Strain identifier

BacDive ID: 140674

Type strain: Yes

Species: Pedobacter psychrophilus

Strain Designation: P4487A

NCBI tax ID(s): 1826909 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 43438

BacDive-ID: 140674

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

description: Pedobacter psychrophilus P4487A is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from fragmentary rock.

NCBI tax id

  • NCBI tax id: 1826909
  • Matching level: species

doi: 10.13145/bacdive140674.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter psychrophilus
  • full scientific name: Pedobacter psychrophilus Švec et al. 2017

@ref: 43438

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter psychrophilus

strain designation: P4487A

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43438negativerod-shapedno
69480no94.879
69480negative99.996

colony morphology

  • @ref: 43438
  • colony size: 1 mm
  • colony color: pink
  • colony shape: circular
  • incubation period: 5 days
  • medium used: R2A agar

pigmentation

@refproductioncolorname
43438yesPink
43438yesCarotenoid
43438noFlexirubin

Culture and growth conditions

culture medium

@refnamegrowth
43438Brain heart infusion agarno
43438Columbia blood agarno
43438MacConkey agarno
43438Nutrient agar (NA)no
43438Reasoner's 2A agar (R2A)yes
43438Trypticase Soy Agar (TSA)no

culture temp

@refgrowthtypetemperaturerange
43438positivegrowth5-25
43438nogrowth1psychrophilic
43438nogrowth30mesophilic
43438nogrowth35mesophilic
43438positiveoptimum20psychrophilic

culture pH

@refabilitytypepHPH range
43438positivegrowth6-9alkaliphile
43438positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 43438
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43438no
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43438NaClpositivegrowth2 %(w/v)
43438NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4343828757fructose-builds acid from
4343829864mannitol-builds acid from
43438casein-hydrolysis
434385291gelatin-hydrolysis
4343861995lecithin-hydrolysis
4343853426tween 80-hydrolysis
4343818186tyrosine-hydrolysis
4343817632nitrate-reduction
4343816301nitrite-reduction
43438645522-hydroxybutyrate-respiration
43438309162-oxoglutarate-respiration
43438286442-oxopentanoate-respiration
43438620642,3-butanediol-respiration
43438370543-hydroxybutyrate-respiration
43438167244-hydroxybutyrate-respiration
43438181014-hydroxyphenylacetic acid-respiration
4343815963ribitol-respiration
4343873706bromosuccinate-respiration
4343816383cis-aconitate-respiration
4343816947citrate-respiration
4343815570D-alanine-respiration
4343818333D-arabitol-respiration
4343815824D-fructose-respiration
4343815895D-galactonic acid lactone-respiration
4343812936D-galactose-respiration
4343818024D-galacturonic acid-respiration
434388391D-gluconate-respiration
4343817784D-glucosaminic acid-respiration
4343814314D-glucose 6-phosphate-respiration
4343815748D-glucuronate-respiration
4343816899D-mannitol-respiration
4343816024D-mannose-respiration
4343827605D-psicose-respiration
4343833801D-saccharate-respiration
4343816523D-serine-respiration
4343817924D-sorbitol-respiration
4343817126DL-carnitine-respiration
4343817113erythritol-respiration
4343816000ethanolamine-respiration
4343815740formate-respiration
4343816865gamma-aminobutyric acid-respiration
4343829042glucose 1-phosphate-respiration
4343832323glucuronamide-respiration
4343814336glycerol 1-phosphate-respiration
4343873804glycyl L-aspartic acid-respiration
4343824741hydroxyproline-respiration
4343816411indole-3-acetic acid-respiration
4343817596inosine-respiration
4343817240itaconate-respiration
4343821217L-alaninamide-respiration
4343816977L-alanine-respiration
4343873786L-alanylglycine-respiration
4343830849L-arabinose-respiration
4343817196L-asparagine-respiration
4343829991L-aspartate-respiration
4343818287L-fucose-respiration
4343815971L-histidine-respiration
4343815603L-leucine-respiration
4343815729L-ornithine-respiration
4343817295L-phenylalanine-respiration
4343817203L-proline-respiration
4343818183L-pyroglutamic acid-respiration
4343862345L-rhamnose-respiration
4343817115L-serine-respiration
4343816857L-threonine-respiration
4343824996lactate-respiration
434386359lactulose-respiration
4343815792malonate-respiration
4343837657methyl D-glucoside-respiration
4343851850methyl pyruvate-respiration
4343875146monomethyl succinate-respiration
4343817268myo-inositol-respiration
4343828037N-acetylgalactosamine-respiration
4343850048phenylethylamine-respiration
4343817272propionate-respiration
4343817148putrescine-respiration
4343826490quinate-respiration
4343816634raffinose-respiration
4343841865sebacic acid-respiration
43438143136succinamate-respiration
4343830031succinate-respiration
4343817992sucrose-respiration
4343817748thymidine-respiration
4343827082trehalose-respiration
4343853423tween 40-respiration
4343853426tween 80-respiration
4343816704uridine-respiration
4343827248urocanic acid-respiration
4343817151xylitol-respiration
4343817306maltose+builds acid from
4343818222xylose+builds acid from
434384853esculin+hydrolysis
4343828017starch+hydrolysis
43438645522-hydroxybutyrate+respiration
4343840585alpha-cyclodextrin+respiration
4343817925alpha-D-glucose+respiration
4343817057cellobiose+respiration
4343823652dextrin+respiration
4343828066gentiobiose+respiration
4343828087glycogen+respiration
4343829985L-glutamate+respiration
4343817716lactose+respiration
4343817306maltose+respiration
4343828053melibiose+respiration
43438506227N-acetylglucosamine+respiration
4343873784glycyl-l-glutamate+respiration
4343832528turanose+respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.group IDis resistantresistance conc.
4343828971ampicillinyesyes10 µg (disc)
434383393carbenicillinyesyes100 µg (disc)
434383508ceftazidimeyesyes10 µg (disc)
434383542cephalothinyesyes30 µg (disc)
43438100241ciprofloxacinyesyes5 µg (disc)
4343817833gentamicinyesyes10 µg (disc)
4343817698chloramphenicolyesyes30 µg (disc)
43438471744imipenemyesyes10 µg (disc)
434386104kanamycinyesyes30 µg (disc)
434388232piperacillinyesyes30 µg (disc)
434388309polymyxin byesyes300 Unit (disc)
4343817076streptomycinyesyes10 µg (disc)
4343827902tetracyclineyesyes30 µg (disc)
4343845924trimethoprimyesyes25 µg (disc)26
434389332sulfamethoxazoleyesyes25 µg (disc)26
43438161680aztreonamyesyes30 µg (disc)
43438472657cefiximeyesyes5 µg (disc)

