Nocardioides phosphati (DSM 104026, CGMCC 4.7371, WYH11-7)

Name: Nocardioides phosphati (DSM 104026, CGMCC 4.7371, WYH11-7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133104

Type strain

Strain Designation WYH11-7

Culture col. no. DSM 104026 CGMCC 4.7371 WYH11-7

NCBI tax ID(s) 1867775

Special Collections DSMZ Literature strains

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

Links

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.

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

Name and taxonomic classification

SI-ID 406119

DSM 104026

@ref 20215

Last LPSN update 2026-05-29 08:38:01

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides phosphati

Full scientific name Nocardioides phosphati Xie et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25299	positive	0.7-2.0 µm	0.4-0.6 µm	rod-shaped
25299				coccus-shaped
125439	positive				99.201
125438					90.5
125438	positive				91.287

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
25299	creamy white	circular	2 days	R2A agar

Multicellular morphology

25299

Forms multicellular complexyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
25299	Reasoner's 2A agar (R2A)
25299	PDA (potato-dextrose agar)
25299	LB media
64132	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
25299	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
25299	positive	growth	4-38
25299	positive	optimum	30
64132	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
25299	positive	optimum	7
25299	positive	growth	5.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	95.694

Spore formation

25299

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25299	NaCl	positive	growth	0-1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25299	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	-	hydrolysis
25299	17128 ChEBI	adipate	+	assimilation
25299	27613 ChEBI	amygdalin	-	builds acid from
25299	17968 ChEBI	butyrate	-	assimilation
25299	16947 ChEBI	citrate	+	assimilation
25299	15824 ChEBI	D-fructose	-	assimilation
25299	12936 ChEBI	D-galactose	-	assimilation
25299	17634 ChEBI	D-glucose	+	builds acid from
25299	17634 ChEBI	D-glucose	+	assimilation
25299	16899 ChEBI	D-mannitol	-	assimilation
25299	16899 ChEBI	D-mannitol	+	builds acid from
25299	16024 ChEBI	D-mannose	-	assimilation
25299	63150 ChEBI	D-rhamnose	-	assimilation
25299	17924 ChEBI	D-sorbitol	-	builds acid from
25299	4853 ChEBI	esculin	-	hydrolysis
25299	16236 ChEBI	ethanol	-	assimilation
25299	24265 ChEBI	gluconate	+	assimilation
25299	17754 ChEBI	glycerol	-	assimilation
25299	15428 ChEBI	glycine	+	assimilation
25299	30849 ChEBI	L-arabinose	-	assimilation
25299	30849 ChEBI	L-arabinose	+	builds acid from
25299	16467 ChEBI	L-arginine	+	assimilation
25299	29991 ChEBI	L-aspartate	-	assimilation
25299	17561 ChEBI	L-cysteine	-	assimilation
25299	29985 ChEBI	L-glutamate	-	assimilation
25299	15971 ChEBI	L-histidine	+	assimilation
25299	15603 ChEBI	L-leucine	-	assimilation
25299	16643 ChEBI	L-methionine	-	assimilation
25299	17295 ChEBI	L-phenylalanine	-	assimilation
25299	17203 ChEBI	L-proline	-	assimilation
25299	62345 ChEBI	L-rhamnose	-	builds acid from
25299	17115 ChEBI	L-serine	-	assimilation
25299	17266 ChEBI	L-sorbose	-	assimilation
25299	17716 ChEBI	lactose	-	assimilation
25299	25115 ChEBI	malate	+	assimilation
25299	17306 ChEBI	maltose	+	assimilation
25299	28053 ChEBI	melibiose	+	builds acid from
25299	17790 ChEBI	methanol	-	assimilation
25299	17268 ChEBI	myo-inositol	-	builds acid from
25299	506227 ChEBI	N-acetylglucosamine	-	assimilation
25299	17632 ChEBI	nitrate	-	reduction
25299	16634 ChEBI	raffinose	-	assimilation
25299	17992 ChEBI	sucrose	-	builds acid from
25299	17992 ChEBI	sucrose	-	assimilation
25299	27082 ChEBI	trehalose	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
25299	2637	amikacin	30 µg
25299	2676	amoxicillin	10 µg
25299	28971	ampicillin	10 µg
25299	2955	azithromycin	15 µg
25299	28669	bacitracin		0.04 Unit
25299	204928	cefotaxime	30 µg
25299	3508	ceftazidime	30 µg
25299	17698	chloramphenicol	30 µg
25299	100241	ciprofloxacin	5 µg
25299	3745	clindamycin		2 µg
25299	48923	erythromycin	15 µg
25299	17833	gentamicin	10 µg
25299	7507	neomycin	30 µg
25299	100246	norfloxacin	10 µg
25299	28368	novobiocin		5 µg
25299	18208	penicillin g	10
25299	8232	piperacillin	100 µg
25299	28077	rifampicin	5 µg
25299	9332	sulfamethoxazole		300 µg
25299	27902	tetracycline	30 µg
25299	28001	vancomycin	30 µg

