Strain identifier

BacDive ID: 464

Type strain: Yes

Species: Microbulbifer elongatus

Strain history: CIP <- 2004, DSMZ <- NCIMB <- ATCC <- H.S. Levinson <- H. Humm.

NCBI tax ID(s): 86173 (species)

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General

@ref: 2834

BacDive-ID: 464

DSM-Number: 6810

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative, rod-shaped

description: Microbulbifer elongatus DSM 6810 is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from liquefies agar.

NCBI tax id

  • NCBI tax id: 86173
  • Matching level: species

strain history

@refhistory
2834<- NCIMB <- ATCC <- H.S. Levinson <- H. Humm
119018CIP <- 2004, DSMZ <- NCIMB <- ATCC <- H.S. Levinson <- H. Humm.

doi: 10.13145/bacdive464.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Microbulbiferaceae
  • genus: Microbulbifer
  • species: Microbulbifer elongatus
  • full scientific name: Microbulbifer elongatus (Humm 1946) Yoon et al. 2003

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas elongata

@ref: 2834

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Microbulbiferaceae

genus: Microbulbifer

species: Microbulbifer elongatus

full scientific name: Microbulbifer elongatus (Humm 1946) Yoon et al. 2003

type strain: yes

Morphology

cell morphology

  • @ref: 119018
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2834SEA WATER AGAR (DSMZ Medium 246)yeshttps://mediadive.dsmz.de/medium/246Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water
34962MEDIUM 609 - for Microbulbifer elongatusyesAgar (20.000 g);Peptone (10.000 g);Beef extract (10.000 g);Tap water(250.000 ml);Synthetic sea solution - M01068 (750.000 ml)
119018CIP Medium 609yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=609

culture temp

@refgrowthtypetemperaturerange
2834positivegrowth20psychrophilic
34962positivegrowth25mesophilic
119018positivegrowth25-37mesophilic
119018nogrowth5psychrophilic
119018nogrowth10psychrophilic
119018nogrowth41thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
119018NaClpositivegrowth4-6 %
119018NaClnogrowth0 %
119018NaClnogrowth2 %
119018NaClnogrowth8 %
119018NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate-reduction
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11901817108D-arabinose-degradation
11901815824D-fructose-degradation
11901817634D-glucose-degradation
11901816024D-mannose-degradation
11901865327D-xylose-degradation
11901817057cellobiose-degradation
11901817716lactose-degradation
11901817306maltose-degradation
11901817814salicin-degradation
11901817992sucrose-degradation
1190184853esculin+hydrolysis
11901817632nitrate-reduction
11901816301nitrite-reduction
683764853esculin-hydrolysis
6837618333D-arabitol-builds acid from
6837665327D-xylose-builds acid from
6837662345L-rhamnose-builds acid from
68376320061methyl alpha-D-glucopyranoside-builds acid from
6837616988D-ribose-builds acid from
6837629042glucose 1-phosphate-builds acid from
6837616443D-tagatose-builds acid from

antibiotic resistance

  • @ref: 119018
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11901835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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
68376alpha-mannosidase-3.2.1.24
68376beta-glucosidase-3.2.1.21
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
119018oxidase+
119018beta-galactosidase+3.2.1.23
119018alcohol dehydrogenase-1.1.1.1
119018gelatinase+
119018amylase+
119018DNase-
119018caseinase-3.4.21.50
119018catalase+1.11.1.6
119018tween esterase-
119018lecithinase-
119018lipase-
119018lysine decarboxylase-4.1.1.18
119018ornithine decarboxylase-4.1.1.17
119018protease+
119018tryptophan deaminase-
119018urease-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
119018-+++-+----++-----+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUINOSorRHASACMELNO2N2
119018-------------------

API LIST

@refDIMESCalpha MANDARLXYLRHAMDGRIBG1PTAG
119018----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119018---------------+--------------------------------------------------------+-----------+---+----------

Isolation, sampling and environmental information

isolation

@refsample type
2834liquefies agar
119018Liquefies agar

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Laboratory
  • Cat3: #Lab enrichment

taxonmaps

  • @ref: 69479
  • File name: preview.99_2325.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_1255;97_1489;98_1814;99_2325&stattab=map
  • Last taxonomy: Microbulbifer elongatus
  • 16S sequence: AF500006
  • Sequence Identity:
  • Total samples: 271
  • soil counts: 2
  • aquatic counts: 265
  • animal counts: 3
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
28341Risk group (German classification)
1190181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbulbifer elongatus gene for 16S rRNA, strain: ATCC 10144AB0213681514ena86173
2834Pseudomonas elongata strain DSM 6810 16S ribosomal RNA gene, partial sequenceAF5000061491ena86173

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbulbifer elongatus DSM 6810GCA_021165935completencbi86173
66792Microbulbifer elongatus DSM 6810GCA_022554105scaffoldncbi86173
66792Microbulbifer elongatus strain DSM 681086173.18completepatric86173

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes74.862no
gram-positiveno99.127no
anaerobicno98.614no
aerobicyes94.356no
halophileyes83.855no
spore-formingno96.14no
motileyes81.632no
thermophileno98.254no
glucose-utilyes88.695no
glucose-fermentno89.108no

External links

@ref: 2834

culture collection no.: DSM 6810, ATCC 10144, LMG 2182, NCIB 1141, CIP 108580, NCIMB 1141

straininfo link

  • @ref: 70143
  • straininfo: 265483

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130018Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov.Yoon JH, Kim H, Kang KH, Oh TK, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.02464-02003Alteromonadaceae/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityMetabolism
Phylogeny19701665Characterization of Microbulbifer strain CMC-5, a new biochemical variant of Microbulbifer elongatus type strain DSM6810T isolated from decomposing seaweeds.Jonnadula R, Verma P, Shouche YS, Ghadi SCCurr Microbiol10.1007/s00284-009-9480-12009Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gammaproteobacteria/*classification/isolation & purification/metabolism, Gracilaria/metabolism/*microbiology, Molecular Sequence Data, Phylogeny, Polysaccharides/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sargassum/*microbiology, Seaweed/genetics/*microbiology, Sequence Analysis, DNA, Species Specificity, Water MicrobiologyMetabolism
Phylogeny23243090Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove.Vashist P, Nogi Y, Ghadi SC, Verma P, Shouche YSInt J Syst Evol Microbiol10.1099/ijs.0.042978-02012Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Genetics24907394Draft genome sequence of Microbulbifer elongatus strain HZ11, a brown seaweed-degrading bacterium with potential ability to produce bioethanol from alginate.Sun C, Chen YJ, Zhang XQ, Pan J, Cheng H, Wu MMar Genomics10.1016/j.margen.2014.05.0092014Alginates/metabolism, Base Composition, Base Sequence, *Biofuels, Cluster Analysis, DNA Primers/genetics, Ethanol/*metabolism, Gammaproteobacteria/*genetics/*metabolism, Genome, Bacterial/*genetics, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Laminaria/*chemistry/microbiology, Molecular Sequence Data, Sequence Analysis, DNAMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2834Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6810)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6810
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
34962Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6219
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)
68368Automatically annotated from API 20E
68376Automatically annotated from API LIST
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
70143Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265483.1StrainInfo: A central database for resolving microbial strain identifiers
119018Curators of the CIPCollection of Institut Pasteur (CIP 108580)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108580