Pedobacter zeae (DSM 100774, CGMCC 1.15287, 22)

Name: Pedobacter zeae (DSM 100774, CGMCC 1.15287, 22)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140255

Type strain

Strain Designation 22

Culture col. no. DSM 100774 CGMCC 1.15287 22

NCBI tax ID(s) 1737356

Special Collections DSMZ Literature strains

History <- J. Gao, Beijing Academy of Agriculture and Forestry Science; 22

Links

Pedobacter zeae 22 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize.

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

Name and taxonomic classification

SI-ID 407605

DSM 100774

@ref 20215

Last LPSN update 2026-02-09 11:33:34

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter zeae

Full scientific name Pedobacter zeae Gao et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25201	negative	0.6-1.8 µm	0.2-0.3 µm	rod-shaped
125439	negative				99.9
125438	negative				97.444

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25201	0.5-1.0 mm	pinkish-yellow	circular	3 days	LB agar plates

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
25201	LB (Luria-Bertani) MEDIUM
25201	LB agar plates
25201	nutrient agar (NA)
25201	Reasoner's 2A agar (R2A)
25201	tryptic soy agar (TSA)
25201	Ashby nitrogen-free medium
42862	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)
25201	positive	growth	15.0-30.0
25201	positive	optimum	30
42862	positive	growth	28

Culture pH

@ref	Ability	Type	PH
25201	positive	optimum	7
25201	positive	growth	6.0-7.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25201	aerobe
125439	obligate aerobe	97.1

Spore formation

@ref	Spore formation	Confidence
125439		99.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25201	NaCl		optimum	1 %
25201	NaCl	positive	growth	0.0-1.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25201	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
25201	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
25201	17128 ChEBI	adipate	-	assimilation
25201	27613 ChEBI	amygdalin	+	builds acid from
25201	18305 ChEBI	arbutin	+	builds acid from
25201	73706 ChEBI	bromosuccinate	+	oxidation
25201	17057 ChEBI	cellobiose	+	builds acid from
25201	17108 ChEBI	D-arabinose	+	builds acid from
25201	18333 ChEBI	D-arabitol	-	builds acid from
25201	15824 ChEBI	D-fructose	+	builds acid from
25201	78697 ChEBI	D-fructose 6-phosphate	+	oxidation
25201	28847 ChEBI	D-fucose	-	builds acid from
25201	12936 ChEBI	D-galactose	+	builds acid from
25201	12936 ChEBI	D-galactose	+	oxidation
25201	8391 ChEBI	D-gluconate	+	oxidation
25201	17634 ChEBI	D-glucose	+	assimilation
25201	17634 ChEBI	D-glucose	+	builds acid from
25201	14314 ChEBI	D-glucose 6-phosphate	+	oxidation
25201	62318 ChEBI	D-lyxose	+	builds acid from
25201	16899 ChEBI	D-mannitol	-	assimilation
25201	16899 ChEBI	D-mannitol	-	builds acid from
25201	16024 ChEBI	D-mannose	+	assimilation
25201	16024 ChEBI	D-mannose	+	builds acid from
25201	16988 ChEBI	D-ribose	+	builds acid from
25201	17924 ChEBI	D-sorbitol	-	builds acid from
25201	16443 ChEBI	D-tagatose	+	builds acid from
25201	16551 ChEBI	D-trehalose	+	builds acid from
25201	65327 ChEBI	D-xylose	+	builds acid from
25201	27689 ChEBI	decanoate	-	assimilation
25201	17113 ChEBI	erythritol	-	builds acid from
25201	4853 ChEBI	esculin	+	hydrolysis
25201	4853 ChEBI	esculin	+	builds acid from
25201	16813 ChEBI	galactitol	-	builds acid from
25201	5291 ChEBI	gelatin	+	hydrolysis
25201	28066 ChEBI	gentiobiose	-	builds acid from
25201	24265 ChEBI	gluconate	-	builds acid from
25201	17234 ChEBI	glucose	+	fermentation
25201	17754 ChEBI	glycerol	-	builds acid from
25201	28087 ChEBI	glycogen	+	builds acid from
25201	15443 ChEBI	inulin	-	builds acid from
25201	30849 ChEBI	L-arabinose	+	assimilation
25201	30849 ChEBI	L-arabinose	+	builds acid from
25201	18403 ChEBI	L-arabitol	-	builds acid from
25201	18287 ChEBI	L-fucose	+	builds acid from
25201	18287 ChEBI	L-fucose	+	oxidation
25201	15971 ChEBI	L-histidine	+	oxidation
25201	15589 ChEBI	L-malate	+	oxidation
25201	62345 ChEBI	L-rhamnose	-	builds acid from
25201	62345 ChEBI	L-rhamnose	-	oxidation
25201	17115 ChEBI	L-serine	+	oxidation
25201	17266 ChEBI	L-sorbose	-	builds acid from
25201	65328 ChEBI	L-xylose	-	builds acid from
25201	17716 ChEBI	lactose	+	builds acid from
25201	25115 ChEBI	malate	-	assimilation
25201	17306 ChEBI	maltose	+	builds acid from
25201	17306 ChEBI	maltose	+	assimilation
25201	6731 ChEBI	melezitose	-	builds acid from
25201	28053 ChEBI	melibiose	+	builds acid from
25201	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
25201	320061 ChEBI	methyl alpha-D-glucopyranoside	+	oxidation
25201	43943 ChEBI	methyl alpha-D-mannoside	+	builds acid from
25201	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
25201	17268 ChEBI	myo-inositol	-	builds acid from
25201	28037 ChEBI	N-acetylgalactosamine	+	oxidation
25201	506227 ChEBI	N-acetylglucosamine	+	assimilation
25201	506227 ChEBI	N-acetylglucosamine	+	builds acid from
25201	17632 ChEBI	nitrate	-	reduction
25201	17309 ChEBI	pectin	-	oxidation
25201	18401 ChEBI	phenylacetate	-	assimilation
25201	32032 ChEBI	potassium gluconate	-	assimilation
25201	16634 ChEBI	raffinose	+	builds acid from
25201	16634 ChEBI	raffinose	+	oxidation
25201	15963 ChEBI	ribitol	-	builds acid from
25201	28077 ChEBI	rifampicin	+	oxidation
25201	17814 ChEBI	salicin	+	builds acid from
25201	53258 ChEBI	sodium citrate	+	assimilation
25201	75228 ChEBI	sodium lactate	+	oxidation
25201	17164 ChEBI	stachyose	+	oxidation
25201	28017 ChEBI	starch	-	builds acid from
25201	17992 ChEBI	sucrose	+	builds acid from
25201	27082 ChEBI	trehalose	+	oxidation
25201	27897 ChEBI	tryptophan	-	energy source
25201	32528 ChEBI	turanose	+	builds acid from
25201	32528 ChEBI	turanose	+	oxidation
25201	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25201	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25201	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
25201	acid phosphatase	+	3.1.3.2
25201	alkaline phosphatase	+	3.1.3.1
25201	alpha-chymotrypsin	-	3.4.21.1
25201	alpha-fucosidase	+	3.2.1.51
25201	alpha-galactosidase	+	3.2.1.22
25201	alpha-glucosidase	+	3.2.1.20
25201	alpha-mannosidase	+	3.2.1.24
25201	arginine dihydrolase	-	3.5.3.6
25201	beta-galactosidase	+	3.2.1.23
25201	beta-glucosidase	+	3.2.1.21
25201	beta-glucuronidase	+	3.2.1.31
25201	catalase	+	1.11.1.6
25201	cystine arylamidase	+	3.4.11.3
25201	cytochrome oxidase	+	1.9.3.1
25201	esterase (C 4)	+
25201	esterase Lipase (C 8)	+
25201	leucine arylamidase	+	3.4.11.1
25201	lipase (C 14)	-
25201	N-acetyl-beta-glucosaminidase	+	3.2.1.52
25201	naphthol-AS-BI-phosphohydrolase	+
25201	trypsin	+	3.4.21.4
25201	tryptophan deaminase	-	4.1.99.1
25201	urease	-	3.5.1.5
25201	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

