Strain identifier
BacDive ID: 23123
Type strain:
Species: Phytohabitans flavus
Strain Designation: K09-0627
Strain history: A. Matsumoto K09-0627.
NCBI tax ID(s): 1076124 (species)
General
@ref: 19188
BacDive-ID: 23123
DSM-Number: 45551
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Phytohabitans flavus K09-0627 is an aerobe, spore-forming, mesophilic bacterium that was isolated from orchid root.
NCBI tax id
- NCBI tax id: 1076124
- Matching level: species
strain history
@ref | history |
---|---|
19188 | <- Y. Takahashi, Kitasato Univ., Tokyo, Japan; K09-0627 <- Y. Inahashi |
67770 | A. Matsumoto K09-0627. |
doi: 10.13145/bacdive23123.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Phytohabitans
- species: Phytohabitans flavus
- full scientific name: Phytohabitans flavus Inahashi et al. 2012
@ref: 19188
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Phytohabitans
species: Phytohabitans flavus
full scientific name: Phytohabitans flavus Inahashi et al. 2012
strain designation: K09-0627
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
30512 | positive | ||
69480 | no | 93.044 | |
69480 | positive | 100 |
pigmentation
- @ref: 30512
- production: yes
multimedia
- @ref: 19188
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45551.jpg
- caption: Medium 554 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
19188 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf | |
19188 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf | |
19188 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
19188 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19188 | positive | growth | 28 | mesophilic |
30512 | positive | growth | 20-35 | |
30512 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30512 | positive | growth | 07-11 | alkaliphile |
30512 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 30512
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30512 | yes | |
69481 | yes | 97 |
69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H8), MK-9(H6), MK-10(H8), MK-10(H6)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30512 | 22599 | arabinose | + | carbon source |
30512 | 28757 | fructose | + | carbon source |
30512 | 17234 | glucose | + | carbon source |
30512 | 29864 | mannitol | + | carbon source |
30512 | 26546 | rhamnose | + | carbon source |
30512 | 18222 | xylose | + | carbon source |
enzymes
- @ref: 30512
- value: alkaline phosphatase
- activity: +
- ec: 3.1.3.1
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
19188 | orchid root | Okinawa Prefecture | Japan | JPN | Asia |
67770 | Roots of an orchid | Okinawa Pref. | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
Safety information
risk assessment
- @ref: 19188
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19188
- description: Phytohabitans flavus gene for 16S rRNA, partial sequence
- accession: AB663558
- length: 1466
- database: ena
- NCBI tax ID: 1076124
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Phytohabitans flavus NBRC 107702 | GCA_011764545 | complete | ncbi | 1076124 |
66792 | Phytohabitans flavus strain NBRC 107702 | 1076124.3 | complete | patric | 1076124 |
GC content
@ref | GC-content | method |
---|---|---|
19188 | 71 | high performance liquid chromatography (HPLC) |
30512 | 71 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 97 | no |
motile | no | 91.286 | no |
flagellated | no | 98.28 | no |
gram-positive | yes | 86.486 | yes |
anaerobic | no | 99.235 | no |
aerobic | yes | 93.288 | yes |
halophile | no | 96.365 | no |
spore-forming | yes | 92.587 | yes |
glucose-util | yes | 88.166 | no |
thermophile | no | 96.839 | no |
glucose-ferment | no | 92.553 | no |
External links
@ref: 19188
culture collection no.: DSM 45551, JCM 17387, NBRC 107702
straininfo link
- @ref: 87359
- straininfo: 398319
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22228668 | Phytohabitans flavus sp. nov., Phytohabitans rumicis sp. nov. and Phytohabitans houttuyneae sp. nov., isolated from plant roots, and emended description of the genus Phytohabitans. | Inahashi Y, Matsumoto A, Omura S, Takahashi Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.037747-0 | 2012 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Houttuynia/microbiology, Japan, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rumex/microbiology, Sequence Analysis, DNA | Genetics |
Phylogeny | 27126122 | Phytohabitans kaempferiae sp. nov., an endophytic actinomycete isolated from the leaf of Kaempferia larsenii. | Niemhom N, Chutrakul C, Suriyachadkun C, Thawai C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001121 | 2016 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistry, Zingiberaceae/*microbiology | Transcriptome |
33120960 | Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans. | Komaki H, Tamura T | Life (Basel) | 10.3390/life10110257 | 2020 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19188 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45551) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45551 | |||
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 | |||
30512 | 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 | 26844 | 28776041 | |
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
87359 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398319.1 | StrainInfo: A central database for resolving microbial strain identifiers |