Name: Rubrobacter indicoceani DSM 105148
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158426

Type strain:

Species: Rubrobacter indicoceani

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

Strain history: CGMCC 1.16398 <-- L.-J. Long and X.-P. Tian; South China Sea Inst. of Oceanol., CAS, China; SCSIO 08198.

NCBI tax ID(s): 2051957 (species)

SI-ID 398232

DSM 105148

Special Collections

Section

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

colony-forming
Gram-positive
rod-shaped
aerobe
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	*Rubrobacteria*
	Order	*Rubrobacterales*
	Family	*Rubrobacteraceae*
	Genus	*Rubrobacter*
	Species	**Rubrobacter indicoceani**
	Full Scientific Name (LPSN)	Rubrobacter indicoceani Chen et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66732]	Gram stain	positive

[Ref.: #66732]	Cell length	1.0-2.4 µm

[Ref.: #66732]	Cell width	0.3-0.6 µm

[Ref.: #66732]	Cell shape	rod-shaped

[Ref.: #66732]	Motility	no

[Ref.: #66732]	Colony color	salmon pink
[Ref.: #66732]	Colony shape	circular
[Ref.: #66732]	Incubation period	14 days
[Ref.: #66732]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65102]

Culture medium

MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)

[Ref.: #65102]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #65102]

Culture medium composition

expand / minimize

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Culture medium

Marine agar (MA)

[Ref.: #66732]

Culture medium growth

		Temperature
[Ref.: #65102]	growth	28 °C
[Ref.: #66732]	optimum	28 °C
[Ref.: #66732]	growth	20-37 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #66732]			optimum	7
[Ref.: #66732]			growth	7.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66732]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66732]		NaCl		growth	1-5	%(w/v)
[Ref.: #66732]		NaCl		optimum	3	%(w/v)

[Ref.: #66732]	Observation	Sensitive to short ultraviolet radiation.
[Ref.: #67770]	Observation	quinones: MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66732]	acetic acid ChEBI	-	carbon source
[Ref.: #66732]	adenine ChEBI	-	nitrogen source
[Ref.: #66732]	amygdalin ChEBI	-	carbon source
[Ref.: #66732]	casein	-	hydrolysis
[Ref.: #66732]	cellobiose ChEBI	+	carbon source
[Ref.: #66732]	D-arabinose ChEBI	+	carbon source
[Ref.: #66732]	D-fructose ChEBI	-	carbon source
[Ref.: #66732]	D-galactose ChEBI	+	carbon source
[Ref.: #66732]	D-ribose ChEBI	+	carbon source
[Ref.: #66732]	D-xylose ChEBI	+	carbon source
[Ref.: #66732]	dextrin ChEBI	+	carbon source
[Ref.: #66732]	esculin ChEBI	+	carbon source
[Ref.: #66732]	galactitol ChEBI	+	carbon source
[Ref.: #66732]	gelatin ChEBI	-	hydrolysis
[Ref.: #66732]	gluconate ChEBI	+	carbon source
[Ref.: #66732]	glucose ChEBI	+	carbon source
[Ref.: #66732]	glycine ChEBI	+	nitrogen source
[Ref.: #66732]	hydroxyproline ChEBI	-	nitrogen source
[Ref.: #66732]	L-alanine ChEBI	+	nitrogen source
[Ref.: #66732]	L-arginine ChEBI	+	nitrogen source
[Ref.: #66732]	L-asparagine ChEBI	+	nitrogen source
[Ref.: #66732]	L-cysteine ChEBI	-	nitrogen source
[Ref.: #66732]	L-glutamate ChEBI	+	nitrogen source
[Ref.: #66732]	L-histidine ChEBI	+	nitrogen source
[Ref.: #66732]	L-lysine ChEBI	+	nitrogen source
[Ref.: #66732]	L-methionine ChEBI	-	nitrogen source
[Ref.: #66732]	L-phenylalanine ChEBI	-	nitrogen source
[Ref.: #66732]	L-proline ChEBI	+	nitrogen source
[Ref.: #66732]	L-rhamnose ChEBI	+	carbon source
[Ref.: #66732]	L-tryptophan ChEBI	-	nitrogen source
[Ref.: #66732]	L-valine ChEBI	-	nitrogen source
[Ref.: #66732]	lactose ChEBI	-	carbon source
[Ref.: #66732]	maltose ChEBI	+	carbon source
[Ref.: #66732]	melibiose ChEBI	-	carbon source
[Ref.: #66732]	milk	-	degradation
[Ref.: #66732]	myo-inositol ChEBI	-	carbon source
[Ref.: #66732]	nitrate ChEBI	-	reduction
[Ref.: #66732]	raffinose ChEBI	-	carbon source
[Ref.: #66732]	ribitol ChEBI	+	carbon source
[Ref.: #66732]	salicin ChEBI	+	carbon source
[Ref.: #66732]	sorbitol ChEBI	+	carbon source
[Ref.: #66732]	sorbose ChEBI	-	carbon source
[Ref.: #66732]	starch ChEBI	-	hydrolysis
[Ref.: #66732]	sucrose ChEBI	+	carbon source
[Ref.: #66732]	tartrate ChEBI	-	carbon source
[Ref.: #66732]	turanose ChEBI	-	carbon source
[Ref.: #66732]	tween 40 ChEBI	-	hydrolysis
[Ref.: #66732]	tween 60 ChEBI	-	hydrolysis
[Ref.: #66732]	tyrosine ChEBI	+	nitrogen source
[Ref.: #66732]	xylitol ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66732]		hydrogen sulfide ChEBI	no
[Ref.: #66732]		melanin ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66732]	catalase	+	1.11.1.6
[Ref.: #66732]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66732]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #65102]	Sample type/isolated from	marine sediment
[Ref.: #65102]	Geographic location (country and/or sea, region)	Indian Ocean
[Ref.: #65102]	Country	International waters
[Ref.: #65102]	Geographic location	0.0062°/81.0311°

[Ref.: #66732]	Sample type/isolated from	a deep-sea sediment sample
[Ref.: #66732]	Geographic location (country and/or sea, region)	in the Indian Ocean at a water depth of 4602 m
[Ref.: #66732]	Geographic location	0.0062°/81.0312°
[Ref.: #66732]	Enrichment culture	actinomycete isolation agar
[Ref.: #66732]	Enrichment culture duration	4 weeks
[Ref.: #66732]	Enrichment culture temperature	28 ̊C
[Ref.: #66732]	Isolation/enrichment procedure	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.

[Ref.: #67770]	Sample type/isolated from	Marine sediment from Indian Ocean at a depth of about 4602 m
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #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

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.: #65102]	Rubrobacter indicoceani strain SCSIO 08198 16S ribosomal RNA gene, partial sequence	MF919580	1372	GenBank ENA	2051957 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rubrobacter indicoceani SCSIO 08198	GCA_003568865	complete	GenBank ENA	2051957 tax ID

[Ref.: #65102]	GC-content	63.8 mol%
[Ref.: #66732]	GC-content	63.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	63.8 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	63.7-64.7 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #65102]

Culture collection no.

DSM 105148, CGMCC 1.16398, SCSIO 08198, JCM 33406

[Ref.: #111227]

SI-ID 398232

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#111227

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-ID398232.1 )

* These data were automatically processed and therefore are not curated

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