Strain identifier

BacDive ID: 133132

Type strain: Yes

Species: Streptomyces phyllanthi

Strain Designation: PA1-07

Strain history: <- Somboon Tanasupawat, Chulalongkorn Univ.

NCBI tax ID(s): 1803180 (species)

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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

@refhistory
67770S. Tanasupawat; Chulalongkorn Univ., Thailand; PA1-07.
67771<- Somboon Tanasupawat, Chulalongkorn Univ.

doi: 10.13145/bacdive133132.20250331.9.3

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

@refgram stainconfidencemotility
24894positive
125439positive99.8
12543991.2no

Culture and growth conditions

culture medium

@refnamegrowthlink
24894Yeast extract-malt extract agar (ISP2)yes
24894Inorganic salts-starch agar (ISP4)yes
24894Oatmeal agar (ISP3)yes
24894Glycerol-asparagine agar (ISP5)yes
24894Peptone Yeast Extract Iron Agar (ISP6)yes
24894Tyrosine Agar (ISP7)yes
24894NA (Nutrient Agar)yes
125195GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
125195STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf

culture temp

@refgrowthtypetemperature
24894positivegrowth20.0-40.0
67770positivegrowth28
67771positivegrowth28
125195positivegrowth28

culture pH

  • @ref: 24894
  • ability: positive
  • type: growth
  • pH: 5.0-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
24894aerobe
67771aerobe
125439obligate aerobe97.1

spore formation

@refspore descriptiontype of sporespore formationconfidence
24894ovule,rugose surfacesporeyes
125438yes93.752

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2489433942ribose-assimilation
2489417814salicin-assimilation
2489417992sucrose-assimilation
2489417057cellobiose+assimilation
2489416899D-mannitol+assimilation
2489465327D-xylose+assimilation
2489428757fructose+assimilation
2489428260galactose+assimilation
2489417234glucose+assimilation
2489417268myo-inositol+assimilation
2489430849L-arabinose+assimilation
2489462345L-rhamnose+assimilation
2489417632nitrate+reduction
2489416634raffinose+assimilation

enzymes

@refvalueactivityec
24894acid phosphatase+3.1.3.2
24894alkaline phosphatase+3.1.3.1
24894alpha-chymotrypsin+3.4.21.1
24894alpha-galactosidase-3.2.1.22
24894alpha-glucosidase+3.2.1.20
24894alpha-mannosidase+3.2.1.24
24894beta-galactosidase+3.2.1.23
24894beta-glucosidase+3.2.1.21
24894beta-glucuronidase-3.2.1.31
24894cystine arylamidase+3.4.11.3
24894esterase (C 4)+
24894esterase lipase (C 8)+
24894leucine arylamidase+3.4.11.1
24894lipase (C 14)-
24894N-acetyl-beta-glucosaminidase+3.2.1.52
24894naphthol-AS-BI-phosphohydrolase+
24894trypsin+3.4.21.4
24894valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
24894stem of Phyllanthus amarusbotanical garden of the Faculty of Pharmaceutical Sciences,Chulalongkorn University,BangkokThailandTHAAsia
67770Stem of Phyllanthus amarusThailandTHAAsiaPhyllanthus amarus
67771From stem of plant (Phyllanthus amarus, Euphobiaceae)BangkokThailandTHAAsia
125195stem of Phyllanthus amarusChulalongkorn UniversityThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces phyllanthi strain TISTR 23461803180.3wgspatric1803180
67770Streptomyces phyllanthi TISTR 2346GCA_009377205contigncbi1803180

GC content

  • @ref: 24894
  • GC-content: 71
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes85.312no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.065no
125438spore-formingspore-formingAbility to form endo- or exosporesyes93.752yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.333yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.4yes
125438motile2+flagellatedAbility to perform flagellated movementno87no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes88
125439BacteriaNetmotilityAbility to perform movementno91.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.1

External links

@ref: 24894

culture collection no.: JCM 30865, KCTC 39785, TISTR 2346, DSM 117319

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27393329Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus.Klykleung N, Phongsopitanun W, Pittayakhajonwut P, Ohkuma M, Kudo T, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0012892016Bacterial 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/chemistryTranscriptome
Phylogeny32139879Streptomyces acidicola sp. nov., isolated from a peat swamp forest in Thailand.Lipun K, Chantavorakit T, Mingma R, Duangmal KJ Antibiot (Tokyo)10.1038/s41429-020-0294-52020Amino 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, WetlandsEnzymology
Phylogeny34775568Streptomyces blattellae, a novel actinomycete isolated from the in vivo of a Blattella germanica.Liu GM, Yuan LL, Zhang LL, Zeng HAntonie Van Leeuwenhoek10.1007/s10482-021-01681-w2021*Actinobacteria/genetics, DNA, Bacterial/genetics, Humans, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/geneticsPathogenicity

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24894N. P. Klykleung, Wongsakorn,Pittayakhajonwut, Pattama,Ohkuma, Moriya,Kudo, Takuji,Tanasupawat, SomboonStreptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus10.1099/ijsem.0.001289IJSEM 66: 3923-3928 201627393329
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
125195Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-117319Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 117319)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG