Strain identifier

BacDive ID: 2937

Type strain: Yes

Species: Comamonas composti

Strain Designation: YY287

Strain history: <- LMG <- W.-M. Chen, Dep. of Seafood Science, Nat. Kaohsiung Marine University Taiwan

NCBI tax ID(s): 1121349 (strain), 408558 (species)

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General

@ref: 15895

BacDive-ID: 2937

DSM-Number: 21721

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

description: Comamonas composti YY287 is an aerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from food waste compost.

NCBI tax id

NCBI tax idMatching level
408558species
1121349strain

strain history

  • @ref: 15895
  • history: <- LMG <- W.-M. Chen, Dep. of Seafood Science, Nat. Kaohsiung Marine University Taiwan

doi: 10.13145/bacdive2937.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Comamonas
  • species: Comamonas composti
  • full scientific name: Comamonas composti Young et al. 2008

@ref: 15895

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Comamonas

species: Comamonas composti

full scientific name: Comamonas composti Young et al. 2008

strain designation: YY287

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23082negative1.0-2.0 µm0.5 µmrod-shapedyes
69480yes97.63
69480negative99.999

colony morphology

  • @ref: 23082
  • colony size: 3.0 mm
  • colony color: semi-transparent
  • colony shape: irregular
  • incubation period: 2 days
  • medium used: nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15895REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
23082Nutrient agar (NA)yes

culture temp

@refgrowthtypetemperaturerange
15895positivegrowth28mesophilic
23082positivegrowth15.0-35.0
23082positiveoptimum25.0-35.0mesophilic

culture pH

@refabilitytypepHPH range
23082positiveoptimum6.0-8.0
23082positivegrowth6.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 23082
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
23082no
69481no100
69480no99.982

halophily

@refsalttested relationconcentrationgrowth
23082NaCloptimum0.0-1.0 %
23082NaClgrowth0.0-3.0 %positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2308217234glucose-fermentation
2308222599arabinose-growth
2308227689decanoate-growth
2308216947citrate-growth
2308217234glucose-growth
2308217306maltose-growth
2308237684mannose-growth
23082506227N-acetylglucosamine-growth
2308218401phenylacetate-growth
230824853esculin-hydrolysis
230825291gelatin-hydrolysis
2308217521(-)-quinic acid-oxidation
23082620642,3-butanediol-oxidation
23082181014-hydroxyphenylacetic acid-oxidation
2308215963ribitol-oxidation
2308240585alpha-cyclodextrin-oxidation
2308217925alpha-D-glucose-oxidation
2308236219alpha-lactose-oxidation
2308215570D-alanine-oxidation
2308218333D-arabitol-oxidation
2308217057cellobiose-oxidation
2308215824D-fructose-oxidation
2308215895D-galactonic acid lactone-oxidation
2308212936D-galactose-oxidation
2308218024D-galacturonic acid-oxidation
2308230612D-glucarate-oxidation
230828391D-gluconate-oxidation
2308217784D-glucosaminic acid-oxidation
2308214314D-glucose 6-phosphate-oxidation
2308215748D-glucuronate-oxidation
2308216899D-mannitol-oxidation
2308216024D-mannose-oxidation
2308227605D-psicose-oxidation
2308216523D-serine-oxidation
2308217924D-sorbitol-oxidation
2308223652dextrin-oxidation
2308217126DL-carnitine-oxidation
2308216000ethanolamine-oxidation
2308216865gamma-aminobutyric acid-oxidation
2308228066gentiobiose-oxidation
2308229042glucose 1-phosphate-oxidation
2308232323glucuronamide-oxidation
2308217754glycerol-oxidation
2308214336glycerol 1-phosphate-oxidation
2308273804glycyl L-aspartic acid-oxidation
2308217596inosine-oxidation
2308221217L-alaninamide-oxidation
2308216977L-alanine-oxidation
2308273786L-alanylglycine-oxidation
2308230849L-arabinose-oxidation
2308218287L-fucose-oxidation
2308229985L-glutamate-oxidation
2308215971L-histidine-oxidation
2308215729L-ornithine-oxidation
2308217295L-phenylalanine-oxidation
2308217203L-proline-oxidation
2308262345L-rhamnose-oxidation
2308217115L-serine-oxidation
2308216857L-threonine-oxidation
230826359lactulose-oxidation
2308215792malonate-oxidation
2308217306maltose-oxidation
2308228053melibiose-oxidation
23082320055methyl beta-D-glucopyranoside-oxidation
2308217268myo-inositol-oxidation
2308228037N-acetylgalactosamine-oxidation
23082506227N-acetylglucosamine-oxidation
2308250048phenylethylamine-oxidation
2308217148putrescine-oxidation
2308216634raffinose-oxidation
2308217992sucrose-oxidation
2308217748thymidine-oxidation
2308227082trehalose-oxidation
2308232528turanose-oxidation
2308216704uridine-oxidation
2308217151xylitol-oxidation
2308217128adipate+growth
2308224265gluconate+growth
2308225115malate+growth
23082645522-hydroxybutyrate+oxidation
23082167632-oxobutanoate+oxidation
23082309162-oxoglutarate+oxidation
23082286442-oxopentanoate+oxidation
23082370543-hydroxybutyrate+oxidation
23082182404-hydroxy-L-proline+oxidation
23082167244-hydroxybutyrate+oxidation
2308230089acetate+oxidation
2308273706bromosuccinate+oxidation
2308216383cis-aconitate+oxidation
2308216947citrate+oxidation
2308224996lactate+oxidation
2308217113erythritol+oxidation
2308215740formate+oxidation
2308228087glycogen+oxidation
2308217240itaconate+oxidation
2308217196L-asparagine+oxidation
2308215603L-leucine+oxidation
2308218183L-pyroglutamic acid+oxidation
2308251850methyl pyruvate+oxidation
2308275146monomethyl succinate+oxidation
2308217272propionate+oxidation
23082576065-oxoproline+oxidation
2308241865sebacic acid+oxidation
23082143136succinamate+oxidation
2308230031succinate+oxidation
2308253423tween 40+oxidation
2308253426tween 80+oxidation
2308227248urocanic acid+oxidation
2308217632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2308217833gentamicinyesyes
2308217076streptomycinyesyes
2308228971ampicillinyesyes
2308217698chloramphenicolyesyes
230823770co-trimoxazoleyesyes
230826104kanamycinyesyes
23082100147nalidixic acidyesyes
2308228368novobiocinyesyes
2308218208penicillin gyesyes
2308228077rifampicinyesyes
2308227902tetracyclineyesyes

metabolite production

  • @ref: 23082
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
23082acid phosphatase+3.1.3.2
23082alkaline phosphatase+3.1.3.1
23082alpha-chymotrypsin-3.4.21.1
23082alpha-fucosidase-3.2.1.51
23082alpha-galactosidase-3.2.1.22
23082alpha-glucosidase-3.2.1.20
23082alpha-mannosidase-3.2.1.24
23082arginine dihydrolase-3.5.3.6
23082beta-galactosidase-3.2.1.23
23082beta-glucosidase-3.2.1.21
23082beta-glucuronidase-3.2.1.31
23082catalase+1.11.1.6
23082cystine arylamidase-3.4.11.3
23082cytochrome oxidase+1.9.3.1
23082esterase (C 4)+
23082esterase lipase (C 8)+
23082leucine arylamidase+3.4.11.1
23082lipase (C 14)+
23082N-acetyl-beta-glucosaminidase-3.2.1.52
23082naphthol-AS-BI-phosphohydrolase+
23082trypsin-3.4.21.4
23082urease-3.5.1.5
23082valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
15895food waste compostTaiwanChinaCHNAsia
23082Kinmen Countynutrient agar (BD Difco)3 days32.0

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Food production#Food
#Engineered#Waste#Domestic waste

Safety information

risk assessment

  • @ref: 15895
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15895
  • description: Comamonas composti strain YY287 16S ribosomal RNA gene, partial sequence
  • accession: EF015884
  • length: 1472
  • database: ena
  • NCBI tax ID: 408558

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Comamonas composti DSM 21721GCA_000429845scaffoldncbi1121349
66792Comamonas composti DSM 217211121349.4wgspatric1121349
66792Comamonas composti DSM 217212524614759draftimg1121349

GC content

  • @ref: 23082
  • GC-content: 62.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.371yes
flagellatedyes68.951no
gram-positiveno98.26yes
anaerobicno98.535yes
aerobicyes93.779yes
halophileno95.279no
spore-formingno95.285no
thermophileno96.82yes
glucose-utilno74.507yes
glucose-fermentno88.956no

External links

@ref: 15895

culture collection no.: DSM 21721, BCRC 17659, LMG 24008

straininfo link

  • @ref: 72459
  • straininfo: 294564

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175717Comamonas composti sp. nov., isolated from food waste compost.Young CC, Chou JH, Arun AB, Yen WS, Sheu SY, Shen FT, Lai WA, Rekha PD, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65277-02008Bacterial Typing Techniques, Comamonas/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, Fatty Acids/analysis, *Food Microbiology, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, Species Specificity, TaiwanGenetics
Phylogeny20148250Characterization of Comamonas thiooxidans sp. nov., and comparison of thiosulfate oxidation with Comamonas testosteroni and Comamonas composti.Narayan KD, Pandey SK, Das SKCurr Microbiol10.1007/s00284-010-9602-92010*Bacterial Typing Techniques, Base Composition, Comamonas/*classification/genetics/isolation & purification/*metabolism, Comamonas testosteroni/genetics/*metabolism, DNA Fingerprinting, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/genetics, Oxidation-Reduction, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil Microbiology, Sulfur/*metabolism, Thiosulfates/*metabolismMetabolism
Phylogeny24633862Comamonas faecalis sp. nov., isolated from domestic pig feces.Kim D, Lee SSCurr Microbiol10.1007/s00284-014-0561-42014Animals, Base Composition, Base Sequence, Comamonas/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/*analysis, Feces/microbiology, Gram-Negative Bacterial Infections/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA/veterinary, Sus scrofa, Swine, Swine Diseases/*microbiology, Ubiquinone/*analysisGenetics
Phylogeny25242539Description of Comamonas serinivorans sp. nov., isolated from wheat straw compost.Zhu D, Xie C, Huang Y, Sun J, Zhang WInt J Syst Evol Microbiol10.1099/ijs.0.066688-02014Bacterial Typing Techniques, Base Composition, China, Comamonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Triticum/*microbiology, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15895Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21721)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21721
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
23082Chiu-Chung Young,Jui-Hsing Chou,A. B. Arun,Wen-Shao Yen,Shih-Yi Sheu,Fo-Ting Shen,Wai-An Lai,P. D. Rekha,Wen-Ming Chen10.1099/ijs.0.65277-0Comamonas composti sp. nov., isolated from food waste compostIJSEM 58: 251-256 200818175717
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)
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
72459Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294564.1StrainInfo: A central database for resolving microbial strain identifiers