Strain identifier

BacDive ID: 5633

Type strain: Yes

Species: Riemerella columbina

Strain Designation: x183-89, 01024

Strain history: CIP <- 1999, LMG <- 1991, MCCM: strain 01024 <- K.H. Hinz, Klinik für Geflügel, Hanover, Germany: strain Hinz x 183-89

NCBI tax ID(s): 1123058 (strain), 103810 (species)

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General

@ref: 6460

BacDive-ID: 5633

DSM-Number: 16469

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, rod-shaped, animal pathogen

description: Riemerella columbina x183-89 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from pigeon palatine cleft.

NCBI tax id

NCBI tax idMatching level
103810species
1123058strain

strain history

@refhistory
6460<- CIP <- LMG <- MCCM <- K.-H. Hinz, Clinic for Poultry, University of Veterinary Medicine, Hannover, Germany; x183-89
118708CIP <- 1999, LMG <- 1991, MCCM: strain 01024 <- K.H. Hinz, Klinik für Geflügel, Hanover, Germany: strain Hinz x 183-89

doi: 10.13145/bacdive5633.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Riemerella
  • species: Riemerella columbina
  • full scientific name: Riemerella columbina Vancanneyt et al. 1999

@ref: 6460

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Riemerella

species: Riemerella columbina

full scientific name: Riemerella columbina Vancanneyt et al. 1999 emend. Rubbenstroth et al. 2013

strain designation: x183-89, 01024

type strain: yes

Morphology

cell morphology

  • @ref: 118708
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 118708
  • hemolysis ability: 1

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_16469_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16469_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16469_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16469_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_16469_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6460CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
37399MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
118708CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
6460positivegrowth37mesophilic
37399positivegrowth37mesophilic
118708positivegrowth25-41

Physiology and metabolism

oxygen tolerance

  • @ref: 6460
  • oxygen tolerance: microaerophile

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
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
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
118708hippurate-hydrolysis606565
118708nitrate-builds gas from17632
118708nitrate-reduction17632
118708nitrite-builds gas from16301
118708nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
11870835581indoleno
118708polysaccharidesno

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
118708oxidase+
118708beta-galactosidase-3.2.1.23
118708alcohol dehydrogenase-1.1.1.1
118708gelatinase+
118708amylase-
118708DNase+
118708caseinase+3.4.21.50
118708catalase+1.11.1.6
118708tween esterase-
118708lecithinase-
118708lipase-
118708lysine decarboxylase-4.1.1.18
118708ornithine decarboxylase-4.1.1.17
118708protease-
118708urease+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
118708-+-+-+++-+++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118708----------+-------------+/---+-------++/-------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
6460pigeon palatine cleftGermanyDEUEurope
57818Pigeon palatine cleftGermanyDEUEurope
118708Animal, Pigeon, palatine cleftGermanyDEUEuropeHanover1989

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host Body-Site#Oral cavity and airways#Mouth
#Host Body-Site#Organ#Nose

taxonmaps

  • @ref: 69479
  • File name: preview.99_2824.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_1349;97_1790;98_2189;99_2824&stattab=map
  • Last taxonomy: Riemerella columbina subclade
  • 16S sequence: AF181448
  • Sequence Identity:
  • Total samples: 1240
  • soil counts: 50
  • aquatic counts: 390
  • animal counts: 749
  • plant counts: 51

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6460yes2Risk group (German classification)
1187081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6460
  • description: Riemerella columbina 16S ribosomal RNA gene, partial sequence
  • accession: AF181448
  • length: 1460
  • database: ena
  • NCBI tax ID: 1123058

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Riemerella columbina DSM 16469GCA_000374405scaffoldncbi1123058
66792Riemerella columbina DSM 164691123058.4wgspatric1123058
66792Riemerella columbina DSM 164692517434010draftimg1123058

GC content

  • @ref: 6460
  • GC-content: 36

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.82no
flagellatedno97.182no
gram-positiveno98.229no
anaerobicno98.551yes
aerobicno71.542yes
halophileno76.533no
spore-formingno96.498no
glucose-utilyes77.237no
thermophileno99.172yes
glucose-fermentno88.467no

External links

@ref: 6460

culture collection no.: DSM 16469, CIP 106288, LMG 11607, CCUG 47689, Hinz x183-89, Hinz x 183-89

straininfo link

  • @ref: 75116
  • straininfo: 14424

literature

  • topic: Phylogeny
  • Pubmed-ID: 19542118
  • title: Planobacterium taklimakanense gen. nov., sp. nov., a member of the family Flavobacteriaceae that exhibits swimming motility, isolated from desert soil.
  • authors: Peng F, Liu M, Zhang L, Dai J, Luo X, An H, Fang C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.006619-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, *Desert Climate, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Molecular Sequence Data, *Movement, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6460Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16469)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16469
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
37399Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18402
57818Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47689)https://www.ccug.se/strain?id=47689
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 life 35: 676-683 201728604660
68371Automatically annotated from API 50CH acid
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
75116Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14424.1StrainInfo: A central database for resolving microbial strain identifiers
118708Curators of the CIPCollection of Institut Pasteur (CIP 106288)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106288