Metabolite production

@ref	Chebi-ID	Metabolite
25299	15688 ChEBI	acetoin
25299	16136 ChEBI	hydrogen sulfide
25299	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
25299	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
25299	acid phosphatase	+	3.1.3.2
25299	alkaline phosphatase	+	3.1.3.1
25299	alpha-chymotrypsin	-	3.4.21.1
25299	alpha-fucosidase	-	3.2.1.51
25299	alpha-galactosidase	-	3.2.1.22
25299	alpha-glucosidase	+	3.2.1.20
25299	alpha-mannosidase	-	3.2.1.24
25299	amylase	+
25299	arginine dihydrolase	+	3.5.3.6
25299	beta-galactosidase	-	3.2.1.23
25299	beta-glucosidase	-	3.2.1.21
25299	beta-glucuronidase	-	3.2.1.31
25299	catalase	+	1.11.1.6
25299	cystine arylamidase	+/-	3.4.11.3
25299	cytochrome oxidase	-	1.9.3.1
25299	esterase (C 4)	+
25299	esterase Lipase (C 8)	+
25299	gelatinase	+
25299	leucine arylamidase	+	3.4.11.1
25299	lipase (C 14)	-
25299	lysine decarboxylase	-	4.1.1.18
25299	N-acetyl-beta-glucosaminidase	-	3.2.1.52
25299	naphthol-AS-BI-phosphohydrolase	+
25299	ornithine decarboxylase	-	4.1.1.17
25299	trypsin	-	3.4.21.4
25299	tryptophan deaminase	-	4.1.99.1
25299	urease	-	3.5.1.5
25299	valine arylamidase	+/-

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
25299	phosphate rock powder samples collected at a phosphate mining field in Kunming	Kunming, Yunnan Province, PR China	China	CHN	Asia
64132	phosphate rock powder from a phosphate mining field	Yunnan Province, suburb of Kunming	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64132	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1464637v1 assembly for Nocardioides phosphati CGMCC 4.7371	scaffold	GCA_014646375	1867775.3	2989587868	1867775	71.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64132	Nocardioides phosphati strain WYH11-7 16S ribosomal RNA gene, partial sequence	KX426598	1478		1867775

GC content

@ref	GC-content (mol%)	Method
64132	71.2	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1464637v1 assembly for Nocardioides phosphati CGMCC 4.7371
BV-BRC: 1867775.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.69	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	spore_formation	BacteriaNetⓘ	no	74.13	no
125439	motility	BacteriaNetⓘ	no	85.71	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides phosphati CGMCC 4.7371
NCBI: GCA_014646375.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.29	yes
125438	anaerobic	anaerobicⓘ	no	94.15	no
125438	aerobic	aerobicⓘ	yes	86.62	no
125438	spore-forming	spore-formingⓘ	no	72.11	yes
125438	thermophilic	thermophileⓘ	no	96.60	yes
125438	flagellated	motile2+ⓘ	no	90.50	yes

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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Nocardioides phosphati (DSM 104026, CGMCC 4.7371, WYH11-7)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014646375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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