Mycetohabitans rhizoxinica (DSM 19002, CIP 109453, HKI 454)

Name: Mycetohabitans rhizoxinica (DSM 19002, CIP 109453, HKI 454)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1976

Type strain

Culture col. no. DSM 19002 CIP 109453 HKI 454

NCBI tax ID(s) 882378 412963

Special Collections DSMZ CIP Literature strains

History DSMZ <- L. P. Partida-Martinez; HKI 454 CIP <- 2007, L.P. Partida-Martinez, Hans-Knoell Inst., Jena, Germany: strain HKI 454

Links

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

Gram-negative motile ovoid-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 319367

CIP 109453,DSM 19002,LMG 24679

@ref 20215

Last LPSN update 2026-05-29 08:25:23

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Mycetohabitans

Species Mycetohabitans rhizoxinica

Full scientific name Mycetohabitans rhizoxinica (Partida-Martinez et al. 2007) Estrada-de Los Santos et al. 2018

Synonyms (3)

"Burkholderia rhizoxina"
Burkholderia rhizoxinica
Paraburkholderia rhizoxinica

BacDive ID	Other strains from **Mycetohabitans rhizoxinica** (1)	Type strain
100245	M. rhizoxinica SF006403,

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31924	negative	1.6 µm	0.9 µm	ovoid-shaped
122215	negative			rod-shaped
125438	negative				98.375
125439	negative				92.686

Colony morphology

7825

Incubation period3-7 days

Pigmentation

31924

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7825	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
37309	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122215	CIP Medium 328	Medium recipe at CIP
122215	CIP Medium 72	Medium recipe at CIP
7825	BCYE alpha agar (DSMZ Medium 585a)	Medium recipe provided by DSMZ
7825	BCYE-AGAR (DSMZ Medium 585)	Medium recipe at MediaDive	Name: BCYE-AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
7825	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)
7825	positive	growth	28
31924	positive	growth	16-45
31924	positive	optimum	30.5
37309	positive	growth	30

Culture pH

@ref	Ability	Type	PH
31924	positive	optimum	6.25
31924	positive	growth	5.0-7.4

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31924	aerobe
122215	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.054

Compound production

7825

Compoundrhizoxin

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31924	NaCl	positive	growth	0-3 %
31924	NaCl	positive	optimum	1 %

Observation

31924

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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
31924	17754 ChEBI	glycerol	+	carbon source
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
31924	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
122215	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
122215	16301 ChEBI	nitrite	-	reduction
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
122215	35581 ChEBI	indole

Metabolite tests

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

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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
7825	catalase	+	1.11.1.6
31924	catalase	+	1.11.1.6
122215	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31924	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
7825	cytochrome-c oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
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
122215	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
122215	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
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
122215	-	-	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	+	-

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
7825	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	-	+
7825	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	not determinedn.d.
7825	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fungi

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent	Isolation date
7825	fungus Rhizopus microsporus van Tieghem var. chinensis (ATCC 62417)	Rhizopus microsporus van Tieghem var. chinensis	Germany	DEU	Europe
122215	Other, Fungus, Rhizopus microsporus		Japan	JPN	Asia	2004

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7825	1	Risk group (German classification) According to TRBA 466
122215	1	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
66792	ASM19877v1 assembly for Mycetohabitans rhizoxinica HKI 454	complete	GCA_000198775	882378.3	650716014	882378	93.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7825	Burkholderia rhizoxinica 16S rRNA gene, type strain HKI 454T	AJ938142	1525		882378

