Devosia limi (DSM 17137, CIP 109005, LMG 22951)

Name: Devosia limi (DSM 17137, CIP 109005, LMG 22951)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6165

Type strain

Culture col. no. DSM 17137 CIP 109005 LMG 22951

NCBI tax ID(s) 1121477 288995

Special Collections DSMZ CIP Literature strains

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

Links

Devosia limi DSM 17137 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from commercial nitrifying inoculum.

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

Name and taxonomic classification

SI-ID 137492

LMG 22951,DSM 17137,CIP 109005

@ref 20215

Last LPSN update 2026-05-29 08:26:20

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Devosiaceae

Genus Devosia

Species Devosia limi

Full scientific name Devosia limi Vanparys et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31510	negative	2 µm	0.75 µm	rod-shaped
120599	negative			rod-shaped
125438	negative				97.833

Colony morphology

120599

Hemolysis ability0

Pigmentation

31510

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6784	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
33275	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120599	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6784	positive	growth	28
31510	positive	growth	28
31510	positive	optimum	28
33275	positive	growth	30

Culture pH

@ref	Ability	Type	PH
31510	positive	optimum	6.8
31510	positive	growth	6.8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6784	aerobe
31510	aerobe
120599	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
31510
125439		97.881

Observation

31510

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31510	4853 ChEBI	esculin	+	hydrolysis
31510	25017 ChEBI	leucine	+	carbon source
120599	17632 ChEBI	nitrate	-	reduction
120599	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120599	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
120599	alcohol dehydrogenase	-	1.1.1.1
31510	alkaline phosphatase	+	3.1.3.1
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
31510	catalase	+	1.11.1.6
120599	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31510	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
120599	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
120599	ornithine decarboxylase	-	4.1.1.17
120599	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120599	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	denitrification	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	allantoin degradation	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	palmitate biosynthesis	95.45	21 of 22
66794	citric acid cycle	92.86	13 of 14
66794	pyrimidine metabolism	91.11	41 of 45
66794	proline metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	ketogluconate metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	phenylalanine metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	purine metabolism	81.91	77 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	tyrosine metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	biotin biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of pentoses	75	21 of 28
66794	lactate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	d-xylose degradation	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	propionate fermentation	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	leucine metabolism	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	histidine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of hexoses	61.11	11 of 18
66794	gallate degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	lysine metabolism	59.52	25 of 42
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	d-mannose degradation	55.56	5 of 9
66794	vitamin B1 metabolism	53.85	7 of 13
66794	ribulose monophosphate pathway	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	coenzyme A metabolism	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	sphingosine metabolism	50	3 of 6
66794	metabolism of disaccharids	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	sulfate reduction	38.46	5 of 13
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	androgen and estrogen metabolism	25	4 of 16
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

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
120599	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Engineered product
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6784	commercial nitrifying inoculum	Gent	Belgium	BEL	Europe
120599	Commercial nitrifying inoculum		Belgium	BEL	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ786801 (>99% sequence identity) for Devosia limi subclade from Microbeatlas

Aquatic Samples	211
Soil Samples	532
Animal Samples	425
Plant Samples	149
Total Samples	1317

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6784	1	Risk group (German classification) According to TRBA 466
120599	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 2582580747 annotated assembly for Devosia limi DSM 17137	scaffold	GCA_900128975	1121477.5	2582580747	1121477	71.3
66792	ASM97043v1 assembly for Devosia limi DSM 17137	contig	GCA_000970435	1121477.3	2627853739	1121477	42.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6784	Devosia sp. R-21940 partial 16S rRNA gene, type strain R-21940T	AJ786801	1437		288995
124043	Devosia limi strain DSM 17137(T) 16S ribosomal RNA gene, partial sequence.	MW111211	609		288995

GC content

6784

GC-content (mol%)61.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2582580747 annotated assembly for Devosia limi DSM 17137
BV-BRC: 1121477.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	73.66	no
125439	gram_stain	BacteriaNetⓘ	negative	72.72	no
125439	motility	BacteriaNetⓘ	yes	45.92	no
125439	spore_formation	BacteriaNetⓘ	no	97.88	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Devosia limi DSM 17137 DSM 17137
NCBI: GCA_900128975.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.83	no
125438	anaerobic	anaerobicⓘ	no	96.52	no
125438	aerobic	aerobicⓘ	yes	83.95	no
125438	spore-forming	spore-formingⓘ	no	89.78	yes
125438	thermophilic	thermophileⓘ	no	97.06	yes
125438	flagellated	motile2+ⓘ	yes	67.58	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The Identification of DepB: An Enzyme Responsible for the Final Detoxification Step in the Deoxynivalenol Epimerization Pathway in Devosia mutans 17-2-E-8.	Carere J, Hassan YI, Lepp D, Zhou T.	Front Microbiol	10.3389/fmicb.2018.01573	2018
Metabolism	Characterization of Endofungal Bacteria and Their Role in the Ectomycorrhizal Fungus Helvella bachu.	Wei C, Liu M, Meng G, Wang M, Zhou X, Xu J, Hu J, Zhang L, Dong C.	J Fungi (Basel)	10.3390/jof10120889	2024
Phylogeny	Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study.	Karakasidou K, Nikolouli K, Amoutzias GD, Pournou A, Manassis C, Tsiamis G, Mossialos D.	Microbiologyopen	10.1002/mbo3.596	2018
	Temporal changes in the bacterial community of animal feces and their correlation with stable fly oviposition, larval development, and adult fitness.	Albuquerque TA, Zurek L.	Front Microbiol	10.3389/fmicb.2014.00590	2014
	Devosia rhodophyticola sp. nov. and Devosia algicola sp. nov., isolated from a marine red alga.	Kim JM, Baek W, Choi BJ, Bayburt H, Baek JH, Han DM, Lee SC, Jeon CO.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006223	2024
Phylogeny	Devosia epidermidihirudinis sp. nov. isolated from the surface of a medical leech.	Galatis H, Martin K, Kampfer P, Glaeser SP.	Antonie Van Leeuwenhoek	10.1007/s10482-013-9895-3	2013
Phylogeny	Devosia subaequoris sp. nov., isolated from beach sediment.	Lee SD.	Int J Syst Evol Microbiol	10.1099/ijs.0.65185-0	2007
Phylogeny	Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea.	Zhang YX, Yu Y, Luo W, Zeng YX, Du ZJ, Li HR	Int J Syst Evol Microbiol	10.1099/ijsem.0.004995	2021
Phylogeny	Devosia limi sp. nov., isolated from a nitrifying inoculum.	Vanparys B, Heylen K, Lebbe L, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.63714-0	2005

References

#6784	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17137
#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 )
#27806	IJSEM 1997 2005 ( DOI 10.1099/ijs.0.63714-0 , PubMed 16166701 )
#31510	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 #27806
#33275	; 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) .
#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 )
#68382	Automatically annotated from API zym .
#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 .
#120599	Collection of Institut Pasteur ; Curators of the CIP; CIP 109005
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Content

About us

Devosia limi (DSM 17137, CIP 109005, LMG 22951)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900128975

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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