Pedobacter vanadiisoli (XNV015, KCTC 42866, CCTCC AB 2015319)

Name: Pedobacter vanadiisoli (XNV015, KCTC 42866, CCTCC AB 2015319)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133249

Type strain

Strain Designation XNV015

Culture col. no. XNV015 KCTC 42866 CCTCC AB 2015319

NCBI tax ID(s) 1761975

Special Collections KCTC Literature strains

History KCTC <- Zhiyong Wang, Huzhong Agricultural Univ.

Links

Pedobacter vanadiisoli XNV015 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil of a vanadium mine.

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

Name and taxonomic classification

SI-ID 287643

KCTC 42866

@ref 20215

Last LPSN update 2026-05-29 08:38:02

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter vanadiisoli

Full scientific name Pedobacter vanadiisoli Wang et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25116	negative	1.0-1.5 µm	0.5-0.6 µm	rod-shaped
67771				rod-shaped
67771	negative
125439	negative				99.811

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25116	2.0-4.0 mm	light pink	circular	2 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
25116	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
25116	positive	growth	10-37
25116	positive	optimum	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
25116	positive	optimum	7
25116	positive	growth	4.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25116	aerobe
67771	aerobe
125439	aerobe	94.472

Spore formation

@ref	Type of spore	Spore formation	Confidence
25116	endospore
125439			99.915

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25116	NaCl	positive	growth	0-2.0 %(w/v)

