Rubrobacter indicoceani (DSM 105148, CGMCC 1.16398, SCSIO 08198)

Name: Rubrobacter indicoceani (DSM 105148, CGMCC 1.16398, SCSIO 08198)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158426

Type strain

Culture col. no. DSM 105148 CGMCC 1.16398 SCSIO 08198 JCM 33406

NCBI tax ID(s) 2051957

Special Collections DSMZ JCM Literature strains

History DSMZ <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 08198 JCM <-- CGMCC 1.16398 <-- L.-J. Long and X.-P. Tian; South China Sea Inst. of Oceanol., CAS, China; SCSIO 08198.

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Rubrobacter indicoceani DSM 105148 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from marine sediment.

Gram-positive rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398232

DSM 105148

@ref 20215

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

Domain Bacteria

Phylum Actinomycetota

Class Rubrobacteria

Order Rubrobacterales

Family Rubrobacteraceae

Genus Rubrobacter

Species Rubrobacter indicoceani

Full scientific name Rubrobacter indicoceani Chen et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
66732	positive	1.0-2.4 µm	0.3-0.6 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
66732	salmon pink	circular	14 days	Marine agar (MA)

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65102	MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)		Medium recipe at MediaDive	Name: MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d) Composition: Difco marine broth 37.4 g/l Agar 15.0 g/l Malt extract 1.0 g/l Soy peptone 1.0 g/l Pancreatic digest of casein 1.0 g/l Distilled water
66732	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)
65102	positive	growth	28
66732	positive	optimum	28
66732	positive	growth	20-37
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH
66732	positive	optimum	7
66732	positive	growth	7.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66732	aerobe
125439	facultative anaerobe	93.176

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66732	NaCl	positive	growth	1-5 %(w/v)
66732	NaCl	positive	optimum	3 %(w/v)

Observation

@ref	Observation
66732	Sensitive to short ultraviolet radiation.
67770	quinones: MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66732	16411 ChEBI	acetic acid	-	carbon source
66732	16708 ChEBI	adenine	-	nitrogen source
66732	27613 ChEBI	amygdalin	-	carbon source
66732		casein	-	hydrolysis
66732	17057 ChEBI	cellobiose	+	carbon source
66732	17108 ChEBI	D-arabinose	+	carbon source
66732	15824 ChEBI	D-fructose	-	carbon source
66732	12936 ChEBI	D-galactose	+	carbon source
66732	16988 ChEBI	D-ribose	+	carbon source
66732	65327 ChEBI	D-xylose	+	carbon source
66732	23652 ChEBI	dextrin	+	carbon source
66732	4853 ChEBI	esculin	+	carbon source
66732	16813 ChEBI	galactitol	+	carbon source
66732	5291 ChEBI	gelatin	-	hydrolysis
66732	24265 ChEBI	gluconate	+	carbon source
66732	17234 ChEBI	glucose	+	carbon source
66732	15428 ChEBI	glycine	+	nitrogen source
66732	24741 ChEBI	hydroxyproline	-	nitrogen source
66732	16977 ChEBI	L-alanine	+	nitrogen source
66732	16467 ChEBI	L-arginine	+	nitrogen source
66732	17196 ChEBI	L-asparagine	+	nitrogen source
66732	17561 ChEBI	L-cysteine	-	nitrogen source
66732	29985 ChEBI	L-glutamate	+	nitrogen source
66732	15971 ChEBI	L-histidine	+	nitrogen source
66732	18019 ChEBI	L-lysine	+	nitrogen source
66732	16643 ChEBI	L-methionine	-	nitrogen source
66732	17295 ChEBI	L-phenylalanine	-	nitrogen source
66732	17203 ChEBI	L-proline	+	nitrogen source
66732	62345 ChEBI	L-rhamnose	+	carbon source
66732	16828 ChEBI	L-tryptophan	-	nitrogen source
66732	16414 ChEBI	L-valine	-	nitrogen source
66732	17716 ChEBI	lactose	-	carbon source
66732	17306 ChEBI	maltose	+	carbon source
66732	28053 ChEBI	melibiose	-	carbon source
66732		milk	-	degradation
66732	17268 ChEBI	myo-inositol	-	carbon source
66732	17632 ChEBI	nitrate	-	reduction
66732	16634 ChEBI	raffinose	-	carbon source
66732	15963 ChEBI	ribitol	+	carbon source
66732	17814 ChEBI	salicin	+	carbon source
66732	30911 ChEBI	sorbitol	+	carbon source
66732	27922 ChEBI	sorbose	-	carbon source
66732	28017 ChEBI	starch	-	hydrolysis
66732	17992 ChEBI	sucrose	+	carbon source
66732	132950 ChEBI	tartrate	-	carbon source
66732	32528 ChEBI	turanose	-	carbon source
66732	53423 ChEBI	tween 40	-	hydrolysis
66732	53425 ChEBI	tween 60	-	hydrolysis
66732	18186 ChEBI	tyrosine	+	nitrogen source
66732	17151 ChEBI	xylitol	-	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66732	16136 ChEBI	hydrogen sulfide
66732	89634 ChEBI	melanin

