Arachnia rubra (DSM 100122, SK-1, JCM 31317)

Name: Arachnia rubra (DSM 100122, SK-1, JCM 31317)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158418

Type strain

Strain Designation SK-1

Culture col. no. DSM 100122 SK-1 JCM 31317

NCBI tax ID(s) 1547448

Special Collections DSMZ JCM

History DSMZ <- M. Saito, Nihon Univ., School of Dentistry, Matsudo; SK-1 JCM <-- M. Saito; Nihon Univ. Sch. of Dent. at Matsudo, Japan; SK-1.

Links

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

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407908

JCM 31317,DSM 100122

@ref 20215

Last LPSN update 2026-05-29 08:43:57

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Propionibacteriaceae

Genus Arachnia

Species Arachnia rubra

Full scientific name Arachnia rubra (Saito et al. 2018) Tindall 2019

Synonyms (1)

Pseudopropionibacterium rubrum

Morphology

Cell morphology

@ref	Motility	Confidence
125438		95.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65094	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
65094	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	91.54

Spore formation

@ref	Spore formation	Confidence
125439		97.507

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	+	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	+		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
65094	-	-	-	+	-	+	-	-	-	+	-	-	-	-	+	-	-	+/-	-	-	+	+/-	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Gingiva
#Infection	#Patient	-
#Host Body-Site	#Other	#Wound

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
65094	human gingival sulcus	Homo sapiens		Japan	JPN	Asia
67770	Gingival sulcus samples from healthy dental patients at Nihon University Hospital at Matsudo	Homo sapiens	Chiba Pref.	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1997373v1 assembly for Arachnia rubra SK-1	complete	GCA_019973735	1547448.4	8064415275	1547448	95.28

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65094	Pseudopropionibacterium rubrum gene for 16S ribosomal RNA, partial sequence	LC002971	1480		1547448

GC content

@ref	GC-content (mol%)	Method
67770	61.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1997373v1 assembly for Arachnia rubra SK-1
NCBI: GCA_019973735

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.54	no
125439	gram_stain	BacteriaNetⓘ	positive	63.21	no
125439	motility	BacteriaNetⓘ	no	65.82	no
125439	spore_formation	BacteriaNetⓘ	no	97.51	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arachnia rubra SK-1
NCBI: GCA_019973735.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.96	no
125438	anaerobic	anaerobicⓘ	no	77.14	no
125438	aerobic	aerobicⓘ	no	63.20	no
125438	spore-forming	spore-formingⓘ	no	73.11	no
125438	thermophilic	thermophileⓘ	no	97.99	yes
125438	flagellated	motile2+ⓘ	no	95.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
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

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 .
#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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Arachnia rubra (DSM 100122, SK-1, JCM 31317)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_019973735

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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