Strain identifier

BacDive ID: 158279

Type strain: Yes

Species: Phenylobacterium deserti

Strain history: <- A. Iftikhar, Institute of Microbial Culture Collection of Pakistan, National Agricultural Research Centre, Islamabad, Pakistan <- F. Hussain, Yunnan Institute of Microbiology, University Yunnan, China

NCBI tax ID(s): 1914756 (species)

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General

@ref: 64939

BacDive-ID: 158279

DSM-Number: 103871

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

description: Phenylobacterium deserti DSM 103871 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from desert soil.

NCBI tax id

  • NCBI tax id: 1914756
  • Matching level: species

strain history

  • @ref: 64939
  • history: <- A. Iftikhar, Institute of Microbial Culture Collection of Pakistan, National Agricultural Research Centre, Islamabad, Pakistan <- F. Hussain, Yunnan Institute of Microbiology, University Yunnan, China

doi: 10.13145/bacdive158279.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Caulobacterales
  • family: Caulobacteraceae
  • genus: Phenylobacterium
  • species: Phenylobacterium deserti
  • full scientific name: Phenylobacterium deserti Khan et al. 2017

@ref: 64939

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Caulobacteraceae

genus: Phenylobacterium

species: Phenylobacterium deserti

full scientific name: Phenylobacterium deserti Khan et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65414negative1.4-2.9 µm0.6-1.7 µmrod-shapedyes
69480negative99.952

pigmentation

  • @ref: 65414
  • production: yes
  • name: melanin

Culture and growth conditions

culture medium

  • @ref: 64939
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
64939positivegrowth37mesophilic
65414positivegrowth20-40
65414positiveoptimum30-37mesophilic

culture pH

@refabilitytypepH
65414positivegrowth5.0-8.0
65414positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 65414
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.99
69481no100

observation

@refobservation
65414predominant isoprenoid quinone is Q-10
65414The polar lipid profile consists of phosphatidylglycerol and four unidentified glycolipids

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6541416004(R)-lactate-carbon source
6541416651(S)-lactate-carbon source
65414309162-oxoglutarate-carbon source
65414739183-O-methyl-D-glucose-carbon source
6541413705acetoacetate+carbon source
6541417925alpha-D-glucose-carbon source
6541417057cellobiose-carbon source
6541418333D-arabitol-carbon source
6541429990D-aspartate+carbon source
6541478697D-fructose 6-phosphate+carbon source
6541428847D-fucose-carbon source
6541412936D-galactose-carbon source
654148391D-gluconate+carbon source
6541415588D-malate+carbon source
6541416899D-mannitol-carbon source
6541417924D-sorbitol-carbon source
6541423652dextrin-carbon source
654144853esculin+hydrolysis
6541415740formate-carbon source
6541471321fusidate+carbon source
654145291gelatin-carbon source
654145291gelatin+hydrolysis
6541415978glycerol 3-phosphate-carbon source
6541485249hydroxyethylcellulose-assimilation
6541417596inosine-carbon source
6541416467L-arginine+carbon source
6541429991L-aspartate+carbon source
6541418287L-fucose-carbon source
6541429985L-glutamate-carbon source
6541415971L-histidine+carbon source
6541415589L-malate+carbon source
6541417295L-phenylalanine+carbon source
6541462345L-rhamnose-carbon source
6541417306maltose-carbon source
65414320055methyl beta-D-glucopyranoside-carbon source
65414milk+assimilation
6541417268myo-inositol+carbon source
6541463154N-acetyl-beta-D-mannosamine-carbon source
6541428037N-acetylgalactosamine-carbon source
65414506227N-acetylglucosamine-carbon source
6541435418n-acetylneuraminate+carbon source
6541417632nitrate+reduction
6541417309pectin-carbon source
6541417272propionate+carbon source
65414576065-oxoproline-carbon source
6541416634raffinose-carbon source
6541464103sodium butyrate-carbon source
6541475228sodium lactate-carbon source
6541428017starch-assimilation
6541417992sucrose-carbon source
6541427082trehalose-carbon source
6541432528turanose-carbon source
6541453424tween 20-assimilation
6541453423tween 40-assimilation
6541453425tween 60-assimilation
6541453426tween 80-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6541417833gentamicinyesyes10 µg (disc)
654142637amikacinyesyes30 µg (disc)
6541417698chloramphenicolyesyes30 µg (disc)
6541427902tetracyclineyesyes30 µg (disc)
6541428001vancomycinyesyes30 µg (disc)
65414100246norfloxacinyesyes10 µg (disc)
6541418208penicillin gyesyes10 µg (disc)
6541448923erythromycinyesyes15 µg (disc)
654143517cefuroxime sodiumyesyes30 µg (disc)
65414100241ciprofloxacinyesyes30 µg (disc)
6541428368novobiocinyesyes30 µg (disc)
654147809oxacillinyesyes30 µg (disc)
654148309polymyxin byesyes30 µg (disc)
654148232piperacillinyesyes30 µg (disc)
654149332sulfamethoxazoleyesyes30 µg (disc)

