Strain identifier

BacDive ID: 159787

Type strain: Yes

Species: Pedobacter yulinensis

Strain Designation: YL28-9

Strain history: <- Wei Yahong, Northwest Agriculture and Forestry Univ.

NCBI tax ID(s): 2126353 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 8.1 (current version)

General

@ref: 66791

BacDive-ID: 159787

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

description: Pedobacter yulinensis YL28-9 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from sandy soil in in the Mu Us in Yulin.

NCBI tax id

  • NCBI tax id: 2126353
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Wei Yahong, Northwest Agriculture and Forestry Univ.

doi: 10.13145/bacdive159787.20230509.8.1

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 yulinensis
  • full scientific name: Pedobacter yulinensis Wei et al. 2018

@ref: 66791

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter yulinensis

strain designation: YL28-9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66791negative0.9-1.2 µm0.3-0.5 µmrod-shapedno
69480negative99.985

colony morphology

  • @ref: 66791
  • colony size: 1-1.55 mm
  • colony color: orange
  • colony shape: circular
  • incubation period: 2-3 days
  • medium used: Nutrient agar (NA)

pigmentation

  • @ref: 66791
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
66791LB (Luria-Bertani) agaryes
66791MacConkey agaryes
66791Nutrient agar (NA)yes
66791Reasoner's 2A agar (R2A)yes
66791Trypticase soy agaryes

culture temp

@refgrowthtypetemperaturerange
66791positiveoptimum30mesophilic
66791positivegrowth15-42
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
66791positiveoptimum7
66791positivegrowth6-9alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66791aerobe
67771aerobe

spore formation

@refspore formationconfidence
66791no
69480no99.96
69481no100

halophily

@refsaltgrowthtested relationconcentration
66791NaClpositivegrowth0-2 %(w/v)
66791NaClpositiveoptimum0 %(w/v)

observation

@refobservation
66791The only respiratory quinone is MK-7.
66791The polar lipids contain phosphatidylethanolamine as the major polar lipid as well as four unidentified aminolipids and five unidentified lipids.
66791They do not contain glycolipids.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6679116024D-mannose-assimilation
6679116899D-mannitol-assimilation
6679117128adipate-assimilation
6679117968butyrate-assimilation
6679118401phenylacetate-assimilation
6679124265gluconate-assimilation
6679125115malate-assimilation
6679130849L-arabinose-assimilation
6679153258sodium citrate-assimilation
6679117306maltose+assimilation
6679117634D-glucose+assimilation
6679159640N-acetylglucosamine+assimilation
6679117754glycerol-builds acid from
667916731melezitose+builds acid from
6679112936D-galactose+builds acid from
6679116634raffinose+builds acid from
6679117057cellobiose+builds acid from
6679117113erythritol+builds acid from
6679117306maltose+builds acid from
6679117634D-glucose+builds acid from
6679117716lactose+builds acid from
6679117814salicin+builds acid from
6679117992sucrose+builds acid from
6679118305arbutin+builds acid from
6679127082trehalose+builds acid from
6679127613amygdalin+builds acid from
6679128017starch+builds acid from
6679128053melibiose+builds acid from
6679132528turanose+builds acid from
6679137684mannose+builds acid from
6679171422beta-gentiobiose+builds acid from
66791320061methyl alpha-D-glucopyranoside+builds acid from
66791esculin ferric citrate+builds acid from
6679116411acetic acid-carbon source
6679117596inosine-carbon source
6679117790methanol-carbon source
66791143136succinamate-carbon source
6679117295L-phenylalanine+carbon source
667915291gelatin-hydrolysis
6679117895L-tyrosine-hydrolysis
6679153426tween 80-hydrolysis
6679185146carboxymethylcellulose-hydrolysis
66791casein-hydrolysis
667914853esculin+hydrolysis
6679116991dna+hydrolysis
6679128017starch+hydrolysis
6679153424tween 20+hydrolysis
6679117632nitrate+reduction

