Metallibacterium scheffleri (DSM 24874, JCM 17596, DKE6)

Name: Metallibacterium scheffleri (DSM 24874, JCM 17596, DKE6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23347

Type strain

Strain Designation DKE6

Culture col. no. DSM 24874 JCM 17596 DKE6

NCBI tax ID(s) 993689

Special Collections DSMZ JCM Literature strains

History <- J. Gescher, Albert-Ludwigs-Univ. Freiburg, Freiburg, Germany; DKE6 <- S. Ziegler; {2009} J. Gescher DKE6.

Links

Metallibacterium scheffleri DKE6 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from acid mine drainage biofilm.

Gram-negative rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399465

JCM 17596,DSM 24874

@ref 20215

Last LPSN update 2026-02-09 11:23:44

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Metallibacterium

Species Metallibacterium scheffleri

Full scientific name Metallibacterium scheffleri Ziegler et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30721	negative	1.95 µm	0.5 µm	rod-shaped
125438	negative					97.222

Colony morphology

19298

Incubation period3-7 days

Pigmentation

30721

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19298	METALLIBACTERIUM MEDIUM (DSMZ Medium 1475)		Medium recipe at MediaDive	Name: METALLIBACTERIUM MEDIUM (DSMZ Medium 1475) Composition: Trypticase peptone 1.39721 g/l (NH4)2SO4 0.131737 g/l MgCl2 x 6 H2O 0.0528942 g/l MgSO4 x 7 H2O 0.0299401 g/l KH2PO4 0.0269461 g/l NaCl 0.00998004 g/l FeSO4 x 7 H2O 0.00998004 g/l MnSO4 x H2O 0.00499002 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00279441 g/l ZnSO4 x 7 H2O 0.00179641 g/l CoCl2 x 6 H2O 0.00179641 g/l CaCl2 x 2 H2O 0.000998004 g/l VOSO4 x 5 H2O 0.000499002 g/l AlK(SO4)2 x 12 H2O 0.000179641 g/l Na2MoO4 x 2 H2O 9.98004e-05 g/l H3BO3 9.98004e-05 g/l Na2WO4 x 2 H2O 9.98004e-05 g/l CuSO4 x 5 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l Na2SeO4 9.98004e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l Vitamin B12 9.98004e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19298	positive	growth	25
30721	positive	optimum	27.5
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
30721	positive	optimum	5.5
30721	positive	growth	2-6.5	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30721	facultative anaerobe
125439	obligate aerobe	97.5

Spore formation

@ref	Spore formation	Confidence
30721
125438		92.954
125439		91.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30721	NaCl	positive	growth	0-1 %

Observation

67770

Observationquinones: Q-8

Enzymes

@ref	Value	Activity	Ec
30721	catalase	+	1.11.1.6
30721	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	denitrification	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	hydrogen production	100	5 of 5
66794	photosynthesis	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	cardiolipin biosynthesis	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	95.45	21 of 22
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycine betaine biosynthesis	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	lipid A biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	purine metabolism	73.4	69 of 94
66794	alanine metabolism	72.41	21 of 29
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	methionine metabolism	69.23	18 of 26
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	IAA biosynthesis	66.67	2 of 3
66794	valine metabolism	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	glutathione metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	lysine metabolism	61.9	26 of 42
66794	urea cycle	61.54	8 of 13
66794	tryptophan metabolism	60.53	23 of 38
66794	Entner Doudoroff pathway	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	D-cycloserine biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	arginine metabolism	54.17	13 of 24
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	heme metabolism	50	7 of 14
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	oxidative phosphorylation	42.86	39 of 91
66794	cellulose degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	3-chlorocatechol degradation	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	sulfate reduction	38.46	5 of 13
66794	metabolism of disaccharids	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	lactate fermentation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	catecholamine biosynthesis	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	carnitine metabolism	25	2 of 8
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Aquatic	-
#Environmental	#Biofilm	-
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19298	acid mine drainage biofilm	Harz Mountains, pyrite mine "Drei Kronen und Ehrt"	Germany	DEU	Europe
67770	Acidic biofilum (pH 2.5) in the pyrite mine Drei Kronen und Ehrt		Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence HQ909259 (>99% sequence identity) for Metallibacterium scheffleri subclade from Microbeatlas

Aquatic Samples	445
Soil Samples	363
Animal Samples	10
Plant Samples	6
Total Samples	824

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19298	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
67770	ASM207713v1 assembly for Metallibacterium scheffleri DKE6	scaffold	GCA_002077135	993689.15	2988929297	993689	72.82
67770	ASM479895v1 assembly for Metallibacterium scheffleri DSM 24874	contig	GCA_004798955	993689.18	8062449935	993689	52.81

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19298	Metallibacterium scheffleri strain DKE6 16S ribosomal RNA gene, partial sequence	HQ909259	1479		993689

GC content

@ref	GC-content (mol%)	Method
19298	66.6	high performance liquid chromatography (HPLC)
30721	66.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Metallibacterium scheffleri DKE6
NCBI: GCA_002077135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.70	no
125439	motility	BacteriaNetⓘ	yes	73.20	no
125439	gram_stain	BacteriaNetⓘ	negative	87.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Metallibacterium scheffleri strain DSM 24874
PATRIC: 993689.18

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.22	no
125438	anaerobic	anaerobicⓘ	no	85.15	no
125438	aerobic	aerobicⓘ	yes	71.21	no
125438	spore-forming	spore-formingⓘ	no	92.95	yes
125438	thermophilic	thermophileⓘ	no	89.47	no
125438	flagellated	motile2+ⓘ	no	71.97	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Phylogenomics insights into order and families of Lysobacterales.	Kumar S, Bansal K, Patil PP, Patil PB.	Access Microbiol	10.1099/acmi.0.000015	2019
Phylogeny	Metallibacterium scheffleri gen. nov., sp. nov., an alkalinizing gammaproteobacterium isolated from an acidic biofilm.	Ziegler S, Waidner B, Itoh T, Schumann P, Spring S, Gescher J	Int J Syst Evol Microbiol	10.1099/ijs.0.042986-0	2012

References

#19298	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24874
#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 )
#27052	IJSEM 1499 2013 ( DOI 10.1099/ijs.0.042986-0 , PubMed 22863988 )
#30721	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 #27052
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Metallibacterium scheffleri (DSM 24874, JCM 17596, DKE6)

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

Halophily

Observation

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002077135

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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