Name: Oribacterium sinus DSM 17245
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6360

Type strain:

Species: Oribacterium sinus

Culture col. no.: DSM 17245, CCUG 48084, CIP 107991, AIP 354-02

Strain history: CIP <- 2003, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 354-02 <- Nancy Hosp., Nancy, France

NCBI tax ID(s): 237576 (species)

SI-ID 134303

CCUG 48084, CIP 107991, DSM 17245

Section

Oribacterium sinus DSM 17245 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from human, maxillary sinus.

Gram-positive
motile
ovoid-shaped
anaerobe
human pathogen
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Oribacterium*
	Species	**Oribacterium sinus**
	Full Scientific Name (LPSN)	Oribacterium sinus Carlier et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #31215]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.719

[Ref.: #31215]	Cell shape	ovoid-shaped
[Ref.: #122636]	Cell shape	rod-shaped

[Ref.: #31215]	Motility	yes
[Ref.: #122636]	Motility	yes

[Ref.: #57977]

Incubation period

4 days

[Ref.: #31215]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6852]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #6852]

Culture medium growth

[Ref.: #6852]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6852]

Culture medium composition

expand / minimize

[Ref.: #6852]

Culture medium

WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)

[Ref.: #6852]

Culture medium growth

[Ref.: #6852]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6852]

Culture medium composition

expand / minimize

[Ref.: #38250]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #38250]

Culture medium growth

[Ref.: #38250]

Culture medium composition

expand / minimize

[Ref.: #122636]

Culture medium

CIP Medium 20

[Ref.: #122636]

Culture medium growth

[Ref.: #122636]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6852]	growth	37 °C
[Ref.: #38250]	growth	37 °C
[Ref.: #57977]	growth	37 °C

[Ref.: #6852]	Temperature range	mesophilic
[Ref.: #38250]	Temperature range	mesophilic
[Ref.: #57977]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6852]	Oxygen tolerance	anaerobe
[Ref.: #31215]	Oxygen tolerance	anaerobe
[Ref.: #57977]	Oxygen tolerance	anaerobe
[Ref.: #122636]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.486

[Ref.: #31215]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #122636]	cellobiose ChEBI	-	degradation
[Ref.: #122636]	D-arabinose ChEBI	-	degradation
[Ref.: #122636]	D-fructose ChEBI	+	degradation
[Ref.: #122636]	D-glucose ChEBI	+	degradation
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #122636]	D-xylose ChEBI	-	degradation
[Ref.: #122636]	esculin ChEBI	-	hydrolysis
[Ref.: #31215]	galactose ChEBI	+	carbon source
[Ref.: #31215]	glucose ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #122636]	lactose ChEBI	-	degradation
[Ref.: #122636]	maltose ChEBI	-	degradation
[Ref.: #122636]	nitrate ChEBI	+	reduction
[Ref.: #122636]	nitrate ChEBI	+	respiration
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #122636]	nitrite ChEBI	-	reduction
[Ref.: #31215]	raffinose ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #122636]	salicin ChEBI	-	degradation
[Ref.: #31215]	sucrose ChEBI	+	carbon source
[Ref.: #122636]	sucrose ChEBI	+	degradation
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #31215]	indole ChEBI	yes
[Ref.: #122636]	indole ChEBI	yes
[Ref.: #68380]	indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #31215]		indole ChEBI	+
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym, API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym, API rID32A
[Ref.: #31215]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym, API rID32A
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API rID32A
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #122636]	amylase	-
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #122636]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API rID32A
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API rID32A
[Ref.: #122636]	caseinase	-	3.4.21.50
[Ref.: #122636]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #122636]	DNase	-
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #122636]	gelatinase	-
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	+		* from API rID32A
[Ref.: #68380]	histidine arylamidase	+		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	+		* from API rID32A
[Ref.: #122636]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #122636]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API rID32A
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122636]	oxidase	-
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	+	3.4.11.5	* from API rID32A
[Ref.: #122636]	protease	-
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	+		* from API rID32A
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #122636]	tween esterase	-
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #122636]	urease	-	3.5.1.5
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

