Rubrobacter aplysinae (DSM 27440, CECT 8425, RV 113)

Name: Rubrobacter aplysinae (DSM 27440, CECT 8425, RV 113)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24540

Type strain

Culture col. no. DSM 27440 CECT 8425 RV 113 JCM 31709

NCBI tax ID(s) 909625

Special Collections DSMZ JCM

History <- U. R. Abdelmosen, Univ. Würzburg; RV113 CECT 8425 <-- U. R. Abdelmosen; Univ. Würzburg, Germany; RV113.

Links

Rubrobacter aplysinae DSM 27440 is a bacterium that was isolated from Mediterranean sponge Aplysina aerophoba.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 392960

DSM 27440,CECT 8425

@ref 20215

Last LPSN update 2026-02-09 11:24:00

Domain Bacteria

Phylum Actinomycetota

Class Rubrobacteria

Order Rubrobacterales

Family Rubrobacteraceae

Genus Rubrobacter

Species Rubrobacter aplysinae

Full scientific name Rubrobacter aplysinae Kämpfer et al. 2014

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20789	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 19.45 g/l Starch 10.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
20789	positive	growth	25
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	91.7

Observation

67770

Observationquinones: MK-8, MK-7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Porifera (Sponges)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
20789	Mediterranean sponge Aplysina aerophoba	Aplysina aerophoba	Rovinj	Croatia	HRV	Europe
67770	Sponge Aplysina aerophoba	Aplysina aerophoba	close to Rovinj	Croatia	HRV	Europe

Taxonmaps

69479

Global distribution of 16S sequence GU318365 (>99% sequence identity) for Rubrobacter aplysinae subclade from Microbeatlas

Aquatic Samples	124
Soil Samples	663
Animal Samples	161
Plant Samples	41
Total Samples	989

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20789	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM102950v1 assembly for Rubrobacter aplysinae RV113	scaffold	GCA_001029505	909625.5	2867637810	909625	58.74

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20789	Rubrobacter aplysinae strain RV113 from Croatia 16S ribosomal RNA gene, partial sequence	GU318365	1512		909625

GC content

@ref	GC-content (mol%)	Method
67770	65.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rubrobacter aplysinae RV113
NCBI: GCA_001029505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	86.20	no
125439	motility	BacteriaNetⓘ	no	54.00	no
125439	gram_stain	BacteriaNetⓘ	negative	78.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	91.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rubrobacter aplysinae strain RV113
PATRIC: 909625.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	70.62	no
125438	anaerobic	anaerobicⓘ	no	79.88	no
125438	aerobic	aerobicⓘ	yes	73.08	no
125438	spore-forming	spore-formingⓘ	no	54.28	no
125438	thermophilic	thermophileⓘ	no	69.66	no
125438	flagellated	motile2+ⓘ	no	76.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rubrobacter aplysinae sp. nov., isolated from the marine sponge Aplysina aerophoba.	Kampfer P, Glaeser SP, Busse HJ, Abdelmohsen UR, Hentschel U	Int J Syst Evol Microbiol	10.1099/ijs.0.055152-0	2013

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 )
#20789	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27440
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Rubrobacter aplysinae (DSM 27440, CECT 8425, RV 113)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001029505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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