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25116	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
25116	16193 ChEBI	3-hydroxybenzoate	-	assimilation
25116	37054 ChEBI	3-hydroxybutyrate	-	assimilation
25116	17879 ChEBI	4-hydroxybenzoate	-	assimilation
25116	17426 ChEBI	5-dehydro-D-gluconate	-	assimilation
25116	30089 ChEBI	acetate	-	assimilation
25116	17128 ChEBI	adipate	-	assimilation
25116	17968 ChEBI	butyrate	-	assimilation
25116	17057 ChEBI	cellobiose	+	builds acid from
25116	16947 ChEBI	citrate	-	assimilation
25116	15824 ChEBI	D-fructose	-	builds acid from
25116	17634 ChEBI	D-glucose	+	builds acid from
25116	17634 ChEBI	D-glucose	+	assimilation
25116	16899 ChEBI	D-mannitol	-	assimilation
25116	16024 ChEBI	D-mannose	+	assimilation
25116	16988 ChEBI	D-ribose	-	builds acid from
25116	16988 ChEBI	D-ribose	-	assimilation
25116	17924 ChEBI	D-sorbitol	-	builds acid from
25116	17924 ChEBI	D-sorbitol	-	assimilation
25116	27689 ChEBI	decanoate	-	assimilation
25116	4853 ChEBI	esculin	+	hydrolysis
25116	16236 ChEBI	ethanol	+	builds acid from
25116	5291 ChEBI	gelatin	+	hydrolysis
25116	24265 ChEBI	gluconate	-	assimilation
25116	28087 ChEBI	glycogen	+	assimilation
25116	17240 ChEBI	itaconate	-	assimilation
25116	16977 ChEBI	L-alanine	-	assimilation
25116	30849 ChEBI	L-arabinose	+	builds acid from
25116	30849 ChEBI	L-arabinose	+	assimilation
25116	18287 ChEBI	L-fucose	-	assimilation
25116	15971 ChEBI	L-histidine	-	assimilation
25116	17203 ChEBI	L-proline	-	assimilation
25116	62345 ChEBI	L-rhamnose	+	assimilation
25116	17115 ChEBI	L-serine	-	assimilation
25116	24996 ChEBI	lactate	-	assimilation
25116	17716 ChEBI	lactose	+	builds acid from
25116	25115 ChEBI	malate	+	assimilation
25116	15792 ChEBI	malonate	-	assimilation
25116	17306 ChEBI	maltose	+	builds acid from
25116	17306 ChEBI	maltose	+	assimilation
25116	28053 ChEBI	melibiose	+	assimilation
25116	17268 ChEBI	myo-inositol	-	assimilation
25116	506227 ChEBI	N-acetylglucosamine	+	assimilation
25116	17632 ChEBI	nitrate	-	reduction
25116	64681 ChEBI	phenyl beta-D-glucuronide	+	assimilation
25116	18401 ChEBI	phenylacetate	-	assimilation
25116	17272 ChEBI	propionate	-	assimilation
25116	26546 ChEBI	rhamnose	+	builds acid from
25116	17814 ChEBI	salicin	+	assimilation
25116	30911 ChEBI	sorbitol	-	builds acid from
25116	9300 ChEBI	suberic acid	-	assimilation
25116	17992 ChEBI	sucrose	+	builds acid from
25116	17992 ChEBI	sucrose	+	assimilation
25116	27897 ChEBI	tryptophan	-	energy source
25116	31011 ChEBI	valerate	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite
25116	2637	amikacin
25116	28971	ampicillin
25116	3393	carbenicillin
25116	3508	ceftazidime
25116	3515	cefuroxime
25116	3534	cephalexin
25116	3547	cephradine
25116	17698	chloramphenicol
25116	17113	erythritol
25116	17833	gentamicin
25116	6104	kanamycin
25116	6472	lincomycin
25116	7507	neomycin
25116	7809	oxacillin
25116	17334	penicillin
25116	8232	piperacillin
25116	28077	rifampicin
25116	17076	streptomycin
25116	27902	tetracycline
25116	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25116	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25116	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
25116	acid phosphatase	+	3.1.3.2
25116	alkaline phosphatase	+	3.1.3.1
25116	alpha-galactosidase	+	3.2.1.22
25116	alpha-glucosidase	+	3.2.1.20
25116	arginine dihydrolase	-	3.5.3.6
25116	beta-galactosidase	+	3.2.1.23
25116	beta-glucosidase	+	3.2.1.21
25116	beta-glucuronidase	-	3.2.1.31
25116	catalase	+	1.11.1.6
25116	chymotrypsin	-	3.4.4.5
25116	cytochrome oxidase	+	1.9.3.1
25116	esterase	-
25116	esterase lipase (C 8)	+
25116	leucine arylamidase	+	3.4.11.1
25116	N-acetyl-beta-glucosaminidase	+	3.2.1.52
25116	naphthol-AS-BI-phosphohydrolase	+
25116	phenylalanine ammonia-lyase	+	4.3.1.24
25116	phenylalanine deaminase	+	4.3.1.5
25116	trypsin	+	3.4.21.4
25116	tryptophan deaminase	-	4.1.99.1
25116	urease	-	3.5.1.5
25116	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture temperature	Isolation procedure
25116	soil of a vanadium mine	Xianning, Hubei province	China	CHN	Asia	29	114 29/114	1/10 TSB	28	dilution-plating method
67771	From soil, vanadium mine	Xianning, Hubei province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KU179044 (>99% sequence identity) for Pedobacter vanadiisoli from Microbeatlas

Aquatic Samples	7
Soil Samples	6
Animal Samples	0
Plant Samples	28
Total Samples	41

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4268438v1 assembly for Pedobacter vanadiisoli KCTC 42866	contig	GCA_042684385	1761975	67.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25116	Pedobacter vanadiisoli strain XNV015 16S ribosomal RNA gene, partial sequence	KU179044	1444		1761975

GC content

@ref	GC-content (mol%)	Method
25116	43.8	high performance liquid chromatography (HPLC)
67771	43.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4268438v1 assembly for Pedobacter vanadiisoli KCTC 42866
NCBI: GCA_042684385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.47	no
125439	gram_stain	BacteriaNetⓘ	negative	99.81	no
125439	motility	BacteriaNetⓘ	no	69.44	no
125439	spore_formation	BacteriaNetⓘ	no	99.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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

References

#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 )
#25116	Z. T. Wang, Y.,Xu, D.,Wang, G.,Yuan, J.,Zheng, S.: Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine. IJSEM 66: 5112 - 5117 2016 ( DOI 10.1099/ijsem.0.001480 , PubMed 27600161 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Content

About us

Pedobacter vanadiisoli (XNV015, KCTC 42866, CCTCC AB 2015319)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_042684385

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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