Orbus hercynius (DSM 22228, CCUG 57622, CN 3)

Name: Orbus hercynius (DSM 22228, CCUG 57622, CN 3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17917

Type strain

Culture col. no. DSM 22228 CCUG 57622 CN 3

NCBI tax ID(s) 593135

Special Collections DSMZ CCUG Literature strains

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

ovoid-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402530

DSM 22228,CCUG 57622

@ref 20215

Last LPSN update 2025-12-16 09:51:13

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Orbales

Family Orbaceae

Genus Orbus

Species Orbus hercynius

Full scientific name Orbus hercynius Volkmann et al. 2010

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape
29700	1-1.5 µm	0.8 µm	ovoid-shaped
125439
125438
125438

Pigmentation

29700

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16215	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16215	positive	growth	28	mesophilic
29700	positive	growth	04-37
29700	positive	optimum	20-30
61393	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
29700	positive	optimum	7.5
29700	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29700	facultative anaerobe
61393	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.7

Observation

29700

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29700	4853 ChEBI	esculin	+	hydrolysis
29700	17234 ChEBI	glucose	+	carbon source
29700	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
29700	catalase	+	1.11.1.6
29700	cytochrome oxidase	+	1.9.3.1
29700	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	threonine metabolism	100	10 of 10
66794	CMP-KDO biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	lipoate biosynthesis	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	palmitate biosynthesis	95.45	21 of 22
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	purine metabolism	69.15	65 of 94
66794	formaldehyde oxidation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	alanine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	non-pathway related	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	methionine metabolism	61.54	16 of 26
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	glycogen metabolism	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	glutathione metabolism	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	proline metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	leucine metabolism	53.85	7 of 13
66794	histidine metabolism	51.72	15 of 29
66794	ethanol fermentation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	arginine metabolism	50	12 of 24
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	butanoate fermentation	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	ketogluconate metabolism	50	4 of 8
66794	tryptophan metabolism	47.37	18 of 38
66794	oxidative phosphorylation	47.25	43 of 91
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	tyrosine metabolism	42.86	6 of 14
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of sugar acids	32	8 of 25
66794	ascorbate metabolism	31.82	7 of 22
66794	phenol degradation	30	6 of 20
66794	coenzyme M biosynthesis	30	3 of 10
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16215	faeces of wild boar	Halberstadt	Germany	DEU	Europe
61393	Wild boar,feces	Halberstadt	Germany	DEU	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16215	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
66792	ASM363427v1 assembly for Orbus hercynius DSM 22228	scaffold	GCA_003634275	593135.5	2770939645	593135	72.46

Genome browser: GCA_003634275

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16215	Orbus hercynius strain CN3 16S ribosomal RNA gene, partial sequence	FJ612598	1522		593135

GC content

@ref	GC-content (mol%)	Method
16215	36.4	high performance liquid chromatography (HPLC)
29700	36.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Orbus hercynius DSM 22228
NCBI: GCA_003634275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	60.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Orbus hercynius DSM 22228
NCBI: GCA_003634275.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	85.40	yes
125438	aerobic	aerobicⓘ	no	75.35	no
125438	spore-forming	spore-formingⓘ	no	89.71	no
125438	thermophilic	thermophileⓘ	no	96.58	no
125438	flagellated	motile2+ⓘ	no	90.33	yes

Literature

Title	Authors	Journal	DOI	Year
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.	Elston KM, Phillips LE, Leonard SP, Young E, Holley JC, Ahsanullah T, McReynolds B, Moran NA, Barrick JE.	ISME Commun	10.1038/s43705-023-00255-3	2023
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
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
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 .
#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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Orbus hercynius (DSM 22228, CCUG 57622, CN 3)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

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_003634275

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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