Cupriavidus sp. (DSM 25816, USMAHM13)

Name: Cupriavidus sp. (DSM 25816, USMAHM13)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158071

Type strain

Strain Designation USMAHM13

Culture col. no. DSM 25816 USMAHM13

NCBI tax ID(s) 1873897

Special Collections DSMZ

History <- A. Al-Ashraf Abdullah, University Sains Malaysia, Minden, Penang; USMAHM13 <- H. Ramachandran

Links

USMAHM13 is a bacterium that was isolated from paddy field soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404411

DSM 25816

@ref 20215

Last LPSN update 2026-02-09 11:38:13

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Cupriavidus

Full scientific name Cupriavidus Makkar and Casida 1987

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.5
125438	negative	95.985

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64645	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
64645	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.3

Spore formation

@ref	Spore formation	Confidence
125439		97.2
125438		90.332

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
64645	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
64645	paddy field soil	Sg. Manik, Perak	Malaysia	MYS	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM185428v1 assembly for Cupriavidus sp. USMAHM13	complete	GCA_001854285	1389192.3	2721755522	1389192	95.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64645	Cupriavidus sp. USMAHM13 16S ribosomal RNA gene, complete sequence	KF460028	1522		1389192

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cupriavidus sp. USMAHM13
NCBI: GCA_001854285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.20	no
125439	motility	BacteriaNetⓘ	yes	83.00	no
125439	gram_stain	BacteriaNetⓘ	negative	96.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cupriavidus sp. USMAHM13 USMAHM13
NCBI: GCA_001854285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.99	no
125438	anaerobic	anaerobicⓘ	no	97.12	no
125438	aerobic	aerobicⓘ	yes	89.93	no
125438	spore-forming	spore-formingⓘ	no	90.33	no
125438	thermophilic	thermophileⓘ	no	98.74	no
125438	flagellated	motile2+ⓘ	yes	81.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Enhanced production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer and antimicrobial yellow pigmentation from Cupriavidus sp. USMAHM13 with antibiofilm capability.	Ismail I, Gurusamy TP, Ramachandran H, Al-Ashraf Amirul A	Prep Biochem Biotechnol	10.1080/10826068.2016.1252925	2016
Cultivation	Identification and characterization of the yellow pigment synthesized by Cupriavidus sp. USMAHM13.	Ramachandran H, Iqbal MA, Amirul AA	Appl Biochem Biotechnol	10.1007/s12010-014-1080-2	2014
Metabolism	Bioconversion of glycerine pitch into a novel yellow-pigmented P(3HB-co-4HB) copolymer: synergistic effect of ammonium acetate and polymer characteristics.	Ramachandran H, Amirul AA	Appl Biochem Biotechnol	10.1007/s12010-013-0552-0	2014
Genetics	Complete Genome Sequences of Three Cupriavidus Strains Isolated from Various Malaysian Environments.	Shafie NA, Lau NS, Ramachandran H, Amirul AA	Genome Announc	10.1128/genomeA.01498-16	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 )
#64645	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25816
#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) .
#68369	Automatically annotated from API 20NE .
#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 )

Rate our new design

Content

About us

Cupriavidus sp. (DSM 25816, USMAHM13)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001854285

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media