Name: Porphyromonas circumdentaria DSM 103022
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132059

Type strain:

Species: Porphyromonas circumdentaria

Culture col. no.: DSM 103022, ATCC 51356, CCUG 41934, JCM 13864, NCTC 12469, VPB 3329

Strain history: CCUG 41934 <-- NCTC 12469 <-- D. N. Love VPB 3329.

NCBI tax ID(s): 29524 (species)

SI-ID 42946

ATCC 51356, NCTC 12469, CCUG 33479, CCUG 41934, JCM 13864, DSM 103022

Section

Porphyromonas circumdentaria DSM 103022 is an anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from cat, subcutaneous abscess.

Gram-negative
anaerobe
animal 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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Porphyromonadaceae*
	Genus	*Porphyromonas*
	Species	**Porphyromonas circumdentaria**
	Full Scientific Name (LPSN)	Porphyromonas circumdentaria Love et al. 1992

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.898

Information on culture and growth conditions Culture and growth conditions

[Ref.: #23850]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #23850]

Culture medium growth

[Ref.: #23850]

Culture medium link

Medium recipe at MediaDive

[Ref.: #23850]

Culture medium composition

expand / minimize

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Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #23850]

Culture medium growth

[Ref.: #23850]

Culture medium link

Medium recipe at MediaDive

[Ref.: #23850]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #23850]	growth	37 °C
[Ref.: #55269]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #23850]	Temperature range	mesophilic
[Ref.: #55269]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #55269]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.225

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

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	+	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	yes	* from API rID32A

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

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	+	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	-	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* 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.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	+	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	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.: #23850]	12961	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	+	-	-	-	-	+	-	-	+/-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	57.14	16 of 28
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	non-pathway related	42.11	16 of 38
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phenylalanine metabolism	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	histidine metabolism	37.93	11 of 29
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	isoleucine metabolism	37.5	3 of 8
[Ref.: #66794]	tryptophan metabolism	36.84	14 of 38
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	oxidative phosphorylation	31.87	29 of 91
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	arginine metabolism	29.17	7 of 24
[Ref.: #66794]	lipid metabolism	29.03	9 of 31
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	urea cycle	23.08	3 of 13
[Ref.: #66794]	leucine metabolism	23.08	3 of 13
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	tyrosine metabolism	21.43	3 of 14
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		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.: #23850]	Sample type/isolated from	cat, subcutaneous abscess
[Ref.: #23850]	Country	Australia
[Ref.: #23850]	Country ISO 3 Code	AUS
[Ref.: #23850]	Continent	Australia and Oceania

[Ref.: #55269]	Sample type/isolated from	Cat abscess,subcutaneous
[Ref.: #55269]	Sampling date	1978

[Ref.: #67770]	Sample type/isolated from	Subcutaneous abscess of a cat
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Felidae (Cat)
#Host Body-Site	#Other	#Abscess

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB547657 (>99% sequence identity) for Porphyromonas circumdentaria from Microbeatlas

Aquatic Samples	40
Soil Samples	73
Animal Samples	3347
Plant Samples	25
Total Samples	3485

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

[Ref.: #23850]	Pathogenicity (animal)	yes
[Ref.: #23850]	Biosafety level	2	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.: #67770]	Porphyromonas circumdentaria gene for 16S ribosomal RNA, partial sequence, strain: JCM 13864	AB547657	1476	ENA	29524 tax ID
[Ref.: #23850]	Porphyromonas circumdentaria strain NCTC 12469 16S ribosomal RNA gene, partial sequence	L26102	1470	ENA	29524 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Porphyromonas circumdentaria ATCC 51356	GCA_900167105	scaffold	GenBank	29524 tax ID	*
[Ref.: #66792]	Porphyromonas circumdentaria DSM 103022	GCA_014206885	contig	GenBank	29524 tax ID	*
[Ref.: #66792]	Porphyromonas circumdentaria strain ATCC 51356	29524.4	wgs	PATRIC	29524 tax ID	*
[Ref.: #66792]	Porphyromonas circumdentaria strain DSM 103022	29524.6	wgs	PATRIC	29524 tax ID	*
[Ref.: #66792]	Porphyromonas circumdentaria ATCC 51356	2582581320	draft	JGI IMG/M	29524 tax ID	*
[Ref.: #66792]	Porphyromonas circumdentaria DSM 103022	2828459078	draft	JGI IMG/M	29524 tax ID	*

[Ref.: #67770]

GC-content

40-42 mol%

thermal denaturation, midpoint method (Tm)

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: Porphyromonas circumdentaria ATCC 51356 NCBI: GCA_900167105.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Porphyromonas circumdentaria ATCC 51356 NCBI: GCA_900167105.1
[Ref.: #69480]	motile	no	91.863	no
[Ref.: #69480]	flagellated	no	96.637	no
[Ref.: #69480]	gram-positive	no	95.912	no
[Ref.: #69480]	anaerobic	yes	98.532	yes
[Ref.: #69480]	aerobic	no	98.842	yes
[Ref.: #69480]	halophile	no	77.153	no
[Ref.: #69480]	spore-forming	no	97.11	no
[Ref.: #69480]	thermophile	no	97.869	yes
[Ref.: #69480]	glucose-util	yes	84.885	no
[Ref.: #69480]	glucose-ferment	no	52.514	no

Availability in culture collections External links

[Ref.: #23850]

Culture collection no.

DSM 103022, ATCC 51356, CCUG 41934, JCM 13864, NCTC 12469, VPB 3329

[Ref.: #90417]

SI-ID 42946

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Porphyromonas gingivicanis sp. nov. and Porphyromonas crevioricanis sp. nov., isolated from beagles.	Hirasawa M, Takada K	Int J Syst Bacteriol	10.1099/00207713-44-4-637	1994	*
Phylogeny	Porphyromonas canoris sp. nov., an asaccharolytic, black-pigmented species from the gingival sulcus of dogs.	Love DN, Karjalainen J, Kanervo A, Forsblom B, Sarkiala E, Bailey GD, Wigney DI, Jousimies-Somer H	Int J Syst Bacteriol	10.1099/00207713-44-2-204	1994	*
Phylogeny	Description of Porphyromonas circumdentaria sp. nov. and reassignment of Bacteroides salivosus (Love, Johnson, Jones, and Calverley 1987) as Porphyromonas (Shah and Collins 1988) salivosa comb. nov.	Love DN, Bailey GD, Collings S, Briscoe DA	Int J Syst Bacteriol	10.1099/00207713-42-3-434	1992	*
Pathogenicity	Structural characterization of the O-antigenic polysaccharide chain of Porphyromonas circumdentaria NCTC 12469.	Matsuo K, Isogai E, Araki Y	Microbiol Immunol	10.1111/j.1348-0421.2001.tb02622.x	2001	*

References

#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 )

#23850

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103022

#55269 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 41934

#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;

#68380

Automatically annotated from API rID32A .

#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 )

#90417

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-ID42946.1 )

* These data were automatically processed and therefore are not curated

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Porphyromonas circumdentaria ATCC 51356

Porphyromonas circumdentaria ATCC 51356

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