Pseudonocardia acaciae (DSM 45401, BCC 28481, NBRC 104274)

Name: Pseudonocardia acaciae (DSM 45401, BCC 28481, NBRC 104274)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13400

Type strain

Culture col. no. DSM 45401 BCC 28481 NBRC 104274 NRRL B-24609 GMKU 095 3 more

NCBI tax ID(s) 551276

Special Collections DSMZ JCM CIP Literature strains

History CIP <- 2009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095 DSMZ <- C Suriyachadkun, BIOTEC Culture Collection (BCC); BCC 28481 <- K. Duangmal JCM <-- TISTR 1862 <-- K. Duangmal GMKU095. CIP <- 2009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095

Links

Pseudonocardia acaciae DSM 45401 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from roots of Acacia auriculiformis A. Cunn. ex. Benth..

spore-forming Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 362848

BCC 28481,NBRC 104274,NRRL B-24609,TISTR 1862,JCM 16707,DSM 45401,CIP 110060

@ref 20215

Last LPSN update 2026-05-29 08:28:02

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Pseudonocardia

Species Pseudonocardia acaciae

Full scientific name Pseudonocardia acaciae Duangmal et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29165	positive
115987	positive	rod-shaped
125438			90.1
125439			94.253
125439	positive		99.79

Pigmentation

29165

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16604	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
33650	MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
115987	CIP Medium 116	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
16604	positive	growth	37
29165	positive	growth	18-42
29165	positive	optimum	37
33650	positive	growth	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
29165	positive	optimum	6.5
29165	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29165	aerobe
115987	facultative anaerobe
125439	obligate aerobe	99.325

Spore formation

29165

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29165	NaCl	positive	growth	0-5 %
29165	NaCl	positive	optimum	2.5 %

Observation

@ref	Observation
29165	aggregates in chains
67770	quinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29165	22599 ChEBI	arabinose	+	carbon source
29165	28757 ChEBI	fructose	+	carbon source
29165	17234 ChEBI	glucose	+	carbon source
29165	17754 ChEBI	glycerol	+	carbon source
29165	29864 ChEBI	mannitol	+	carbon source
29165	37684 ChEBI	mannose	+	carbon source
29165	17268 ChEBI	myo-inositol	+	carbon source
29165	17632 ChEBI	nitrate	+	reduction
115987	17632 ChEBI	nitrate	+	reduction
115987	16301 ChEBI	nitrite	-	reduction
29165	26546 ChEBI	rhamnose	+	carbon source
29165	15963 ChEBI	ribitol	+	carbon source
29165	33942 ChEBI	ribose	+	carbon source
29165	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
115987	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
29165	catalase	+	1.11.1.6
115987	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
115987	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
29165	urease	+	3.5.1.5
115987	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
115987	-	+	+	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16604	roots of Acacia auriculiformis A. Cunn. ex. Benth.		Bangkok, Kasetsart University	Thailand	THA	Asia
67770	Roots of Acacia auriculiformis A. Cunn. ex Benth. from Kasetsart Univ.	Acacia auriculiformis	Bangkok	Thailand	THA	Asia
115987	Plant, Roots, Acacia auriculiformis		Bangkok	Thailand	THA	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU921261 (>99% sequence identity) for Pseudonocardia acaciae subclade from Microbeatlas

Aquatic Samples	89
Soil Samples	964
Animal Samples	115
Plant Samples	262
Total Samples	1430

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16604	1	Risk group (German classification) According to TRBA 466
115987	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM62078v1 assembly for Pseudonocardia acaciae DSM 45401	scaffold	GCA_000620785	1123023.3	2558860112	1123023	56.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16604	Pseudonocardia acaciae strain GMKU095 16S ribosomal RNA gene, partial sequence	EU921261	1483		1123023

GC content

@ref	GC-content (mol%)	Method
16604	71.6
67770	71.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM62078v1 assembly for Pseudonocardia acaciae DSM 45401
BV-BRC: 1123023.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	99.79	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.33	no
125439	motility	BacteriaNetⓘ	no	94.25	no
125439	spore_formation	BacteriaNetⓘ	yes	89.25	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudonocardia acaciae DSM 45401
PATRIC: 1123023.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.71	yes
125438	anaerobic	anaerobicⓘ	no	97.13	yes
125438	spore-forming	spore-formingⓘ	yes	71.31	yes
125438	aerobic	aerobicⓘ	yes	85.42	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	90.10	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Characterizing an amidase and its operon from actinomycete bacteria responsible for paraben catabolism.	Takenoya M, Hiratsuka Y, Shimamura K, Ito S, Sasaki Y, Yajima S.	Biosci Biotechnol Biochem	10.1093/bbb/zbae083	2024
Genetics	Environmental Potential for Microbial 1,4-Dioxane Degradation Is Sparse despite Mobile Elements Playing a Role in Trait Distribution.	Goff KL, Hug LA.	Appl Environ Microbiol	10.1128/aem.02091-21	2022
Metabolism	Expanding the Toolbox of R-Selective Amine Transaminases by Identification and Characterization of New Members.	Telzerow A, Paris J, Hakansson M, Gonzalez-Sabin J, Rios-Lombardia N, Groger H, Moris F, Schurmann M, Schwab H, Steiner K.	Chembiochem	10.1002/cbic.202000692	2021
Metabolism	Hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides.	Oinuma K, Takuwa A, Taniyama K, Doi Y, Takaya N.	J Bacteriol	10.1128/jb.02443-14	2015
Phylogeny	Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree.	Kaewkla O, Franco CMM	Int J Syst Evol Microbiol	10.1099/ijs.0.022327-0	2010
Phylogeny	Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth.	Duangmal K, Thamchaipenet A, Matsumoto A, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.007724-0	2009

References

#16604	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45401
#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 )
#25589	IJSEM 1487 2009 ( DOI 10.1099/ijs.0.007724-0 , PubMed 19502340 )
#29165	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 #25589
#33650	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#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 .
#115987	Collection of Institut Pasteur ; Curators of the CIP; CIP 110060
#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 )

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Pseudonocardia acaciae (DSM 45401, BCC 28481, NBRC 104274)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000620785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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