Pedobacter caeni (DSM 16990, CIP 109035, LMG 22862)

Name: Pedobacter caeni (DSM 16990, CIP 109035, LMG 22862)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14099

Type strain

Culture col. no. DSM 16990 CIP 109035 LMG 22862

NCBI tax ID(s) 288992

Special Collections DSMZ CIP Literature strains

History <- B. Vanparys, LMG 2005, DSMZ CIP <- 2005, DSMZ

Links

Pedobacter caeni DSM 16990 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from nitrifying inoculum.

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

Name and taxonomic classification

SI-ID 129690

LMG 22862,DSM 16990,CIP 109035,VTT E-072688

@ref 20215

Last LPSN update 2026-02-09 11:21:19

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter caeni

Full scientific name Pedobacter caeni Vanparys et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31473	negative	6.5 µm	0.75 µm	rod-shaped
117094	negative			rod-shaped
125438	negative				96
125439	negative				99.4

Colony morphology

117094

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6593	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
34022	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117094	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6593	positive	growth	28
31473	positive	growth	28-37
31473	positive	optimum	28
34022	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6593	aerobe
31473	aerobe
117094	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
31473
125439		98.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
117094	17632 ChEBI	nitrate	-	reduction
117094	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
31473	16634 ChEBI	raffinose	+	carbon source
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
31473	17151 ChEBI	xylitol	+	carbon source
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
117094	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
117094	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31473	catalase	+	1.11.1.6
117094	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31473	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
117094	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
117094	ornithine decarboxylase	-	4.1.1.17
117094	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
117094	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
117094	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	+	-	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
117094	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6593	nitrifying inoculum	Gent	Belgium	BEL	Europe
117094	Commercial nitrifying inoculum	Ghent	Belgium	BEL	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6593	1	Risk group (German classification) According to TRBA 466
117094	1	Risk group (French 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	IMG-taxon 2622736434 annotated assembly for Pedobacter caeni DSM 16990	scaffold	GCA_900129215	288992.5	2622736434	288992	71.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6593	Pedobacter caeni partial 16S rRNA gene, type strain LMG 22862T	AJ786798	1337		288992

GC content

31473

GC-content (mol%)42.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter caeni DSM 16990
NCBI: GCA_900129215

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	no	72.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	84.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter caeni DSM 16990
NCBI: GCA_900129215.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.00	no
125438	anaerobic	anaerobicⓘ	no	97.37	no
125438	aerobic	aerobicⓘ	yes	87.83	yes
125438	spore-forming	spore-formingⓘ	no	84.44	no
125438	thermophilic	thermophileⓘ	no	98.99	yes
125438	flagellated	motile2+ⓘ	no	86.25	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana.	Qi SS, Cnockaert M, Carlier A, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijsem.0.004667	2021
Phylogeny	Pedobacter quisquiliarum sp. nov., isolated from activated sludge.	Zhang B, Liu ZQ, Zheng YG	Int J Syst Evol Microbiol	10.1099/ijsem.0.002531	2017
Phylogeny	Pedobacter humi sp. nov., isolated from a playground soil.	Trinh H, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001032	2016
Phylogeny	Pedobacter lotistagni sp. nov. isolated from lotus pond water.	Singh H, Du J, Ngo HT, Kim KY, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-015-0387-5	2015
Phylogeny	Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field.	Ngo HT, Son HM, Park SY, Kim KY, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0154-z	2014
Phylogeny	Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet.	Muurholm S, Cousin S, Pauker O, Brambilla E, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.65166-0	2007
Phylogeny	Parapedobacter koreensis gen. nov., sp. nov.	Kim MK, Na JR, Cho DH, Soung NK, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64677-0	2007
Phylogeny	Pedobacter panaciterrae sp. nov., isolated from soil in South Korea.	Yoon MH, Ten LN, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64693-0	2007
Phylogeny	Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea.	Ten LN, Liu QM, Im WT, Lee M, Yang DC, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64414-0	2006
Phylogeny	Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum.	Vanparys B, Heylen K, Lebbe L, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.63635-0	2005

References

#6593	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16990
#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 )
#27773	IJSEM 1315 2005 ( DOI 10.1099/ijs.0.63635-0 , PubMed 15879274 )
#31473	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 #27773
#34022	; 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) .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#117094	Collection of Institut Pasteur ; Curators of the CIP; CIP 109035
#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 caeni (DSM 16990, CIP 109035, LMG 22862)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900129215

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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