Strain identifier

BacDive ID: 133287

Type strain: Yes

Species: Chromobacterium alkanivorans

Strain Designation: IITR-71

Strain history: S. Mayilraj IITR-71.

NCBI tax ID(s): 1071719 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 9.3 (current version)

General

@ref: 25102

BacDive-ID: 133287

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

description: Chromobacterium alkanivorans IITR-71 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from collected from an industrial site.

NCBI tax id

  • NCBI tax id: 1071719
  • Matching level: species

strain history

  • @ref: 67770
  • history: S. Mayilraj IITR-71.

doi: 10.13145/bacdive133287.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Chromobacterium
  • species: Chromobacterium alkanivorans
  • full scientific name: Chromobacterium alkanivorans Bajaj et al. 2016

@ref: 25102

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Chromobacterium

species: Chromobacterium alkanivorans

strain designation: IITR-71

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25102negative0.8-2.4 µm0.3-0.6 µmrod-shapedyes
125438negative98.994
125439negative99.2

colony morphology

  • @ref: 25102
  • colony color: creamish-yellow
  • colony shape: circular

Culture and growth conditions

culture temp

@refgrowthtypetemperature
25102positivegrowth12.0-37.0
25102positiveoptimum30
25102nogrowth12
25102nogrowth42
67770positivegrowth30

culture pH

@refabilitytypepHPH range
25102positivegrowth5.0-10.0alkaliphile
25102positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 25102
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99

halophily

  • @ref: 25102
  • salt: NaCl
  • tested relation: maximum
  • concentration: 2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2510217521(-)-quinic acid-carbon source
25102645522-hydroxybutyrate-carbon source
25102167632-oxobutanoate-carbon source
25102286442-oxopentanoate-carbon source
25102620642,3-butanediol-carbon source
25102167244-hydroxybutyrate-carbon source
25102181014-hydroxyphenylacetic acid-carbon source
2510215963ribitol-builds acid from
2510215963ribitol-carbon source
2510240585alpha-cyclodextrin-carbon source
2510236219alpha-lactose-carbon source
2510222599arabinose-builds acid from
2510217126carnitine-carbon source
2510217057cellobiose-builds acid from
2510216383cis-aconitate-carbon source
2510216947citrate-carbon source
2510217057cellobiose-carbon source
2510215895D-galactonic acid lactone-carbon source
2510212936D-galactose-carbon source
2510218024D-galacturonic acid-carbon source
2510230612D-glucarate-carbon source
2510217784D-glucosaminic acid-carbon source
2510215748D-glucuronate-carbon source
2510216899D-mannitol-carbon source
2510216024D-mannose-carbon source
2510228053melibiose-carbon source
2510227605D-psicose-carbon source
2510216634raffinose-carbon source
2510217113erythritol-carbon source
2510216000ethanolamine-carbon source
2510215740formate-carbon source
2510216813galactitol-builds acid from
2510228260galactose-builds acid from
2510228066gentiobiose-carbon source
2510217234glucose-fermentation
2510229042glucose 1-phosphate-carbon source
2510232323glucuronamide-carbon source
2510217754glycerol-carbon source
2510214336glycerol 1-phosphate-carbon source
2510273804glycyl L-aspartic acid-carbon source
2510217596inosine-carbon source
2510215443inulin-builds acid from
2510217240itaconate-carbon source
2510273786L-alanylglycine-carbon source
2510230849L-arabinose-carbon source
2510218287L-fucose-carbon source
2510215971L-histidine-assimilation
2510215589L-malate-assimilation
2510215729L-ornithine-carbon source
2510217295L-phenylalanine-carbon source
2510218183L-pyroglutamic acid-carbon source
2510262345L-rhamnose-carbon source
2510216857L-threonine-carbon source
2510224996lactate-assimilation
2510217716lactose-builds acid from
251026359lactulose-carbon source
2510215792malonate-carbon source
2510217306maltose-builds acid from
2510217306maltose-carbon source
2510229864mannitol-builds acid from
2510228053melibiose-builds acid from
2510237657methyl D-glucoside-carbon source
2510251850methyl pyruvate-carbon source
2510228037N-acetylgalactosamine-carbon source
2510273784glycyl-l-glutamate-carbon source
2510217632nitrate-reduction
2510250048phenylethylamine-carbon source
2510216634raffinose-builds acid from
2510226546rhamnose-builds acid from
2510217814salicin-builds acid from
2510241865sebacic acid-carbon source
2510228017starch-hydrolysis
25102143136succinamate-carbon source
2510217992sucrose-builds acid from
2510217992sucrose-carbon source
2510217748thymidine-carbon source
2510227897tryptophan-energy source
2510232528turanose-carbon source
2510227248urocanic acid-carbon source
2510217151xylitol-carbon source
2510218222xylose-builds acid from
251021-chlorobutane+degradation
251021-chloropropane+degradation
25102277891,2-dichloroethane+degradation
25102309162-oxoglutarate+carbon source
25102370543-hydroxybutyrate+carbon source
25102182404-hydroxy-L-proline+carbon source
2510230089acetate+carbon source
2510217925alpha-D-glucose+carbon source
2510228938ammonium+nitrogen source
2510273706bromosuccinate+carbon source
25102casein+hydrolysis
2510216947citrate+carbon source
2510215570D-alanine+carbon source
2510218333D-arabitol+carbon source
2510215824D-fructose+carbon source
251028391D-gluconate+carbon source
2510214314D-glucose 6-phosphate+carbon source
2510216523D-serine+carbon source
2510216551D-trehalose+carbon source
2510223652dextrin+carbon source
2510228757fructose+builds acid from
2510216865gamma-aminobutyric acid+carbon source
251025291gelatin+hydrolysis
2510217234glucose+builds acid from
2510217234glucose+fermentation
2510228087glycogen+carbon source
2510217268myo-inositol+builds acid from
2510217268myo-inositol+carbon source
2510221217L-alaninamide+carbon source
2510216977L-alanine+carbon source
2510217196L-asparagine+carbon source
2510229991L-aspartate+carbon source
2510215971L-histidine+carbon source
2510215603L-leucine+carbon source
25102L-proline-4-nitroanilide+carbon source
2510217115L-serine+carbon source
2510224996lactate+carbon source
2510237684mannose+builds acid from
2510275146monomethyl succinate+carbon source
25102506227N-acetylglucosamine+carbon source
2510273784glycyl-l-glutamate+carbon source
2510217272propionate+carbon source
2510217148putrescine+carbon source
2510230911sorbitol+builds acid from
2510230031succinate+carbon source
2510227082trehalose+builds acid from
2510253423tween 40+carbon source
2510253426tween 80+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
2510215688acetoinno
2510216136hydrogen sulfideno
2510235581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole testcitrate test
2510217234glucose-
2510215688acetoin-
2510235581indole-
2510216947citrate+

