Strain identifier

BacDive ID: 13731

Type strain: Yes

Species: Phaeobacter inhibens

Strain Designation: T5

Strain history: CIP <- 2006, DSMZ <- T. Martens, T5 <- T. Brinkhoff

NCBI tax ID(s): 999548 (strain), 221822 (species)

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General

@ref: 6411

BacDive-ID: 13731

DSM-Number: 16374

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, ovoid-shaped

description: Phaeobacter inhibens T5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water sample.

NCBI tax id

NCBI tax idMatching level
999548strain
221822species

strain history

@refhistory
6411<- T. Martens; T5 <- T. Brinkhoff
375022006, DSMZ
120118CIP <- 2006, DSMZ <- T. Martens, T5 <- T. Brinkhoff

doi: 10.13145/bacdive13731.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Phaeobacter
  • species: Phaeobacter inhibens
  • full scientific name: Phaeobacter inhibens Martens et al. 2006

@ref: 6411

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Phaeobacter

species: Phaeobacter inhibens

full scientific name: Phaeobacter inhibens Martens et al. 2006 emend. Vandecandelaere et al. 2008 emend. Dogs et al. 2013

strain designation: T5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31517negative1.4-1.9 µm0.6-0.8 µmovoid-shapedyes
120118negativerod-shapedno

colony morphology

  • @ref: 6411
  • incubation period: 1-2 days

pigmentation

  • @ref: 31517
  • production: yes

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_16374_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6411BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37502Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120118CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6411positivegrowth25mesophilic
31517positivegrowth04-36
31517positiveoptimum27-29mesophilic
37502positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
31517positivegrowth6-9.5alkaliphile
31517positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31517aerobe
120118obligate aerobe

spore formation

  • @ref: 31517
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31517NaClpositivegrowth0.05-8.6 %
31517NaClpositiveoptimum2.96-3.94 %

observation

  • @ref: 31517
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3151716449alanine+carbon source
3151729016arginine+carbon source
3151722653asparagine+carbon source
3151735391aspartate+carbon source
3151717057cellobiose+carbon source
3151728757fructose+carbon source
3151728260galactose+carbon source
3151717234glucose+carbon source
3151717754glycerol+carbon source
3151715428glycine+carbon source
3151727570histidine+carbon source
3151725017leucine+carbon source
3151737684mannose+carbon source
3151726271proline+carbon source
3151717272propionate+carbon source
3151733942ribose+carbon source
3151730911sorbitol+carbon source
3151726986threonine+carbon source
3151727082trehalose+carbon source
3151718222xylose+carbon source
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836917306maltose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12011817632nitrate-reduction
12011816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12011835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
6411catalase+1.11.1.6
6411cytochrome-c oxidase+1.9.3.1
31517catalase+1.11.1.6
31517cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
120118oxidase+
120118catalase+1.11.1.6
120118urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120118-+++-++---+++--+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
6411---------+-+-----+/---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
6411--------+/-+/-+/-+/-+/-++/--+++/-+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6411water sampleWadden SeaGermanyDEUEurope
120118Environment, Water, tidal mud flatWadden SeaGermanyDEUEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1899.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_566;98_1495;99_1899&stattab=map
  • Last taxonomy: Phaeobacter
  • 16S sequence: KC176240
  • Sequence Identity:
  • Total samples: 7469
  • soil counts: 318
  • aquatic counts: 6774
  • animal counts: 295
  • plant counts: 82

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64111Risk group (German classification)
1201181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6411Phaeobacter inhibens DSM 16374 16S ribosomal RNA gene, partial sequenceAY1777121386ena999548
6411Phaeobacter inhibens DSM 16374 16S ribosomal RNA gene, partial sequenceKC1762401380ena999548

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phaeobacter inhibens DSM 16374GCA_000473105scaffoldncbi999548
66792Phaeobacter inhibens DSM 16374999548.6wgspatric999548
66792Phaeobacter inhibens T5, DSM 163742574179718completeimg999548

GC content

  • @ref: 6411
  • GC-content: 55.7

External links

@ref: 6411

culture collection no.: DSM 16374, CIP 109289, LMG 22475

straininfo link

  • @ref: 82913
  • straininfo: 131523

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738106Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera.Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff TInt J Syst Evol Microbiol10.1099/ijs.0.63724-02006Chromosomes, Bacterial, DNA, Bacterial/genetics, Fatty Acids/analysis, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Roseobacter/*classification/drug effects/growth & development/isolation & purification/ultrastructureGenetics
Phylogeny24187021Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395.Buddruhs N, Pradella S, Goker M, Pauker O, Pukall R, Sproer C, Schumann P, Petersen J, Brinkhoff TInt J Syst Evol Microbiol10.1099/ijs.0.053900-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Electrophoresis, Gel, Pulsed-Field, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Hybridization, *Phylogeny, Plasmids/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/growth & development, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationEnzymology
Phylogeny25355001Phaeobacter marinintestinus sp. nov., isolated from the intestine of a sea cucumber (Apostichopus japonicus).Lee MH, Song EJ, Seo MJ, Hyun DW, Bae JW, Lee SY, Roh SW, Nam YDAntonie Van Leeuwenhoek10.1007/s10482-014-0318-x2014Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Intestines/microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Stichopus/*microbiology, TemperatureGenetics
Phylogeny31913437Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench.Ding W, Liu P, Xu Y, Fang J, Cao JFEMS Microbiol Lett10.1093/femsle/fnaa0042019Base Composition, China, Chromosomes, Bacterial, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Phospholipids/analysis, *Phylogeny, Plasmids/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6411Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16374)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16374
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
31517Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2781228776041
37502Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7013
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82913Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131523.1StrainInfo: A central database for resolving microbial strain identifiers
120118Curators of the CIPCollection of Institut Pasteur (CIP 109289)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109289