Strain identifier

BacDive ID: 2457

Type strain: Yes

Species: Rheinheimera pacifica

Strain history: CIP <- 2003, CCUG <- 2002, L.A. Romanenko, KMM, Vladivostok, Russia

NCBI tax ID(s): 173990 (species)

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General

@ref: 7089

BacDive-ID: 2457

DSM-Number: 17616

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative

description: Rheinheimera pacifica DSM 17616 is an aerobe, Gram-negative bacterium that was isolated from sea-water sample that was obtained from a depth of 5000 m in the northwestern part of the Pacific Ocean.

NCBI tax id

  • NCBI tax id: 173990
  • Matching level: species

strain history

@refhistory
7089<- CCUG <- L. A. Romanenko, KMM
67770M. Uchino <-- KMM 1406.
121499CIP <- 2003, CCUG <- 2002, L.A. Romanenko, KMM, Vladivostok, Russia

doi: 10.13145/bacdive2457.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Chromatiales
  • family: Chromatiaceae
  • genus: Rheinheimera
  • species: Rheinheimera pacifica
  • full scientific name: Rheinheimera pacifica Romanenko et al. 2003

@ref: 7089

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Chromatiaceae

genus: Rheinheimera

species: Rheinheimera pacifica

full scientific name: Rheinheimera pacifica Romanenko et al. 2003

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121499negativerod-shapedyes
69480negative99.5

colony morphology

  • @ref: 121499

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7089NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37417MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121499CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
121499CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7089positivegrowth28
37417positivegrowth37
57258positivegrowth30
67770positivegrowth30
121499positivegrowth10-37
121499nogrowth5
121499nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57258aerobe
121499obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
121499NaClpositivegrowth2 %
121499NaClnogrowth0 %
121499NaClnogrowth4 %
121499NaClnogrowth6 %
121499NaClnogrowth8 %
121499NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121499citrate-carbon source16947
121499esculin+hydrolysis4853
121499nitrate-reduction17632
121499nitrite-reduction16301
121499nitrate-respiration17632

antibiotic resistance

  • @ref: 121499
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121499
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121499oxidase+
121499beta-galactosidase+3.2.1.23
121499alcohol dehydrogenase+1.1.1.1
121499gelatinase+/-
121499amylase+
121499DNase+
121499caseinase+3.4.21.50
121499catalase-1.11.1.6
121499tween esterase-
121499lecithinase-
121499lipase-
121499lysine decarboxylase-4.1.1.18
121499ornithine decarboxylase-4.1.1.17
121499phenylalanine ammonia-lyase-4.3.1.24
121499tryptophan deaminase-
121499urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121499-+++-++-++-+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121499------------------------+------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121499++++---++++----+--+-++-------------+-----------------+++---+--------------------------+--+---++----

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryisolation date
7089sea-water sample that was obtained from a depth of 5000 m in the northwestern part of the Pacific Ocean
57258Seawater,at a depth of 5000 meter1985-07-01Pacific Ocean
67770Pacific deep-sea water
121499Environment, Seawater, and a depth of 5000 meterPacific Ocean1985

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70891Risk group (German classification)
1214991Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rheinheimera pacifica gene for 16S rRNA, partial sequence, strain: NBRC 103167AB6819741450nuccore173990
7089Rheinheimera pacifica gene for 16S rRNA, partial sequenceAB0731321402nuccore173990

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rheinheimera pacifica strain DSM 17616173990.3wgspatric173990
66792Rheinheimera pacifica DSM 176162599185208draftimg173990
67770Rheinheimera pacifica DSM 17616GCA_900108485scaffoldncbi173990

GC content

@refGC-contentmethod
708949.6
6777049.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.772yes
69480spore-formingspore-formingAbility to form endo- or exosporesno86.863no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes69.981yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.357yes
69480flagellatedmotile2+Ability to perform flagellated movementyes86.41no

