Strain identifier
BacDive ID: 133132
Type strain:
Species: Streptomyces phyllanthi
Strain Designation: PA1-07
Strain history: <- Somboon Tanasupawat, Chulalongkorn Univ.
NCBI tax ID(s): 1803180 (species)
General
@ref: 24894
BacDive-ID: 133132
DSM-Number: 117319
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive
description: Streptomyces phyllanthi PA1-07 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from stem of Phyllanthus amarus.
NCBI tax id
- NCBI tax id: 1803180
- Matching level: species
strain history
@ref | history |
---|---|
67770 | S. Tanasupawat; Chulalongkorn Univ., Thailand; PA1-07. |
67771 | <- Somboon Tanasupawat, Chulalongkorn Univ. |
doi: 10.13145/bacdive133132.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Kitasatosporales
- family: Streptomycetaceae
- genus: Streptomyces
- species: Streptomyces phyllanthi
- full scientific name: Streptomyces phyllanthi Klykleung et al. 2016
@ref: 24894
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Streptomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces phyllanthi
full scientific name: Streptomyces phyllanthi Klykleung et al. 2016
strain designation: PA1-07
type strain: yes
Morphology
cell morphology
- @ref: 24894
- gram stain: positive
Culture and growth conditions
culture medium
@ref | name | growth | link |
---|---|---|---|
24894 | Yeast extract-malt extract agar (ISP2) | yes | |
24894 | Inorganic salts-starch agar (ISP4) | yes | |
24894 | Oatmeal agar (ISP3) | yes | |
24894 | Glycerol-asparagine agar (ISP5) | yes | |
24894 | Peptone Yeast Extract Iron Agar (ISP6) | yes | |
24894 | Tyrosine Agar (ISP7) | yes | |
24894 | NA (Nutrient Agar) | yes | |
125195 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf |
125195 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf |
culture temp
@ref | growth | type | temperature |
---|---|---|---|
24894 | positive | growth | 20.0-40.0 |
67770 | positive | growth | 28 |
67771 | positive | growth | 28 |
125195 | positive | growth | 28 |
culture pH
- @ref: 24894
- ability: positive
- type: growth
- pH: 5.0-9.0
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
24894 | aerobe |
67771 | aerobe |
spore formation
@ref | spore description | type of spore | spore formation | confidence |
---|---|---|---|---|
24894 | ovule,rugose surface | spore | yes | |
69480 | yes | 93.752 | ||
69481 | yes | 100 |
halophily
- @ref: 24894
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: >5.0 %(w/v)
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H6), MK-9(H8)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
24894 | 33942 | ribose | - | assimilation |
24894 | 17814 | salicin | - | assimilation |
24894 | 17992 | sucrose | - | assimilation |
24894 | 17057 | cellobiose | + | assimilation |
24894 | 16899 | D-mannitol | + | assimilation |
24894 | 65327 | D-xylose | + | assimilation |
24894 | 28757 | fructose | + | assimilation |
24894 | 28260 | galactose | + | assimilation |
24894 | 17234 | glucose | + | assimilation |
24894 | 17268 | myo-inositol | + | assimilation |
24894 | 30849 | L-arabinose | + | assimilation |
24894 | 62345 | L-rhamnose | + | assimilation |
24894 | 17632 | nitrate | + | reduction |
24894 | 16634 | raffinose | + | assimilation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
24894 | acid phosphatase | + | 3.1.3.2 |
24894 | alkaline phosphatase | + | 3.1.3.1 |
24894 | alpha-chymotrypsin | + | 3.4.21.1 |
24894 | alpha-galactosidase | - | 3.2.1.22 |
24894 | alpha-glucosidase | + | 3.2.1.20 |
24894 | alpha-mannosidase | + | 3.2.1.24 |
24894 | beta-galactosidase | + | 3.2.1.23 |
24894 | beta-glucosidase | + | 3.2.1.21 |
24894 | beta-glucuronidase | - | 3.2.1.31 |
24894 | cystine arylamidase | + | 3.4.11.3 |
24894 | esterase (C 4) | + | |
24894 | esterase lipase (C 8) | + | |
24894 | leucine arylamidase | + | 3.4.11.1 |
24894 | lipase (C 14) | - | |
24894 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
24894 | naphthol-AS-BI-phosphohydrolase | + | |
24894 | trypsin | + | 3.4.21.4 |
24894 | valine arylamidase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | host species |
---|---|---|---|---|---|---|
24894 | stem of Phyllanthus amarus | botanical garden of the Faculty of Pharmaceutical Sciences,Chulalongkorn University,Bangkok | Thailand | THA | Asia | |
67770 | Stem of Phyllanthus amarus | Thailand | THA | Asia | Phyllanthus amarus | |
67771 | From stem of plant (Phyllanthus amarus, Euphobiaceae) | Bangkok | Thailand | THA | Asia | |
125195 | stem of Phyllanthus amarus | Chulalongkorn University | Thailand | THA | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Stem (Branch) |
Safety information
risk assessment
- @ref: 125195
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24894
- description: Streptomyces phyllanthi gene for 16S ribosomal RNA, partial sequence
- accession: LC125632
- length: 1462
- database: nuccore
- NCBI tax ID: 1803180
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces phyllanthi strain TISTR 2346 | 1803180.3 | wgs | patric | 1803180 |
67770 | Streptomyces phyllanthi TISTR 2346 | GCA_009377205 | contig | ncbi | 1803180 |
GC content
- @ref: 24894
- GC-content: 71
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
@ref | trait | model | description | prediction | confidence | training_data |
---|---|---|---|---|---|---|
69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 85.312 | no |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.065 | no |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 93.752 | yes |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.333 | yes |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.4 | yes |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 87 | no |
External links
@ref: 24894
culture collection no.: JCM 30865, KCTC 39785, TISTR 2346, DSM 117319
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 27393329 | Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus. | Klykleung N, Phongsopitanun W, Pittayakhajonwut P, Ohkuma M, Kudo T, Tanasupawat S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001289 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, Phyllanthus/*microbiology, *Phylogeny, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 32139879 | Streptomyces acidicola sp. nov., isolated from a peat swamp forest in Thailand. | Lipun K, Chantavorakit T, Mingma R, Duangmal K | J Antibiot (Tokyo) | 10.1038/s41429-020-0294-5 | 2020 | Amino Acids, Diamino/genetics, Bacterial Typing Techniques/methods, Base Composition/genetics, DNA, Bacterial/genetics, Diaminopimelic Acid, Fatty Acids/genetics, Forests, Galactose/genetics, Glucose/genetics, Mannose/genetics, Nucleic Acid Hybridization/genetics, Phospholipids/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribose/genetics, Soil, Soil Microbiology, Streptomyces/genetics/*isolation & purification, Thailand, Wetlands | Enzymology |
Phylogeny | 34775568 | Streptomyces blattellae, a novel actinomycete isolated from the in vivo of a Blattella germanica. | Liu GM, Yuan LL, Zhang LL, Zeng H | Antonie Van Leeuwenhoek | 10.1007/s10482-021-01681-w | 2021 | *Actinobacteria/genetics, DNA, Bacterial/genetics, Humans, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/genetics | Pathogenicity |
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
24894 | N. P. Klykleung, Wongsakorn,Pittayakhajonwut, Pattama,Ohkuma, Moriya,Kudo, Takuji,Tanasupawat, Somboon | Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus | 10.1099/ijsem.0.001289 | IJSEM 66: 3923-3928 2016 | 27393329 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
125195 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-117319 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 117319) |