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

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #6852]	12649	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	+	+	+	-	+

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122636]	10802	-	-	-	-	-	+	-	-	-	-	-	+	+	+	-	+	-	-	-	-

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

[Ref.: #6852]	Sample type/isolated from	human, maxillary sinus
[Ref.: #6852]	Geographic location (country and/or sea, region)	Nancy
[Ref.: #6852]	Country	France
[Ref.: #6852]	Country ISO 3 Code	FRA
[Ref.: #6852]	Continent	Europe

[Ref.: #57977]	Sample type/isolated from	Human maxillary sinus
[Ref.: #57977]	Geographic location (country and/or sea, region)	Nancy
[Ref.: #57977]	Country	France
[Ref.: #57977]	Country ISO 3 Code	FRA
[Ref.: #57977]	Continent	Europe

[Ref.: #122636]	Sample type/isolated from	Human, Maxillary sinus
[Ref.: #122636]	Geographic location (country and/or sea, region)	Nancy
[Ref.: #122636]	Country	France
[Ref.: #122636]	Country ISO 3 Code	FRA
[Ref.: #122636]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY323228 (>99% sequence identity) for Oribacterium from Microbeatlas

Aquatic Samples	598
Soil Samples	511
Animal Samples	46753
Plant Samples	264
Total Samples	48126

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

[Ref.: #6852]	Pathogenicity (human)	yes, in single cases
[Ref.: #6852]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122636]	Biosafety level	1	Risk group (French classification)

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.: #6852]	Oribacterium sinus 16S ribosomal RNA gene, partial sequence	AY323228	1374	ENA	237576 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Oribacterium sinus DSM 17245	GCA_014202695	scaffold	GenBank	237576 tax ID	*
[Ref.: #66792]	Oribacterium sinus strain DSM 17245	237576.163	wgs	PATRIC	237576 tax ID	*
[Ref.: #66792]	Oribacterium sinus DSM 17245	2861591105	draft	JGI IMG/M	237576 tax ID	*

[Ref.: #6852]

GC-content

42.4 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: Oribacterium sinus DSM 17245 NCBI: GCA_014202695.1
[Ref.: #69481]	spore-forming	yes	78	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Oribacterium sinus DSM 17245 NCBI: GCA_014202695.1
[Ref.: #69480]	flagellated	no	69.623	no
[Ref.: #69480]	gram-positive	yes	66.217	no
[Ref.: #69480]	anaerobic	yes	98.496	no
[Ref.: #69480]	aerobic	no	98.482	no
[Ref.: #69480]	halophile	no	74.356	no
[Ref.: #69480]	spore-forming	no	82.865	no
[Ref.: #69480]	glucose-util	yes	85.412	yes
[Ref.: #69480]	thermophile	no	98.316	no
[Ref.: #69480]	motile	yes	81.784	no
[Ref.: #69480]	glucose-ferment	yes	74.913	no

Availability in culture collections External links

[Ref.: #6852]

Culture collection no.

DSM 17245, CCUG 48084, CIP 107991, AIP 354-02

[Ref.: #75833]

SI-ID 134303

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oribacterium sinus gen. nov., sp. nov., within the family 'Lachnospiraceae' (phylum Firmicutes).	Carlier JP, K'ouas G, Bonne I, Lozniewski A, Mory F	Int J Syst Evol Microbiol	10.1099/ijs.0.63060-0	2004	*

References

#6852

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17245

#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 )

#31215

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 #27541 (see below)

#38250 ; Curators of the CIP;
#57977 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48084

#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) .

#68380

Automatically annotated from API rID32A .

#68382

Automatically annotated from API zym .

#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 )

#75833

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-ID134303.1 )

#122636 Collection of Institut Pasteur ; Curators of the CIP; CIP 107991

#27541

IJSEM 1611 2004 ( DOI 10.1099/ijs.0.63060-0 , PubMed 15388717 )

* These data were automatically processed and therefore are not curated

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