Name: Arachnia rubra SK-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158418

Type strain:

Species: Arachnia rubra

Strain Designation: SK-1

Culture col. no.: DSM 100122, JCM 31317

Strain history: M. Saito; Nihon Univ. Sch. of Dent. at Matsudo, Japan; SK-1.

NCBI tax ID(s): 1547448 (species)

SI-ID 407908

DSM 100122

Section

Arachnia rubra SK-1 is a mesophilic bacterium that was isolated from human gingival sulcus.

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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Propionibacteriaceae*
	Genus	*Arachnia*
	Species	**Arachnia rubra**
	Full Scientific Name (LPSN)	Arachnia rubra (Saito et al. 2018) Tindall 2019

Synonym

Pseudopropionibacterium rubrum

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65094]

Culture medium

BHI MEDIUM (DSMZ Medium 215)

[Ref.: #65094]

Culture medium growth

[Ref.: #65094]

Culture medium link

Medium recipe at MediaDive

[Ref.: #65094]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #65094]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #65094]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	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	no	* 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]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* 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.: #65094]	12880	-	-	-	+	-	+	-	-	-	+	-	-	-	-	+	-	-	+/-	-	-	+	+/-	-	+	-	-	-	-	-

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

[Ref.: #65094]	Sample type/isolated from	human gingival sulcus
[Ref.: #65094]	Country	Japan
[Ref.: #65094]	Country ISO 3 Code	JPN
[Ref.: #65094]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Gingival sulcus samples from healthy dental patients at Nihon University Hospital at Matsudo
[Ref.: #67770]	Geographic location (country and/or sea, region)	Chiba Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Gingiva
#Infection	#Patient	-
#Host Body-Site	#Other	#Wound

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC002971 (>99% sequence identity) for Arachnia rubra subclade from Microbeatlas

Aquatic Samples	17
Soil Samples	38
Animal Samples	662
Plant Samples	1
Total Samples	718

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.: #65094]	Pseudopropionibacterium rubrum gene for 16S ribosomal RNA, partial sequence	LC002971	1480	ENA	1547448 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Arachnia rubra SK-1	GCA_019973735	complete	GenBank	1547448 tax ID	*

[Ref.: #67770]

GC-content

61.8 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Arachnia rubra SK-1 NCBI: GCA_019973735.1
[Ref.: #69480]	flagellated	no	97.549	no
[Ref.: #69480]	gram-positive	yes	91.087	no
[Ref.: #69480]	anaerobic	no	82.825	no
[Ref.: #69480]	aerobic	no	81.797	no
[Ref.: #69480]	halophile	no	89.045	no
[Ref.: #69480]	spore-forming	no	89.192	no
[Ref.: #69480]	motile	no	93.636	no
[Ref.: #69480]	thermophile	no	93.936	no
[Ref.: #69480]	glucose-util	yes	83.856	no
[Ref.: #69480]	glucose-ferment	yes	68.973	no

Availability in culture collections External links

[Ref.: #65094]

Culture collection no.

DSM 100122, JCM 31317

[Ref.: #111221]

SI-ID 407908

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudopropionibacterium rubrum sp. nov., a novel red-pigmented species isolated from human gingival sulcus.	Saito M, Shinozaki-Kuwahara N, Tsudukibashi O, Hashizume-Takizawa T, Kobayashi R, Kurita-Ochiai T	Microbiol Immunol	10.1111/1348-0421.12592	2018	*
Genetics	Complete Genome Sequence of Arachnia rubra Strain DSM 100122(T), a Cultured Member of the Human Oral Microbiome.	Ouellette M, Bejian AA, Chen T, Jones DS, Johnston CD, Dewhirst FE	Microbiol Resour Announc	10.1128/MRA.00959-21	2021	*

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 )

#65094

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100122

#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) .

#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) .

#111221

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-ID407908.1 )

* These data were automatically processed and therefore are not curated

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