Strain identifier
BacDive ID: 11335
Type strain:
Species: Massilia niastensis
Strain Designation: 5516S-1
Strain history: CIP <- 2009, DSMZ <- S.-W. Kwon, KACC, Korea: strain 5516S-1
NCBI tax ID(s): 1122215 (strain), 544911 (species)
General
@ref: 15506
BacDive-ID: 11335
DSM-Number: 21313
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Massilia niastensis 5516S-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from air sample.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1122215 | strain |
544911 | species |
strain history
@ref | history |
---|---|
15506 | <- S.-W. Kwon; 5516S-1 {2008} |
121291 | CIP <- 2009, DSMZ <- S.-W. Kwon, KACC, Korea: strain 5516S-1 |
doi: 10.13145/bacdive11335.20230509.8.1
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 niastensis
- full scientific name: Massilia niastensis Weon et al. 2009
synonyms
- @ref: 20215
- synonym: Telluria niastensis
@ref: 15506
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Massilia
species: Massilia niastensis
full scientific name: Massilia niastensis Weon et al. 2009
strain designation: 5516S-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29130 | negative | 2.75 µm | 0.7 µm | rod-shaped | yes | |
69480 | yes | 98.119 | ||||
69480 | negative | 99.994 | ||||
121291 | negative | rod-shaped | yes |
pigmentation
- @ref: 29130
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15506 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
33671 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
121291 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15506 | positive | growth | 30 | mesophilic |
29130 | positive | growth | 05-40 | |
29130 | positive | optimum | 28 | mesophilic |
33671 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29130 | positive | growth | 06-08 |
29130 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29130
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.982 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29130 | NaCl | positive | growth | 0-1 % |
29130 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29130 | 16193 | 3-hydroxybenzoate | + | carbon source |
29130 | 37054 | 3-hydroxybutyrate | + | carbon source |
29130 | 17879 | 4-hydroxybenzoate | + | carbon source |
29130 | 16449 | alanine | + | carbon source |
29130 | 22599 | arabinose | + | carbon source |
29130 | 17234 | glucose | + | carbon source |
29130 | 17240 | itaconate | + | carbon source |
29130 | 15792 | malonate | + | carbon source |
29130 | 17306 | maltose | + | carbon source |
29130 | 37684 | mannose | + | carbon source |
29130 | 506227 | N-acetylglucosamine | + | carbon source |
29130 | 26271 | proline | + | carbon source |
29130 | 26546 | rhamnose | + | carbon source |
29130 | 17814 | salicin | + | carbon source |
29130 | 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 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
121291 | 17632 | nitrate | - | reduction |
121291 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121291 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
29130 | acid phosphatase | + | 3.1.3.2 |
29130 | alkaline phosphatase | + | 3.1.3.1 |
29130 | catalase | + | 1.11.1.6 |
29130 | cytochrome oxidase | + | 1.9.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121291 | oxidase | + | |
121291 | catalase | + | 1.11.1.6 |
121291 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121291 | - | + | - | - | - | + | + | + | - | + | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15506 | - | - | - | - | - | + | + | + | - | + | + | - | - | + | - | - | - | + | + | + | + |
15506 | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
15506 | air sample | Suwon region (37°16'46" N, 126°59'10" E) | Republic of Korea | KOR | Asia | 37.2794 | 126.986 |
121291 | Environment, Air samples | Suwon | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Air
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15506 | 1 | Risk group (German classification) |
121291 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 15506
- description: Massilia niastensis strain 5516S-1 16S ribosomal RNA gene, partial sequence
- accession: EU808005
- length: 1394
- database: ena
- NCBI tax ID: 544911
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Massilia niastensis DSM 21313 | GCA_000382345 | scaffold | ncbi | 1122215 |
66792 | Massilia niastensis DSM 21313 | 1122215.3 | wgs | patric | 1122215 |
66792 | Massilia niastensis DSM 21313 | 2521172636 | draft | img | 1122215 |
GC content
@ref | GC-content | method |
---|---|---|
15506 | 66.6 | high performance liquid chromatography (HPLC) |
29130 | 66.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.928 | no |
flagellated | yes | 80.751 | no |
gram-positive | no | 98.628 | yes |
anaerobic | no | 98.032 | yes |
aerobic | yes | 88.736 | yes |
halophile | no | 93.401 | yes |
spore-forming | no | 93.473 | no |
thermophile | no | 98.992 | yes |
glucose-util | yes | 78.565 | no |
glucose-ferment | no | 90.553 | yes |
External links
@ref: 15506
culture collection no.: DSM 21313, CIP 110038, KACC 12599
straininfo link
- @ref: 80568
- straininfo: 363416
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19542125 | Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples. | Weon HY, Kim BY, Hong SB, Jeon YA, Koo BS, Kwon SW, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.006908-0 | 2009 | *Air Microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
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 | 24810317 | Massilia kyonggiensis sp. nov., isolated from forest soil in Korea. | Kim J | J Microbiol | 10.1007/s12275-014-4010-7 | 2014 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Forests, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature | Genetics |
Phylogeny | 26220552 | Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia. | Singh H, Du J, Won K, Yang JE, Yin C, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000477 | 2015 | Agriculture, Bacterial Typing Techniques, Base Composition, Brassica, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
Phylogeny | 26449383 | Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing. | Feng GD, Yang SZ, Li HP, Zhu HH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000670 | 2015 | Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Disulfides/metabolism, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tungsten, Ubiquinone/chemistry | Genetics |
Phylogeny | 27334790 | Massiliapinisoli sp. nov., isolated from forest soil. | Altankhuu K, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001249 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15506 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21313) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21313 | |||
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 | |||
29130 | 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 | 25556 | 28776041 | |
33671 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7851 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
80568 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID363416.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121291 | Curators of the CIP | Collection of Institut Pasteur (CIP 110038) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110038 |