Strain identifier

BacDive ID: 159574

Type strain: Yes

Species: Actinomadura logoneensis

Strain Designation: NEAU-G17

Strain history: <- J. Zhao; Northeast Agricultural University, Harbin, P.R. CHINA; NEAU-G17<-J. Zhao; School of Life Science, Northeast Agricultural University

NCBI tax ID(s): 2293572 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 9.3 (current version)

General

@ref: 66400

BacDive-ID: 159574

DSM-Number: 105122

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

description: Actinomadura logoneensis NEAU-G17 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 2293572
  • Matching level: species

strain history

  • @ref: 66400
  • history: <- J. Zhao; Northeast Agricultural University, Harbin, P.R. CHINA; NEAU-G17<-J. Zhao; School of Life Science, Northeast Agricultural University

doi: 10.13145/bacdive159574.20250331.9.3

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 logoneensis
  • full scientific name: Actinomadura logoneensis Shi et al. 2019

@ref: 66400

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Streptosporangiales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura logoneensis

full scientific name: Actinomadura logoneensis Shi et al. 2019

strain designation: NEAU-G17

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: positive
  • confidence: 99.9

colony morphology

@refcolony colormedium used
69284Beige (1001), Light ivory (1015)ISP 2
69284Beige (1001), Light ivory (1015)suter with tyrosine
69284Beige (1001)ISP 7
68183yellow
69284Light ivory (1015)ISP 3
69284Light ivory (1015)suter without tyrosine
69284Ochre yellow (1024)ISP 6
69284Oyster white (1013)ISP 4
69284Oyster white (1013)ISP 5

multicellular morphology

@refforms multicellular complexcomplex colormedium namefurther descriptioncomplex name
68183yesdepending on medium aerial mycelium: greenish yellow (ISP1, ISP2, ISP7, Czapek's agar), yellow (ISP3, ISP4, ISP6, Bennett's agar) and orange yellow (ISP5)ISP1, ISP2, ISP3, ISP4, ISP5, ISP6, ISP7, Bennett's agar, Czapek's agarwell-developed, branched substrate hyphae and aerial mycelium that differentiates into flexuous spore chains consisted of cylindrical spores
69284noISP 2Aerial mycelium
69284noISP 3Aerial mycelium
69284noISP 4Aerial mycelium
69284noISP 5Aerial mycelium
69284noISP 6Aerial mycelium
69284noISP 7Aerial mycelium
69284nosuter with tyrosineAerial mycelium
69284nosuter without tyrosineAerial mycelium

pigmentation

@refproductionnamecolor
69284noMelanin
69284yessoluble pigmentSand yellow (1002), ivory (1014)

multimedia

  • @ref: 66400
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105122.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66400BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
66400GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
66400N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf

culture temp

@refgrowthtypetemperature
66400positivegrowth28
68183positivegrowth25-42
68183positiveoptimum37

culture pH

@refabilitytypepHPH range
68183positivegrowth5.0-10.0alkaliphile
68183positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
68183aerobe
125439obligate aerobe99.4

spore formation

@refspore descriptiontype of sporespore formationconfidence
68183flexuous spore chains consisted of cylindrical spores (0.5-0.7 µm x 0.8-1.0 µm)sporeyes
125439yes95.4

halophily

@refsaltgrowthtested relationconcentration
68183NaClpositivegrowth0-4.0 %(w/v)
69284NaClpositivegrowth0-5 %

observation

  • @ref: 68183
  • observation: forms well-developed, branched substrate hyphae and aerial mycelium that differentiates into flexuous spore chains consisted of cylindrical spores