25201

Fatty acid	Percentage
C15:0 iso	37
C16:1ω7c / C16:1ω6c	31.4
C17:0 iso 3OH	7.9
C17:1 iso ω9c / C16:0 10-methyl	4.5
C19:1ω11c / C19:1ω9c	4.1
C15:0 iso 3OH	3
C14:0	2.6
C16:1ω5c	1.4
C15:1 iso h / C13:0 3OH	1
C17:1 iso I /C17:1 anteiso B	0.9
C16:0 iso 3OH	0.9
C16:0	0.8
C16:0 3OH	0.8
C15:1ω6c	0.6
C15:0 anteiso	0.5
C11:0 iso	0.4
C18:1ω5c	0.4
C13:1 at 12-13	0.4
C13:0 iso	0.3
C14:0 2OH	0.3
C14:1ω5c	0.3
C15:1 iso F	0.2
C17:0 iso	0.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
25201	surface-sterilized root tissue of maize	Fangshan District of Beijing	Republic of China	CHN	Asia	Ashby nitrogen-free medium	3 days	28
42862	surface-sterilized root tissue of maize	Fangshan District of Beijing	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42862	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419671v1 assembly for Pedobacter zeae DSM 100774	scaffold	GCA_014196715	1737356.3	2829961646	1737356	74.92
66792	ASM1464157v1 assembly for Pedobacter zeae CGMCC 1.15287	scaffold	GCA_014641575	1737356.4	8113157366	1737356	73.42

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
25201	Pedobacter zeae strain 22 16S ribosomal RNA gene, partial sequence	KR610524.2	1480	1737356
42862	Pedobacter zeae strain 22 16S ribosomal RNA gene, partial sequence	KR610524	1480	1737356
124043	Pedobacter zeae strain CGMCC 1.15287 16S ribosomal RNA gene, partial sequence.	MT759967	1345	1737356

GC content

@ref	GC-content (mol%)	Method
25201	40.7-41.7	thermal denaturation, midpoint method (Tm)
42862	41.2	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter zeae CGMCC 1.15287
NCBI: GCA_014641575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	no	74.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter zeae CGMCC 1.15287
NCBI: GCA_014641575.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.44	yes
125438	anaerobic	anaerobicⓘ	no	95.34	yes
125438	aerobic	aerobicⓘ	yes	89.69	no
125438	spore-forming	spore-formingⓘ	no	83.83	no
125438	thermophilic	thermophileⓘ	no	97.99	yes
125438	flagellated	motile2+ⓘ	no	89.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001603	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 )
#25201	J. L. S. Gao, P.,Mao, X. J.,Du, Y. L.,Liu, B. Y.,Sun, J. G.: Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root. IJSEM 67: 231 - 236 2017 ( DOI 10.1099/ijsem.0.001603 , PubMed 27902277 )
#42862	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100774
#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) .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Pedobacter zeae (DSM 100774, CGMCC 1.15287, 22)

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

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014196715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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