Name: Cupriavidus sp. USMAHM13
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158071

Type strain:

Species: Cupriavidus sp.

Strain Designation: USMAHM13

Culture col. no.: DSM 25816

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

NCBI tax ID(s): 1873897 (species)

SI-ID 404411

DSM 25816

Special Collections

DSMZ

Other strains from Cupriavidus sp.

Section

When using BacDive for research please cite our paper

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

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Cupriavidus*
	Full Scientific Name (LPSN)	Cupriavidus Makkar and Casida 1987

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	negative Confidence in %96.5
[Ref.: #125438]	Gram stain	negative Confidence in %95.985

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64645]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #64645]

Culture medium growth

[Ref.: #64645]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64645]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #64645]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %97.3

[Ref.: #125439]	Ability of spore formation	no Confidence in %97.2
[Ref.: #125438]	Ability of spore formation	no Confidence in %90.332

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #64645]	27460	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+

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

[Ref.: #64645]	Sample type/isolated from	paddy field soil
[Ref.: #64645]	Geographic location (country and/or sea, region)	Sg. Manik, Perak
[Ref.: #64645]	Country	Malaysia
[Ref.: #64645]	Country ISO 3 Code	MYS
[Ref.: #64645]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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.: #64645]	Cupriavidus sp. USMAHM13 16S ribosomal RNA gene, complete sequence	KF460028	1522	GenBank ENA	1389192 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cupriavidus sp. USMAHM13	GCA_001854285	complete	GenBank ENA	1389192 tax ID	*
[Ref.: #66792]	Cupriavidus sp. USMAHM13	1389192.4	plasmid	PATRIC	1389192 tax ID	*
[Ref.: #66792]	Cupriavidus sp. USMAHM13	1389192.3	complete	PATRIC	1389192 tax ID	*
[Ref.: #66792]	Cupriavidus sp. USMAHM13	2721755522	complete	JGI IMG/M	1389192 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	no	95.985	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.118	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.932	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.332	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.738	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	81.707	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cupriavidus sp. USMAHM13 NCBI: GCA_001854285
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.2
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	83
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	96.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.3

Availability in culture collections External links

[Ref.: #64645]

Culture collection no.

DSM 25816

[Ref.: #110914]

SI-ID 404411

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 .

#110914

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-ID404411.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Cupriavidus sp. USMAHM13 USMAHM13

Cupriavidus sp. USMAHM13

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