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6928422599arabinose+growth
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
6837917632nitrate+reduction
6818328017starch-hydrolysis
6818353424tween 20-hydrolysis
6818353423tween 40-hydrolysis
6818353426tween 80-hydrolysis
681834853esculin-assimilation
6818362968cellulose-assimilation
681835291gelatin-hydrolysis
6818317632nitrate-reduction
68183milk-assimilation
6818330849L-arabinose+carbon source
6818315824D-fructose+carbon source
6818312936D-galactose+carbon source
6818317634D-glucose+carbon source
6818317268myo-inositol+carbon source
6818317716lactose+carbon source
6818317306maltose+carbon source
6818316024D-mannose+carbon source
6818316634raffinose+carbon source
6818362345L-rhamnose+carbon source
6818317992sucrose+carbon source
6818316813galactitol-carbon source
6818316899D-mannitol-carbon source
6818316988D-ribose-carbon source
6818317924D-sorbitol-carbon source
6818365327D-xylose-carbon source
6818316977L-alanine+nitrogen source
6818390350L-arginine-2-naphthylamide+nitrogen source
6818317196L-asparagine+nitrogen source
6818329991L-aspartate+nitrogen source
6818318050L-glutamine+nitrogen source
6818315428glycine+nitrogen source
6818317203L-proline+nitrogen source
6818317115L-serine+nitrogen source
6818316919creatine-nitrogen source
6818329985L-glutamate-nitrogen source
6818316857L-threonine-nitrogen source
6818317895L-tyrosine-nitrogen source
6928462968cellulose+growth
6928428757fructose+growth
6928417234glucose+growth
6928417268inositol+growth
6928437684mannose+growth
6928416634raffinose+growth
6928426546rhamnose+growth
6928417992sucrose+growth
6928418222xylose+growth
6837928087glycogen-fermentation
6837917306maltose-fermentation
683794853esculin-hydrolysis

metabolite production

  • @ref: 68183
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
68183catalase-1.11.1.6
68183urease-3.5.1.5
68379urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379gelatinase-
68379beta-glucosidase-3.2.1.21
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68183C16:033.2
    68183C18:1 w9c13.8
    68183C17:010.1
    68183C16:0 iso10.5
    68183C18:09.7
    68183C19:0 10-methly9.7
    68183C17:1 w7c5.5
    68183C18:0 10-methly3.3
    68183C15:0 iso2.8
    68183C16:1 w7c1.4
  • type of FA analysis: whole cell analysis
  • incubation medium: GY broth
  • incubation temperature: 28
  • incubation time: 6
  • system: MIS MIDI

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69284+------+-----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69284+/-+++/-+++/---++-+/--+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
66400soilLogone riverbank, N’Djamena (12° 06' N, 15° 03' E)ChadTCDAfrica12.115.05
68183muddy soil collected from Logone riverbankN'DjamenaChadTCDAfrica12.115.05sodium succinate-asparagine agar21 days28

isolation source categories

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

Sequence information

16S sequences

  • @ref: 66400
  • description: Actinomadura logoneensis strain NEAU-G17 16S ribosomal RNA gene, partial sequence
  • accession: MG189967
  • length: 1520
  • database: nuccore
  • NCBI tax ID: 1989

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura logoneensis NEAU-G172841009013draftimg2293572
68183Actinomadura logoneensis NEAU-G17GCA_003428695contigncbi2293572

GC content

@refGC-contentmethod
6640073.1sequence analysis
6818373.1genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes95.4
125439BacteriaNetmotilityAbility to perform movementno89.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.4

External links

@ref: 66400

culture collection no.: DSM 105122, CGMCC 4.7411

straininfo link

  • @ref: 112050
  • straininfo: 402472

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny31287395Actinomadura logoneensis sp. nov., a novel actinomycete isolated from the soil.Shi L, Han L, Guo X, Zhao J, Wang J, Wang H, Jiang S, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0035792019Actinobacteria/*classification, Bacterial Typing Techniques, Base Composition, Chad, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31671050Actinomadura harenae sp. nov., a novel actinomycete isolated from sea sand in Sanya.Hu J, Han C, Yu B, Zhao J, Guo X, Shen Y, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0038192020Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sand/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
66400Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105122Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105122)
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
68183Linlin Shi, Liyuan Han, Xiaowei Guo, Junwei Zhao, Jiabin Wang, Han Wang, Shanwen Jiang, Wensheng Xiang and Xiangjing WangActinomadura logoneensis sp. nov., a novel actinomycete isolated from the soil10.1099/ijsem.0.003579IJSEM 69: 2914-2920 2019
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69284Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%20105122.pdf
112050Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402472.1
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