Strain identifier

BacDive ID: 158603

Type strain: Yes

Species: Pedobacter quisquiliarum

Strain Designation: C62-2

NCBI tax ID(s): 1834438 (species)

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General

@ref: 65319

BacDive-ID: 158603

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

description: Pedobacter quisquiliarum C62-2 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 1834438
  • Matching level: species

doi: 10.13145/bacdive158603.20230509.8.1

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 quisquiliarum
  • full scientific name: Pedobacter quisquiliarum Zhang et al. 2018

@ref: 65319

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter quisquiliarum

strain designation: C62-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65319negative0.7-1.8 µm0.45-0.68 µmrod-shapedno
69480no90.594
69480negative99.989

colony morphology

  • @ref: 65319
  • colony size: 1 mm
  • colony color: light-yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A

pigmentation

  • @ref: 65319
  • production: no
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 65319
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65319positivegrowth20-37
65319positiveoptimum30mesophilic

culture pH

@refabilitytypepH
65319positivegrowth5-8
65319positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 65319
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
65319no
69480no99.998
69481no100

halophily

@refsaltgrowthtested relationconcentration
65319NaClpositivegrowth0-3 %(w/v)
65319NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65319168082-dehydro-D-gluconate+builds acid from
65319581435-dehydro-D-gluconate-builds acid from
6531915963ribitol-builds acid from
6531927613amygdalin+builds acid from
6531918305arbutin+builds acid from
6531917057cellobiose+builds acid from
6531917108D-arabinose-builds acid from
6531918333D-arabitol-builds acid from
6531915824D-fructose+builds acid from
6531928847D-fucose-builds acid from
6531912936D-galactose+builds acid from
6531917634D-glucose+builds acid from
6531962318D-lyxose+builds acid from
6531916024D-mannose+builds acid from
6531916988D-ribose-builds acid from
6531916443D-tagatose-builds acid from
6531965327D-xylose+builds acid from
6531916813galactitol-builds acid from
6531917113erythritol-builds acid from
653194853esculin+builds acid from
653194853esculin+hydrolysis
6531928066gentiobiose+builds acid from
6531924265gluconate+builds acid from
6531917234glucose-fermentation
6531917754glycerol-builds acid from
6531928087glycogen-builds acid from
6531917268myo-inositol-builds acid from
6531915443inulin+builds acid from
6531930849L-arabinose+builds acid from
6531918403L-arabitol-builds acid from
6531917266L-sorbose-builds acid from
6531965328L-xylose-builds acid from
6531917716lactose+builds acid from
6531917306maltose+builds acid from
6531929864mannitol-builds acid from
653196731melezitose+builds acid from
6531928053melibiose+builds acid from
6531943943methyl alpha-D-mannoside-builds acid from
6531974863methyl beta-D-xylopyranoside-builds acid from
6531937657methyl D-glucoside+builds acid from
65319506227N-acetylglucosamine+builds acid from
6531917632nitrate-reduction
6531916634raffinose+builds acid from
6531917814salicin+builds acid from
6531930911sorbitol-builds acid from
6531928017starch+builds acid from
6531917992sucrose+builds acid from
6531927082trehalose+builds acid from
6531932528turanose+builds acid from
6531953426tween 80-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6531915688acetoinno
6531916136hydrogen sulfideno
6531935581indoleno

metabolite tests

  • @ref: 65319
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
65319catalase+1.11.1.6
65319cytochrome oxidase+1.9.3.1
65319alkaline phosphatase+3.1.3.1
65319esterase Lipase (C 8)+
65319esterase (C 4)+
65319leucine arylamidase+3.4.11.1
65319naphthol-AS-BI-phosphohydrolase+
65319acid phosphatase+3.1.3.2
65319N-acetyl-beta-glucosaminidase+3.2.1.52
65319beta-galactosidase-3.2.1.23
65319lipase (C 14)-
65319valine arylamidase-
65319alpha-chymotrypsin-3.4.21.1
65319beta-glucuronidase-3.2.1.31
65319beta-glucosidase-3.2.1.21
65319alpha-glucosidase-3.2.1.20
65319urease-3.5.1.5
65319cystine arylamidase-3.4.11.3
65319alpha-galactosidase-3.2.1.22
65319alpha-mannosidase-3.2.1.24
65319alpha-fucosidase-3.2.1.51
65319arginine dihydrolase-3.5.3.6

Isolation, sampling and environmental information

isolation

  • @ref: 65319
  • sample type: activated sludge
  • geographic location: Shanghang county, Fujian Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 25.6286
  • longitude: 116.82
  • enrichment culture: R2A
  • enrichment culture temperature: 30
  • isolation procedure: Activated sludge (1 g) was incubated at 30°C using R2A agar (Difco). After enriching three times, the enriched culture was serially diluted (10-fold) intubes containing 0.9 ml of R2A broth. Aliquots of 0.2 ml were spread on R2A agar plates to cultivate separated colonies.

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

Sequence information

16S sequences

  • @ref: 65319
  • description: 16S rRNA gene sequence
  • accession: KU973598
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter quisquiliarum CGMCC 1.15343GCA_014642175contigncbi1834438
66792Pedobacter quisquiliarum strain CGMCC 1.153431834438.3wgspatric1834438

GC content

  • @ref: 65319
  • GC-content: 43.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.372no
gram-positiveno96.509yes
anaerobicno99.283yes
aerobicyes89.375yes
halophileno91.635no
spore-formingno95.955no
glucose-utilyes90.735no
flagellatedno95.79yes
thermophileno99.184no
glucose-fermentno89.585no

External links

@ref: 65319

culture collection no.: CGMCC 1.15343, NBRC 111767

literature

  • topic: Phylogeny
  • Pubmed-ID: 29231155
  • title: Pedobacter quisquiliarum sp. nov., isolated from activated sludge.
  • authors: Zhang B, Liu ZQ, Zheng YG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002531
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/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
65319Bo Zhang, Zhi-Qiang Liu, Yu-Guo ZhengPedobacter quisquiliarum sp. nov., isolated from activated sludge10.1099/ijsem.0.002531IJSEM 68: 438-442 201829231155
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
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