Strain identifier

BacDive ID: 140518

Type strain: Yes

Species: Flavobacterium pedocola

Strain Designation: UCM-R36

NCBI tax ID(s): 1778664 (species)

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General

@ref: 43098

BacDive-ID: 140518

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

description: Flavobacterium pedocola UCM-R36 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil samples.

NCBI tax id

  • NCBI tax id: 1778664
  • Matching level: species

doi: 10.13145/bacdive140518.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium pedocola
  • full scientific name: Flavobacterium pedocola Nguyen and Kim 2016

@ref: 43098

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium pedocola

strain designation: UCM-R36

type strain: yes

Morphology

cell morphology

  • @ref: 43098
  • gram stain: negative
  • cell length: 1.1-1.4 µm
  • cell width: 0.25-0.3 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43098
  • colony color: opaque
  • colony shape: circular
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
43098Reasoner's 2A agar (R2A)yes
43098nutritient agar (NA)yes
43098LB (Luria-Bertani) MEDIUMyes
43098MacConkeyno
43098trypticase soy agar (TSA)no

culture temp

  • @ref: 43098
  • growth: positive
  • type: growth
  • temperature: 15-35

culture pH

  • @ref: 43098
  • ability: positive
  • type: growth
  • pH: 5.5-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43098
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 43098
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43098NaClnogrowth0.5 %
43098NaClnogrowth1 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43098milk+hydrolysis
43098starch-hydrolysis28017
43098dna-hydrolysis16991
43098urea-hydrolysis16199
43098esculin ferric citrate+hydrolysis
43098glucose-builds acid from17234
43098myo-inositol-assimilation17268
43098sucrose-assimilation17992
43098sodium acetate-assimilation32954
43098glycogen-assimilation28087
43098D-mannitol-assimilation16899
43098salicin-assimilation17814
43098melibiose-assimilation28053
430983-hydroxybutyrate-assimilation37054
43098L-arginine-assimilation16467
43098D-glucose-assimilation17634
43098D-mannose-assimilation16024
43098N-acetylglucosamine-assimilation506227
43098maltose-assimilation17306
43098potassium gluconate-assimilation32032
43098malate-assimilation25115
43098itaconate-assimilation17240
43098suberic acid-assimilation9300
43098sodium malonate-assimilation62983
43098lactate-assimilation24996
43098L-alanine-assimilation16977
43098potassium 5-dehydro-D-gluconate-assimilation
430983-hydroxybenzoate-assimilation16193
43098L-serine-assimilation17115
43098L-fucose-assimilation18287
43098D-sorbitol-assimilation17924
43098L-arabinose-assimilation30849
43098propionate-assimilation17272
43098decanoate-assimilation27689
43098valerate-assimilation31011
43098sodium citrate-assimilation53258
43098L-histidine-assimilation15971
43098potassium 2-dehydro-D-gluconate-assimilation
430984-hydroxybenzoate-assimilation17879
43098L-proline-assimilation17203
43098L-tryptophan-assimilation16828
430984-nitrophenyl beta-D-galactopyranoside-assimilation355715
43098adipate-assimilation17128
43098phenylacetate-assimilation18401

metabolite production

@refChebi-IDmetaboliteproduction
4309835581indoleno
4309816136hydrogen sulfideno

enzymes

@refvalueactivityec
43098acid phosphatase+3.1.3.2
43098alkaline phosphatase+3.1.3.1
43098cystine arylamidase+3.4.11.3
43098leucine arylamidase+3.4.11.1
43098esterase Lipase (C 8)+
43098naphthol-AS-BI-phosphohydrolase+
43098trypsin+3.4.21.4
43098valine arylamidase+
43098esterase (C 4)+
43098alpha-chymotrypsin+3.4.21.1
43098alpha-fucosidase-3.2.1.51
43098alpha-galactosidase-3.2.1.22
43098beta-galactosidase-3.2.1.23
43098N-acetyl-beta-glucosaminidase-3.2.1.52
43098alpha-glucosidase-3.2.1.20
43098beta-glucosidase-3.2.1.21
43098beta-glucuronidase-3.2.1.31
43098lipase (C 14)-
43098alpha-mannosidase-3.2.1.24

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43098C14:02.2
    43098C16:03.7
    43098C17:0 2OH1.3
    43098C16:0 3OH2.1
    43098C15:1 iso G6.5
    43098C15:1 anteiso A0.5
    43098C15:0 iso32.9
    43098C15:0 anteiso5.8
    43098C15:0 iso 3OH6
    43098C16:0 iso1.8
    43098C17:0 iso 3OH11.6
    43098C16:1ω7c / C16:1ω6c7.7
    43098iso-C17:1ω7c / C16:0 10-methyl17.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • system: MIS MIDI
  • instrument: Hewlett-Packard 6890 series

Isolation, sampling and environmental information

isolation

  • @ref: 43098
  • sample type: soil samples
  • geographic location: Yuseong-gu, Daejeon
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 36
  • longitude: 127
  • enrichment culture: VL55 medium
  • enrichment culture duration: 4 weeks
  • enrichment culture temperature: 25

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_116629.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1250;97_1483;98_78787;99_116629&stattab=map
  • Last taxonomy: Flavobacterium pedocola subclade
  • 16S sequence: KU052688
  • Sequence Identity:
  • Total samples: 10
  • soil counts: 7
  • aquatic counts: 2
  • plant counts: 1

Sequence information

16S sequences

  • @ref: 43098
  • description: Flavobacterium pedocola strain UCM-R36 16S ribosomal RNA gene, partial sequence
  • accession: KU052688
  • length: 1458
  • database: nuccore
  • NCBI tax ID: 1778664

GC content

  • @ref: 43098
  • GC-content: 39
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43098

culture collection no.: KACC 18668, NBRC 111765

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27188996Flavobacterium fulvum sp. nov., Flavobacterium pedocola sp. nov. and Flavobacterium humicola sp. nov., three new members of the family Flavobacteriaceae, isolated from soil.Nguyen TM, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0011542016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28809147Flavobacterium flaviflagrans sp. nov., a bacterium of the family Flavobacteriaceae isolated from forest soil.Dahal RH, Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0020002017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, *Forests, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29713912Flavobacterium zaozhuangense sp. nov., a new member of the family Flavobacteriaceae, isolated from metolachlor-contaminated soil.Chen Q, Wang HM, Zhuang W, Sun ZG, Chen J, Ge Y, Qiu JG, He JAntonie Van Leeuwenhoek10.1007/s10482-018-1090-02018Acetamides/*chemistry, Environmental Pollution, Flavobacterium/genetics/*isolation & purification/metabolism, Glycolipids/metabolism, Phosphatidylethanolamines/metabolism, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyMetabolism

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
43098Tuan Manh Nguyen, Jaisoo KimFlavobacterium fulvum sp. nov., Flavobacterium pedocola sp. nov. and Flavobacterium humicola sp. nov., three new members of the family Flavobacteriaceae, isolated from soil10.1099/ijsem.0.001154IJSEM 66: 3108-3118 201627188996
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/