Strain identifier

BacDive ID: 11325

Type strain: Yes

Species: Massilia albidiflava

Strain Designation: 45

Strain history: CIP <- 2006, KCTC

NCBI tax ID(s): 321983 (species)

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General

@ref: 7007

BacDive-ID: 11325

DSM-Number: 17472

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

description: Massilia albidiflava 45 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 321983
  • Matching level: species

strain history

@refhistory
7007<- W.-J. Li, Yunnan Univ.
369982006, KCTC
116185CIP <- 2006, KCTC

doi: 10.13145/bacdive11325.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Massilia
  • species: Massilia albidiflava
  • full scientific name: Massilia albidiflava Zhang et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella albidiflava

@ref: 7007

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia albidiflava

full scientific name: Massilia albidiflava Zhang et al. 2006

strain designation: 45

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31701negative3-3.5 µm1.8-2 µmrod-shapedyes
69480yes95.901
69480negative99.999
116185negativerod-shapedno

colony morphology

@refincubation period
594673 days
116185

pigmentation

  • @ref: 31701
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7007R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
7007TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium545.pdf
7007TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
36998MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116185CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7007positivegrowth30mesophilic
31701positivegrowth10-45
31701positiveoptimum28-30mesophilic
36998positivegrowth30mesophilic
59467positivegrowth30mesophilic
7007positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31701positivegrowth6.5-8.5alkaliphile
31701positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31701aerobe
59467aerobe
116185facultative anaerobe

spore formation

@refspore formationconfidence
31701no
69481no100
69480no99.976

halophily

@refsaltgrowthtested relationconcentration
31701NaClpositivegrowth0-1 %
31701NaClpositiveoptimum0-1 %

observation

  • @ref: 31701
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170117234glucose+carbon source
3170117992sucrose+carbon source
3170117632nitrate+reduction
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-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
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
11618517632nitrate+reduction
11618516301nitrite-reduction

metabolite production

  • @ref: 116185
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31701alpha-galactosidase+3.2.1.22
31701catalase+1.11.1.6
31701cytochrome oxidase+1.9.3.1
31701urease+3.5.1.5
116185oxidase+
116185catalase+1.11.1.6
116185urease+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
116185-+++-++---+++++-+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7007-+/---+-+---+/-+/-++-+------+--+-++--+++--++-+/-----+-+/-++/-+/-
7007----+-+---++++-+------+-+/-++++--+++--++-+----------
7007----+-+---++++-+------+-+++++--+++--+++-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7007soilJiangsu provinceChinaCHNAsia
116185Environment, Heavy metal, polluted farm soilNanjing, JiangsuChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_127045.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_429;97_2883;98_85215;99_127045&stattab=map
  • Last taxonomy: Massilia
  • 16S sequence: AY965999
  • Sequence Identity:
  • Total samples: 370
  • soil counts: 111
  • aquatic counts: 20
  • animal counts: 137
  • plant counts: 102

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70071Risk group (German classification)
1161851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7007
  • description: Massilia albidiflava strain 45 16S ribosomal RNA gene, partial sequence
  • accession: AY965999
  • length: 1470
  • database: ena
  • NCBI tax ID: 321983

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella albidiflava DSM 17472GCA_004322755completencbi321983
66792Pseudoduganella albidiflava KCTC 12343GCA_014651415scaffoldncbi321983
66792Massilia albidiflava strain DSM 17472321983.3completepatric321983
66792Massilia albidiflava strain KCTC 12343321983.5wgspatric321983
66792Massilia albidiflava DSM 174722843757166completeimg321983

GC content

  • @ref: 31701
  • GC-content: 65.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.184yes
flagellatedyes83.385no
gram-positiveno98.52yes
anaerobicno98.133no
aerobicyes87.101yes
halophileno93.932yes
spore-formingno93.645no
glucose-utilyes90.417yes
thermophileno99.568yes
glucose-fermentno88.452no

External links

@ref: 7007

culture collection no.: CCUG 52214, DSM 17472, CCTCC AB 204071, KCTC 12343, CIP 109189

straininfo link

  • @ref: 80558
  • straininfo: 232830

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449458Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China.Zhang YQ, Li WJ, Zhang KY, Tian XP, Jiang Y, Xu LH, Jiang CL, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.64083-02006Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/*genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny19783608Massilia jejuensis sp. nov. and Naxibacter suwonensis sp. nov., isolated from air samples.Weon HY, Yoo SH, Kim SJ, Kim YS, Anandham R, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.015479-02009*Air Microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny21515701Massilia flava sp. nov., isolated from soil.Wang J, Zhang J, Pang H, Zhang Y, Li Y, Fan JInt J Syst Evol Microbiol10.1099/ijs.0.031344-02011Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysisGenetics
Phylogeny24030691Massilia umbonata sp. nov., able to accumulate poly-beta-hydroxybutyrate, isolated from a sewage sludge compost-soil microcosm.Rodriguez-Diaz M, Cerrone F, Sanchez-Peinado M, SantaCruz-Calvo L, Pozo C, Lopez JGInt J Syst Evol Microbiol10.1099/ijs.0.049874-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification/metabolism, *Phylogeny, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Soil, *Soil Microbiology, Spain, Ubiquinone/chemistryMetabolism
Pathogenicity33361781Massiliamide, a cyclic tetrapeptide with potent tyrosinase inhibitory properties from the Gram-negative bacterium Massilia albidiflava DSM 17472(T).Frediansyah A, Straetener J, Brotz-Oesterhelt H, Gross HJ Antibiot (Tokyo)10.1038/s41429-020-00394-y2020Drug Evaluation, Preclinical, Enzyme Inhibitors/chemistry/*pharmacology, HeLa Cells, Humans, Monophenol Monooxygenase/*antagonists & inhibitors, Nuclear Magnetic Resonance, Biomolecular, Oxalobacteraceae/*chemistry, Peptides, Cyclic/*chemistry/isolation & purification/*pharmacology, Spectrometry, Mass, Electrospray IonizationEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7007Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17472)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17472
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
31701Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797828776041
36998Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6902
59467Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52214)https://www.ccug.se/strain?id=52214
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
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
80558Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232830.1StrainInfo: A central database for resolving microbial strain identifiers
116185Curators of the CIPCollection of Institut Pasteur (CIP 109189)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109189