Strain identifier
BacDive ID: 11333
Type strain: 
Species: Massilia varians
Strain Designation: R-3575, RSTN 96/5182
Strain history: <- P. Kämpfer, Univ. Giessen <- CCUG <- S.-T. Thomassen, Tromsø, Norway; RSTN 96/5182
NCBI tax ID(s): 457921 (species)
version 8.1 (current version)
General
@ref: 16006
BacDive-ID: 11333
DSM-Number: 21873
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, human pathogen
description: Massilia varians R-3575 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from human eye, 90-year-old man.
NCBI tax id
- NCBI tax id: 457921
- Matching level: species
strain history
- @ref: 16006
- history: <- P. Kämpfer, Univ. Giessen <- CCUG <- S.-T. Thomassen, Tromsø, Norway; RSTN 96/5182
doi: 10.13145/bacdive11333.20230509.8.1
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 varians
- full scientific name: Massilia varians (Kämpfer et al. 2008) Kämpfer et al. 2011
synonyms
@ref synonym 20215 Naxibacter varians 20215 Telluria varians
@ref: 16006
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Massilia
species: Massilia varians
full scientific name: Massilia varians (Kämpfer et al. 2008) Kämpfer et al. 2011
strain designation: R-3575, RSTN 96/5182
type strain: yes
Morphology
cell morphology
- @ref: 32451
- gram stain: negative
- cell length: 2 µm
- cell width: 1 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 32451
- production: yes
Culture and growth conditions
culture medium
- @ref: 16006
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: 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
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16006 | positive | growth | 28 | mesophilic |
| 32451 | positive | growth | 15-37 | |
| 32451 | positive | optimum | 25-30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32451 | positive | growth | 5.5-11.5 | alkaliphile |
| 32451 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32451
- oxygen tolerance: aerobe
spore formation
- @ref: 32451
- spore formation: no
observation
- @ref: 32451
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32451 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 32451 | 30089 | acetate | + | carbon source |
| 32451 | 15361 | pyruvate | + | carbon source |
| 32451 | 4853 | esculin | + | hydrolysis |
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 17306 | maltose | + | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | + | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | + | hydrolysis |
| 68369 | 4853 | esculin | + | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32451 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | + | |
| 68369 | beta-glucosidase | + | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 16006 | - | - | - | - | - | + | + | + | + | + | - | - | + | + | - | - | - | + | - | + | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 16006 | human eye, 90-year-old man | Tromsø | Norway | NOR | Europe | |
| 52657 | Human eye,90-yr-old man | Tromsö | Norway | NOR | Europe | 1996-01-01 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | #Male |
| #Host Body-Site | #Organ | #Eye |
taxonmaps
- @ref: 69479
- File name: preview.99_6685.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_429;97_3881;98_4931;99_6685&stattab=map
- Last taxonomy: Massilia
- 16S sequence: AM774587
- Sequence Identity:
- Total samples: 438
- soil counts: 34
- aquatic counts: 118
- animal counts: 196
- plant counts: 90
Safety information
risk assessment
- @ref: 16006
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16006
- description: Naxibacter varians partial 16S rRNA gene, type strain CCUG 35299T
- accession: AM774587
- length: 1362
- database: ena
- NCBI tax ID: 457921
External links
@ref: 16006
culture collection no.: DSM 21873, CCM 7478, CCUG 35299
straininfo link
- @ref: 80566
- straininfo: 16235
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18599716 | Naxibacter varians sp. nov. and Naxibacter haematophilus sp. nov., and emended description of the genus Naxibacter. | Kampfer P, Falsen E, Busse HJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.65516-0 | 2008 | Adult, Aged, 80 and over, Fatty Acids/metabolism, Humans, Japan, Male, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/chemistry/*classification/genetics/isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity | Pathogenicity |
| Phylogeny | 20656816 | Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. | Kampfer P, Lodders N, Martin K, Falsen E | Int J Syst Evol Microbiol | 10.1099/ijs.0.025585-0 | 2010 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Pathogenicity |
| Phylogeny | 22140160 | Massilia tieshanensis sp. nov., isolated from mining soil. | Du Y, Yu X, Wang G | Int J Syst Evol Microbiol | 10.1099/ijs.0.034306-0 | 2011 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysis | Genetics |
| Phylogeny | 28809142 | Massilia agri sp. nov., isolated from reclaimed grassland soil. | Chaudhary DK, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002002 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Nepal, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16006 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21873) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21873 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 32451 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28673 | 28776041 | |
| 52657 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 35299) | https://www.ccug.se/strain?id=35299 | |||
| 68369 | Automatically annotated from API 20NE | |||||
| 69479 | João 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 | |||
| 80566 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID16235.1 | StrainInfo: A central database for resolving microbial strain identifiers |