Strain identifier

BacDive ID: 158548

Type strain: Yes

Species: Ruegeria profundi

Strain Designation: ZGT108

Strain history: U. Stingl ZGT108.

NCBI tax ID(s): 1685378 (species)

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General

@ref: 65241

BacDive-ID: 158548

keywords: genome sequence, 16S sequence, Bacteria, aerobe, moderately halophilic, Gram-negative, rod-shaped, colony-forming

description: Ruegeria profundi ZGT108 is an aerobe, moderately halophilic, Gram-negative bacterium that forms circular colonies and was isolated from water sample.

NCBI tax id

  • NCBI tax id: 1685378
  • Matching level: species

strain history

  • @ref: 67770
  • history: U. Stingl ZGT108.

doi: 10.13145/bacdive158548.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Ruegeria
  • species: Ruegeria profundi
  • full scientific name: Ruegeria profundi Zhang et al. 2017

@ref: 65241

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Ruegeria

species: Ruegeria profundi

strain designation: ZGT108

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65241negative1-3 µm0.5-1 µmrod-shapedno
69480negative99.996

colony morphology

  • @ref: 65241
  • colony size: 2-3 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: marine agar

Culture and growth conditions

culture medium

  • @ref: 65241
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65241positivegrowth15-42
65241positiveoptimum33-35mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65241positivegrowth5.5-9alkaliphile
65241positiveoptimum7.5-8

Physiology and metabolism

oxygen tolerance

  • @ref: 65241
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.999
69481no100

halophily

@refhalophily levelsaltgrowthtested relationconcentration
65241moderately halophilicNaClpositivegrowth0.5-1.9 M
65241moderately halophilicNaClpositiveoptimum1-1.5 M

observation

  • @ref: 65241
  • observation: A few cells are longer than 5 µm.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6524116651(S)-lactate-carbon source
652411 % sodium lactate+carbon source
65241167632-oxobutanoate-carbon source
65241309162-oxoglutarate-carbon source
65241370543-hydroxybutyrate-carbon source
65241739183-O-methyl-D-glucose-carbon source
65241181014-hydroxyphenylacetic acid-carbon source
6524130089acetate-assimilation
6524130089acetate-carbon source
6524113705acetoacetate-carbon source
6524117925alpha-D-glucose-carbon source
6524136219alpha-lactose+carbon source
65241645522-hydroxybutyrate+carbon source
65241161680aztreonam-carbon source
6524173706bromosuccinate-carbon source
65241casein-assimilation
6524116947citrate-carbon source
6524118333D-arabitol+carbon source
6524129990D-aspartate-carbon source
6524117057cellobiose-carbon source
6524115824D-fructose+carbon source
6524178697D-fructose 6-phosphate-carbon source
6524128847D-fucose-carbon source
6524112936D-galactose-carbon source
6524118024D-galacturonic acid-carbon source
6524117634D-glucose-fermentation
6524114314D-glucose 6-phosphate-carbon source
6524115748D-glucuronate-carbon source
6524115588D-malate-carbon source
6524117306maltose-carbon source
6524116899D-mannitol+carbon source
6524116024D-mannose+carbon source
6524128053melibiose+carbon source
6524116634raffinose+carbon source
6524133801D-saccharate-carbon source
6524116523D-serine-carbon source
6524116523D-serine+carbon source
6524117924D-sorbitol-carbon source
6524116551D-trehalose-carbon source
6524132528turanose-carbon source
6524123652dextrin+carbon source
6524115740formate-carbon source
6524171321fusidate+carbon source
6524116537galactarate-carbon source
6524116865gamma-aminobutyric acid+carbon source
652415291gelatin-assimilation
652415291gelatin-carbon source
6524128066gentiobiose-carbon source
6524132323glucuronamide-carbon source
6524117754glycerol-carbon source
6524170744glycine-proline-carbon source
6524117596inosine-carbon source
6524116977L-alanine-carbon source
6524116467L-arginine-carbon source
6524129991L-aspartate-carbon source
6524118287L-fucose-carbon source
6524117464L-galactonic acid gamma-lactone+carbon source
6524129985L-glutamate-carbon source
6524115971L-histidine-carbon source
6524115589L-malate-carbon source
6524118183L-pyroglutamic acid-carbon source
6524162345L-rhamnose-carbon source
6524117115L-serine-carbon source
6524148607lithium chloride-carbon source
6524174611methyl (R)-lactate-carbon source
65241320055methyl beta-D-glucopyranoside-carbon source
6524151850methyl pyruvate-carbon source
6524117268myo-inositol-carbon source
6524163153N-acetyl-D-mannosamine-carbon source
6524128037N-acetylgalactosamine-carbon source
65241506227N-acetylglucosamine-carbon source
6524135418n-acetylneuraminate-carbon source
65241100147nalidixic acid-carbon source
6524117632nitrate-reduction
6524117309pectin-carbon source
6524175248potassium tellurite-carbon source
6524117272propionate-carbon source
6524126490quinate-carbon source
6524117814salicin-carbon source
6524175229sodium bromate-carbon source
6524164103sodium butyrate-carbon source
6524117164stachyose-carbon source
6524117992sucrose+carbon source
6524127897tryptophan+energy source
6524153423tween 40-carbon source
6524153426tween 80-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6524128971ampicillinyesyes10 µg (disc)
6524118208penicillin gyesyes10 µg (disc)
6524117076streptomycinyesyes10 µg (disc)
6524148923erythromycinyesyes15 µg (disc)
6524128001vancomycinyesyes30 µg (disc)
6524117698chloramphenicolyesyes30 µg (disc)
652416104kanamycinyesyes30 µg (disc)
6524127902tetracyclineyesyes30 µg (disc)
652418309polymyxin byesyes30 µg (disc)
6524117833gentamicinyesyes10 µg (disc)

