Strain identifier

BacDive ID: 1467

Type strain: Yes

Species: Gracilibacillus ureilyticus

Strain Designation: MF38

Strain history: X.-W. Xu MF38.

NCBI tax ID(s): 531814 (species)

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General

@ref: 17412

BacDive-ID: 1467

DSM-Number: 23863

keywords: genome sequence, 16S sequence, Bacteria, halotolerant, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, colony-forming

description: Gracilibacillus ureilyticus MF38 is a halotolerant, spore-forming, mesophilic bacterium that forms irregular colonies and was isolated from saline–alkaline soil.

NCBI tax id

  • NCBI tax id: 531814
  • Matching level: species

strain history

@refhistory
17412<- JCM <- X.-W. Xu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China
67770X.-W. Xu MF38.

doi: 10.13145/bacdive1467.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Gracilibacillus
  • species: Gracilibacillus ureilyticus
  • full scientific name: Gracilibacillus ureilyticus Huo et al. 2010

@ref: 17412

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Gracilibacillus

species: Gracilibacillus ureilyticus

full scientific name: Gracilibacillus ureilyticus Huo et al. 2010

strain designation: MF38

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23049positive1.5-4.5 µm0.7-1.0 µmrod-shapedyesperitrichous
69480yes99.187
69480positive100

colony morphology

  • @ref: 23049
  • colony size: 1.0-2.0 mm
  • colony color: cream
  • colony shape: irregular
  • incubation period: 2 days
  • medium used: MA medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17412BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
23049Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
17412positivegrowth28mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
23049positivegrowth6.5-8.5alkaliphile
23049positiveoptimum7.0

Physiology and metabolism

spore formation

@reftype of sporespore formationconfidence
23049sporeyes
69481yes100
69480yes100

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23049halotolerantNaClpositivegrowth0.0-15.0 %(w/v)
23049NaCloptimum3.0 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2304917924D-sorbitol-builds acid from
2304917266L-sorbose-builds acid from
2304917790methanol-builds acid from
2304915963ribitol-builds acid from
2304916947citrate-carbon source
2304927897tryptophan-energy source
2304927613amygdalin-fermentation
2304917634D-glucose-fermentation
2304916899D-mannitol-fermentation
2304917924D-sorbitol-fermentation
2304917268myo-inositol-fermentation
2304930849L-arabinose-fermentation
2304962345L-rhamnose-fermentation
2304928053melibiose-fermentation
2304917992sucrose-fermentation
23049casein-hydrolysis
2304916991dna-hydrolysis
23049O-nitrophenyl-beta-D-galactopyranosid-hydrolysis
2304953423tween 40-hydrolysis
2304953425tween 60-hydrolysis
2304953426tween 80-hydrolysis
2304918186tyrosine-hydrolysis
2304917057cellobiose+builds acid from
2304915824D-fructose+builds acid from
2304912936D-galactose+builds acid from
2304916899D-mannitol+builds acid from
2304965327D-xylose+builds acid from
2304917234glucose+builds acid from
2304930849L-arabinose+builds acid from
2304962345L-rhamnose+builds acid from
2304917716lactose+builds acid from
2304917306maltose+builds acid from
2304916634raffinose+builds acid from
2304917814salicin+builds acid from
2304928017starch+builds acid from
2304917992sucrose+builds acid from
2304927082trehalose+builds acid from
2304917057cellobiose+growth
2304912936D-galactose+growth
2304916899D-mannitol+growth
2304916024D-mannose+growth
2304965327D-xylose+growth
2304924265gluconate+growth
2304917234glucose+growth
2304930849L-arabinose+growth
2304962345L-rhamnose+growth
2304917716lactose+growth
2304917306maltose+growth
2304916634raffinose+growth
2304917814salicin+growth
2304928017starch+growth
2304917992sucrose+growth
2304927082trehalose+growth
230494853esculin+hydrolysis
230495291gelatin+hydrolysis
2304928017starch+hydrolysis
2304953424tween 20+hydrolysis
2304916199urea+hydrolysis
2304917632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistantresistance conc.sensitivity conc.
2304917076streptomycinyesnoyes10 µg
230497660nystatinyesnoyes100 µg
2304928669bacitracinyesyes0.04 Unit
2304918208penicillin gyesyes10 Unit
230492676amoxicillinyesyes10 µg
2304928971ampicillinyesyes10 µg
2304927902tetracyclineyesyes10 µg
2304928864tobramycinyesyes10 µg
230493393carbenicillinyesyes100 µg
2304948923erythromycinyesyes15 µg
23049209807cefoxitinyesyes30 µg
23049204928cefotaximeyesyes30 µg
2304917698chloramphenicolyesyes30 µg
230496104kanamycinyesyes30 µg
230497507neomycinyesyes30 µg
2304928368novobiocinyesyes30 µg
2304971415nitrofurantoinyesyes300 µg
2304928077rifampicinyesyes5 µg

