Strain identifier

BacDive ID: 6083

Type strain: Yes

Species: Kushneria avicenniae

Strain Designation: Mw2a

Strain history: CIP <- 2007, CECT <- 2006, A. Ventosa, Sevilla Univ., Sevilla, Spain <- R. Montalvo-Rodriguez, Puerto-Rico Univ., Puerto-Rico: strain MW2a

NCBI tax ID(s): 402385 (species)

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General

@ref: 17211

BacDive-ID: 6083

DSM-Number: 23439

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

description: Kushneria avicenniae Mw2a is an aerobe, mesophilic, Gram-negative bacterium that was isolated from leaves of the black mangrove Avicennia germinans.

NCBI tax id

  • NCBI tax id: 402385
  • Matching level: species

strain history

@refhistory
17211<- CECT <- A. Ventosa <- R. Montalvo-Rodríguez; Mw2a
67770DSM 23439 <-- CECT 7193 <-- A. Ventosa <-- R. Montalvo-Rodríguez Mw2a.
116663CIP <- 2007, CECT <- 2006, A. Ventosa, Sevilla Univ., Sevilla, Spain <- R. Montalvo-Rodriguez, Puerto-Rico Univ., Puerto-Rico: strain MW2a

doi: 10.13145/bacdive6083.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Kushneria
  • species: Kushneria avicenniae
  • full scientific name: Kushneria avicenniae (Soto-Ramírez et al. 2007) Sánchez-Porro et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Halomonas avicenniae

@ref: 17211

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Kushneria

species: Kushneria avicenniae

full scientific name: Kushneria avicenniae (Soto-Ramírez et al. 2007) Sánchez-Porro et al. 2009

strain designation: Mw2a

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32017negative2.3 µm1.5 µmrod-shaped
116663negativeoval-shapedyes
125438negative100
125439negative99.9

pigmentation

  • @ref: 32017
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17211BACTO 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
37819MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116663CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116663CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
17211positivegrowth28
32017positivegrowth12-40
32017positiveoptimum32.5
37819positivegrowth30
67770positivegrowth30

culture pH

@refabilitytypepHPH range
32017positivegrowth05-09alkaliphile
32017positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32017aerobe
116663obligate aerobe

spore formation

@refspore formationconfidence
32017no
125439no99.6

halophily

@refsaltgrowthtested relationconcentration
32017NaClpositivegrowth0-25 %
32017NaClpositiveoptimum5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3201722599arabinose+carbon source
3201716947citrate+carbon source
3201728757fructose+carbon source
3201728260galactose+carbon source
320175291gelatin+carbon source
3201717234glucose+carbon source
3201717754glycerol+carbon source
3201717306maltose+carbon source
3201729864mannitol+carbon source
3201717992sucrose+carbon source
3201718222xylose+carbon source
320174853esculin+hydrolysis
11666317632nitrate-reduction
11666316301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117754glycerol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

metabolite production

  • @ref: 116663
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32017catalase+1.11.1.6
32017gelatinase+
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
116663oxidase-
116663catalase+1.11.1.6
116663urease-3.5.1.5
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116663-++-------++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116663---+/-+/-+/----+/-+/-+/-+/--+/----------+/--+/-+/-+/--+/---------+/-+/--+/-------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17211leaves of the black mangrove Avicennia germinansAvicennia germinansCape RedPuerto RicoPRIMiddle and South America
67770Leaf surface of Avicennia germinans (black mangrove)Avicennia germinans
116663Plant, Leaves, Avicennia germinansCape Red, Puerto RicoUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_13502.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_6462;97_7747;98_10197;99_13502&stattab=map
  • Last taxonomy: Kushneria avicenniae
  • 16S sequence: DQ888315
  • Sequence Identity:
  • Total samples: 36
  • soil counts: 3
  • aquatic counts: 14
  • animal counts: 18
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
172111Risk group (German classification)
1166631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17211
  • description: Halomonas avicenniae strain MW2a 16S ribosomal RNA gene, partial sequence
  • accession: DQ888315
  • length: 1433
  • database: nuccore
  • NCBI tax ID: 402385

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kushneria avicenniae strain DSM 23439402385.4wgspatric402385
66792Kushneria avicenniae DSM 234392684623008draftimg402385
67770Kushneria avicenniae DSM 23439GCA_900112585contigncbi402385

GC content

@refGC-contentmethod
3201761.5
6777061.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.954yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.366yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.95no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.286yes
125438motile2+flagellatedAbility to perform flagellated movementyes76.955no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.6
125439BacteriaNetmotilityAbility to perform movementyes86
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe86.3

External links

@ref: 17211

culture collection no.: DSM 23439, CECT 7193, CIP 109711, JCM 18993, CCM 7396

straininfo link

  • @ref: 75571
  • straininfo: 308612

literature

  • topic: Phylogeny
  • Pubmed-ID: 17473230
  • title: Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico.
  • authors: Soto-Ramirez N, Sanchez-Porro C, Rosas S, Gonzalez W, Quinones M, Ventosa A, Montalvo-Rodriguez R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64818-0
  • year: 2007
  • mesh: Avicennia/*microbiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Environmental Microbiology, Fatty Acids/analysis, Genes, rRNA/genetics, Gentian Violet, Halomonas/chemistry/*classification/*isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phenazines, Phylogeny, Plant Leaves/*microbiology, Puerto Rico, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17211Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23439)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23439
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
32017Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2826928776041
37819Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7485
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/
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
75571Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308612.1StrainInfo: A central database for resolving microbial strain identifiers
116663Curators of the CIPCollection of Institut Pasteur (CIP 109711)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109711
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1