Name: Mycetohabitans rhizoxinica DSM 19002
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1976

Type strain:

Species: Mycetohabitans rhizoxinica

Culture col. no.: DSM 19002, CIP 109453, HKI 454

Strain history: CIP <- 2007, L.P. Partida-Martinez, Hans-Knoell Inst., Jena, Germany: strain HKI 454

NCBI tax ID(s): 882378 (strain), 412963 (species)

SI-ID 319367

CIP 109453, DSM 19002, LMG 24679

Special Collections

Other strains from Mycetohabitans rhizoxinica

Section

When using BacDive for research please cite our paper

Mycetohabitans rhizoxinica DSM 19002 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fungus Rhizopus microsporus van Tieghem var. chinensis .

Gram-negative
motile
ovoid-shaped
aerobe
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	*Mycetohabitans*
	Species	**Mycetohabitans rhizoxinica**
	Full Scientific Name (LPSN)	Mycetohabitans rhizoxinica (Partida-Martinez et al. 2007) Estrada-de Los Santos et al. 2018

	Synonym	"Burkholderia* rhizoxina"*
	Synonym	Paraburkholderia rhizoxinica
	Synonym	Burkholderia rhizoxinica

Information on morphological and physiological properties Morphology

[Ref.: #31924]	Gram stain	negative
[Ref.: #122215]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %97.3
[Ref.: #125438]	Gram stain	negative Confidence in %98.375

[Ref.: #31924]	Cell length	1.6 µm

[Ref.: #31924]	Cell width	0.9 µm

[Ref.: #31924]	Cell shape	ovoid-shaped
[Ref.: #122215]	Cell shape	rod-shaped

[Ref.: #31924]	Motility	yes
[Ref.: #122215]	Motility	no

[Ref.: #7825]

Incubation period

3-7 days

[Ref.: #31924]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7825]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7825]

Culture medium growth

[Ref.: #7825]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7825]

Culture medium composition

expand / minimize

[Ref.: #37309]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37309]

Culture medium growth

[Ref.: #37309]

Culture medium composition

expand / minimize

[Ref.: #122215]

Culture medium

CIP Medium 328

[Ref.: #122215]

Culture medium growth

[Ref.: #122215]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122215]

Culture medium

CIP Medium 72

[Ref.: #122215]

Culture medium growth

[Ref.: #122215]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #7825]

Culture medium

BCYE alpha agar (DSMZ Medium 585a)

[Ref.: #7825]

Culture medium growth

[Ref.: #7825]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #7825]

Culture medium

BCYE-AGAR (DSMZ Medium 585)

[Ref.: #7825]

Culture medium growth

[Ref.: #7825]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #7825]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #7825]

Culture medium growth

[Ref.: #7825]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7825]	growth	28 °C
[Ref.: #31924]	growth	16-45 °C
[Ref.: #31924]	optimum	30.5 °C
[Ref.: #37309]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31924]			optimum	6.25
[Ref.: #31924]			growth	5.0-7.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31924]	Oxygen tolerance	aerobe
[Ref.: #122215]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	aerobe Confidence in %91.1

[Ref.: #125439]

Ability of spore formation

no Confidence in %96.9

[Ref.: #7825]

Name of produced compound

rhizoxin

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31924]		NaCl		growth	0-3	%
[Ref.: #31924]		NaCl		optimum	1	%

[Ref.: #31924]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[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.: #31924]	glycerol ChEBI	+	carbon source
[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.: #31924]	mannose ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #122215]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #122215]	nitrite ChEBI	-	reduction
[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.: #122215]		indole ChEBI	no
[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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #7825]	catalase	+	1.11.1.6
[Ref.: #31924]	catalase	+	1.11.1.6
[Ref.: #122215]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31924]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #7825]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122215]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122215]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #7825]	26487	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	+
[Ref.: #7825]	26486	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	not determinedn.d.
[Ref.: #7825]	26485	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	not determinedn.d.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122215]	11875	-	-	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	+	-

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

[Ref.: #7825]	Sample type/isolated from	fungus Rhizopus microsporus van Tieghem var. chinensis (ATCC 62417)
[Ref.: #7825]	Host species	Rhizopus microsporus van Tieghem var. chinensis
[Ref.: #7825]	Country	Germany
[Ref.: #7825]	Country ISO 3 Code	DEU
[Ref.: #7825]	Continent	Europe

[Ref.: #122215]	Sample type/isolated from	Other, Fungus, Rhizopus microsporus
[Ref.: #122215]	Country	Japan
[Ref.: #122215]	Country ISO 3 Code	JPN
[Ref.: #122215]	Continent	Asia
[Ref.: #122215]	Isolation date	2004
* marker position based on {}

Isolation sources categories

#Host

#Fungi

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ938142 (>99% sequence identity) for Burkholderia from Microbeatlas

Aquatic Samples	1257
Soil Samples	4868
Animal Samples	2903
Plant Samples	2896
Total Samples	11924

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

[Ref.: #7825]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122215]	Biosafety level	1	Risk group (French classification)

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.: #7825]	Burkholderia rhizoxinica 16S rRNA gene, type strain HKI 454T	AJ938142	1525	GenBank ENA	882378 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Mycetohabitans rhizoxinica HKI 454	GCA_000198775	complete	GenBank ENA	882378 tax ID	*
[Ref.: #66792]	Burkholderia rhizoxinica HKI 454	882378.3	complete	PATRIC	882378 tax ID	*
[Ref.: #66792]	Paraburkholderia rhizoxinica HKI 454	882378.20	plasmid	PATRIC	882378 tax ID	*
[Ref.: #66792]	Paraburkholderia rhizoxinica HKI 454	882378.19	plasmid	PATRIC	882378 tax ID	*
[Ref.: #66792]	Mycetohabitans rhizoxinica HKI 454	650716014	complete	JGI IMG/M	882378 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: Mycetohabitans rhizoxinica HKI 454 HKI 454 NCBI: GCA_000198775.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.375	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.697	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	77.98	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.659	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	91.771	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	51.826	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Burkholderia rhizoxinica HKI 454 PATRIC: 882378.3
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	73.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	91.1

Availability in culture collections External links

[Ref.: #7825]

Culture collection no.

DSM 19002, CIP 109453, HKI 454

[Ref.: #71621]

SI-ID 319367

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica.	Sharmin D, Guo Y, Nishizawa T, Ohshima S, Sato Y, Takashima Y, Narisawa K, Ohta H	Microbes Environ	10.1264/jsme2.ME17138	2018	*
Phylogeny	Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporus.	Partida-Martinez LP, Groth I, Schmitt I, Richter W, Roth M, Hertweck C	Int J Syst Evol Microbiol	10.1099/ijs.0.64660-0	2007	*

References

#7825

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19002

#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 )

#31924

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 #28181 (see below)

#37309 ; Curators of the CIP;

#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 .

#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 .

#71621

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-ID319367.1 )

#122215 Collection of Institut Pasteur ; Curators of the CIP; CIP 109453

#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 .

#28181

IJSEM 2583 2007 ( DOI 10.1099/ijs.0.64660-0 , PubMed 17978222 )

* These data were automatically processed and therefore are not curated

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Mycetohabitans rhizoxinica HKI 454 HKI 454

Burkholderia rhizoxinica HKI 454

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