Strain identifier

BacDive ID: 140490

Type strain: Yes

Species: Actinomadura montaniterrae

Strain Designation: CYP1-1B

Strain history: <- Somboon Tanasupawat

NCBI tax ID(s): 1803903 (species)

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General

@ref: 43102

BacDive-ID: 140490

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

description: Actinomadura montaniterrae CYP1-1B is an aerobe, spore-forming, Gram-positive bacterium that builds a substrate mycelium and was isolated from mountain soil sample.

NCBI tax id

  • NCBI tax id: 1803903
  • Matching level: species

strain history

@refhistory
67770S. Tanasupawat; Chulalongkorn Univ., Thailand; CYP1-1B.
67771<- Somboon Tanasupawat

doi: 10.13145/bacdive140490.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura montaniterrae
  • full scientific name: Actinomadura montaniterrae Songsumanus et al. 2016

@ref: 43102

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Streptosporangiales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura montaniterrae

strain designation: CYP1-1B

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
43102positive
69480positive100

colony morphology

  • @ref: 43102
  • colony color: dark greyish yellow
  • medium used: ISP 2

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium namefurther description
43102yessubstrate myceliumdark greyish yellowISP2extensively branched non-fragmenting substrate mycelium
43102yesaerial myceliumpale greenISP2

Culture and growth conditions

culture medium

@refnamegrowth
43102ISP 7yes
43102nutritient agar (NA)yes
43102ISP 2yes

culture temp

@refgrowthtypetemperaturerange
43102positivegrowth20-45
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

  • @ref: 43102
  • ability: positive
  • type: growth
  • pH: 4.5-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43102aerobe
67771aerobe

spore formation

@refspore descriptionspore formationconfidence
43102oval to ellipsoid spores formed along the sporogenous hyphae and its branchesyes
69481yes100
69480yes100

halophily

  • @ref: 43102
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4310217634D-glucose+carbon source
4310216899D-mannitol+carbon source
4310262345L-rhamnose+carbon source
4310217716lactose+carbon source
4310230849L-arabinose+carbon source
4310215824D-fructose+carbon source
4310217057cellobiose+carbon source
4310217992sucrose+carbon source
4310265327D-xylose+carbon source
4310212936D-galactose-carbon source
4310217754glycerol-carbon source
4310228053melibiose-carbon source
4310216634raffinose-carbon source
4310216988D-ribose-carbon source
4310217814salicin-carbon source
4310228017starch+hydrolysis
431025291gelatin-hydrolysis
4310217632nitrate-reduction
43102milk-hydrolysis

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43102C14:04.6
    43102C16:031.2
    43102C17:00.5
    43102C18:03.3
    43102C16:1ω7c5.4
    43102C18:1ω9c17.1
    43102C16:0 10-methyl1.9
    43102C18:0 10-methyl19
    43102C16:0 2OH10.5
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP 2
  • agar/liquid: liquid
  • incubation temperature: 30
  • incubation time: 7
  • software version: Sherlock 6.0
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
43102mountain soil sampleChaiyaphum ProvinceThailandTHAAsiastarch casein nitrate agarsupplemented with nystatin (50 mg/l) and nalidixic acid (20 mg/l)21 days30
67770Mountain soilThailandTHAAsia
67771From Mountain soilThailandTHAAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_147423.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_1053;97_1231;98_1478;99_147423&stattab=map
  • Last taxonomy: Actinomadura
  • 16S sequence: LC126428
  • Sequence Identity:
  • Total samples: 93
  • soil counts: 69
  • aquatic counts: 10
  • animal counts: 7
  • plant counts: 7

Sequence information

16S sequences

  • @ref: 43102
  • description: Actinomadura sp. CYP1-1B gene for 16S ribosomal RNA, partial sequence
  • accession: LC126428
  • length: 1488
  • database: nuccore
  • NCBI tax ID: 1803903

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura montaniterrae CYP1-1BGCA_008923365scaffoldncbi1803903
66792Actinomadura montaniterrae CYP1-1B2898631135draftimg1803903

GC content

  • @ref: 43102
  • GC-content: 74.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.066no
flagellatedno98.318no
gram-positiveyes88.261no
anaerobicno98.692yes
aerobicyes89.553yes
halophileno93.076no
spore-formingyes92.772yes
thermophileno97.14yes
glucose-utilyes88.5yes
glucose-fermentno88.663no

External links

@ref: 43102

culture collection no.: JCM 16995, KCTC 39784, PCU 349, TISTR 2400

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27255441Actinomadura montaniterrae sp. nov., isolated from mountain soil.Songsumanus A, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0011962016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/chemistryTranscriptome
Phylogeny31900710Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr].Zhuang X, Peng C, Wang Z, Zhao J, Shen Y, Liu C, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-019-01380-72020*Actinomycetales/classification/genetics/isolation & purification, Bacterial Typing Techniques, Bryophyta/*microbiology, Carbohydrates/analysis, Cell Wall/chemistry, China, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genome, Bacterial, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny34870574Actinomadura violacea sp. nov., a madurastatin A1-producing strain isolated from lichen in Thailand.Kanchanasin P, Phongsopitanun W, Yuki M, Kudo T, Ohkuma M, Nakashima T, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0051262021Actinomadura/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lichens/microbiology, Nucleic Acid Hybridization, Oligopeptides/*biosynthesis, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43102Apakorn Songsumanus, Takuji Kudo, Moriya Ohkuma, Wongsakorn Phongsopitanun, Somboon TanasupawatActinomadura montaniterrae sp. nov., isolated from mountain soil10.1099/ijsem.0.001196IJSEM 66: 3310-3316 201627255441
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
69479João 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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1