Cite this strain

Pedobacter terrae (DSM 17933, KCTC 12762, CCM 9056)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14100

Type strain

Strain Designation DS-57

Culture col. no. DSM 17933 KCTC 12762 CCM 9056 DS-57

NCBI tax ID(s) 405671

Special Collections DSMZ KCTC Literature strains

Links

Name and taxonomic classification

Pedobacter terrae DS-57 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

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

SI-ID 402122

DSM 17933

Last LPSN update 2024-12-09 10:44:39

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter terrae

Full scientific name Pedobacter terrae Yoon et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
31965	negative	2.15 µm	0.4 µm	rod-shaped
67771				rod-shaped
67771	negative
125439	negative
125438	negative

Pigmentation

31965

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7174	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)	Range
7174	positive	growth	25	mesophilic
31965	positive	growth	04-35
31965	positive	optimum	25	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
31965	positive	optimum	7
31965	positive	growth	5.5-9.0

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31965	NaCl	positive	growth	<3 %
31965	NaCl	positive	optimum	0.5 %

Observation

67771

Observationquinones: MK-7

Spore formation

@ref	Spore formation
31965
67771
125439

Enzymes

@ref	Value	Activity	Ec
31965	acid phosphatase	+	3.1.3.2
31965	alkaline phosphatase	+	3.1.3.1
31965	catalase	+	1.11.1.6
31965	cytochrome oxidase	+	1.9.3.1
31965	gelatinase	+

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31965	22599 ChEBI	arabinose	+	carbon source
31965	17057 ChEBI	cellobiose	+	carbon source
31965	4853 ChEBI	esculin	+	hydrolysis
31965	28757 ChEBI	fructose	+	carbon source
31965	28260 ChEBI	galactose	+	carbon source
31965	17234 ChEBI	glucose	+	carbon source
31965	17716 ChEBI	lactose	+	carbon source
31965	17306 ChEBI	maltose	+	carbon source
31965	37684 ChEBI	mannose	+	carbon source
31965	28053 ChEBI	melibiose	+	carbon source
31965	37657 ChEBI	methyl D-glucoside	+	carbon source
31965	506227 ChEBI	N-acetylglucosamine	+	carbon source
31965	17814 ChEBI	salicin	+	carbon source
31965	17992 ChEBI	sucrose	+	carbon source
31965	27082 ChEBI	trehalose	+	carbon source
31965	18222 ChEBI	xylose	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
67771	aerobe
125439	obligate aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7174	soil	Dokdo	Republic of Korea	KOR	Asia
67771	From soil	Dokdo	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ889723 (>99% sequence identity) for Pedobacter from Microbeatlas

Aquatic Samples	64
Soil Samples	113
Animal Samples	279
Plant Samples	109
Total Samples	565

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
7174	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
7174	39.7	high performance liquid chromatography (HPLC)
31965	39.7

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7174	Pedobacter terrae strain DS-57 16S ribosomal RNA gene, partial sequence	DQ889723	1477		405671

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Pedobacter terrae DSM 17933	GCA_900100705	scaffold		405671
66792	Pedobacter terrae strain DSM 17933	405671.6	wgs	PATRIC	405671
66792	Pedobacter terrae DSM 17933	2675903222	draft	JGI IMG/M	405671

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Pedobacter terrae DSM 17933
NCBI: GCA_900100705

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	no	77.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from Diaspora project based on:
Pedobacter terrae DSM 17933
NCBI: GCA_900100705.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.44	no
125438	anaerobic	anaerobicⓘ	no	95.93	yes
125438	aerobic	aerobicⓘ	yes	86.67	yes
125438	spore-forming	spore-formingⓘ	no	84.17	yes
125438	thermophilic	thermophileⓘ	no	96.99	yes
125438	flagellated	motile2+ⓘ	no	83.00	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter fastidiosus sp. nov., isolated from glacial habitats of maritime Antarctica.	Svec P, Kralova S, Stankova E, Holochova P, Sedlar K, Koudelkova S, Krsek D, Grzesiak J, Sedo O, Vaczi P, Urvashi, Gupta V, Sood U, Lal R, Korpole S, Sedlacek I	Int J Syst Evol Microbiol	10.1099/ijsem.0.005309	2022
Phylogeny	Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil.	Chaudhary DK, Lee SD, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002428	2017
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
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 ardleyensis sp. nov., isolated from soil in Antarctica.	Da X, Jiang F, Chang X, Ren L, Qiu X, Kan W, Zhang Y, Deng S, Fang C, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.000504	2015
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 terrae sp. nov., isolated from soil.	Yoon JH, Kang SJ, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64727-0	2007

Straininfo Link

@ref	Straininfo	Culture collections
83268	402122	DSM 17933

Culture collection no.

Culture collection no.
DSM 17933
KCTC 12762
CCM 9056
DS-57

References

#7174	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17933
#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 )
#31965	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28220 (see below)
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#83268	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID402122.1 )
#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 .

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