Strain identifier

BacDive ID: 158426

Type strain: Yes

Species: Rubrobacter indicoceani

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)

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General

@ref: 65102

BacDive-ID: 158426

DSM-Number: 105148

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped, colony-forming

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

NCBI tax id

  • NCBI tax id: 2051957
  • Matching level: species

strain history

@refhistory
65102<- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 08198
67770CGMCC 1.16398 <-- L.-J. Long and X.-P. Tian; South China Sea Inst. of Oceanol., CAS, China; SCSIO 08198.

doi: 10.13145/bacdive158426.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Rubrobacteria
  • order: Rubrobacterales
  • family: Rubrobacteraceae
  • genus: Rubrobacter
  • species: Rubrobacter indicoceani
  • full scientific name: Rubrobacter indicoceani Chen et al. 2018

@ref: 65102

domain: Bacteria

phylum: Actinobacteria

class: Rubrobacteria

order: Rubrobacterales

family: Rubrobacteraceae

genus: Rubrobacter

species: Rubrobacter indicoceani

full scientific name: Rubrobacter indicoceani Chen et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 66732
  • gram stain: positive
  • cell length: 1.0-2.4 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 66732
  • colony color: salmon pink
  • colony shape: circular
  • incubation period: 14 days
  • medium used: Marine agar (MA)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65102MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)yeshttps://mediadive.dsmz.de/medium/514dName: 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
66732Marine agar (MA)yes

culture temp

@refgrowthtypetemperature
65102positivegrowth28
66732positiveoptimum28
66732positivegrowth20-37
67770positivegrowth28

culture pH

@refabilitytypepH
66732positiveoptimum7
66732positivegrowth7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 66732
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
66732NaClpositivegrowth1-5 %(w/v)
66732NaClpositiveoptimum3 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6673215824D-fructose-carbon source
6673216411acetic acid-carbon source
6673216634raffinose-carbon source
6673217151xylitol-carbon source
6673217268myo-inositol-carbon source
6673217716lactose-carbon source
6673227613amygdalin-carbon source
6673227922sorbose-carbon source
6673228053melibiose-carbon source
6673232528turanose-carbon source
66732132950tartrate-carbon source
667324853esculin+carbon source
6673212936D-galactose+carbon source
6673215963ribitol+carbon source
6673216813galactitol+carbon source
6673216988D-ribose+carbon source
6673217057cellobiose+carbon source
6673217108D-arabinose+carbon source
6673217234glucose+carbon source
6673217306maltose+carbon source
6673217814salicin+carbon source
6673217992sucrose+carbon source
6673223652dextrin+carbon source
6673224265gluconate+carbon source
6673230911sorbitol+carbon source
6673262345L-rhamnose+carbon source
6673265327D-xylose+carbon source
66732milk-degradation
667325291gelatin-hydrolysis
6673228017starch-hydrolysis
6673253423tween 40-hydrolysis
6673253425tween 60-hydrolysis
66732casein-hydrolysis
6673216414L-valine-nitrogen source
6673216643L-methionine-nitrogen source
6673216708adenine-nitrogen source
6673216828L-tryptophan-nitrogen source
6673217295L-phenylalanine-nitrogen source
6673217561L-cysteine-nitrogen source
6673224741hydroxyproline-nitrogen source
6673215428glycine+nitrogen source
6673215971L-histidine+nitrogen source
6673216467L-arginine+nitrogen source
6673216977L-alanine+nitrogen source
6673217196L-asparagine+nitrogen source
6673217203L-proline+nitrogen source
6673218019L-lysine+nitrogen source
6673218186tyrosine+nitrogen source
6673229985L-glutamate+nitrogen source
6673217632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6673216136hydrogen sulfideno
6673289634melaninno

enzymes

@refvalueactivityec
66732urease-3.5.1.5
66732catalase+1.11.1.6
66732cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    66732unknown ECL 15.4761.115.476
    66732C16:00.915.999
    66732C16:0 12-methyl75.216.516
    66732C17:0 anteiso2.116.723
    66732C17:1 w6c8.716.869
    66732C17:05.116.999
    66732C17:0 10-methyl0.717.405
    66732C17:0 12-methyl3.417.46
    66732C18:3 w6c (6,9,12)1.517.587
    66732C18:00.718.002
  • type of FA analysis: whole cell analysis
  • incubation medium: MB supplemented with 1 % soluble starch
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 1
  • software version: Sherlock 4.5
  • library/peak naming table: TSBA40
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountrylatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65102marine sedimentIndian OceanInternational waters0.006281.0311
66732a deep-sea sediment samplein the Indian Ocean at a water depth of 4602 m0.00615481.0312actinomycete isolation agar4 weeks28a 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.
67770Marine sediment from Indian Ocean at a depth of about 4602 m

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_52411.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_408;96_2983;97_9328;98_11447;99_52411&stattab=map
  • Last taxonomy: Rubrobacter indicoceani subclade
  • 16S sequence: MF919580
  • Sequence Identity:
  • Total samples: 216
  • soil counts: 21
  • aquatic counts: 106
  • animal counts: 72
  • plant counts: 17

Sequence information

16S sequences

  • @ref: 65102
  • description: Rubrobacter indicoceani strain SCSIO 08198 16S ribosomal RNA gene, partial sequence
  • accession: MF919580
  • length: 1372
  • database: nuccore
  • NCBI tax ID: 2051957

Genome sequences

  • @ref: 67770
  • description: Rubrobacter indicoceani SCSIO 08198
  • accession: GCA_003568865
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2051957

GC content

@refGC-contentmethod
6510263.8
6673263.8high performance liquid chromatography (HPLC)
6777063.8genome sequence analysis
6777063.7-64.7high performance liquid chromatography (HPLC)

External links

@ref: 65102

culture collection no.: DSM 105148, CGMCC 1.16398, SCSIO 08198, JCM 33406

straininfo link

  • @ref: 111227
  • straininfo: 398232

literature

  • topic: Phylogeny
  • Pubmed-ID: 30300120
  • title: Rubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment.
  • authors: Chen RW, Wang KX, Wang FZ, He YQ, Long LJ, Tian XP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003018
  • year: 2018
  • mesh: Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ultraviolet Rays, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
65102Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105148Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105148)
66732Rou-Wen Chen, Ke-Xin Wang, Fa-Zuo Wang, Yuan-Qiu He, Li-Juan Long, Xin-Peng TianRubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment10.1099/ijsem.0.003018IJSEM 68: 3487-3493 201830300120
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/
111227Reimer, 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 identifiers10.60712/SI-ID398232.1