External links

@ref: 7089

culture collection no.: DSM 17616, CCUG 46544, IAM 15043, JCM 12090, KMM 1406, NBRC 103167, NRIC 0539, CIP 108198, CGMCC 1.7099

straininfo link

  • @ref: 72001
  • straininfo: 128013

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657132Rheinheimera pacifica sp. nov., a novel halotolerant bacterium isolated from deep sea water of the Pacific.Romanenko LA, Uchino M, Falsen E, Zhukova NV, Mikhailov VV, Uchimura TInt J Syst Evol Microbiol10.1099/ijs.0.02252-02003Chromatiaceae/*classification/genetics/growth & development/isolation & purification, Fatty Acids/analysis, Glucose/metabolism, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Pacific Ocean, Phenotype, *Phylogeny, Seawater/microbiologyStress
Phylogeny17684273Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass.Halpern M, Senderovich Y, Snir SInt J Syst Evol Microbiol10.1099/ijs.0.64927-02007Animals, Chironomidae/*microbiology, Chromatiaceae/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Ovum/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolismGenetics
Phylogeny20511463Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007.Li HJ, Zhang XY, Zhang YJ, Zhou MY, Gao ZM, Chen XL, Dang HY, Zhang YZInt J Syst Evol Microbiol10.1099/ijs.0.019281-02010Chromatiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny22268075Rheinheimera longhuensis sp. nov., isolated from a slightly alkaline lake, and emended description of genus Rheinheimera Brettar et al. 2002.Liu Y, Jiang JT, Xu CJ, Liu YH, Song XF, Li H, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.036020-02012Bacterial Typing Techniques, Base Composition, China, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Lakes/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysis, *Water MicrobiologyGenetics
Phylogeny24408524Rheinheimera tuosuensis sp. nov., isolated from a saline lake.Zhong ZP, Liu Y, Liu LZ, Wang F, Zhou YG, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.056473-02014Bacterial Typing Techniques, Base Composition, China, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny24408528Rheinheimera hassiensis sp. nov. and Rheinheimera muenzenbergensis sp. nov., two species from the rhizosphere of Hordeum secalinum.Suarez C, Ratering S, Geissler-Plaum R, Schnell SInt J Syst Evol Microbiol10.1099/ijs.0.061200-02014Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Hordeum/*microbiology, Molecular Sequence Data, Nitrogen Fixation, Nucleic Acid Hybridization, Oxidoreductases/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNAEnzymology
Phylogeny25702316Rheinheimera japonica sp. nov., a novel bacterium with antimicrobial activity from seashore sediments of the Sea of Japan.Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI, Mikhailov VVArch Microbiol10.1007/s00203-015-1095-22015Anti-Bacterial Agents/*metabolism/pharmacology, Base Sequence, Chromatiaceae/classification/genetics/isolation & purification/*metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Gram-Negative Bacteria/*drug effects, Gram-Positive Bacteria/*drug effects, Japan, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny25957052Rheinheimera aestuari sp. nov., a marine bacterium isolated from coastal sediment.Baek K, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.0003122015Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny29111971Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera.Hayashi K, Busse HJ, Golke J, Anderson J, Wan X, Hou S, Chain PSG, Prescott RD, Donachie SPInt J Syst Evol Microbiol10.1099/ijsem.0.0024122017Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hawaii, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/*chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34882530Rheinheimera lutimaris sp. nov., a marine bacterium isolated from coastal sediment.Yu Q, Qi Y, Pu JInt J Syst Evol Microbiol10.1099/ijsem.0.0051432021Bacterial Typing Techniques, Base Composition, China, Chromatiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny35687392Rheinheimera maricola sp. nov., isolated from seawater of the Yellow Sea.Kim KH, Baek JH, Wenting R, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0054232022Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, *Platyhelminths, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7089Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17616)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17616
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37417Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5793
57258Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46544)https://www.ccug.se/strain?id=46544
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72001Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128013.1StrainInfo: A central database for resolving microbial strain identifiers
121499Curators of the CIPCollection of Institut Pasteur (CIP 108198)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108198