Strain identifier

BacDive ID: 138793

Type strain: Yes

Species: Roseibium hamelinense

Strain history: CIP <- 2001, Y. Nishimura, Tokyo Univ., Tokyo, Japan <- T. Shiba: strain Och 368

NCBI tax ID(s): 150831 (species)

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General

@ref: 40665

BacDive-ID: 138793

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Roseibium hamelinense CIP 107048 is an obligate aerobe, mesophilic, motile bacterium of the family Stappiaceae.

NCBI tax id

  • NCBI tax id: 150831
  • Matching level: species

strain history

@refhistory
67770Y. Nishimura <-- T. Shida OCh 368.
40665CIP <- 2001, Y. Nishimura, Tokyo Univ., Tokyo, Japan <- T. Shiba: strain Och 368

doi: 10.13145/bacdive138793.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Stappiaceae
  • genus: Roseibium
  • species: Roseibium hamelinense
  • full scientific name: Roseibium hamelinense Suzuki et al. 2000

@ref: 40665

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhodobacteraceae

genus: Roseibium

species: Roseibium hamelinense

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.96
6948099.998negative
40665yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40665Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
40665CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
40665positivegrowth25mesophilic
67770positivegrowth30mesophilic
40665positivegrowth15-37
40665nogrowth5psychrophilic
40665nogrowth41thermophilic
40665nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 40665
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
40665NaClpositivegrowth0-8 %
40665NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4066516947citrate-carbon source
406654853esculin-hydrolysis
40665606565hippurate-hydrolysis
4066517632nitrate-builds gas from
4066517632nitrate-reduction
4066516301nitrite-builds gas from
4066516301nitrite-reduction
4066515792malonate-assimilation
4066517234glucose-degradation

antibiotic resistance

  • @ref: 40665
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 40665
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
4066515688acetoin-
4066517234glucose-

enzymes

@refvalueactivityec
40665oxidase+
40665beta-galactosidase+3.2.1.23
40665alcohol dehydrogenase-1.1.1.1
40665gelatinase-
40665amylase-
40665DNase-
40665caseinase-3.4.21.50
40665catalase+1.11.1.6
40665tween esterase-
40665gamma-glutamyltransferase+2.3.2.2
40665lecithinase-
40665lipase-
40665lysine decarboxylase-4.1.1.18
40665ornithine decarboxylase-4.1.1.17
40665phenylalanine ammonia-lyase-4.3.1.24
40665tryptophan deaminase-
40665urease+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
40665-+++-+--+-++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
40665++-++--+-------+---+-----------+-+-++----------------------+------------------------------+--+-----

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
40665Shark BayAustraliaAUSAustralia and Oceania
67770Shark BayAustraliaAUSAustralia and OceaniaSands at Hamelin Pool
40665Shark bayAustraliaAUSAustralia and OceaniaEnvironment, Sands

Safety information

risk assessment

  • @ref: 40665
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Roseibium hamelinense gene for 16S rRNA, partial sequence, strain: OCh 368D858361362ena150831
67770Roseibium hamelinense JCM 10544 gene for 16S ribosomal RNA, partial sequenceLC5061431403ena150831

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseibium hamelinense strain NBRC 16783150831.5wgspatric150831
67770Roseibium hamelinense NBRC 16783GCA_009711505scaffoldncbi150831
67770Roseibium hamelinense ATCC BAA-252GCA_007830545contigncbi150831

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.999no
gram-positiveno98.408no
anaerobicno98.439no
aerobicyes93.673no
halophileyes64.444no
spore-formingno94.282no
thermophileno95.109no
glucose-utilyes88.514no
flagellatedno59.905no
glucose-fermentno89.765no

External links

@ref: 40665

culture collection no.: CIP 107048, JCM 10544, ATCC BAA 252, IFO 16783, NBRC 16783, Och 368

straininfo link

  • @ref: 95444
  • straininfo: 60979

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11155991Roseigium denhamense gen. nov., sp. nov. and Roseibium hemelinense sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from the east and west coasts of Australia.Suzuki T, Muroga Y, Takahama M, Nishimura YInt J Syst Evol Microbiol10.1099/00207713-50-6-21512000Aerobiosis, Alphaproteobacteria/*classification/genetics/*growth & development, Australia, Bacteriochlorophylls/*metabolism, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny28857737Roseibium sediminis sp. nov., isolated from sea surface sediment.Liu J, Wang Y, Yang X, Sun Z, Ren Q, Zhang Y, Liu J, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0020342017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

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
40665Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107048Collection of Institut Pasteur (CIP 107048)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
95444Reimer, 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-ID60979.1