Name: Metallibacterium scheffleri DKE6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23347

Type strain:

Species: Metallibacterium scheffleri

Strain Designation: DKE6

Culture col. no.: DSM 24874, JCM 17596

Strain history: J. Gescher DKE6.

NCBI tax ID(s): 993689 (species)

SI-ID 399465

DSM 24874

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Metallibacterium*
	Species	**Metallibacterium scheffleri**
	Full Scientific Name (LPSN)	Metallibacterium scheffleri Ziegler et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30721]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.987

[Ref.: #30721]	Cell length	1.95 µm

[Ref.: #30721]	Cell width	0.5 µm

[Ref.: #30721]	Cell shape	rod-shaped

[Ref.: #30721]	Motility	no

[Ref.: #19298]

Incubation period

3-7 days

[Ref.: #30721]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19298]

Culture medium

METALLIBACTERIUM MEDIUM (DSMZ Medium 1475)

[Ref.: #19298]

Culture medium growth

[Ref.: #19298]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19298]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19298]	growth	25 °C
[Ref.: #30721]	optimum	27.5 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #19298]	Temperature range	mesophilic
[Ref.: #30721]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30721]			optimum	5.5
[Ref.: #30721]			growth	2-6.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30721]

Oxygen tolerance

facultative anaerobe

[Ref.: #30721]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30721]		NaCl		growth	0-1	%

[Ref.: #67770]

Observation

quinones: Q-8

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30721]		catalase	+	1.11.1.6
[Ref.: #30721]		cytochrome oxidase	+	1.9.3.1

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #19298]	Sample type/isolated from	acid mine drainage biofilm
[Ref.: #19298]	Geographic location (country and/or sea, region)	Harz Mountains, pyrite mine "Drei Kronen und Ehrt"
[Ref.: #19298]	Country	Germany
[Ref.: #19298]	Country ISO 3 Code	DEU
[Ref.: #19298]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Acidic biofilum (pH 2.5) in the pyrite mine Drei Kronen und Ehrt
[Ref.: #67770]	Country	Germany
[Ref.: #67770]	Country ISO 3 Code	DEU
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Aquatic	-
#Environmental	#Biofilm	-
#Condition	#Acidic	-

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #19298]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #19298]	Metallibacterium scheffleri strain DKE6 16S ribosomal RNA gene, partial sequence	HQ909259	1479	ENA	993689 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Metallibacterium scheffleri DKE6	GCA_002077135	scaffold	GenBank	993689 tax ID
[Ref.: #67770]	Metallibacterium scheffleri DSM 24874	GCA_004798955	contig	GenBank	993689 tax ID
[Ref.: #66792]	Metallibacterium scheffleri strain DSM 24874	993689.18	wgs	PATRIC	993689 tax ID	*

[Ref.: #19298]	GC-content	66.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30721]	GC-content	66.6 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Metallibacterium scheffleri DKE6 NCBI: GCA_002077135.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Metallibacterium scheffleri strain DSM 24874 PATRIC: 993689.18
[Ref.: #69480]	motile	no	86.692	yes
[Ref.: #69480]	flagellated	no	97.208	yes
[Ref.: #69480]	gram-positive	no	98.392	no
[Ref.: #69480]	anaerobic	no	96.388	yes
[Ref.: #69480]	halophile	no	96.603	yes
[Ref.: #69480]	spore-forming	no	94.931	yes
[Ref.: #69480]	glucose-util	yes	78.028	no
[Ref.: #69480]	aerobic	no	65.484	yes
[Ref.: #69480]	thermophile	no	87.583	yes
[Ref.: #69480]	glucose-ferment	no	85.594	no

Availability in culture collections External links

[Ref.: #19298]

Culture collection no.

DSM 24874, JCM 17596

[Ref.: #87563]

SI-ID 399465

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#87563

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID399465.1 )

#27052

IJSEM 1499 2013 ( DOI 10.1099/ijs.0.042986-0 , PubMed 22863988 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Metallibacterium scheffleri in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Metallibacterium scheffleri DKE6

Metallibacterium scheffleri strain DSM 24874

Change proposal

Change proposal