metabolite production

  • @ref: 43438
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43438catalase+1.11.1.6
43438cytochrome oxidase+/-1.9.3.1
43438DNase+
43438esterase (C 4)+
43438esterase Lipase (C 8)+/-
43438leucine arylamidase+3.4.11.1
43438valine arylamidase+
43438naphthol-AS-BI-phosphohydrolase+
43438beta-galactosidase+3.2.1.23
43438alpha-glucosidase+3.2.1.20
43438alkaline phosphatase+3.1.3.1
43438acid phosphatase+3.1.3.2
43438urease-3.5.1.5
43438arginine dihydrolase-3.5.3.6
43438lysine decarboxylase-4.1.1.18
43438ornithine decarboxylase-4.1.1.17
43438lipase (C 14)-
43438cystine arylamidase-3.4.11.3
43438trypsin-3.4.21.4
43438chymotrypsin-3.4.4.5
43438beta-glucuronidase-3.2.1.31
43438beta-glucosidase-3.2.1.21
43438alpha-galactosidase-3.2.1.22
43438N-acetyl-beta-glucosaminidase-3.2.1.52
43438alpha-mannosidase-3.2.1.24
43438alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

  • @ref: 43438
  • sample type: fragmentary rock
  • geographic location: James Ross Island, Antarctica
  • country: Antarctica
  • origin.country: ATA
  • continent: Australia and Oceania

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3021.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1588;97_1895;98_2325;99_3021&stattab=map
  • Last taxonomy: Pedobacter psychrophilus subclade
  • 16S sequence: KX113374
  • Sequence Identity:
  • Total samples: 595
  • soil counts: 70
  • aquatic counts: 250
  • animal counts: 245
  • plant counts: 30

Sequence information

16S sequences

  • @ref: 43438
  • description: 16S rRNA gene sequence
  • accession: KX113374
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter psychrophilus CCM 8644GCA_001652725contigncbi1826909
66792Pedobacter sp. CCM 86441826909.3wgspatric1826909
66792Pedobacter psychrophilus CCM 86442744054859draftimg1826909

GC content

  • @ref: 43438
  • GC-content: 46.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.102no
gram-positiveno97.796yes
anaerobicno97.427no
aerobicyes87.682yes
halophileno94.802yes
spore-formingno95.675yes
glucose-utilyes87.227yes
flagellatedno97.591yes
glucose-fermentno90.418no
thermophileno98.765no

External links

@ref: 43438

culture collection no.: CCM 8644, LMG 29436

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28771123Pedobacter psychrophilus sp. nov., isolated from fragmentary rock.Svec P, Kralova S, Busse HJ, Kleinhagauer T, Kyrova K, Pantucek R, Maslanova I, Stankova E, Nemec M, Holochova P, Bartak M, Sedlacek IInt J Syst Evol Microbiol10.1099/ijsem.0.0019622017Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingolipids/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35059849Pedobacter segetis sp. nov., a Novel Bacterium Isolated from Soil.Ten LN, Li W, Hong SM, Kim MK, Lee SY, Jung HYCurr Microbiol10.1007/s00284-021-02753-w2022DNA, Bacterial/genetics, *Pedobacter/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil, Soil Microbiology

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
43438Pavel Švec, Stanislava Kralova, Hans-Juergen Busse, Tanita Kleinhagauer, Kamila Kýrova, Roman Pantucek, Ivana Mašlanova, Eva Stankova, Miroslav Nemec, Pavla Holochova, Miloš Bartak, Ivo SedlacekPedobacter psychrophilus sp. nov., isolated from fragmentary rock10.1099/ijsem.0.001962IJSEM 67: 2538-2543 201728771123
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