enzymes

@refvalueactivityec
25102alanine arylamidase-3.4.11.2
25102alpha-galactosidase-3.2.1.22
25102alpha-glucosidase-3.2.1.20
25102beta-galactosidase-3.2.1.23
25102beta-glucosidase-3.2.1.21
25102beta-glucuronidase-3.2.1.31
25102beta-N-acetylgalactosaminidase-
25102catalase+1.11.1.6
25102cytochrome oxidase-1.9.3.1
25102gamma-glutamyltransferase+2.3.2.2
25102glu-gly-arg-arylamidase-
25102glutamyl arylamidase pNA+
25102glycin arylamidase-
25102lipase-
25102lysine decarboxylase-4.1.1.18
25102N-acetyl-beta-glucosaminidase+3.2.1.52
25102ornithine decarboxylase-4.1.1.17
25102phosphatase+
25102proline-arylamidase-3.4.11.5
25102pyrrolidonyl arylamidase+3.4.19.3
25102tripeptide aminopeptidase-3.4.11.4
25102tryptophan deaminase-4.1.99.1
25102tyrosine arylamidase+
25102urease+3.5.1.5
25102xylan 1,4-beta-xylosidase-3.2.1.37

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
25102collected from an industrial siteEloor in the Cochin region ( Hindustan Insecticides Limited (HIL))IndiaINDAsiaLB-agar mediumpeptone 10 g; yeast extract 5.0 g; NaCl 5.0 g; and agar 15.00 g in 1000 ml distilled water, pH 7.52 days30
67770Insecticide-contaminated site

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial

taxonmaps

  • @ref: 69479
  • File name: preview.99_1476.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_48;97_931;98_1091;99_1476&stattab=map
  • Last taxonomy: Chromobacterium
  • 16S sequence: JN210566
  • Sequence Identity:
  • Total samples: 235
  • soil counts: 15
  • aquatic counts: 118
  • animal counts: 41
  • plant counts: 61

Sequence information

16S sequences

  • @ref: 25102
  • description: Chromobacterium alkanivorans strain IITR-71 16S ribosomal RNA gene, partial sequence
  • accession: JN210566
  • length: 1446
  • database: nuccore
  • NCBI tax ID: 1071719

Genome sequences

  • @ref: 66792
  • description: Chromobacterium alkanivorans IITR-71
  • accession: GCA_016937655
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1071719

GC content

  • @ref: 67770
  • GC-content: 61.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.994yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.18yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes51.477yes
125438spore-formingspore-formingAbility to form endo- or exosporesno86.134no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes76.984no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99
125439BacteriaNetmotilityAbility to perform movementyes89.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative aerobe74

External links

@ref: 25102

culture collection no.: MTCC 11059, JCM 30068, KCTC 52433

literature

  • topic: Phylogeny
  • Pubmed-ID: 27619232
  • title: Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes.
  • authors: Bajaj A, Kumar A, Yadav S, Kaur G, Bala M, Singh NK, Mathan Kumar R, Manickam N, Mayilraj S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001500
  • year: 2016
  • mesh: Alkanes/metabolism, Bacterial Typing Techniques, Base Composition, Chromobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Halogenation, India, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/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
25102A. K. Bajaj, A.,Yadav, S.,Kaur, G.,Bala, M.,Singh, N. K.,Mathan Kumar, R.,Manickam, N.,Mayilraj, S.Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes10.1099/ijsem.0.001500IJSEM 66: 5228-5235 201627619232
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/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG