Strain identifier

BacDive ID: 17483

Type strain: Yes

Species: Lysobacter concretionis

Strain Designation: Ko07

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1122185 (strain), 262325 (species)

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General

@ref: 6263

BacDive-ID: 17483

DSM-Number: 16239

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Lysobacter concretionis Ko07 is an aerobe, Gram-negative, motile bacterium that was isolated from granular sludge of an upflow anaerobic slugde blanket reactor.

NCBI tax id

NCBI tax idMatching level
1122185strain
262325species

strain history

@refhistory
6263<- S.-T. Lee; Ko07
67771<- ST Lee, KAIST

doi: 10.13145/bacdive17483.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter concretionis
  • full scientific name: Lysobacter concretionis Bae et al. 2005

@ref: 6263

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter concretionis

full scientific name: Lysobacter concretionis Bae et al. 2005

strain designation: Ko07

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31360negative7.25 µm0.85 µmrod-shapedyes
67771negative
69480negative98.25

pigmentation

  • @ref: 31360
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6263
  • name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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

culture temp

@refgrowthtypetemperature
6263positivegrowth30
31360positivegrowth25-30
31360positiveoptimum27.5
60656positivegrowth30
67771positivegrowth30

culture pH

@refabilitytypepH
31360positivegrowth6.8-7.5
31360positiveoptimum7.15

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31360aerobe
60656aerobe
67771aerobe

spore formation

@refspore formationconfidence
69480no90.026
69481no100

observation

@refobservation
31360aggregates in clumps
67771quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31360370543-hydroxybutyrate+carbon source
3136030089acetate+carbon source
3136028087glycogen+carbon source
3136026271proline+carbon source
3136031011valerate+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
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-galactosidase-3.2.1.23
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
60656-++--+---+++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6263------+-------------+
60656+-----+-------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6263granular sludge of an upflow anaerobic slugde blanket reactorKongjuRepublic of KoreaKORAsia
60656Granular sludge,brewery,UASB reactorKongjuRepublic of KoreaKORAsia
67771From granule sludgeRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Activated sludge
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7663.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_2460;97_3003;98_5233;99_7663&stattab=map
  • Last taxonomy: Lysobacter concretionis subclade
  • 16S sequence: AB161359
  • Sequence Identity:
  • Total samples: 181
  • soil counts: 104
  • aquatic counts: 37
  • animal counts: 35
  • plant counts: 5

Safety information

risk assessment

  • @ref: 6263
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lysobacter concretionis gene for 16S rRNA, partial sequence, strain: NBRC 102010AB6816601470nuccore262325
6263Lysobacter concretionis gene for 16S rRNA, partial sequence, strain: Ko07AB1613591481nuccore262325

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysobacter concretionis Ko07 = DSM 16239GCA_000768345contigncbi1122185
66792Lysobacter concretionis Ko07 = DSM 162391122185.3wgspatric1122185
66792Lysobacter concretionis Ko072574179754draftimg1122185
66792Lysobacter concretionis Ko072645727875draftimg1122185

GC content

  • @ref: 31360
  • GC-content: 63.8

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98.25yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.211no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.026no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.24yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.457no
69480flagellatedmotile2+Ability to perform flagellated movementno55.27no

External links

@ref: 6263

culture collection no.: DSM 16239, KCTC 12205, CCUG 55589, LMG 23352, NBRC 102010

straininfo link

  • @ref: 86480
  • straininfo: 128581

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879248Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor.Bae HS, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63399-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Water Microbiology, Xanthomonadaceae/*classification/cytology/*isolation & purification/physiologyEnzymology
Phylogeny16403891Lysobacter koreensis sp. nov., isolated from a ginseng field.Lee JW, Im WT, Kim MK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.63955-02006Benzoquinones, Fatty Acids, Korea, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, Xanthomonadaceae/chemistry/*classification/isolation & purification/physiologyGenetics
Phylogeny18218933Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge.Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.65391-02008Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny36260505Lysobacter selenitireducens sp. nov., isolated from river sediment.Mao S, Li S, Guo B, Mu W, Hou X, Liu H, Wei S, Liu A, Kong L, Chen ZInt J Syst Evol Microbiol10.1099/ijsem.0.0055502022*Lysobacter/genetics, RNA, Ribosomal, 16S/genetics, Ubiquinone/chemistry, Phylogeny, Phosphatidylethanolamines/metabolism, Base Composition, Rivers, Sodium Chloride, Cardiolipins, Soil Microbiology, *DNA, Bacterial/genetics, Fatty Acids/chemistry, Bacterial Typing Techniques, Sequence Analysis, DNA, Phospholipids/chemistry, Glycolipids/analysis, Amino Acids/metabolism, NucleotidesMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6263Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16239)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16239
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
31360Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127673
60656Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55589)https://www.ccug.se/strain?id=55589
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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)
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
86480Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128581.1StrainInfo: A central database for resolving microbial strain identifiers