Name: Otariodibacter oris Baika1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11759

Type strain:

Species: Otariodibacter oris

Strain Designation: Baika1

Culture col. no.: DSM 23800, CCUG 59994

Strain history: <- M.J. Hansen, Fac. Life Sci., Univ. Copenhagen, Frederiksberg, Denmark; Baika1

NCBI tax ID(s): 1032623 (species)

SI-ID 405975

DSM 23800, CCUG 59994

Special Collections

Section

Otariodibacter oris Baika1 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from oral swab from gingiva of a healthy Californian sea lion.

Gram-negative
rod-shaped
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	*Pasteurellales*
	Family	*Pasteurellaceae*
	Genus	*Otariodibacter*
	Species	**Otariodibacter oris**
	Full Scientific Name (LPSN)	Otariodibacter oris Hansen et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30597]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.604

[Ref.: #30597]	Cell shape	rod-shaped

[Ref.: #30597]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.071

[Ref.: #17373]	Type of hemolysis	gamma
[Ref.: #17373]	Incubation period	1-2 days

[Ref.: #30597]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17373]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #17373]

Culture medium growth

[Ref.: #17373]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17373]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17373]			growth	37 °C
[Ref.: #62178]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30597]	Oxygen tolerance	anaerobe
[Ref.: #62178]	Oxygen tolerance	microaerophile

[Ref.: #69480]	Ability of spore formation	no Confidence in %93.466
[Ref.: #69481]	Ability of spore formation	no Confidence in %99

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30597]	arabinose ChEBI	+	carbon source
[Ref.: #68377]	D-fructose ChEBI	+	builds acid from	* from API NH
[Ref.: #68377]	D-glucose ChEBI	+	builds acid from	* from API NH
[Ref.: #30597]	maltose ChEBI	+	carbon source
[Ref.: #30597]	nitrate ChEBI	+	reduction
[Ref.: #68377]	ornithine ChEBI	-	degradation	* from API NH
[Ref.: #68377]	sucrose ChEBI	-	builds acid from	* from API NH
[Ref.: #30597]	trehalose ChEBI	+	carbon source
[Ref.: #68377]	tryptophan ChEBI	-	energy source	* from API NH
[Ref.: #68377]	urea ChEBI	-	hydrolysis	* from API NH

	Metabolite production	Metabolite	Production
[Ref.: #30597]		indole ChEBI	yes
[Ref.: #68377]		indole ChEBI	no	* from API NH

	Physiological tests	Metabolite	Indole test
[Ref.: #30597]		indole ChEBI	+
[Ref.: #68377]		indole ChEBI	-	* from API NH

	Enzyme	Enzyme activity	EC number
[Ref.: #68377]	beta-galactosidase	-	3.2.1.23	* from API NH
[Ref.: #17373]	catalase	+	1.11.1.6
[Ref.: #30597]	catalase	+	1.11.1.6
[Ref.: #30597]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68377]	gamma-glutamyltransferase	-	2.3.2.2	* from API NH
[Ref.: #68377]	ornithine decarboxylase	-	4.1.1.17	* from API NH
[Ref.: #68377]	proline-arylamidase	-	3.4.11.5	* from API NH
[Ref.: #68377]	tryptophan deaminase	-	4.1.99.1	* from API NH
[Ref.: #68377]	urease	-	3.5.1.5	* from API NH

API® NH:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Penicillinase productionPEN	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from maltoseMAL	Acid from sucroseSAC	Ornithine decarboxylaseODC	Urease/urea hydrolysisURE	LipaseLIP	Alkaline phosphatasePAL	beta-Galactosidasebeta GAL	Proline arylamidaseProA	gamma-Glutamyl transferaseGGT	Indole productionIND
[Ref.: #17373]	6214	+	+	+	-	-	-	-	+	-	-	-	-	-
[Ref.: #17373]	5658	-	+	+	+	-	-	-	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	NAD metabolism	55.56	10 of 18
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	46.43	13 of 28
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	cysteine metabolism	33.33	6 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	arginine metabolism	29.17	7 of 24
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	4-hydroxymandelate degradation	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.: #17373]	Sample type/isolated from	oral swab from gingiva of a healthy Californian sea lion
[Ref.: #17373]	Geographic location (country and/or sea, region)	Copenhagen Zoo
[Ref.: #17373]	Country	Denmark
[Ref.: #17373]	Country ISO 3 Code	DNK
[Ref.: #17373]	Continent	Europe

[Ref.: #62178]	Sample type/isolated from	Californian sea lion gingiva
[Ref.: #62178]	Sampling date	2007-10-25
[Ref.: #62178]	Geographic location (country and/or sea, region)	Copenhagen Zoo
[Ref.: #62178]	Country	Denmark
[Ref.: #62178]	Country ISO 3 Code	DNK
[Ref.: #62178]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Infection	#Patient	#Swab
#Host	#Mammals	-
#Host Body-Site	#Oral cavity and airways	#Gingiva

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HM626613 (>99% sequence identity) for Otariodibacter oris subclade from Microbeatlas

Aquatic Samples	5
Soil Samples	1
Animal Samples	309
Plant Samples
Total Samples	315

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

[Ref.: #17373]

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.: #17373]	Otariodibacter oris strain Baika1 16S ribosomal RNA gene, partial sequence	HM626613	1410	GenBank ENA	1032623 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Otariodibacter oris Baika1	GCA_009684715	complete	GenBank ENA	1032623 tax ID	*
[Ref.: #66792]	Otariodibacter oris DSM 23800	GCA_003634665	scaffold	GenBank ENA	1032623 tax ID	*
[Ref.: #66792]	Otariodibacter oris strain DSM 23800	1032623.3	wgs	PATRIC	1032623 tax ID	*
[Ref.: #66792]	Otariodibacter oris DSM 23800	2770939614	draft	JGI IMG/M	1032623 tax ID	*

[Ref.: #17373]	GC-content	36.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30597]	GC-content	36.2 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: Otariodibacter oris Baika1 NCBI: GCA_009684715.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Otariodibacter oris Baika1 NCBI: GCA_009684715.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.604	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.759	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	82.019	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.466	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	95.071	yes

Availability in culture collections External links

[Ref.: #17373]

Culture collection no.

DSM 23800, CCUG 59994

[Ref.: #80977]

SI-ID 405975

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds.	Hansen MJ, Bertelsen MF, Christensen H, Bojesen AM, Bisgaard M	Int J Syst Evol Microbiol	10.1099/ijs.0.039586-0	2011	*

References

#17373

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23800

#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 )

#30597

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 #26928 (see below)

#62178 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59994

#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 )

#68377

Automatically annotated from API NH .

#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 )

#80977

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-ID405975.1 )

#26928

IJSEM 2572 2012 ( DOI 10.1099/ijs.0.039586-0 , PubMed 22199211 )

* These data were automatically processed and therefore are not curated

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