metabolite production

  • @ref: 65414
  • Chebi-ID: 15138
  • metabolite: sulfide
  • production: yes

enzymes

@refvalueactivityec
65414alkaline phosphatase+3.1.3.1
65414esterase (C 4)+
65414esterase Lipase (C 8)+
65414leucine arylamidase+3.4.11.1
65414valine arylamidase+
65414cystine arylamidase+3.4.11.3
65414acid phosphatase+3.1.3.2
65414beta-glucuronidase+3.2.1.31
65414alpha-glucosidase+3.2.1.20
65414cytochrome oxidase+1.9.3.1
65414catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65414C12:04.5
    65414C14:01.6
    65414C16:027.9
    65414C18:00.5
    65414C12:1 3OH3.2
    65414C12:0 3OH0.6
    65414C15:0 3OH0.5
    65414C16:1ω11c2.1
    65414C17:1ω8c0.7
    65414C19:0cycloω8c5.3
    65414C16:1ω6c and/or C16:1ω7c4.6
    65414C18:1ω7c and/or C 18:1ω6c46.4
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soya agar
  • incubation temperature: 37
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
64939desert soilPunjab, Cholistan Desert, (42° 27' N 60° 57' E)PakistanPAKAsia42.4560.95
65414the Cholistan desertPunjabPakistanPAKAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_73060.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_73;96_31106;97_39341;98_51173;99_73060&stattab=map
  • Last taxonomy: Phenylobacterium deserti subclade
  • 16S sequence: LC193944
  • Sequence Identity:
  • Total samples: 2448
  • soil counts: 1687
  • aquatic counts: 389
  • animal counts: 313
  • plant counts: 59

Safety information

risk assessment

  • @ref: 64939
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64939
  • description: Phenylobacterium sp. YIM 73061 gene for 16S ribosomal RNA, partial sequence
  • accession: LC193944
  • length: 1469
  • database: ena
  • NCBI tax ID: 1914756

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phenylobacterium deserti YIM 73061GCA_003254705contigncbi1914756
66792Phenylobacterium deserti strain YIM 730611914756.3wgspatric1914756
66792Phenylobacterium deserti YIM 730612840414474draftimg1914756

GC content

  • @ref: 64939
  • GC-content: 66.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.374no
gram-positiveno98.279yes
anaerobicno99.15no
aerobicyes92.141no
halophileno94.132no
spore-formingno95.107no
glucose-utilyes85.999no
flagellatedno73.53no
thermophileno98.735yes
glucose-fermentno92.856no

External links

@ref: 64939

culture collection no.: DSM 103871, CCTCC AB 2016297, YIM 73061, NCCP 697

straininfo link

  • @ref: 111097
  • straininfo: 401591

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28984224Phenylobacterium deserti sp. nov., isolated from desert soil.Khan IU, Hussain F, Habib N, Wadaan MAM, Ahmed I, Im WT, Hozzein WN, Zhi XY, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0023662017Bacterial Typing Techniques, Base Composition, Caulobacteraceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Pakistan, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny30821672Phenylobacterium soli sp. nov., isolated from arsenic and cadmium contaminated farmland soil.Li X, Yu Y, Choi L, Song Y, Wu M, Wang G, Li MInt J Syst Evol Microbiol10.1099/ijsem.0.0033252019Arsenic, Bacterial Typing Techniques, Base Composition, Cadmium, Caulobacteraceae/*classification/isolation & purification, China, DNA, Bacterial/genetics, Farms, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Ubiquinone/chemistryTranscriptome

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
64939Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103871Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103871)
65414Inam Ullah Khan, Firasat Hussain, Neeli Habib, Mohammed A. M. Wadaan, Iftikhar Ahmed, Wan-Taek Im, Wael N. Hozzein, Xiao-Yang Zhi, Wen-Jun LiPhenylobacterium deserti sp. nov., isolated from desert soil10.1099/ijsem.0.002366IJSEM 67: 4722-4727 201728984224
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
111097Reimer, 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-ID401591.1