Strain identifier

BacDive ID: 132480

Type strain: Yes

Species: Tessaracoccus flavus

Strain Designation: RP1

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; RP1 <- R. Kumari

NCBI tax ID(s): 1610493 (species)

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General

@ref: 24269

BacDive-ID: 132480

DSM-Number: 100159

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, coccus-shaped, colony-forming

description: Tessaracoccus flavus RP1 is a facultative anaerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from drainage system of a lindane-producing unit.

NCBI tax id

  • NCBI tax id: 1610493
  • Matching level: species

strain history

  • @ref: 24269
  • history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; RP1 <- R. Kumari

doi: 10.13145/bacdive132480.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Tessaracoccus
  • species: Tessaracoccus flavus
  • full scientific name: Tessaracoccus flavus Kumari et al. 2016

@ref: 24269

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Tessaracoccus

species: Tessaracoccus flavus

full scientific name: Tessaracoccus flavus Kumari et al. 2016

strain designation: RP1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
43695positive0.4-1 µmcoccus-shapedno
69480no91.54
69480positive100

colony morphology

  • @ref: 43695
  • colony color: Yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Luria Bertani agar

Culture and growth conditions

culture medium

  • @ref: 43695
  • name: LB (Luria-Bertani) MEDIUM
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43695positivegrowth15-45
43695positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
43695positivegrowth7-10alkaliphile
43695positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 43695
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
43695no
69481no92
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
43695NaClpositivegrowth0-7 %(w/v)
43695NaClpositiveoptimum5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4369517317D-sorbose-assimilation
4369516813galactitol-assimilation
4369516634raffinose-assimilation
43695casein-hydrolysis
436955291gelatin-hydrolysis
4369517368hypoxanthine-hydrolysis
4369528017starch-hydrolysis
4369553424tween 20-hydrolysis
4369553426tween 80-hydrolysis
4369516199urea-hydrolysis
4369515318xanthine-hydrolysis
4369517108D-arabinose+assimilation
4369515824D-fructose+assimilation
4369512936D-galactose+assimilation
4369517634D-glucose+assimilation
4369516899D-mannitol+assimilation
4369516024D-mannose+assimilation
4369517924D-sorbitol+assimilation
4369517113erythritol+assimilation
4369530849L-arabinose+assimilation
4369517306maltose+assimilation
4369517992sucrose+assimilation
4369527082trehalose+assimilation
4369517108D-arabinose+builds acid from
4369515824D-fructose+builds acid from
4369512936D-galactose+builds acid from
4369517634D-glucose+builds acid from
4369516899D-mannitol+builds acid from
4369516024D-mannose+builds acid from
4369517924D-sorbitol+builds acid from
4369517113erythritol+builds acid from
4369530849L-arabinose+builds acid from
4369517306maltose+builds acid from
4369517992sucrose+builds acid from
4369527082trehalose+builds acid from
436954853esculin+hydrolysis
4369517632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4369517698chloramphenicolyesyes30 µg (disc)
4369517833gentamicinyesyes10 µg (disc)
436956104kanamycinyesyes30 µg (disc)
436958309polymyxin byesyes300 µg (disc)
4369528077rifampicinyesyes5 µg (disc)
4369528001vancomycinyesyes30 µg (disc)
436952637amikacinyesyes30 µg (disc)
4369528971ampicillinyesyes10 µg (disc)
43695100241ciprofloxacinyesyes5 µg (disc)
43695100147nalidixic acidyesyes30 µg (disc)
4369527701oxytetracyclineyesyes30 µg (disc)
4369518208penicillin gyesyes10 µg (disc)
4369527902tetracyclineyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4369516136hydrogen sulfideno
4369535581indoleno

enzymes

@refvalueactivityec
43695catalase+1.11.1.6
43695cytochrome oxidase-1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43695C16:07.7
    43695C16:1ω7c / C16:1ω6c1
    43695C18:03.1
    43695C18:1ω7c / C18:1ω6c73
    4369511-methyl C18:1ω7c13.2
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 1
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA60
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24269drainage system of a lindane-producing unitUttar Pradesh, Lucknow, Chinhat (26° 54' N 81° 09' E)IndiaINDAsia26.981.15
43695The drainage system of a lindane-producing unitIndiaIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Engineered#Waste#Industrial wastewater
#Engineered#Industrial#Plant (Factory)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8072.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_1163;97_1367;98_5880;99_8072&stattab=map
  • Last taxonomy: Tessaracoccus flavus subclade
  • 16S sequence: KP265298
  • Sequence Identity:
  • Total samples: 744
  • soil counts: 110
  • aquatic counts: 165
  • animal counts: 456
  • plant counts: 13

Sequence information

16S sequences

  • @ref: 24269
  • description: Tessaracoccus flavus strain RP1 16S ribosomal RNA gene, partial sequence
  • accession: KP265298
  • length: 1396
  • database: ena
  • NCBI tax ID: 1610493

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tessaracoccus flavus RP1GCA_900107385contigncbi1610493
66792Tessaracoccus flavus RP1GCA_001997295completencbi1610493
66792Tessaracoccus flavus strain RP1T1610493.4completepatric1610493

GC content

@refGC-contentmethod
4369566.7Thermal denaturation, fluorometry
2426966.7fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
flagellatedno98.056yes
gram-positiveyes90.23no
anaerobicno97.914yes
aerobicyes79.51no
halophileno93.25no
spore-formingno94.81yes
glucose-utilyes88.793yes
thermophileno96.887yes
glucose-fermentno63.062no
motileno94.297no

External links

@ref: 24269

culture collection no.: DSM 100159, KCTC 39686, MCC 2769

literature

  • topic: Phylogeny
  • Pubmed-ID: 26869509
  • title: Tessaracoccus flavus sp. nov., isolated from the drainage system of a lindane-producing factory.
  • authors: Kumari R, Singh P, Schumann P, Lal R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000958
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Hexachlorocyclohexane, India, *Industrial Waste, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, Propionibacteriaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24269Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100159Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100159)
43695Rashmi Kumari, Priya Singh, Peter Schumann, Rup LalTessaracoccus flavus sp. nov., isolated from the drainage system of a lindane-producing factory10.1099/ijsem.0.000958IJSEM 66: 1862-1868 201626869509
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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