metabolite production

@refChebi-IDmetaboliteproduction
2304935581indoleno
2304916136hydrogen sulfideno
2304915688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testcitrate test
2304915688acetoin+
2304935581indole-
2304916947citrate-

enzymes

@refvalueactivityec
23049acid phosphatase-3.1.3.2
23049alkaline phosphatase+3.1.3.1
23049alpha-chymotrypsin-3.4.21.1
23049alpha-galactosidase+3.2.1.22
23049alpha-glucosidase+3.2.1.20
23049alpha-mannosidase-3.2.1.24
23049arginine dihydrolase-3.5.3.6
23049beta-D-fucosidase-3.2.1.38
23049beta-galactosidase+3.2.1.23
23049beta-glucosidase+3.2.1.21
23049beta-glucuronidase-3.2.1.31
23049catalase+1.11.1.6
23049cystine arylamidase-3.4.11.3
23049cytochrome oxidase+1.9.3.1
23049esterase (C 4)+
23049esterase lipase (C 8)+
23049leucine arylamidase-3.4.11.1
23049lipase (C 14)-
23049lysine decarboxylase-4.1.1.18
23049N-acetyl-beta-glucosaminidase-3.2.1.52
23049naphthol-AS-BI-phosphohydrolase-
23049ornithine decarboxylase-4.1.1.17
23049trypsin-3.4.21.4
23049tryptophan deaminase-4.1.99.1
23049valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
17412saline–alkaline soilMinfeng county, XinjiangChinaCHNAsia
23049modified HM mediumcontaining per l distilled water: NaCl 10 % (w/v), 2.0 g KCl, 1.0 g MgSO4, 0.36 g CaCl2.2H2O, 0.23 g NaBr, 0.06 g NaHCO3, trace FeCl3, 1.0 g yeast extract (Difco), 0.5 g peptone (Difco) and 0.1 g glucose (pH 7.5)3 days25.0
67770Saline-alkaline soil in MinfengXinjiangChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_66320.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2444;97_7991;98_10968;99_66320&stattab=map
  • Last taxonomy: Gracilibacillus
  • 16S sequence: EU709020
  • Sequence Identity:
  • Total samples: 384
  • soil counts: 206
  • aquatic counts: 110
  • animal counts: 29
  • plant counts: 39

Safety information

risk assessment

  • @ref: 17412
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17412
  • description: Gracilibacillus ureilyticus strain MF38 16S ribosomal RNA gene, partial sequence
  • accession: EU709020
  • length: 1485
  • database: ena
  • NCBI tax ID: 531814

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gracilibacillus ureilyticus strain CGMCC 1.7727531814.3wgspatric531814
66792Gracilibacillus ureilyticus CGMCC 1.77272617270788draftimg531814
67770Gracilibacillus ureilyticus CGMCC 1.7727GCA_900111195scaffoldncbi531814

GC content

@refGC-contentmethod
2304935.3
6777035.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes87.786no
anaerobicno98.65no
halophileyes84.634no
spore-formingyes93.151yes
glucose-utilyes87.153no
thermophileno99.135yes
motileyes91.411yes
flagellatedyes90.019no
aerobicyes85.52no
glucose-fermentno85.577yes

External links

@ref: 17412

culture collection no.: DSM 23863, CGMCC 1.7727, JCM 15711

straininfo link

  • @ref: 71113
  • straininfo: 407113

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19671721Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline-alkaline soil.Huo YY, Xu XW, Cui HL, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.016808-02009Base Composition, DNA, Bacterial/genetics, Gram-Positive Endospore-Forming Bacteria/classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Spores, Bacterial/classification/geneticsGenetics
Phylogeny23942614Gracilibacillus marinus sp. nov., isolated from the northern South China Sea.Huang HQ, Wang Y, Yuan WD, Xiao C, Ye JJ, Liu M, Zhu J, Sun QG, Bao SXAntonie Van Leeuwenhoek10.1007/s10482-013-9977-22013Bacillaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolismGenetics
Phylogeny32894210Gracilibacillus oryzae sp. nov., isolated from rice seeds.He SW, Wang X, Guo HB, Han JG, Thin KK, Gao JS, Ma LA, Zhang XXInt J Syst Evol Microbiol10.1099/ijsem.0.0044272020Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17412Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23863)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23863
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
23049Ying-Yi Huo,Xue-Wei Xu,Heng-Lin Cui,Min Wu10.1099/ijs.0.016808-0Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline-alkaline soilIJSEM 60: 1383-1386 201019671721
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/
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)
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
71113Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407113.1StrainInfo: A central database for resolving microbial strain identifiers