Enzymes

@ref	Value	Activity	Ec
66732	catalase	+	1.11.1.6
66732	cytochrome oxidase	+	1.9.3.1
66732	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

66732

Fatty acid	Percentage	ECL
C16:0 12-methyl	75.2	16.516
C17:1 w6c	8.7	16.869
C17:0	5.1	16.999
C17:0 12-methyl	3.4	17.46
C17:0 anteiso	2.1	16.723
C18:3 w6c (6,9,12)	1.5	17.587
unknown ECL 15.476	1.1	15.476
C16:0	0.9	15.999
C17:0 10-methyl	0.7	17.405
C18:0	0.7	18.002

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure	Country
65102	marine sediment	Indian Ocean	0.0062	81.0311 0.0062/81.0311					International waters
66732	a deep-sea sediment sample	in the Indian Ocean at a water depth of 4602 m	0.006154	81.0312 0.006154/81.0312	actinomycete isolation agar	4 weeks	28	a deep-sea sediment sample aseptically collected from the site in the Indian Ocean at a water depth of 4602 m by using a grab-bucket collection sampler. The sample was diluted directly by an equal volume of autoclaved seawater, and shook well before 200 µl was evenly spread onmedium of 50 % actinomycete isolation agar and incubated for four weeks at 28°C.
67770	Marine sediment from Indian Ocean at a depth of about 4602 m

Taxonmaps

69479

Global distribution of 16S sequence MF919580 (>99% sequence identity) for Rubrobacter indicoceani subclade from Microbeatlas

Aquatic Samples	106
Soil Samples	21
Animal Samples	72
Plant Samples	17
Total Samples	216

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM356886v1 assembly for Rubrobacter indicoceani SCSIO 08198	complete	GCA_003568865	2051957.3	2848344536	2051957	87.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65102	Rubrobacter indicoceani strain SCSIO 08198 16S ribosomal RNA gene, partial sequence	MF919580	1372		2051957

GC content

@ref	GC-content (mol%)	Method
65102	63.8
66732	63.8	high performance liquid chromatography (HPLC)
67770	63.8	genome sequence analysis
67770	63.7-64.7	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: ASM356886v1 assembly for Rubrobacter indicoceani SCSIO 08198
NCBI: GCA_003568865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.18	no
125439	gram_stain	BacteriaNetⓘ	positive	45.53	no
125439	motility	BacteriaNetⓘ	no	61.72	no
125439	spore_formation	BacteriaNetⓘ	no	69.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The First Insight into Polyhydroxyalkanoates Accumulation in Multi-Extremophilic Rubrobacter xylanophilus and Rubrobacter spartanus.	Kourilova X, Schwarzerova J, Pernicova I, Sedlar K, Mrazova K, Krzyzanek V, Nebesarova J, Obruca S.	Microorganisms	10.3390/microorganisms9050909	2021
Enzymology	New genus-specific primers for PCR identification of Rubrobacter strains.	Castro JF, Nouioui I, Asenjo JA, Andrews B, Bull AT, Goodfellow M.	Antonie Van Leeuwenhoek	10.1007/s10482-019-01314-3	2019
Phylogeny	Rubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment.	Chen RW, Wang KX, Wang FZ, He YQ, Long LJ, Tian XP	Int J Syst Evol Microbiol	10.1099/ijsem.0.003018	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 )
#65102	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105148
#66732	Rou-Wen Chen, Ke-Xin Wang, Fa-Zuo Wang, Yuan-Qiu He, Li-Juan Long, Xin-Peng Tian: Rubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment. IJSEM 68: 3487 - 3493 2018 ( DOI 10.1099/ijsem.0.003018 , PubMed 30300120 )
#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 .
#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 )

Content

About us

Rubrobacter indicoceani (DSM 105148, CGMCC 1.16398, SCSIO 08198)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003568865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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