Strain identifier

BacDive ID: 12685

Type strain: Yes

Species: Alteromonas nigrifaciens

Strain Designation: DB 574

Strain history: CIP <- 1994, NCIMB <- Div. Bact. Dairy Res., Ottawa, Canada <- A.H. White: strain DB 574, Pseudomonas nigrifaciens

NCBI tax ID(s): 28109 (species)

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General

@ref: 3411

BacDive-ID: 12685

DSM-Number: 8810

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

description: Alteromonas nigrifaciens DB 574 is a mesophilic, motile bacterium that was isolated from butter.

NCBI tax id

  • NCBI tax id: 28109
  • Matching level: species

strain history

@refhistory
3411<- ATCC <- NCIB (Pseudomonas nigrifaciens) <- A. White, DB 574
67770IAM 13010 <-- ATCC 19375 <-- NCIB 8614 ("Pseudomonas nigrifaciens") <-- A. White DB574.
121298CIP <- 1994, NCIMB <- Div. Bact. Dairy Res., Ottawa, Canada <- A.H. White: strain DB 574, Pseudomonas nigrifaciens

doi: 10.13145/bacdive12685.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Alteromonas
  • species: Alteromonas nigrifaciens
  • full scientific name: Alteromonas nigrifaciens (ex White 1940) Baumann et al. 1984

  • synonyms

    • @ref: 20215
    • synonym: Pseudoalteromonas nigrifaciens

@ref: 3411

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Alteromonas

species: Alteromonas nigrifaciens

full scientific name: Alteromonas nigrifaciens (ex White 1940) Baumann et al. 1984 emend. Ivanova et al. 1996

strain designation: DB 574

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.402
6948099.991negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3411BACTO 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
3411NUTRIENT AGAR WITH NaCl (DSMZ Medium 101)yeshttps://mediadive.dsmz.de/medium/101Name: NUTRIENT AGAR or BROTH WITH NaCl (DSMZ Medium 101) Composition: NaCl 30.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
42027Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121298CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
3411positivegrowth26mesophilic
42027positivegrowth22psychrophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.969

Isolation, sampling and environmental information

isolation

@refsample type
3411butter
44480Salted butter showing black discolouration
67770Moderately salted butter
121298Salted butter showing black discoloration

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34111Risk group (German classification)
1212981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudoalteromonas nigrifaciens gene for 16S rRNA, partial sequenceD11173217ena28109
20218Alteromonas nigrifaciens 16S rRNAD11222206ena28109
20218Alteromonas nigrifaciens 16S rRNAD11271196ena28109
20218Pseudoalteromonas nigrifaciens gene for 16S rRNA, partial sequence, strain: NBRC 103036AB6819161461ena28109
20218A.nigrifaciens 16S rRNA gene (NCIMB 8614T)X821461436ena28109

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoalteromonas nigrifaciens KMM 661GCA_002221505completencbi28109
66792Pseudoalteromonas nigrifaciens NCTC10691GCA_900455185contigncbi28109
66792Pseudoalteromonas nigrifaciens NBRC 103036GCA_007991255contigncbi28109
66792Pseudoalteromonas nigrifaciens strain KMM 66128109.6plasmidpatric28109
66792Pseudoalteromonas nigrifaciens strain KMM 66128109.4completepatric28109
66792Pseudoalteromonas nigrifaciens strain NBRC 10303628109.12wgspatric28109
66792Pseudoalteromonas nigrifaciens strain NCTC1069128109.10wgspatric28109
66792Pseudoalteromonas nigrifaciens NCTC 106912808606633draftimg28109
66792Pseudoalteromonas nigrifaciens KMM 6612791355162completeimg1315278

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes84.579no
gram-positiveno98.875no
anaerobicno97.443no
aerobicyes92.452no
halophileno57.824no
spore-formingno94.929no
thermophileno99.018no
glucose-utilyes90.981no
motileyes88.463no
glucose-fermentno76.854no

External links

@ref: 3411

culture collection no.: CCUG 2085, NCTC 10691, ATCC 23327, DSM 8810, ATCC 19375, DSM 6063, NCDO 755, NCIB 8614, JCM 20792, CCUG 16154, CIP 104111, IAM 13010, KMM 661, LMG 2227, NBRC 103036, NCIMB 8614

straininfo link

  • @ref: 81897
  • straininfo: 871

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics9129296Structure of the capsular polysaccharide from Alteromonas nigrifaciens IAM 13010T containing 2-acetamido-2,6-dideoxy-L-talose and 3-deoxy-D-manno-octulosonic acid.Gorshkova RP, Nazarenko EL, Zubkov VA, Shashkov AS, Knirel YA, Paramonov NA, Meshkov SV, Ivanova EPCarbohydr Res10.1016/s0008-6215(96)00339-41997Carbohydrate Conformation, Carbohydrate Sequence, Gram-Negative Aerobic Bacteria/chemistry/growth & development/*immunology, Hexosamines/*analysis, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Oligosaccharides/chemistry/isolation & purification, Polysaccharides, Bacterial/*chemistry/isolation & purification, Sugar Acids/analysisEnzymology
Phylogeny18768597Pseudoalteromonas arctica sp. nov., an aerobic, psychrotolerant, marine bacterium isolated from Spitzbergen.Al Khudary R, Stosser NI, Qoura F, Antranikian GInt J Syst Evol Microbiol10.1099/ijs.0.64963-02008Anaerobiosis, Arctic Regions, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carboxylic Acids/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudoalteromonas/*classification/genetics/*isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3411Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8810)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8810
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
42027Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15984
44480Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2085)https://www.ccug.se/strain?id=2085
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/
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
81897Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID871.1StrainInfo: A central database for resolving microbial strain identifiers
121298Curators of the CIPCollection of Institut Pasteur (CIP 104111)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104111