Pedobacter nutrimenti (DSM 27372, CCUG 64422, J22)

Name: Pedobacter nutrimenti (DSM 27372, CCUG 64422, J22)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24549

Type strain

Strain Designation J22

Culture col. no. DSM 27372 CCUG 64422 J22

NCBI tax ID(s) 1241337

Special Collections DSMZ CCUG

Links

Pedobacter nutrimenti J22 is an aerobe, mesophilic prokaryote that was isolated from refrigerated fresh pasta filled with pork .

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400780

DSM 27372,CCUG 64422

@ref 20215

Last LPSN update 2025-12-16 09:52:52

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter nutrimenti

Full scientific name Pedobacter nutrimenti Derichs et al. 2014

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.444
125439	negative	99.5

Colony morphology

63124

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20727	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
63124	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

63124

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	methylglyoxal degradation	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycine betaine biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	vitamin B1 metabolism	69.23	9 of 13
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	coenzyme M biosynthesis	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tryptophan metabolism	57.89	22 of 38
66794	lysine metabolism	57.14	24 of 42
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	oxidative phosphorylation	52.75	48 of 91
66794	myo-inositol biosynthesis	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	catecholamine biosynthesis	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	degradation of sugar acids	44	11 of 25
66794	degradation of sugar alcohols	43.75	7 of 16
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	phenol degradation	35	7 of 20
66794	polyamine pathway	34.78	8 of 23
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	arachidonic acid metabolism	33.33	6 of 18
66794	degradation of pentoses	28.57	8 of 28
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22
66794	allantoin degradation	22.22	2 of 9
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food
#Engineered	#Food production	#Meat
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
20727	refrigerated fresh pasta filled with pork (tortellini)		Bonn	Germany	DEU	Europe
63124	Food,chilled	2010-03-15	Bonn	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20727	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM320865v1 assembly for Pedobacter nutrimenti DSM 27372	scaffold	GCA_003208655	1241337.3	2619619049	1241337	72.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20727	Pedobacter nutrimenti partial 16S rRNA gene, type strain J22T	HF536497	1457		1241337

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter nutrimenti DSM 27372
NCBI: GCA_003208655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.10	no
125439	motility	BacteriaNetⓘ	no	65.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter nutrimenti DSM 27372
NCBI: GCA_003208655.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.44	no
125438	anaerobic	anaerobicⓘ	no	97.45	no
125438	aerobic	aerobicⓘ	yes	84.93	yes
125438	spore-forming	spore-formingⓘ	no	88.01	no
125438	thermophilic	thermophileⓘ	no	97.85	no
125438	flagellated	motile2+ⓘ	no	84.50	no

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 nutrimenti sp. nov., isolated from chilled food.	Derichs J, Kampfer P, Lipski A	Int J Syst Evol Microbiol	10.1099/ijs.0.058677-0	2014

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 )
#20727	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27372
#63124	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 64422
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 nutrimenti (DSM 27372, CCUG 64422, J22)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003208655

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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