Sphingobacterium zeae (CIP 110975, LMG 29191, CCM 8652)

Name: Sphingobacterium zeae (CIP 110975, LMG 29191, CCM 8652)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 139617

Type strain

Strain Designation JM-1081

Culture col. no. CIP 110975 LMG 29191 CCM 8652 DSM 101567 JM-1081

NCBI tax ID(s) 1776859

Special Collections CIP Literature strains DSMZ

History DSMZ <- P. Kämpfer, Univ. Giessen, Germany; JM-1081 <- J. A. McInroy, Auburn University, USA; JM-1081 CIP <- 2015, P. Kampfer,Giessen Univ., Giessen, Germany: strain JM-1081

Links

Sphingobacterium zeae JM-1081 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 413469

LMG 29191,CIP 110975

@ref 20215

Last LPSN update 2026-05-29 08:39:32

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium zeae

Full scientific name Sphingobacterium zeae Kämpfer et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43625	negative	2 µm	1 µm	rod-shaped
42169	negative			rod-shaped
125439	negative				98.702

Colony morphology

@ref	Colony size	Colony color	Colony shape	Medium used
43625	2 mm	Yellow	circular	Nutrient Agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
68991	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
42169	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
43625	Nutrient agar (NA)
42169	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
43625	positive	growth	4-42
68991	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
43625	positive	growth	5.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43625	aerobe
125439	obligate aerobe	98.492

Spore formation

43625

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43625	NaCl	positive	growth	1-4 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43625		2-deoxythymidine-5'-4-nitrophenyl phosphate	+	hydrolysis
43625	30916 ChEBI	2-oxoglutarate	-	carbon source
43625	16193 ChEBI	3-hydroxybenzoate	-	carbon source
43625	37054 ChEBI	3-hydroxybutyrate	-	carbon source
43625	17879 ChEBI	4-hydroxybenzoate	-	carbon source
43625	91122 ChEBI	4-nitrophenyl alpha-D-glucopyranoside	+	hydrolysis
43625	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	+	hydrolysis
43625	90259 ChEBI	4-nitrophenyl beta-D-glucopyranoside	+/-	hydrolysis
43625	90146 ChEBI	4-nitrophenyl beta-D-glucuronide	-	hydrolysis
43625	90148 ChEBI	4-nitrophenyl beta-D-xylopyranoside	+	hydrolysis
43625	30089 ChEBI	acetate	+/-	carbon source
43625	17128 ChEBI	adipate	-	carbon source
43625	78208 ChEBI	azelaate	-	carbon source
43625	16958 ChEBI	beta-alanine	-	carbon source
43625	3122 ChEBI	bis-4-nitrophenyl phosphate	+	hydrolysis
43625	91050 ChEBI	bis-4-nitrophenyl-phenyl phosphonate	+	hydrolysis
43625	55394 ChEBI	bis-4-nitrophenyl-phosphorylcholine	+	hydrolysis
43625		casein	+	hydrolysis
43625	17057 ChEBI	cellobiose	+	builds acid from
43625	17057 ChEBI	cellobiose	+/-	carbon source
43625	16383 ChEBI	cis-aconitate	-	carbon source
43625	16947 ChEBI	citrate	-	carbon source
43625	18333 ChEBI	D-arabitol	-	builds acid from
43625	15824 ChEBI	D-fructose	+/-	carbon source
43625	12936 ChEBI	D-galactose	+/-	carbon source
43625	17634 ChEBI	D-glucose	+	builds acid from
43625	17634 ChEBI	D-glucose	+/-	carbon source
43625	16899 ChEBI	D-mannitol	-	builds acid from
43625	16899 ChEBI	D-mannitol	-	carbon source
43625	16024 ChEBI	D-mannose	+/-	carbon source
43625	16988 ChEBI	D-ribose	+/-	carbon source
43625	17924 ChEBI	D-sorbitol	-	builds acid from
43625	17924 ChEBI	D-sorbitol	-	carbon source
43625	65327 ChEBI	D-xylose	-	builds acid from
43625	65327 ChEBI	D-xylose	-	carbon source
43625	17113 ChEBI	erythritol	-	builds acid from
43625	4853 ChEBI	esculin	+	hydrolysis
43625	29806 ChEBI	fumarate	-	carbon source
43625	16813 ChEBI	galactitol	-	builds acid from
43625	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
43625		gamma-L-glutamate-4-nitroanilide	+	hydrolysis
43625	5291 ChEBI	gelatin	+	hydrolysis
43625	24265 ChEBI	gluconate	+/-	carbon source
43625	17859 ChEBI	glutaric acid	-	carbon source
43625	17240 ChEBI	itaconate	-	carbon source
43625	16977 ChEBI	L-alanine	-	carbon source
43625		L-alanine 4-nitroanilide	+	hydrolysis
43625	30849 ChEBI	L-arabinose	+	builds acid from
43625	30849 ChEBI	L-arabinose	+/-	carbon source
43625	29991 ChEBI	L-aspartate	-	carbon source
43625	15971 ChEBI	L-histidine	-	carbon source
43625	15603 ChEBI	L-leucine	-	carbon source
43625	15729 ChEBI	L-ornithine	-	carbon source
43625	17295 ChEBI	L-phenylalanine	-	carbon source
43625	17203 ChEBI	L-proline	-	carbon source
43625		L-proline-4-nitroanilide	+	hydrolysis
43625	62345 ChEBI	L-rhamnose	+	builds acid from
43625	62345 ChEBI	L-rhamnose	+/-	carbon source
43625	17115 ChEBI	L-serine	-	carbon source
43625	16828 ChEBI	L-tryptophan	-	carbon source
43625	24996 ChEBI	lactate	-	carbon source
43625	17716 ChEBI	lactose	+	builds acid from
43625	68428 ChEBI	maltitol	+/-	carbon source
43625	17306 ChEBI	maltose	+	builds acid from
43625	17306 ChEBI	maltose	+/-	carbon source
43625	28053 ChEBI	melibiose	-	builds acid from
43625	28053 ChEBI	melibiose	+/-	carbon source
43625	36986 ChEBI	mesaconate	-	carbon source
43625	37657 ChEBI	methyl D-glucoside	+	builds acid from
43625	17268 ChEBI	myo-inositol	-	builds acid from
43625	17268 ChEBI	myo-inositol	-	carbon source
43625	28037 ChEBI	N-acetylgalactosamine	-	carbon source
43625	506227 ChEBI	N-acetylglucosamine	+/-	carbon source
43625	18401 ChEBI	phenylacetate	-	carbon source
43625	17148 ChEBI	putrescine	-	carbon source
43625	15361 ChEBI	pyruvate	-	carbon source
43625	16634 ChEBI	raffinose	+	builds acid from
43625	15963 ChEBI	ribitol	-	builds acid from
43625	15963 ChEBI	ribitol	-	carbon source
43625	17814 ChEBI	salicin	+	builds acid from
43625	17814 ChEBI	salicin	+/-	carbon source
43625	28017 ChEBI	starch	+	hydrolysis
43625	9300 ChEBI	suberic acid	-	carbon source
43625	17992 ChEBI	sucrose	+	builds acid from
43625	17992 ChEBI	sucrose	+/-	carbon source
43625	15708 ChEBI	trans-aconitate	-	carbon source
43625	27082 ChEBI	trehalose	+	builds acid from
43625	16199 ChEBI	urea	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43625	16136 ChEBI	hydrogen sulfide
43625	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43625	arginine dihydrolase	-	3.5.3.6
43625	beta-galactosidase	+	3.2.1.23
43625	catalase	+	1.11.1.6
43625	cytochrome oxidase	+	1.9.3.1
43625	lysine decarboxylase	-	4.1.1.18
43625	ornithine decarboxylase	-	4.1.1.17
43625	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

