBI	-	assimilation
[Ref.: #25299]	D-mannitol ChEBI	+	builds acid from
[Ref.: #25299]	D-mannose ChEBI	-	assimilation
[Ref.: #25299]	D-rhamnose ChEBI	-	assimilation
[Ref.: #25299]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #25299]	esculin ChEBI	-	hydrolysis
[Ref.: #25299]	ethanol ChEBI	-	assimilation
[Ref.: #25299]	gluconate ChEBI	+	assimilation
[Ref.: #25299]	glycerol ChEBI	-	assimilation
[Ref.: #25299]	glycine ChEBI	+	assimilation
[Ref.: #25299]	L-arabinose ChEBI	-	assimilation
[Ref.: #25299]	L-arabinose ChEBI	+	builds acid from
[Ref.: #25299]	L-arginine ChEBI	+	assimilation
[Ref.: #25299]	L-aspartate ChEBI	-	assimilation
[Ref.: #25299]	L-cysteine ChEBI	-	assimilation
[Ref.: #25299]	L-glutamate ChEBI	-	assimilation
[Ref.: #25299]	L-histidine ChEBI	+	assimilation
[Ref.: #25299]	L-leucine ChEBI	-	assimilation
[Ref.: #25299]	L-methionine ChEBI	-	assimilation
[Ref.: #25299]	L-phenylalanine ChEBI	-	assimilation
[Ref.: #25299]	L-proline ChEBI	-	assimilation
[Ref.: #25299]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #25299]	L-serine ChEBI	-	assimilation
[Ref.: #25299]	L-sorbose ChEBI	-	assimilation
[Ref.: #25299]	lactose ChEBI	-	assimilation
[Ref.: #25299]	malate ChEBI	+	assimilation
[Ref.: #25299]	maltose ChEBI	+	assimilation
[Ref.: #25299]	melibiose ChEBI	+	builds acid from
[Ref.: #25299]	methanol ChEBI	-	assimilation
[Ref.: #25299]	myo-inositol ChEBI	-	builds acid from
[Ref.: #25299]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25299]	nitrate ChEBI	-	reduction
[Ref.: #25299]	raffinose ChEBI	-	assimilation
[Ref.: #25299]	sucrose ChEBI	-	builds acid from
[Ref.: #25299]	sucrose ChEBI	-	assimilation
[Ref.: #25299]	trehalose ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25299]	amikacin ChEBI	yes	30	µg
[Ref.: #25299]	amoxicillin ChEBI	yes	10	µg
[Ref.: #25299]	ampicillin ChEBI	yes	10	µg
[Ref.: #25299]	azithromycin ChEBI	yes	15	µg
[Ref.: #25299]	bacitracin ChEBI				yes	0.04	Unit
[Ref.: #25299]	cefotaxime ChEBI	yes	30	µg
[Ref.: #25299]	ceftazidime ChEBI	yes	30	µg
[Ref.: #25299]	chloramphenicol ChEBI	yes	30	µg
[Ref.: #25299]	ciprofloxacin ChEBI	yes	5	µg
[Ref.: #25299]	clindamycin ChEBI				yes	2	µg
[Ref.: #25299]	erythromycin ChEBI	yes	15	µg
[Ref.: #25299]	gentamicin ChEBI	yes	10	µg
[Ref.: #25299]	neomycin ChEBI	yes	30	µg
[Ref.: #25299]	norfloxacin ChEBI	yes	10	µg
[Ref.: #25299]	novobiocin ChEBI				yes	5	µg
[Ref.: #25299]	penicillin g ChEBI	yes	10
[Ref.: #25299]	piperacillin ChEBI	yes	100	µg
[Ref.: #25299]	rifampicin ChEBI	yes	5	µg
[Ref.: #25299]	sulfamethoxazole ChEBI				yes	300	µg
[Ref.: #25299]	tetracycline ChEBI	yes	30	µg
[Ref.: #25299]	vancomycin ChEBI	yes	30	µg
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #25299]	acetoin ChEBI	no
[Ref.: #25299]	hydrogen sulfide ChEBI	no
[Ref.: #25299]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #25299]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25299]	acid phosphatase	+	3.1.3.2
[Ref.: #25299]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25299]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25299]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25299]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25299]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25299]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25299]	amylase	+
[Ref.: #25299]	arginine dihydrolase	+	3.5.3.6
[Ref.: #25299]	beta-galactosidase	-	3.2.1.23
[Ref.: #25299]	beta-glucosidase	-	3.2.1.21
[Ref.: #25299]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25299]	catalase	+	1.11.1.6
[Ref.: #25299]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #25299]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25299]	esterase (C 4)	+
[Ref.: #25299]	esterase Lipase (C 8)	+
[Ref.: #25299]	gelatinase	+
[Ref.: #25299]	leucine arylamidase	+	3.4.11.1
[Ref.: #25299]	lipase (C 14)	-
[Ref.: #25299]	lysine decarboxylase	-	4.1.1.18
[Ref.: #25299]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25299]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25299]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #25299]	trypsin	-	3.4.21.4
[Ref.: #25299]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25299]	urease	-	3.5.1.5
[Ref.: #25299]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25299]

