Sphingomonas zeae (DSM 100049, CCM 8596, LMG 28739)

Name: Sphingomonas zeae (DSM 100049, CCM 8596, LMG 28739)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131402

Type strain

Strain Designation JM-791

Culture col. no. DSM 100049 CCM 8596 LMG 28739 JM-791 CIP 110945 1 more

NCBI tax ID(s) 1646122

Special Collections DSMZ CIP

History <- P. Kämpfer, Univ. Giessen, Germany; JM-791 <- J. McInroy CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-791

Links

Sphingomonas zeae JM-791 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from healthy internal stem tissue of a 4-week-old field-grown corn plant .

Gram-negative rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 403706

LMG 28739,DSM 100049

@ref 20215

Last LPSN update 2026-02-09 11:31:27

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas zeae

Full scientific name Sphingomonas zeae Kämpfer et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		95.548
125439	negative		97.4
124029	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
41950	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
22629	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
124029	CIP Medium 72	Medium recipe at CIP
22629	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22629	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125439		94.1

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
22629	-	-	-	-	-	+	-	+	+	+	+	-	+	-	-	+	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Stem (Branch)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
22629	healthy internal stem tissue of a 4-week-old field-grown corn plant (Zea mays, cultivar ‘Sweet Belle’)	Zea mays	Alabama, Elmore county, Tallassee, Plant Breeding Unit of the E.V. Smith Research Center	USA	USA	North America
124029	Healthy internal stem tissue of corn, Zea mays, cultivar 'Sweet Belle'		Alabama	United States of America	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22629	1	Risk group (German classification)
124029	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419713v1 assembly for Sphingomonas zeae DSM 100049	scaffold	GCA_014197135	1646122.4	2830100248	1646122	69.46
66792	ASM1335979v1 assembly for Sphingomonas zeae DSM 100049	contig	GCA_013359795	1646122.3	8114398002	1646122	64.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22629	Sphingomonas zeae strain JM-791 16S ribosomal RNA gene, partial sequence	KP999966	1408		1646122

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas zeae DSM 100049
NCBI: GCA_014197135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.10	no
125439	motility	BacteriaNetⓘ	yes	55.80	no
125439	gram_stain	BacteriaNetⓘ	negative	97.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas zeae DSM 100049
NCBI: GCA_014197135.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.55	no
125438	anaerobic	anaerobicⓘ	no	91.99	no
125438	aerobic	aerobicⓘ	yes	88.78	no
125438	spore-forming	spore-formingⓘ	no	87.43	no
125438	thermophilic	thermophileⓘ	no	98.36	yes
125438	flagellated	motile2+ⓘ	yes	68.98	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome-based taxonomy and functional prediction of Sphingomonas fuzhouensis sp. nov. and Massilia phyllosphaerae sp. nov. isolated from Pennisetum sp. with plant growth-promoting potential.	Yao L, Liu GH, Zhang SY, Gao P, Rensing C, Yang QE, Zhou SG.	Antonie Van Leeuwenhoek	10.1007/s10482-024-02017-0	2024
Phylogeny	Sphingomonas zeae sp. nov., isolated from the stem of Zea mays.	Kampfer P, Busse HJ, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.000298	2015

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 )
#22629	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100049
#41950	; 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 .
#124029	Collection of Institut Pasteur ; Curators of the CIP; CIP 110945
#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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Sphingomonas zeae (DSM 100049, CCM 8596, LMG 28739)

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

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014197135

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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