Strain identifier

BacDive ID: 158646

Type strain: Yes

Species: Pedobacter mongoliensis

Strain Designation: 1-32

Strain history: <- Kai Yuan, Huzhong Agricultural Univ.

NCBI tax ID(s): 2100740 (species)

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General

@ref: 65371

BacDive-ID: 158646

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

description: Pedobacter mongoliensis 1-32 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from soil sample of subsurface.

NCBI tax id

  • NCBI tax id: 2100740
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Kai Yuan, Huzhong Agricultural Univ.

doi: 10.13145/bacdive158646.20230509.8.1

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 mongoliensis
  • full scientific name: Pedobacter mongoliensis Yuan et al. 2018

@ref: 65371

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter mongoliensis

strain designation: 1-32

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
65371negative1-2 µm0.3.0.6 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative

colony morphology

  • @ref: 65371
  • colony size: 2 mm
  • colony color: light pink
  • colony shape: circular
  • incubation period: 7 days
  • medium used: R2A

pigmentation

  • @ref: 65371
  • production: no
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

@refnamegrowth
65371Reasoner's 2A agar (R2A)yes
65371Nutrient agar (NA)no
65371tryptic soy agarno
65371LB (Luria-Bertani) MEDIUMno

culture temp

@refgrowthtypetemperaturerange
65371positivegrowth4-37
65371positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
65371positivegrowth6-9alkaliphile
65371positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65371aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
65371NaClpositivegrowth0-1 %(w/v)
65371NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65371645522-hydroxybutyrate-respiration
65371167632-oxobutanoate-respiration
65371309162-oxoglutarate-respiration
65371286442-oxopentanoate-respiration
65371620642,3-butanediol-respiration
65371370543-hydroxybutyrate-respiration
65371182404-hydroxy-L-proline-respiration
65371167244-hydroxybutyrate-respiration
65371181014-hydroxyphenylacetic acid-respiration
6537130089acetate-respiration
6537117128adipate-assimilation
6537115963ribitol-respiration
6537140585alpha-cyclodextrin-respiration
6537117925alpha-D-glucose+respiration
6537136219alpha-lactose-respiration
6537173706bromosuccinate-respiration
6537127689decanoate-assimilation
65371casein-hydrolysis
6537162968cellulose-hydrolysis
6537117029chitin-hydrolysis
6537116383cis-aconitate-respiration
6537116947citrate-respiration
6537115570D-alanine-respiration
6537118333D-arabitol-respiration
6537117057cellobiose-respiration
6537115824D-fructose-respiration
6537115895D-galactonic acid lactone-respiration
6537112936D-galactose-builds acid from
6537112936D-galactose-respiration
6537118024D-galacturonic acid-respiration
6537130612D-glucarate-respiration
653718391D-gluconate-respiration
6537117784D-glucosaminic acid-respiration
6537117634D-glucose-builds acid from
6537117634D-glucose-fermentation
6537117634D-glucose+assimilation
6537114314D-glucose 6-phosphate-respiration
6537115748D-glucuronate-respiration
6537116899D-mannitol-assimilation
6537116899D-mannitol-respiration
6537116024D-mannose-builds acid from
6537116024D-mannose+assimilation
6537116024D-mannose+respiration
6537127605D-psicose-respiration
6537116988D-ribose-builds acid from
6537116523D-serine-respiration
6537117924D-sorbitol-respiration
6537165327D-xylose+builds acid from
6537123652dextrin-respiration
6537117126DL-carnitine-respiration
6537124996lactate-respiration
6537116991dna-hydrolysis
6537117113erythritol-respiration
653714853esculin+hydrolysis
6537116000ethanolamine-respiration
6537115740formate-respiration
6537116865gamma-aminobutyric acid-respiration
653715291gelatin-hydrolysis
6537128066gentiobiose-respiration
6537129042glucose 1-phosphate-respiration
6537132323glucuronamide-respiration
6537117754glycerol-respiration
6537114336glycerol 1-phosphate-respiration
6537128087glycogen-respiration
6537173804glycyl L-aspartic acid-respiration
6537117596inosine-respiration
6537117268myo-inositol-builds acid from
6537117240itaconate-respiration
6537121217L-alaninamide-respiration
6537116977L-alanine-respiration
6537173786L-alanylglycine-respiration
6537130849L-arabinose-builds acid from
6537130849L-arabinose+assimilation
6537130849L-arabinose+respiration
6537117196L-asparagine-respiration
6537129991L-aspartate-respiration
6537118287L-fucose-respiration
6537129985L-glutamate-respiration
6537115971L-histidine-respiration
6537115603L-leucine-respiration
6537115729L-ornithine-respiration
6537117295L-phenylalanine-respiration
6537117203L-proline-respiration
6537118183L-pyroglutamic acid-respiration
6537162345L-rhamnose-respiration
6537117115L-serine-respiration
6537116857L-threonine-respiration
6537117716lactose-builds acid from
653716359lactulose-respiration
6537125115malate-assimilation
6537115792malonate-respiration
6537117306maltose-assimilation
6537117306maltose-respiration
6537129864mannitol-builds acid from
6537128053melibiose-respiration
65371320055methyl beta-D-glucopyranoside-respiration
6537151850methyl pyruvate-respiration
6537175146monomethyl succinate-respiration
6537117268myo-inositol-respiration
6537128037N-acetylgalactosamine+respiration
65371506227N-acetylglucosamine-respiration
65371506227N-acetylglucosamine+assimilation
6537173784glycyl-l-glutamate-respiration
6537117632nitrate-reduction
6537118401phenylacetate-assimilation
6537150048phenylethylamine-respiration
6537132032potassium gluconate-assimilation
6537117272propionate-respiration
6537117148putrescine-respiration
6537126490quinate-respiration
6537116634raffinose-builds acid from
6537116634raffinose-respiration
6537126546rhamnose-builds acid from
6537141865sebacic acid-respiration
6537153258sodium citrate-assimilation
6537130911sorbitol-builds acid from
6537127922sorbose-builds acid from
6537128017starch-hydrolysis
65371143136succinamate-respiration
6537130031succinate-respiration
6537117992sucrose-builds acid from
6537117992sucrose-respiration
6537117748thymidine-respiration
6537127082trehalose-builds acid from
6537127082trehalose-respiration
6537132528turanose-respiration
6537153424tween 20-hydrolysis
6537153423tween 40-hydrolysis
6537153423tween 40-respiration
6537153425tween 60-hydrolysis
6537153426tween 80-hydrolysis
6537153426tween 80-respiration
6537118186tyrosine-hydrolysis
6537116704uridine-respiration
6537127248urocanic acid-respiration
6537117151xylitol+respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
653717507neomycinyesyes30 µg (disc)
653712637amikacinyesyes30 µg (disc)
6537150845doxycyclineyesyes30 µg (disc)
653717809oxacillinyesyes1 µg (disc)
6537118208penicillin gyesyes10 µg (disc)
6537148923erythromycinyesyes15 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6537116136hydrogen sulfideno
6537135581indoleno

