Strain identifier

BacDive ID: 130318

Type strain: Yes

Species: Kosakonia sacchari

Strain Designation: SP1

Strain history: CIP <- 2014, LMG <- 2011, Q. An, Zhejiang Univ., Hangzhou, China: strain SP1 <- 1994, 2007, J. Li

NCBI tax ID(s): 1158459 (species)

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General

@ref: 21585

BacDive-ID: 130318

DSM-Number: 100203

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

description: Kosakonia sacchari SP1 is a mesophilic, Gram-negative, motile bacterium that was isolated from stem of sugar cane plant, cultivar GT11.

NCBI tax id

  • NCBI tax id: 1158459
  • Matching level: species

strain history

@refhistory
21585<- LMG <- Q. An, State Key Laboratory of Rice Biology, Zhejiang University; SP1
122331CIP <- 2014, LMG <- 2011, Q. An, Zhejiang Univ., Hangzhou, China: strain SP1 <- 1994, 2007, J. Li

doi: 10.13145/bacdive130318.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Kosakonia
  • species: Kosakonia sacchari
  • full scientific name: Kosakonia sacchari (Zhu et al. 2013) Gu et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Enterobacter sacchari

@ref: 21585

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Kosakonia

species: Kosakonia sacchari

full scientific name: Kosakonia sacchari (Zhu et al. 2013) Gu et al. 2014

strain designation: SP1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30832negative1.35 µm0.6 µmrod-shapedyes
122331positiverod-shapedyes

pigmentation

  • @ref: 30832
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36199MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
21585NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
122331CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
21585positivegrowth28mesophilic
30832positiveoptimum30mesophilic
36199positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30832positivegrowth04-10alkaliphile
30832positiveoptimum7

Physiology and metabolism

halophily

  • @ref: 30832
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3083230089acetate+carbon source
3083216449alanine+carbon source
3083218403L-arabitol+carbon source
3083235391aspartate+carbon source
3083217057cellobiose+carbon source
3083216947citrate+carbon source
3083223652dextrin+carbon source
3083228757fructose+carbon source
3083233984fucose+carbon source
3083224148galactonate+carbon source
3083228260galactose+carbon source
3083224175galacturonate+carbon source
308325291gelatin+carbon source
3083224265gluconate+carbon source
3083217234glucose+carbon source
3083232323glucuronamide+carbon source
3083229987glutamate+carbon source
3083217754glycerol+carbon source
3083217596inosine+carbon source
3083224996lactate+carbon source
3083217716lactose+carbon source
3083225115malate+carbon source
3083217306maltose+carbon source
3083229864mannitol+carbon source
3083237684mannose+carbon source
3083228053melibiose+carbon source
3083237657methyl D-glucoside+carbon source
3083251850methyl pyruvate+carbon source
3083217268myo-inositol+carbon source
30832506227N-acetylglucosamine+carbon source
3083226271proline+carbon source
3083217148putrescine+carbon source
3083216634raffinose+carbon source
3083226546rhamnose+carbon source
3083217814salicin+carbon source
3083217822serine+carbon source
3083230911sorbitol+carbon source
3083230031succinate+carbon source
3083217992sucrose+carbon source
308324853esculin+hydrolysis
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21585++--+----+-+++++++++-
21585++--+----+-+++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
21585stem of sugar cane plant, cultivar GT11Nanning, GuangxiChinaCHNAsia
122331Sugar cane, stemNanning, Guangxi, ChinaChinaCHNAsia1994-01-03

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
215851Risk group (German classification)
1223311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21585
  • description: Enterobacter sacchari strain SP1 16S ribosomal RNA gene, partial sequence
  • accession: JQ001784
  • length: 1500
  • database: ena
  • NCBI tax ID: 1158459

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kosakonia sacchari SP1GCA_000300455completencbi1235834
66792Kosakonia sacchari CGMCC 1.12102GCA_900100995scaffoldncbi1158459
66792Kosakonia sacchari SP11235834.6completepatric1235834
66792Kosakonia sacchari strain CGMCC 1.121021158459.6wgspatric1158459
66792Kosakonia sacchari CGMCC 1.121022596583580draftimg1158459
66792Kosakonia sacchari SP12547132181draftimg1235834

GC content

  • @ref: 30832
  • GC-content: 55

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.002no
motileyes90.002no
motileyes90.002no
flagellatedno60.171no
flagellatedno60.171no
flagellatedno60.171no
gram-positiveno98.445no
gram-positiveno98.445no
gram-positiveno98.445no
anaerobicno94.086no
anaerobicno94.086no
anaerobicno94.086no
aerobicno58.845no
aerobicno58.845no
aerobicno58.845no
halophileno93.135no
halophileno93.135no
halophileno93.135no
spore-formingno92.979no
spore-formingno92.979no
spore-formingno92.979no
glucose-utilyes95.528yes
glucose-utilyes95.528yes
glucose-utilyes95.528yes
thermophileno99.658no
thermophileno99.658no
glucose-fermentyes92.635yes
glucose-fermentyes92.635yes
glucose-fermentyes92.635yes
thermophileno99.658no

External links

@ref: 21585

culture collection no.: DSM 100203, CGMCC 1.12102, LMG 26783, CIP 110705

straininfo link

  • @ref: 88851
  • straininfo: 379007

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23291881Enterobacter sacchari sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.).Zhu B, Zhou Q, Lin L, Hu C, Shen P, Yang L, An Q, Xie G, Li YInt J Syst Evol Microbiol10.1099/ijs.0.045500-02013Bacterial Proteins/analysis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterobacter/*classification/genetics/isolation & purification, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/microbiology, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Rhizosphere, Saccharum/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny24824638Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov.Gu CT, Li CY, Yang LJ, Huo GCInt J Syst Evol Microbiol10.1099/ijs.0.064709-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterobacter/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Genetics25197499Complete genome sequence of Kosakonia sacchari type strain SP1(T.).Chen M, Zhu B, Lin L, Yang L, Li Y, An QStand Genomic Sci10.4056/sigs.57799772014
Phylogeny26597455Kosakonia pseudosacchari sp. nov., an endophyte of Zea mays.Kampfer P, McInroy JA, Doijad S, Chakraborty T, Glaeser SPSyst Appl Microbiol10.1016/j.syapm.2015.09.0042015Alabama, Base Sequence, DNA Gyrase/genetics, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Endophytes, Enterobacteriaceae/*classification/genetics/*isolation & purification, Multilocus Sequence Typing, Phylogeny, Plant Roots/*microbiology, Prokaryotic Initiation Factor-2/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Transcription Factors/genetics, Zea mays/*microbiologyTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21585Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100203Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100203)
30832Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172716228776041
36199Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30512
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
68368Automatically annotated from API 20E
88851Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID379007.1
122331Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110705Collection of Institut Pasteur (CIP 110705)