Strain identifier

BacDive ID: 140838

Type strain: Yes

Species: Kordiimonas lipolytica

Strain Designation: M41

Strain history: Y. Wu; Second Inst. of Oceanogr., State Oceanic Admin., China; M41.

NCBI tax ID(s): 1662421 (species)

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General

@ref: 43641

BacDive-ID: 140838

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

description: Kordiimonas lipolytica M41 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface seawater sample collected from the western Pacific Ocean.

NCBI tax id

  • NCBI tax id: 1662421
  • Matching level: species

strain history

  • @ref: 67770
  • history: Y. Wu; Second Inst. of Oceanogr., State Oceanic Admin., China; M41.

doi: 10.13145/bacdive140838.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Kordiimonadales
  • family: Temperatibacteraceae
  • genus: Kordiimonas
  • species: Kordiimonas lipolytica
  • full scientific name: Kordiimonas lipolytica Wu et al. 2016

@ref: 43641

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Kordiimonadales

family: Kordiimonadaceae

genus: Kordiimonas

species: Kordiimonas lipolytica

strain designation: M41

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43641negative1.8-3 µm0.7-0.9 µmrod-shaped
69480yes95.207
69480negative99.904

colony morphology

  • @ref: 43641
  • colony size: 1-2 mm
  • colony color: Cream-white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA agar

Culture and growth conditions

culture medium

  • @ref: 43641
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43641positivegrowth15-45
43641positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43641positivegrowth5.5-9.5alkaliphile
43641positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43641
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
43641NaClpositivegrowth0.5-10 %(w/v)
43641NaClpositiveoptimum1-3 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4364116947citrate-assimilation
4364117268myo-inositol-builds acid from
4364127082trehalose-builds acid from
4364117128adipate-carbon source
4364127689decanoate-carbon source
4364112936D-galactose-carbon source
4364116899D-mannitol-carbon source
4364116024D-mannose-carbon source
4364125115malate-carbon source
4364130849L-arabinose-carbon source
43641506227N-acetylglucosamine-carbon source
4364118401phenylacetate-carbon source
4364132032potassium gluconate-carbon source
4364153258sodium citrate-carbon source
4364117128adipate-energy source
4364127689decanoate-energy source
4364112936D-galactose-energy source
4364116899D-mannitol-energy source
4364116024D-mannose-energy source
4364125115malate-energy source
4364130849L-arabinose-energy source
43641506227N-acetylglucosamine-energy source
4364118401phenylacetate-energy source
4364132032potassium gluconate-energy source
4364153258sodium citrate-energy source
4364117234glucose-fermentation
4364128017starch-hydrolysis
4364117057cellobiose+builds acid from
4364117234glucose+builds acid from
4364117306maltose+builds acid from
4364117634D-glucose+carbon source
4364117306maltose+carbon source
4364117634D-glucose+energy source
4364117306maltose+energy source
4364116991dna+hydrolysis
436414853esculin+hydrolysis
436415291gelatin+hydrolysis
4364153424tween 20+hydrolysis
4364153423tween 40+hydrolysis
4364153426tween 80+hydrolysis
4364117632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4364117698chloramphenicolyesyes30 µg (disc)
436416104kanamycinyesyes30 µg (disc)
436417507neomycinyesyes30 µg (disc)
4364171415nitrofurantoinyesyes300 µg (disc)
4364128368novobiocinyesyes30 µg (disc)
4364128077rifampicinyesyes5 µg (disc)
4364128864tobramycinyesyes10 µg (disc)
4364128971ampicillinyesyes10 µg (disc)
436412676amoxicillinyesyes20 µg (disc)
4364129007ceftriaxoneyesyes30 µg (disc)
436413745clindamycinyesyes2 µg (disc)
4364117833gentamicinyesyes10 µg (disc)
4364117076streptomycinyesyes10 µg (disc)
4364127902tetracyclineyesyes30 µg (disc)
4364128001vancomycinyesyes30 µg (disc)
4364118208penicillin gyesyes10 Unit (disc)
436418309polymyxin byesyes300 Unit (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4364116136hydrogen sulfideno
4364135581indoleno

enzymes

@refvalueactivityec
43641cytochrome oxidase+1.9.3.1
43641catalase+1.11.1.6
43641arginine dihydrolase-3.5.3.6
43641lysine decarboxylase-4.1.1.18
43641ornithine decarboxylase-4.1.1.17
43641urease-3.5.1.5
43641acid phosphatase+3.1.3.2
43641alkaline phosphatase+3.1.3.1
43641alpha-chymotrypsin+3.4.21.1
43641cystine arylamidase+3.4.11.3
43641esterase (C 4)+
43641esterase Lipase (C 8)+
43641naphthol-AS-BI-phosphohydrolase+
43641valine arylamidase+
43641trypsin+3.4.21.4
43641N-acetyl-beta-glucosaminidase-3.2.1.52
43641alpha-galactosidase-3.2.1.22
43641beta-galactosidase-3.2.1.23
43641alpha-glucosidase-3.2.1.20
43641beta-glucosidase-3.2.1.21
43641beta-glucuronidase-3.2.1.31
43641lipase (C 14)-
43641alpha-mannosidase-3.2.1.24
43641leucine arylamidase-3.4.11.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountrylongitude
43641surface seawater sample collected from the western Pacific OceanPacific OceanPacific Ocean160
67770Surface seawater sample collected from the western Pacific Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_1839.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16030;96_1039;97_1213;98_1454;99_1839&stattab=map
  • Last taxonomy: Kordiimonas lipolytica
  • 16S sequence: KR919608
  • Sequence Identity:
  • Total samples: 693
  • soil counts: 83
  • aquatic counts: 607
  • plant counts: 3

Sequence information

16S sequences

  • @ref: 43641
  • description: 16S rRNA gene sequence
  • accession: KR919608
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kordiimonas lipolytica M412791354939draftimg1662421
67770Kordiimonas lipolytica M41GCA_001550065scaffoldncbi1662421

GC content

@refGC-contentmethod
4364156.3genome sequence analysis
6777056.3

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 43641

culture collection no.: CGMCC 1.15304, JCM 30877

literature

  • topic: Phylogeny
  • Pubmed-ID: 26955805
  • title: Kordiimonas lipolytica sp. nov., isolated from seawater.
  • authors: Wu YH, Jian SL, Meng FX, Maripatay, Tohty D, Wang CS, Xu XW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001007
  • year: 2016
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43641Yue-Hong Wu, Shu-Ling Jian, Fan-Xu Meng, Maripatay, Dilbar Tohty, Chun-Sheng Wang, Xue-Wei XuKordiimonas lipolytica sp. nov., isolated from seawater10.1099/ijsem.0.001007IJSEM 66: 2198-2204 201626955805
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1