Name: Pedobacter antarcticus KS0420
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14093

Type strain:

Species: Pedobacter antarcticus

Strain Designation: KS0420, P-48

Culture col. no.: DSM 11725, CIP 104195, JCM 14985, JCM 7454, AJ 2502, CCM 4602, IFO 14985, KCTC 12489, LMG 14024, NBRC 14985, NCIMB 13704

Strain history: CIP <- 1994, IFO <- JCM <- H. Oyaizu: strain AJ 2502 <- K. Komagata and H. Ogawa: strain P-48

NCBI tax ID(s): 34086 (species)

SI-ID 264392

LMG 14024, CIP 104195, IFO 14985, JCM 7454, NCIMB 13704, CCM 4602, DSM 11725, NBRC 14985, KCTC 12489

Special Collections

Other strains from Pedobacter antarcticus

Section

Pedobacter antarcticus KS0420 is an obligate aerobe, Gram-negative, rod-shaped bacterium that was isolated from frozen rainbow trout.

Gram-negative
rod-shaped
obligate 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 antarcticus**
	Full Scientific Name (LPSN)	Pedobacter antarcticus (Shivaji et al. 1992) Farfán et al. 2014

	Synonym	Sphingobacterium antarcticum
	Synonym	Pedobacter piscium
	Synonym	Sphingobacterium antarcticus
	Synonym	Sphingobacterium piscium

Information on morphological and physiological properties Morphology

[Ref.: #121845]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96

[Ref.: #121845]	Cell shape	rod-shaped

[Ref.: #121845]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4457]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #4457]

Culture medium growth

[Ref.: #4457]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4457]

Culture medium composition

expand / minimize

[Ref.: #41043]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #41043]

Culture medium growth

[Ref.: #41043]

Culture medium composition

expand / minimize

[Ref.: #121845]

Culture medium

CIP Medium 3

[Ref.: #121845]

Culture medium growth

[Ref.: #121845]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #4457]		growth	28 °C
[Ref.: #41043]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #121845]		growth	10-30 °C
[Ref.: #121845]	no	growth	37 °C
[Ref.: #121845]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121845]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #121845]	citrate ChEBI	-	carbon source
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121845]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121845]	nitrate ChEBI	-	reduction
[Ref.: #121845]	nitrate ChEBI	-	respiration
[Ref.: #121845]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121845]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #121845]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #121845]	beta-galactosidase	+	3.2.1.23
[Ref.: #121845]	catalase	+	1.11.1.6
[Ref.: #121845]	DNase	+
[Ref.: #121845]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #121845]	lysine decarboxylase	-	4.1.1.18
[Ref.: #121845]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121845]	oxidase	+
[Ref.: #121845]	phenylalanine ammonia-lyase	+	4.3.1.24
[Ref.: #121845]	tryptophan deaminase	-
[Ref.: #121845]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #121845]	9536	not determinedn.d.	-	-	-	+	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	+/-	-	+	+	+	+	+	+	+	+	+	+	-	-	+	+	-	-	+	+	-	-	-	-	-	-	-	-	-

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #121845]	596	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	-	-	-	-	+	-

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

[Ref.: #4457]	Sample type/isolated from	frozen rainbow trout

[Ref.: #67770]	Sample type/isolated from	Frozen rainbow trout

[Ref.: #121845]	Sample type/isolated from	Frozen rainbow traut
* marker position based on {}

Isolation sources categories

#Host

#Fishes

#Salmonidae

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ438174 (>99% sequence identity) for Pedobacter antarcticus from Microbeatlas

Aquatic Samples	29
Soil Samples	82
Animal Samples	136
Plant Samples	67
Total Samples	314

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

[Ref.: #4457]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121845]	Biosafety level	1	Risk group (French classification)

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.: #4457]	Pedobacter piscium partial 16S rRNA gene, strain DSM 11725T	AJ438174	1494	GenBank ENA	34086 tax ID
[Ref.: #124043]	Pedobacter piscium gene for 16S rRNA, partial sequence, strain: NBRC 14985.	AB680733	1447	GenBank ENA	34086 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter antarcticus DSM 11725	GCA_900103515	scaffold	GenBank ENA	34086 tax ID	*
[Ref.: #66792]	Pedobacter antarcticus strain DSM 11725	34086.10	wgs	PATRIC	34086 tax ID	*
[Ref.: #66792]	Pedobacter piscium DSM 11725	2622736436	draft	JGI IMG/M	34086 tax ID	*

[Ref.: #67770]	GC-content	40.4 mol%
[Ref.: #67770]	GC-content	38.7 mol%	thermal denaturation, midpoint method (Tm)

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 antarcticus DSM 11725 NCBI: GCA_900103515.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter antarcticus DSM 11725 NCBI: GCA_900103515.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.629	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.697	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.194	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.99	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	88.095	no

Availability in culture collections External links

[Ref.: #4457]

Culture collection no.

DSM 11725, CIP 104195, JCM 14985, JCM 7454, AJ 2502, CCM 4602, IFO 14985, KCTC 12489, LMG 14024, NBRC 14985, NCIMB 13704

[Ref.: #83261]

SI-ID 264392

References

#4457

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11725

#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 )

#41043 ; Curators of the CIP;

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#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 )

#83261

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-ID264392.1 )

#121845 Collection of Institut Pasteur ; Curators of the CIP; CIP 104195

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pedobacter antarcticus in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Pedobacter antarcticus DSM 11725

Pedobacter antarcticus DSM 11725

Change proposal

Change proposal