Pedobacter rhizosphaerae (DSM 18610, KACC 14938, NBRC 107690)

Name: Pedobacter rhizosphaerae (DSM 18610, KACC 14938, NBRC 107690)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14103

Type strain

Strain Designation 01-96

Variant Isotype of BacDive ID 131130

Culture col. no. DSM 18610 KACC 14938 NBRC 107690 01-96

NCBI tax ID(s) 390241

Special Collections DSMZ

Links

Pedobacter rhizosphaerae 01-96 is a mesophilic prokaryote that was isolated from rhizosphere soil of Chinese cabbage .

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 412344

NBRC 107690,DSM 18610

@ref 20215

Last LPSN update 2025-12-16 09:50:15

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter rhizosphaerae

Full scientific name Pedobacter rhizosphaerae Kwon et al. 2011

BacDive ID	Other strains from **Pedobacter rhizosphaerae** (1)	Type strain
131130	P. rhizosphaerae 01-96, DSM 25732, KACC 14938 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.922
125439	negative	99.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7624	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
7624	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	94

Spore formation

@ref	Spore formation	Confidence
125439		99

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	kanosamine biosynthesis II	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	L-lactaldehyde degradation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	threonine metabolism	100	10 of 10
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	sulfopterin metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	Entner Doudoroff pathway	90	9 of 10
66794	NAD metabolism	88.89	16 of 18
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glycine betaine biosynthesis	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	leucine metabolism	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	histidine metabolism	68.97	20 of 29
66794	cysteine metabolism	66.67	12 of 18
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	alanine metabolism	65.52	19 of 29
66794	glutathione metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	lipid metabolism	61.29	19 of 31
66794	degradation of hexoses	61.11	11 of 18
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	O-antigen biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	propionate fermentation	60	6 of 10
66794	lysine metabolism	59.52	25 of 42
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	methionine metabolism	57.69	15 of 26
66794	degradation of pentoses	57.14	16 of 28
66794	non-pathway related	55.26	21 of 38
66794	carotenoid biosynthesis	54.55	12 of 22
66794	sulfate reduction	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	oxidative phosphorylation	50.55	46 of 91
66794	selenocysteine biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	arginine metabolism	50	12 of 24
66794	catecholamine biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	androgen and estrogen metabolism	50	8 of 16
66794	degradation of sugar acids	48	12 of 25
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	enterobactin biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	vitamin E metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
7624	rhizosphere soil of Chinese cabbage (Brassica campestris L.)	Brassica campestris	Suwon (37° 16' 38.50'' N 126° 58' 59.60'' E)	Republic of Korea	KOR	Asia	37.2774	126.983 37.2774/126.983

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7624	1	Risk group (German 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	IMG-taxon 2622736586 annotated assembly for Pedobacter rhizosphaerae DSM 18610	scaffold	GCA_900111155	390241.6	2622736586	390241	55.46

Genome browser: GCA_900111155

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7624	Pedobacter rhizosphaerae partial 16S rRNA gene, type strain 01-96T	AM279214	1486		390241

GC content

@ref	GC-content (mol%)	Method
7624	37.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter rhizosphaerae DSM 18610
NCBI: GCA_900111155

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.00	no
125439	motility	BacteriaNetⓘ	no	70.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter rhizosphaerae DSM 18610
NCBI: GCA_900111155.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.92	no
125438	anaerobic	anaerobicⓘ	no	95.21	no
125438	aerobic	aerobicⓘ	yes	85.41	no
125438	spore-forming	spore-formingⓘ	no	84.50	no
125438	thermophilic	thermophileⓘ	no	97.07	yes
125438	flagellated	motile2+ⓘ	no	85.50	no

Literature

Title	Authors	Journal	DOI	Year
CARD domains mediate anti-phage defence in bacterial gasdermin systems.	Wein T, Millman A, Lange K, Yirmiya E, Hadary R, Garb J, Melamed S, Amitai G, Dym O, Steinruecke F, Hill AB, Kranzusch PJ, Sorek R.	Nature	10.1038/s41586-024-08498-3	2025
Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil.	Ngo HTT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000055	2015
Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.	Kim DU, Kim YJ, Shin DH, Weon HY, Kwon SW, Seong CN, Ka JO	J Microbiol	10.1007/s12275-013-2231-9	2013
Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).	Kwon SW, Son JA, Kim SJ, Kim YS, Park IC, Bok JI, Weon HY	Int J Syst Evol Microbiol	10.1099/ijs.0.026781-0	2011

References

#7624	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18610
#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 )
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 rhizosphaerae (DSM 18610, KACC 14938, NBRC 107690)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900111155

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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