Strain identifier

BacDive ID: 6282

Type strain: Yes

Species: Oryzihumus leptocrescens

Strain Designation: KV-628

Strain history: S. ?mura KV-628.

NCBI tax ID(s): 297536 (species)

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General

@ref: 7383

BacDive-ID: 6282

DSM-Number: 18082

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Oryzihumus leptocrescens KV-628 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from paddy soil.

NCBI tax id

  • NCBI tax id: 297536
  • Matching level: species

strain history

@refhistory
7383<- JCM <- S. Omura; KV-628
67770S. ?mura KV-628.

doi: 10.13145/bacdive6282.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Oryzihumus
  • species: Oryzihumus leptocrescens
  • full scientific name: Oryzihumus leptocrescens Kageyama et al. 2005

@ref: 7383

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Oryzihumus

species: Oryzihumus leptocrescens

full scientific name: Oryzihumus leptocrescens Kageyama et al. 2005

strain designation: KV-628

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31553positive1.4 µm0.65 µmrod-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19759Cream (9001)10-14 daysISP 2
19759Light ivory (1015)10-14 daysISP 3
19759Cream (9001)10-14 daysISP 4

multicellular morphology

@refforms multicellular complexmedium name
19759noISP 2
19759noISP 3
19759noISP 4

pigmentation

  • @ref: 31553
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7383R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
19759ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19759ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19759ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml

culture temp

@refgrowthtypetemperaturerange
19759positiveoptimum28mesophilic
7383positivegrowth28mesophilic
31553positivegrowth15-37
31553positiveoptimum26mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31553positivegrowth04-09alkaliphile
31553positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31553
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.961

halophily

@refsaltgrowthtested relationconcentration
31553NaClpositivegrowth<5 %
31553NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3155328260galactose+carbon source
3155317234glucose+carbon source
3155317306maltose+carbon source
3155317992sucrose+carbon source
3155327082trehalose+carbon source

enzymes

@refvalueactivityec
31553acid phosphatase+3.1.3.2
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19759----+------++-+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7383paddy soilJapanJPNAsia
67770Soil from a paddy fieldJapanJPNAsiaSaitama Pref.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Anoxic (anaerobic)
#Condition#Humid

taxonmaps

  • @ref: 69479
  • File name: preview.99_39830.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_18649;97_23075;98_29106;99_39830&stattab=map
  • Last taxonomy: Oryzihumus leptocrescens subclade
  • 16S sequence: AB193172
  • Sequence Identity:
  • Total samples: 2143
  • soil counts: 1493
  • aquatic counts: 370
  • animal counts: 128
  • plant counts: 152

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73831Risk group (German classification)
197591Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Oryzihumus leptocrescens gene for 16S rRNA, partial sequence, strain: NBRC 100762AB5234131481ena297536
7383Oryzihumus leptocrescens gene for 16S rRNA, partial sequence, strain:KV-628AB1931721429ena297536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oryzihumus leptocrescens strain DSM 18082297536.3wgspatric297536
66792Oryzihumus leptocrescens DSM 180822814123533draftimg297536
67770Oryzihumus leptocrescens DSM 18082GCA_006716205contigncbi297536

GC content

@refGC-contentmethod
738372
3155372.5
6777072-73high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno65no
gram-positiveyes89.726yes
anaerobicno98.032no
halophileno96.086no
spore-formingno77.329no
glucose-utilyes88.144yes
motileno66.89yes
flagellatedno94.947yes
thermophileno96.82yes
aerobicyes90.818no
glucose-fermentno91.845no

External links

@ref: 7383

culture collection no.: DSM 18082, JCM 12835, NBRC 100762, NRRL B-24347

straininfo link

  • @ref: 75758
  • straininfo: 281458

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280526Oryzihumus leptocrescens gen. nov., sp. nov.Kageyama A, Takahashi Y, Seki T, Tomoda H, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.63799-02005Actinomycetales/classification/*isolation & purification/physiology/ultrastructure, Base Composition, DNA, Bacterial/analysis/chemistry/isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNAEnzymology
Phylogeny24760799Oryzihumus terrae sp. nov., isolated from soil and emended description of the genus Oryzihumus.Lim JM, Kim SJ, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.060897-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28884678Oryzihumus soli sp. nov., isolated from soil and emended description of the genus Oryzihumus.Kim DU, Kim SG, Lee H, Park AY, Ka JOInt J Syst Evol Microbiol10.1099/ijsem.0.0022312017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7383Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18082)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18082
19759Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18082.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31553Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127844
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
75758Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281458.1StrainInfo: A central database for resolving microbial strain identifiers