Pedobacter soli (DSM 18609, KACC 14939, NBRC 107691)

Name: Pedobacter soli (DSM 18609, KACC 14939, NBRC 107691)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14102

Type strain

Strain Designation 15-51

Variant Isotype of BacDive ID 131129

Culture col. no. DSM 18609 KACC 14939 NBRC 107691 15-51

NCBI tax ID(s) 390242

Special Collections DSMZ

Links

Pedobacter soli 15-51 is a mesophilic prokaryote that was isolated from rhizosphere soil of Chinese cabbage .

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400046

NBRC 107691,DSM 25729,DSM 18609

@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 soli

Full scientific name Pedobacter soli Kwon et al. 2011

BacDive ID	Other strains from **Pedobacter soli** (1)	Type strain
131129	P. soli 15-51, DSM 25729, KACC 14939, NBRC 107691 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.7
125438	negative	98

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7623	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
7623	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.7

Spore formation

@ref	Spore formation	Confidence
125439		98.6

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
7623	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
7623	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 2622736512 annotated assembly for Pedobacter soli DSM 18609	scaffold	GCA_900101435	390242.6	2622736512	390242	69.75

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7623	Pedobacter soli partial 16S rRNA gene, type strain 15-51T	AM279215	1487		390242

GC content

@ref	GC-content (mol%)	Method
7623	38.6	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 soli DSM 18609
NCBI: GCA_900101435

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	no	69.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter soli DSM 18609
NCBI: GCA_900101435.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	96.92	no
125438	aerobic	aerobicⓘ	yes	82.31	no
125438	spore-forming	spore-formingⓘ	no	84.23	no
125438	thermophilic	thermophileⓘ	no	96.49	yes
125438	flagellated	motile2+ⓘ	no	87.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter riviphilus sp. nov., isolated from stream sediment.	Im HS, Joung Y, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004989	2021
Phylogeny	Pedobacter miscanthi sp. nov., isolated from Miscanthus sinensis.	Chen Z, Tian W, Sun F, Chen Y, Han H, Yao L, Zhang Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.003161	2019
Phylogeny	Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine.	Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001480	2016
Phylogeny	Pedobacter kyungheensis sp. nov., with ginsenoside converting activity.	Yang JE, Shin JY, Park SY, T Mavlonov G, Yi EJ, Lee EH, Lee JM, Yi TH	J Gen Appl Microbiol	10.2323/jgam.58.309	2012
Phylogeny	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

#7623	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18609
#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) .
#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 soli (DSM 18609, KACC 14939, NBRC 107691)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900101435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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