metabolite production

  • @ref: 66791
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66791alpha-chymotrypsin-3.4.21.1
66791alpha-mannosidase-3.2.1.24
66791beta-glucuronidase-3.2.1.31
66791cystine arylamidase-3.4.11.3
66791cytochrome oxidase-1.9.3.1
66791esterase (C 4)-
66791lipase (C 14)-
66791protease-
66791trypsin-3.4.21.4
66791acid phosphatase+3.1.3.2
66791alkaline phosphatase+3.1.3.1
66791alpha-fucosidase+3.2.1.51
66791alpha-galactosidase+3.2.1.22
66791alpha-glucosidase+3.2.1.20
66791arginine dihydrolase+3.5.3.6
66791beta-galactosidase+3.2.1.23
66791beta-glucosidase+3.2.1.21
66791catalase+1.11.1.6
66791esterase Lipase (C 8)+
66791leucine arylamidase+3.4.11.1
66791N-acetyl-beta-glucosaminidase+3.2.1.52
66791naphthol-AS-BI-phosphohydrolase+
66791urease+3.5.1.5
66791valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66791C15:1 iso H and/or C13:0 3OH1.1
    66791C14:0 anteiso1.16
    66791C19:01.2
    66791C18:01.6
    66791C16:1 w7c and/or C16:1 w6c26.2
    66791C15:0 anteiso3.3
    66791C16:03.5
    66791C15:0 iso 3OH3.6
    66791C15:0 iso31.7
    66791C14:0 iso4.8
    66791C17:1 iso w9c / C16:0 10-methyl6.5
    66791C17:0 iso 3OH6.7
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic Soy Agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: GC (6890 N; Agilent)

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture durationenrichment culture temperatureisolation procedure
66791sandy soil in in the Mu Us in YulinShaanxi provinceChinaCHNAsia341085 days30A 5.0 g sample of sandy soil was suspended in 45 ml sterile 0.85 % (w/v) NaCl for 30 min at 30°C by vigorously shaking the flask. The soil suspensions were serially diluted (10 ^-1-10^-6) and 0.1 ml of each dilution was inoculated onto nutrient agar (NA; tryptone, 10 g l^-1; beef extract, 3 g l^-1;NaCl, 5 g l^-1; agar 18 g l^-1;pH 7.2-7.4).
67771From soilYulin city, Shaanxi ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_127824.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_49892;97_64242;98_85680;99_127824&stattab=map
  • Last taxonomy: Pedobacter yulinensis subclade
  • 16S sequence: KY120369
  • Sequence Identity:
  • Total samples: 15
  • soil counts: 5
  • aquatic counts: 4
  • animal counts: 4
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 66791
  • description: Pedobacter sp. strain YL28-9 16S ribosomal RNA gene, partial sequence
  • accession: KY120369
  • length: 1484
  • database: ena
  • NCBI tax ID: 2126353

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter yulinensis YL28-9GCA_003029735scaffoldncbi2126353
66792Pedobacter yulinensis YL28-92855540664draftimg2126353

GC content

  • @ref: 66791
  • GC-content: 50.40
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.896no
gram-positiveno97.178yes
anaerobicno99.212yes
halophileno96.149yes
spore-formingno93.728yes
glucose-utilyes86.577no
aerobicyes88.933no
thermophileno98.914yes
motileno89.794yes
glucose-fermentno89.486no

External links

@ref: 66791

culture collection no.: CGMCC 1.16050, KCTC 62104

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29927365Pedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter.Wei Y, Wang B, Zhang L, Zhang J, Chen SInt J Syst Evol Microbiol10.1099/ijsem.0.0028682018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34576992Screening and Characterization of Two Extracellular Polysaccharide-Producing Bacteria from the Biocrust of the Mu Us Desert.Xue Z, Zhao S, Bold N, Zhang J, Hu Z, Hu X, Gao Y, Chen S, Wei YMolecules10.3390/molecules261855212021Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Desert Climate, Extracellular Polymeric Substance Matrix/*chemistry/genetics/metabolism, Extracellular Space/chemistry, Fatty Acids/analysis, Metals, Heavy/pharmacology, Nucleic Acid Hybridization, Pedobacter/cytology/drug effects/*isolation & purification/*physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sinorhizobium meliloti/cytology/drug effects/*isolation & purification/*physiology, Soil MicrobiologyEnzymology

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
66791Yahong Wei, Baodan Wang, Limei Zhang, Jianguo Zhang, Shaolin ChenPedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter10.1099/ijsem.0.002868IJSEM 68: 2523-2529 201829927365
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
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