metabolite production

  • @ref: 65241
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 65241
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
65241catalase+1.11.1.6
65241cytochrome oxidase+1.9.3.1
65241alpha-glucosidase+3.2.1.20
65241valine arylamidase-
65241alkaline phosphatase+3.1.3.1
65241esterase Lipase (C 8)+
65241alpha-mannosidase-3.2.1.24
65241alpha-fucosidase-3.2.1.51
65241esterase (C 4)+
65241beta-galactosidase-3.2.1.23
65241trypsin-3.4.21.4
65241leucine arylamidase+3.4.11.1
65241acid phosphatase+3.1.3.2
65241naphthol-AS-BI-phosphohydrolase-
65241lipase (C 14)-
65241cystine arylamidase-3.4.11.3
65241alpha-chymotrypsin-3.4.21.1
65241alpha-galactosidase-3.2.1.22
65241beta-glucuronidase-3.2.1.31
65241N-acetyl-beta-glucosaminidase-3.2.1.52
65241tryptophan deaminase+4.1.99.1
65241urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65241water sample2011brine-seawater interface at Erba Deep in the Red SeaSaudi ArabiaSAUAsia20.7338.183350 % marine 2216 broth (MB; Difco) and 50 % sterilized in situ brine water1 week285 ml brine was used to inoculate 30 ml enrichment medium [50 % marine 2216 broth (MB; Difco) and 50 % sterilized in situ brine water]. The flasks were incubated at 28°C for 1 week, then plated onto marine 2216 agar (MA; Difco) plates amended to a final concentration of 10 % NaCl, and subsequently purified into single colonies using plates containing the same solidified media
67770Brine-seawater interface at Erba Deep in the Red SeaSaudi ArabiaSAUAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1027.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_588;97_688;98_803;99_1027&stattab=map
  • Last taxonomy: Ruegeria
  • 16S sequence: KP726355
  • Sequence Identity:
  • Total samples: 720
  • soil counts: 17
  • aquatic counts: 619
  • animal counts: 82
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 65241
  • description: 16S rRNA gene sequence
  • accession: KP726355
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruegeria sp. ZGT1081685378.4wgspatric1685378
66792Ruegeria profundi ZGT1082724679119draftimg1685378
67770Ruegeria profundi ZGT108GCA_001507545contigncbi1685378

GC content

  • @ref: 67770
  • GC-content: 56.68
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno67.09yes
gram-positiveno97.982no
anaerobicno98.912yes
aerobicyes89.185yes
halophileyes87.421yes
spore-formingno95.639no
glucose-utilyes58.253yes
flagellatedno89.438yes
thermophileno96.52yes
glucose-fermentno88.951no

External links

@ref: 65241

culture collection no.: JCM 19518, ACCC 19861

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29022541Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea.Zhang G, Haroon MF, Zhang R, Dong X, Wang D, Liu Y, Xun W, Dong X, Stingl UInt J Syst Evol Microbiol10.1099/ijsem.0.0023442017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indian Ocean, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, *Salts, Saudi Arabia, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny32195650Ruegeria sediminis sp. nov., isolated from tidal flat sediment.Baek J, Kim JH, Sukhoom A, Kim WInt J Syst Evol Microbiol10.1099/ijsem.0.0041282020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65241Guishan Zhang, Mohamed Fauzi Haroon, Ruifu Zhang, Xiaoyan Dong, Dandan Wang, Yunpeng Liu, Weibing Xun, Xiuzhu Dong, Ulrich StinglRuegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine–seawater interface at Erba Deep in the Red Sea10.1099/ijsem.0.002344IJSEM 67: 4624-4631 201729022541
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1