Fatty acid	Percentage
C18:1ω9c	31.3
C16:0	22
C17:0	10.1
C17:1ω8c	7.3
10-Methyl C18:0	6.8
C16:1ω6c / C16:1ω7c	5.9
C16:0 2OH	3.5
C10:0 3OH	3.4
C19:1ω9c / C19:1ω11c	2.3
C18:0	2.1
C17:0 2OH	1.9
C14:0	1.3
C15:1ω6c	1.2
C16:1ω9c	1.1
C16:0 iso	1
10-Methyl C17:0	1
C15:0 2OH	0.3
C19:0	0.3
C14:1ω5c	0.3
C15:1ω8c	0.2
C18:0 iso	0.2
C12:0	0.1

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

[Ref.: #25299]	Sample type/isolated from	phosphate rock powder samples collected at a phosphate mining field in Kunming
[Ref.: #25299]	Geographic location (country and/or sea, region)	Kunming, Yunnan Province, PR China
[Ref.: #25299]	Country	China
[Ref.: #25299]	Country ISO 3 Code	CHN
[Ref.: #25299]	Continent	Asia

[Ref.: #64132]	Sample type/isolated from	phosphate rock powder from a phosphate mining field
[Ref.: #64132]	Geographic location (country and/or sea, region)	Yunnan Province, suburb of Kunming
[Ref.: #64132]	Country	China
[Ref.: #64132]	Country ISO 3 Code	CHN
[Ref.: #64132]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX426598 (>99% sequence identity) for Nocardioides phosphati from Microbeatlas

Aquatic Samples	158
Soil Samples	1465
Animal Samples	231
Plant Samples	149
Total Samples	2003

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

[Ref.: #64132]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #64132]	Nocardioides phosphati strain WYH11-7 16S ribosomal RNA gene, partial sequence	KX426598	1478	ENA	1867775 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides phosphati CGMCC 4.7371	GCA_014646375	scaffold	GenBank	1867775 tax ID	*
[Ref.: #66792]	Nocardioides phosphati strain CGMCC 4.7371	1867775.3	wgs	PATRIC	1867775 tax ID	*

[Ref.: #64132]

GC-content

71.2 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nocardioides phosphati CGMCC 4.7371 NCBI: GCA_014646375.1
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides phosphati CGMCC 4.7371 NCBI: GCA_014646375.1
[Ref.: #69480]	flagellated	no	98.134	yes
[Ref.: #69480]	gram-positive	yes	86.891	yes
[Ref.: #69480]	anaerobic	no	98.181	no
[Ref.: #69480]	aerobic	yes	93.372	no
[Ref.: #69480]	halophile	no	92.757	no
[Ref.: #69480]	spore-forming	no	90.634	no
[Ref.: #69480]	thermophile	no	98.555	yes
[Ref.: #69480]	glucose-util	yes	86.174	yes
[Ref.: #69480]	motile	no	98.128	yes
[Ref.: #69480]	glucose-ferment	no	90.274	no

Availability in culture collections External links

[Ref.: #64132]

Culture collection no.

DSM 104026, CGMCC 4.7371

[Ref.: #91366]

SI-ID 406119

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides jejuensis sp. nov., isolated from soil.	Jang JH, Maeng S, Jung HY, Kim MK, Subramani G	Antonie Van Leeuwenhoek	10.1007/s10482-019-01343-y	2019	*
Phylogeny	Nocardioides phosphati sp. nov., an actinomycete isolated from a phosphate mine.	Xie F, Yang Y, Ma H, Quan S, Yue D, Sun Y, Feng F, Zhen J, Liu D	Int J Syst Evol Microbiol	10.1099/ijsem.0.001754	2017	*

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 )

#25299

F. Y. Xie, Y.,Ma, H.,Quan, S.,Yue, D.,Sun, Y.,Feng, F.,Zhen, J.,Liu, D.: Nocardioides phosphati sp. nov., an actinomycete isolated from a phosphate mine. IJSEM 67: 1522 - 1528 2017 ( DOI 10.1099/ijsem.0.001754 , PubMed 28005518 )

#64132

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104026

#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) .

#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.: MicrobeAtlas 1.0 beta .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91366

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-ID406119.1 )

* These data were automatically processed and therefore are not curated

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Nocardioides phosphati CGMCC 4.7371

Nocardioides phosphati CGMCC 4.7371

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