43625

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	19.8
C15:0 iso	18
C17:0 iso 3OH	11.1
C16:0 iso 3OH	10.4
C15:0 iso 3OH	9.4
C15:1 iso G	7.7
C15:1ω6c	4.1
C17:1ω6c	2.7
C16:0 iso	2
C15:0 3OH	2
C16:1 iso H	1.6
C16:0 3OH	1.2
C14:0 iso	1.1
C17:1 iso ω9c	1.1

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	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
42169		Alabama	USA	USA	North America
43625	healthy internal stem tissue of mature maize (Zea mays, cultivar 'Sweet Belle')	E.V. Smith Research Center, Tallassee, Elmore County, AL	USA	USA	North America	1990
42169	Stem-enclophic of field-grown maize	Tallassee, Alabama	United States of America	USA	North America	1990-06-01
68991	healthy internal stem tissue of mature maize (Zea mays, cultivar 'Sweet Belle')	Alabama, Elmore county, Tallassee, E.V. Smith Research Center	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence KU201960 (>99% sequence identity) for Sphingobacterium zeae from Microbeatlas

Aquatic Samples	6
Soil Samples	14
Animal Samples	12
Plant Samples	31
Total Samples	63

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
68991	1	Risk group (German classification)
42169	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4264742v1 assembly for Sphingobacterium zeae CCM 8652	contig	GCA_042647425	1776859	64.39

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43625	Sphingobacterium zeae strain JM-1081 16S ribosomal RNA gene, partial sequence	KU201960
124043	Sphingobacterium zeae strain CCM 8652 16S ribosomal RNA gene, partial sequence.	MT760230	778		1776859

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4264742v1 assembly for Sphingobacterium zeae CCM 8652
NCBI: GCA_042647425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.49	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	spore_formation	BacteriaNetⓘ	no	89.11	no
125439	motility	BacteriaNetⓘ	yes	58.48	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium zeae sp. nov., an endophyte of maize.	Kampfer P, Busse HJ, Kleinhagauer T, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.001100	2016

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 )
#42169	Collection of Institut Pasteur ; Curators of the CIP; CIP 110975
#43625	Peter Kaempfer, Hans-Jürgen Busse, Tanita Kleinhagauer, John A. McInroy, Stefanie P. Glaeser: Sphingobacterium zeae sp. nov., an endophyte of maize. IJSEM 66: 2643 - 2649 2016 ( DOI 10.1099/ijsem.0.001100 , PubMed 27098598 )
#68991	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101567
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Sphingobacterium zeae (CIP 110975, LMG 29191, CCM 8652)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042647425

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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