Name: Pedobacter terrae DS-57
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14100

Type strain:

Species: Pedobacter terrae

Strain Designation: DS-57

Culture col. no.: DSM 17933, KCTC 12762, CCM 9056

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 405671 (species)

SI-ID 402122

DSM 17933

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter terrae**
	Full Scientific Name (LPSN)	Pedobacter terrae Yoon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31965]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.444

[Ref.: #31965]	Cell length	2.15 µm

[Ref.: #31965]	Cell width	0.4 µm

[Ref.: #31965]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31965]	Motility	no

[Ref.: #31965]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7174]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #7174]

Culture medium growth

[Ref.: #7174]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7174]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7174]	growth	25 °C
[Ref.: #31965]	growth	04-35 °C
[Ref.: #31965]	optimum	25 °C
[Ref.: #67771]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #31965]			optimum	7
[Ref.: #31965]			growth	5.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #31965]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31965]		NaCl		growth	<3	%
[Ref.: #31965]		NaCl		optimum	0.5	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31965]	arabinose ChEBI	+	carbon source
[Ref.: #31965]	cellobiose ChEBI	+	carbon source
[Ref.: #31965]	esculin ChEBI	+	hydrolysis
[Ref.: #31965]	fructose ChEBI	+	carbon source
[Ref.: #31965]	galactose ChEBI	+	carbon source
[Ref.: #31965]	glucose ChEBI	+	carbon source
[Ref.: #31965]	lactose ChEBI	+	carbon source
[Ref.: #31965]	maltose ChEBI	+	carbon source
[Ref.: #31965]	mannose ChEBI	+	carbon source
[Ref.: #31965]	melibiose ChEBI	+	carbon source
[Ref.: #31965]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #31965]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31965]	salicin ChEBI	+	carbon source
[Ref.: #31965]	sucrose ChEBI	+	carbon source
[Ref.: #31965]	trehalose ChEBI	+	carbon source
[Ref.: #31965]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #31965]	acid phosphatase	+	3.1.3.2
[Ref.: #31965]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31965]	catalase	+	1.11.1.6
[Ref.: #31965]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31965]	gelatinase	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7174]	Sample type/isolated from	soil
[Ref.: #7174]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #7174]	Country	Republic of Korea
[Ref.: #7174]	Country ISO 3 Code	KOR
[Ref.: #7174]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7174]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7174]	Pedobacter terrae strain DS-57 16S ribosomal RNA gene, partial sequence	DQ889723	1477	GenBank ENA	405671 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter terrae DSM 17933	GCA_900100705	scaffold	GenBank ENA	405671 tax ID	*
[Ref.: #66792]	Pedobacter terrae strain DSM 17933	405671.6	wgs	PATRIC	405671 tax ID	*
[Ref.: #66792]	Pedobacter terrae DSM 17933	2675903222	draft	JGI IMG/M	405671 tax ID	*

[Ref.: #7174]	GC-content	39.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31965]	GC-content	39.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pedobacter terrae DSM 17933 NCBI: GCA_900100705.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter terrae DSM 17933 NCBI: GCA_900100705.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.444	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.928	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.673	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	84.165	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.99	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	83	no

Availability in culture collections External links

[Ref.: #7174]

Culture collection no.

DSM 17933, KCTC 12762, CCM 9056

[Ref.: #83268]

SI-ID 402122

Literature:

Only first 10 entries are displayed. Click here to see all.

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	*

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#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 )

#28220

IJSEM 2462 2007 ( DOI 10.1099/ijs.0.64727-0 , PubMed 17978200 )

* These data were automatically processed and therefore are not curated

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Pedobacter terrae DSM 17933

Pedobacter terrae DSM 17933

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