Name: Orbus hercynius DSM 22228
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17917

Type strain:

Species: Orbus hercynius

Culture col. no.: DSM 22228, CCUG 57622, CN 3

Strain history: <- G. Wilharm, Robert-Koch-Institut, Wernigerode, Germany; CN3 <- M. Volkmann

NCBI tax ID(s): 593135 (species)

SI-ID 402530

DSM 22228, CCUG 57622

Special Collections

Section

Orbus hercynius DSM 22228 is a facultative anaerobe, ovoid-shaped bacterium that was isolated from faeces of wild boar.

ovoid-shaped
facultative anaerobe
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	*Orbales*
	Family	*Orbaceae*
	Genus	*Orbus*
	Species	**Orbus hercynius**
	Full Scientific Name (LPSN)	Orbus hercynius Volkmann et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #29700]	Cell length	1-1.5 µm

[Ref.: #29700]	Cell width	0.8 µm

[Ref.: #29700]	Cell shape	ovoid-shaped

[Ref.: #29700]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.329

[Ref.: #29700]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16215]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #16215]

Culture medium growth

[Ref.: #16215]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16215]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16215]	growth	28 °C
[Ref.: #29700]	growth	04-37 °C
[Ref.: #29700]	optimum	20-30 °C
[Ref.: #61393]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #29700]			optimum	7.5
[Ref.: #29700]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29700]	Oxygen tolerance	facultative anaerobe
[Ref.: #61393]	Oxygen tolerance	aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #29700]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29700]	esculin ChEBI	+	hydrolysis
[Ref.: #29700]	glucose ChEBI	+	carbon source
[Ref.: #29700]	nitrate ChEBI	+	reduction

	Enzyme	Enzyme activity	EC number
[Ref.: #29700]	catalase	+	1.11.1.6
[Ref.: #29700]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29700]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[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.: #16215]	Sample type/isolated from	faeces of wild boar
[Ref.: #16215]	Geographic location (country and/or sea, region)	Halberstadt
[Ref.: #16215]	Country	Germany
[Ref.: #16215]	Country ISO 3 Code	DEU
[Ref.: #16215]	Continent	Europe

[Ref.: #61393]	Sample type/isolated from	Wild boar,feces
[Ref.: #61393]	Sampling date	2008-08-11
[Ref.: #61393]	Geographic location (country and/or sea, region)	Halberstadt
[Ref.: #61393]	Country	Germany
[Ref.: #61393]	Country ISO 3 Code	DEU
[Ref.: #61393]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ612598 (>99% sequence identity) for Orbus hercynius subclade from Microbeatlas

Aquatic Samples	27
Soil Samples	2
Animal Samples	417
Plant Samples	3
Total Samples	449

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

[Ref.: #16215]

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.: #16215]	Orbus hercynius strain CN3 16S ribosomal RNA gene, partial sequence	FJ612598	1522	GenBank ENA	593135 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Orbus hercynius DSM 22228	GCA_003634275	scaffold	GenBank ENA	593135 tax ID	*
[Ref.: #66792]	Orbus hercynius strain DSM 22228	593135.5	wgs	PATRIC	593135 tax ID	*
[Ref.: #66792]	Orbus hercynius DSM 22228	2770939645	draft	JGI IMG/M	593135 tax ID	*

[Ref.: #16215]	GC-content	36.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29700]	GC-content	36.4 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Orbus hercynius DSM 22228 NCBI: GCA_003634275.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Orbus hercynius DSM 22228 NCBI: GCA_003634275.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	85.396	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	75.345	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.705	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.583	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90.329	yes

Availability in culture collections External links

[Ref.: #16215]

Culture collection no.

DSM 22228, CCUG 57622, CN 3

[Ref.: #86906]

SI-ID 402530

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Orbus hercynius gen. nov., sp. nov., isolated from faeces of wild boar, is most closely related to members of the orders 'Enterobacteriales' and Pasteurellales.	Volkmann M, Skiebe E, Kerrinnes T, Faber F, Lepka D, Pfeifer Y, Holland G, Bannert N, Wilharm G	Int J Syst Evol Microbiol	10.1099/ijs.0.019026-0	2009	*
Phylogeny	Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order 'Enterobacteriales' of the Gammaproteobacteria.	Kwong WK, Moran NA	Int J Syst Evol Microbiol	10.1099/ijs.0.044875-0	2012	*
Phylogeny	Orbus sasakiae sp. nov., a bacterium isolated from the gut of the butterfly Sasakia charonda, and emended description of the genus Orbus.	Kim JY, Lee J, Shin NR, Yun JH, Whon TW, Kim MS, Jung MJ, Roh SW, Hyun DW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.041871-0	2012	*

References

#16215

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22228

#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 )

#29700

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 #26083 (see below)

#61393 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57622

#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 )

#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 )

#86906

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-ID402530.1 )

#26083

IJSEM 2601 2010 ( DOI 10.1099/ijs.0.019026-0 , PubMed 20023064 )

* These data were automatically processed and therefore are not curated

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