Pedobacter alluvionis (DSM 19624, LMG 24258, NWER-II11)

Name: Pedobacter alluvionis (DSM 19624, LMG 24258, NWER-II11)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14110

Type strain

Strain Designation NWER-II11

Culture col. no. DSM 19624 LMG 24258 NWER-II11

NCBI tax ID(s) 475253

Special Collections DSMZ Literature strains

Links

Pedobacter alluvionis NWER-II11 is an aerobe, psychrophilic, Gram-negative prokaryote that was isolated from hyporheic sediments.

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

Name and taxonomic classification

SI-ID 310963

LMG 24258,DSM 19624,CCM 8562

@ref 20215

Last LPSN update 2025-12-16 09:50:16

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter alluvionis

Full scientific name Pedobacter alluvionis Gordon et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
28877	negative	2 µm	0.45 µm	rod-shaped
125438	negative
125439	negative

Pigmentation

28877

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8216	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8216	positive	growth	20	psychrophilic
28877	positive	growth	04-30
28877	positive	optimum	17	psychrophilic

Culture pH

@ref	Ability	Type	PH
28877	positive	optimum	7.5
28877	positive	growth	05-10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
28877	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
28877
125439

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28877	22599 ChEBI	arabinose	+	carbon source
28877	17057 ChEBI	cellobiose	+	carbon source
28877	4853 ChEBI	esculin	+	hydrolysis
28877	28757 ChEBI	fructose	+	carbon source
28877	28260 ChEBI	galactose	+	carbon source
28877	17234 ChEBI	glucose	+	carbon source
28877	17716 ChEBI	lactose	+	carbon source
28877	37684 ChEBI	mannose	+	carbon source
28877	28053 ChEBI	melibiose	+	carbon source
28877	506227 ChEBI	N-acetylglucosamine	+	carbon source
28877	16634 ChEBI	raffinose	+	carbon source
28877	26546 ChEBI	rhamnose	+	carbon source
28877	15963 ChEBI	ribitol	+	carbon source
28877	33942 ChEBI	ribose	+	carbon source
28877	17992 ChEBI	sucrose	+	carbon source
28877	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28877	acid phosphatase	+	3.1.3.2
28877	alkaline phosphatase	+	3.1.3.1
28877	alpha-galactosidase	+	3.2.1.22
28877	catalase	+	1.11.1.6
28877	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8216	hyporheic sediments	northwestern Montana, Middle Fork Flathead River, Nyack Floodplain	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence EU030688 (>99% sequence identity) for Pedobacter from Microbeatlas

Aquatic Samples	23
Soil Samples	35
Animal Samples	207
Plant Samples	7
Total Samples	272

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8216	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	ASM366403v1 assembly for Pedobacter alluvionis DSM 19624	scaffold	GCA_003664035	475253.4	2690315623	475253	73.56
66792	ASM440200v1 assembly for Pedobacter alluvionis DSM 19624	scaffold	GCA_004402005	475253.7	8119236617	475253	70.62

Genome browser: GCA_003664035

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8216	Pedobacter alluvionis strain NWER-II11 16S ribosomal RNA gene, partial sequence	EU030688	1400		475253

GC content

@ref	GC-content (mol%)	Method
8216	34.4±0.2	high performance liquid chromatography (HPLC)
8216	39.3	high performance liquid chromatography (HPLC)
28877	34.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter alluvionis DSM 19624
NCBI: GCA_003664035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	no	75.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	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 alluvionis DSM 19624
NCBI: GCA_003664035.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.44	no
125438	anaerobic	anaerobicⓘ	no	96.90	yes
125438	aerobic	aerobicⓘ	yes	88.21	yes
125438	spore-forming	spore-formingⓘ	no	86.05	no
125438	thermophilic	thermophileⓘ	no	97.99	yes
125438	flagellated	motile2+ⓘ	no	84.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter changchengzhani sp. nov., isolated from soil of Antarctica.	He RH, Liu ZW, Yu Y, Li HR, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-019-01305-4	2019
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	Pedobacterpsychrotolerans sp. nov., isolated from soil.	Manandhar P, Zhang G, Lama A, Hu Y, Gao F	Int J Syst Evol Microbiol	10.1099/ijsem.0.001391	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 ureilyticus sp. nov., isolated from tomato rhizosphere soil.	Ngo HTT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000055	2015
Phylogeny	Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter.	Kook M, Park Y, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.058024-0	2014
Phylogeny	Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil.	Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE	Int J Syst Evol Microbiol	10.1099/ijs.0.000158-0	2009
Phylogeny	Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic.	Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.005448	2022

References

#8216	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19624
#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 )
#28877	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 #25317 (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) .
#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 .
#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 alluvionis (DSM 19624, LMG 24258, NWER-II11)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003664035

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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