enzymes

@refvalueactivityec
65371cytochrome oxidase+1.9.3.1
65371catalase+1.11.1.6
65371heparin lyase+4.2.2.7
65371alkaline phosphatase+3.1.3.1
65371esterase (C 4)+
65371esterase Lipase (C 8)+
65371leucine arylamidase+3.4.11.1
65371acid phosphatase+3.1.3.2
65371naphthol-AS-BI-phosphohydrolase+
65371beta-galactosidase+3.2.1.23
65371beta-glucosidase+3.2.1.21
65371N-acetyl-beta-glucosaminidase+3.2.1.52
65371lipase (C 14)-
65371valine arylamidase-
65371cystine arylamidase-3.4.11.3
65371alpha-chymotrypsin-3.4.21.1
65371trypsin-3.4.21.4
65371alpha-galactosidase-3.2.1.22
65371beta-glucuronidase-3.2.1.31
65371alpha-glucosidase-3.2.1.20
65371alpha-mannosidase-3.2.1.24
65371alpha-fucosidase-3.2.1.51
65371arginine dihydrolase-3.5.3.6
65371urease-3.5.1.5
65371gelatinase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65371C16:002.3
    65371C15:1ω6c2.6
    65371C16:1ω5c5.9
    65371C13:0 iso1.9
    65371C15:0 iso33
    65371C15:0 anteiso2.8
    65371C15:0 iso 3OH6.5
    65371C16:0 3OH0.6
    65371C17:0 iso 3OH18.4
    65371iso-C15:1 and/or C13:0 3-OH0.7
    65371C16:1ω7c and/or C16:1ω6c18.7
    65371C17:1 iso I and/or anteiso B0.6
    65371iso-C17:1ω9c and/or 10-methyl C16:03.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65371soil sample of subsurfaceOrdos grassland of Inner MongoliaChinaCHNAsia39.8106108.623R2A1 week28dilution-plating method
67771From soilerdos plateau, Nei Monggol Autonomous Region, the Ordos grassland of Inner MongoliaChinaCHNAsia

isolation source categories

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

Sequence information

16S sequences

  • @ref: 67771
  • description: Pedobacter mongoliensis strain 1-32 16S ribosomal RNA gene, partial sequence
  • accession: KY933307
  • length: 1483
  • database: ena
  • NCBI tax ID: 2100740

Genome sequences

  • @ref: 66792
  • description: Pedobacter mongoliensis KCTC 52859
  • accession: GCA_024436395
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 2100740

GC content

@refGC-contentmethod
6537143.4high performance liquid chromatography (HPLC)
6777143.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.421yes
gram-positiveno96.795no
anaerobicno98.973yes
aerobicyes89.387no
halophileno93.881yes
spore-formingno95.914no
motileno90no
glucose-fermentno90.754yes
thermophileno96.474no
glucose-utilyes88.797yes

External links

@ref: 65371

culture collection no.: KCTC 52859, CCTCC AB 2017084

literature

  • topic: Phylogeny
  • Pubmed-ID: 29461180
  • title: Pedobacter mongoliensis sp. nov., isolated from grassland soil.
  • authors: Yuan K, Cao M, Li J, Wang G
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002637
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Grassland, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil 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
65371Kai Yuan, Min Cao, Jingxin Li, Gejiao WangPedobacter mongoliensis sp. nov., isolated from grassland soil10.1099/ijsem.0.002637IJSEM 68: 1112-1117 201829461180
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc