Strain identifier

BacDive ID: 8018

Type strain: Yes

Species: Micromonospora humi

Strain Designation: P0402

Strain history: S. Tanasupawat; Chulalongkorn Univ., Thailand; P0402.

NCBI tax ID(s): 745366 (species)

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General

@ref: 17970

BacDive-ID: 8018

DSM-Number: 45647

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

description: Micromonospora humi P0402 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from peat swamp forest soil.

NCBI tax id

  • NCBI tax id: 745366
  • Matching level: species

strain history

@refhistory
17970<- JCM; JCM 15292 <- S. Tanasupawat; P0402
67770S. Tanasupawat; Chulalongkorn Univ., Thailand; P0402.

doi: 10.13145/bacdive8018.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora humi
  • full scientific name: Micromonospora humi Songsumanus et al. 2011

@ref: 17970

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora humi

full scientific name: Micromonospora humi Songsumanus et al. 2011

strain designation: P0402

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colormedium used
69415Dahlia yellow (1033)ISP 3
69415Light ivory (1015), yellow orange (2000)ISP 7
69415Nut brown (8011), olive brown (8008)ISP 2
69415Ochre brown (8001), daffodil yellow (1007)ISP 6
69415Ochre brown (8001), fawn brown (8007)suter with tyrosine
69415Ochre brown (8001), fawn brown (8007)suter without tyrosine
69415Oyster white (1013), yellow orange (2000)ISP 4
69415Oyster white (1013), yellow orange (2000)ISP 5

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69415noAerial myceliumISP 2
69415noAerial myceliumISP 3
69415noAerial myceliumISP 4
69415noAerial myceliumISP 5
69415noAerial myceliumISP 6
69415noAerial myceliumISP 7
69415noAerial myceliumsuter with tyrosine
69415noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69415noMelanin
69415nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69415DSM_45647_image3.jpegPlates (554, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69415DSM_45647_image4.jpegPlates (554, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17970N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: 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
17970GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
17970GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf

culture temp

@refgrowthtypetemperaturerange
17970positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes99.72

halophily

  • @ref: 69415
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6941522599arabinose+growth
6941562968cellulose+/-growth
6941528757fructose+growth
6941517234glucose+growth
6941517268inositol+/-growth
6941537684mannose+growth
6941516634raffinose+/-growth
6941526546rhamnose+/-growth
6941517992sucrose+growth
6941518222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
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
68382leucine arylamidase+3.4.11.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69415------+---+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69415+/-+/-+/-+/-++/-+/-+++-++/--+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17970peat swamp forest soilPhayao Province, Phu Sang National ParkThailandTHAAsia
67770Peat swamp forest soil at Phu Sang National ParkPhayao ProvinceThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)
#Condition#Acidic

Safety information

risk assessment

  • @ref: 17970
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17970
  • description: Micromonospora humi strain P0402 16S ribosomal RNA gene, partial sequence
  • accession: GU459068
  • length: 1478
  • database: ena
  • NCBI tax ID: 745366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora humi strain DSM 45647745366.4wgspatric745366
66792Micromonospora humi DSM 456472622736513draftimg745366
67770Micromonospora humi DSM 45647GCA_900090105scaffoldncbi745366

GC content

@refGC-contentmethod
1797073high performance liquid chromatography (HPLC)
6777073.56genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.367no
flagellatedno97.508no
gram-positiveyes92.546no
anaerobicno99.143no
aerobicyes94.375no
halophileno94.615no
spore-formingyes94.17no
glucose-utilyes89.094no
thermophileno98.912yes
glucose-fermentno91.887yes

External links

@ref: 17970

culture collection no.: DSM 45647, JCM 15292, PCU 315, TISTR 1883

straininfo link

  • @ref: 77448
  • straininfo: 404173

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20562246Micromonospora humi sp. nov., isolated from peat swamp forest soil.Songsumanus A, Tanasupawat S, Thawai C, Suwanborirux K, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.024281-02010DNA, Bacterial/genetics, Micromonospora/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Thailand, Trees/microbiologyGenetics
Phylogeny22523171Micromonospora maritima sp. nov., isolated from mangrove soil.Songsumanus A, Tanasupawat S, Igarashi Y, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.039180-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/metabolism, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analysisGenetics
Phylogeny26395026Micromonospora nickelidurans sp. nov., isolated from soil from a nickel-mining site.Lin YB, Fan MC, Guo YQ, Di XH, Dong DH, Zhang X, Wei GHInt J Syst Evol Microbiol10.1099/ijsem.0.0006232015Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, *Mining, Molecular Sequence Data, *Nickel, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
17970Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45647)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45647
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69415Wink, J.https://cdn.dsmz.de/wink/DSM%2045647.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77448Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404173.1StrainInfo: A central database for resolving microbial strain identifiers