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM19877v1 assembly for Mycetohabitans rhizoxinica HKI 454
BV-BRC: 882378.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.69	no
125439	gram_stain	BacteriaNetⓘ	negative	92.69	no
125439	motility	BacteriaNetⓘ	yes	65.83	no
125439	spore_formation	BacteriaNetⓘ	no	99.05	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.38	yes
125438	anaerobic	anaerobicⓘ	no	94.70	yes
125438	aerobic	aerobicⓘ	yes	77.98	no
125438	spore-forming	spore-formingⓘ	no	89.66	no
125438	thermophilic	thermophileⓘ	no	91.77	yes
125438	flagellated	motile2+ⓘ	no	51.83	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Endofungal Mycetohabitans rhizoxinica Bacteremia Associated with Rhizopus microsporus Respiratory Tract Infection.	Yang S, Anikst V, Adamson PC.	Emerg Infect Dis	10.3201/eid2810.220507	2022
Pathogenicity	Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction.	Richter I, Hasan M, Kramer JW, Wein P, Krabbe J, Wojtas KP, Stinear TP, Pidot SJ, Kloss F, Hertweck C, Lackner G.	ISME J	10.1093/ismejo/wrae074	2024
	Transcription activator-like effector protects bacterial endosymbionts from entrapment within fungal hyphae.	Richter I, Wein P, Uzum Z, Stanley CE, Krabbe J, Molloy EM, Moebius N, Ferling I, Hillmann F, Hertweck C.	Curr Biol	10.1016/j.cub.2023.05.028	2023
	The development of Burkholderia bacteria as heterologous hosts.	Heard SC, Eustaquio AS.	Nat Prod Rep	10.1039/d5np00024f	2025
Pathogenicity	Identification of novel toxins associated with the extracellular contractile injection system using machine learning.	Danov A, Pollin I, Moon E, Ho M, Wilson BA, Papathanos PA, Kaplan T, Levy A.	Mol Syst Biol	10.1038/s44320-024-00053-6	2024
Enzymology	Pilot Scale Production of a F₄₂₀ Precursor Under Microaerobic Conditions.	Lenic A, Bardl B, Kloss F, Peschel G, Schlembach I, Lackner G, Regestein L, Rosenbaum MA.	Biotechnol J	10.1002/biot.70002	2025
Pathogenicity	Transcription activator-like effectors from endosymbiotic bacteria control the reproduction of their fungal host.	Richter I, Uzum Z, Wein P, Molloy EM, Moebius N, Stinear TP, Pidot SJ, Hertweck C.	mBio	10.1128/mbio.01824-23	2023
	Biotechnology approaches for natural product discovery, engineering, and production based on Burkholderia bacteria.	Adaikpoh BI, Fernandez HN, Eustaquio AS.	Curr Opin Biotechnol	10.1016/j.copbio.2022.102782	2022
	Symbiotic and toxinogenic Rhizopus spp. isolated from soils of different papaya producing regions in Mexico.	Cabrera-Rangel JF, Mendoza-Servin JV, Cordova-Lopez G, Alcalde-Vazquez R, Garcia-Estrada RS, Winkler R, Partida-Martinez LP.	Front Fungal Biol	10.3389/ffunb.2022.893700	2022
Metabolism	Heterologous Production of Lasso Peptide Capistruin in a Burkholderia Host.	Kunakom S, Eustaquio AS.	ACS Synth Biol	10.1021/acssynbio.9b00438	2020
	A bacterial endosymbiont of the fungus Rhizopus microsporus drives phagocyte evasion and opportunistic virulence.	Itabangi H, Sephton-Clark PCS, Tamayo DP, Zhou X, Starling GP, Mahamoud Z, Insua I, Probert M, Correia J, Moynihan PJ, Gebremariam T, Gu Y, Ibrahim AS, Brown GD, King JS, Ballou ER, Voelz K.	Curr Biol	10.1016/j.cub.2022.01.028	2022
	Biosynthesis and engineering of the nonribosomal peptides with a C-terminal putrescine.	Chen H, Zhong L, Zhou H, Bai X, Sun T, Wang X, Zhao Y, Ji X, Tu Q, Zhang Y, Bian X.	Nat Commun	10.1038/s41467-023-42387-z	2023
Metabolism	Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism.	Lastovetsky OA, Krasnovsky LD, Qin X, Gaspar ML, Gryganskyi AP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Pawlowska TE.	mBio	10.1128/mbio.02088-20	2020
	Narnaviruses: novel players in fungal-bacterial symbioses.	Espino-Vazquez AN, Bermudez-Barrientos JR, Cabrera-Rangel JF, Cordova-Lopez G, Cardoso-Martinez F, Martinez-Vazquez A, Camarena-Pozos DA, Mondo SJ, Pawlowska TE, Abreu-Goodger C, Partida-Martinez LP.	ISME J	10.1038/s41396-020-0638-y	2020
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	'Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov., an endosymbiotic bacterium associated with nematode species of the genus Xiphinema (Nematoda, Longidoridae).	Palomares-Rius JE, Gutierrez-Gutierrez C, Mota M, Bert W, Claeys M, Yushin VV, Suzina NE, Ariskina EV, Evtushenko LI, Subbotin SA, Castillo P.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004888	2021
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 )
#28181	IJSEM 2583 2007 ( DOI 10.1099/ijs.0.64660-0 , PubMed 17978222 )
#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
#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 .
#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 .
#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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Mycetohabitans rhizoxinica (DSM 19002, CIP 109453, HKI 454)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000198775

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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