Strain identifier

BacDive ID: 141079

Type strain: Yes

Species: Pedobacter humi

NCBI tax ID(s): 1517591 (species)

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General

@ref: 43973

BacDive-ID: 141079

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

description: Pedobacter humi KCTC 42735 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from playground soil in Sindorim-dong, Guro-gu, Seoul, South Korea.

NCBI tax id

  • NCBI tax id: 1517591
  • Matching level: species

doi: 10.13145/bacdive141079.20230509.8.1

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 humi
  • full scientific name: Pedobacter humi Trinh and Yi 2016

@ref: 43973

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter humi

type strain: yes

Morphology

cell morphology

  • @ref: 43973
  • gram stain: negative
  • cell length: 1.28-1.96 µm
  • cell width: 0.43-0.52 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43973
  • colony size: 0.5-1.5 mm
  • colony color: yellow
  • colony shape: circular
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowth
43973LB (Luria-Bertani) MEDIUMyes
43973MacConkey agarno
43973Nutrient agar (NA)yes
43973Reasoner's 2A agar (R2A)yes
43973Tryptone soya agaryes

culture temp

@refgrowthtypetemperature
43973positivegrowth4-33
43973positiveoptimum24-28

culture pH

  • @ref: 43973
  • ability: positive
  • type: growth
  • pH: 6.0-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43973
  • oxygen tolerance: aerobe

halophily

  • @ref: 43973
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4397317128adipate-assimilation
4397327689decanoate-assimilation
4397316947citrate-assimilation
4397324265gluconate-assimilation
4397325115malate-assimilation
4397318401phenylacetate-assimilation
4397316899D-mannitol-builds acid from
4397385146carboxymethylcellulose-hydrolysis
43973casein-hydrolysis
4397317029chitin-hydrolysis
4397316991dna-hydrolysis
4397317895L-tyrosine-hydrolysis
4397328017starch-hydrolysis
4397353424tween 20-hydrolysis
4397353426tween 80-hydrolysis
4397317632nitrate-reduction
4397317634D-glucose+builds acid from
4397317306maltose+builds acid from
4397316024D-mannose+builds acid from
4397328053melibiose+builds acid from
4397328087glycogen+builds acid from
4397330849L-arabinose+builds acid from
4397317203L-proline+builds acid from
4397362345L-rhamnose+builds acid from
43973506227N-acetylglucosamine+builds acid from
4397364681phenyl beta-D-glucuronide+builds acid from
4397317814salicin+builds acid from
4397317992sucrose+builds acid from
439734853esculin+hydrolysis

metabolite production

  • @ref: 43973
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43973catalase-1.11.1.6
43973cytochrome oxidase-1.9.3.1
43973alkaline phosphatase+3.1.3.1
43973leucine arylamidase+3.4.11.1
43973valine arylamidase+
43973alpha-chymotrypsin+3.4.21.1
43973acid phosphatase+3.1.3.2
43973N-acetyl-beta-glucosaminidase+3.2.1.52
43973esterase (C 4)+/-
43973cystine arylamidase+/-3.4.11.3
43973esterase Lipase (C 8)-
43973lipase (C 14)-
43973trypsin-3.4.21.4
43973naphthol-AS-BI-phosphohydrolase-
43973alpha-galactosidase-3.2.1.22
43973beta-galactosidase-3.2.1.23
43973beta-glucuronidase-3.2.1.31
43973alpha-glucosidase-3.2.1.20
43973alpha-mannosidase-3.2.1.24
43973alpha-fucosidase-3.2.1.51
43973beta-glucosidase+3.2.1.21
43973beta-galactosidase+3.2.1.23
43973arginine dihydrolase-3.5.3.6
43973urease-3.5.1.5
43973protease-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43973C15:0 anteiso1.4
    43973C14:01.7
    43973C16:010.9
    43973C16:1ω5c2.1
    43973C16:1ω7c / C16:1ω6c33.3
    43973C17:0 2OH1.2
    43973C18:05
    43973C18:1ω6c (6,9,12)1.7
    43973C15:0 iso21.6
    43973C15:0 iso 3OH1.9
    43973C16:0 iso1.9
    43973C16:0 iso 3OH1.3
    43973C17:0 iso 3OH6.1
    43973C17:1 iso ω9c2.4
  • type of FA analysis: whole cell analysis
  • incubation medium: Nutrient agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA60
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43973
  • sample type: playground soil in Sindorim-dong, Guro-gu, Seoul, South Korea
  • geographic location: Sindorim-dong, Guro-gu, Seoul
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • enrichment culture: Nutrient agar
  • enrichment culture duration: 7 days
  • enrichment culture temperature: 28

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_64142.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_404;98_3973;99_64142&stattab=map
  • Last taxonomy: Pedobacter
  • 16S sequence: KM073965
  • Sequence Identity:
  • Total samples: 511
  • soil counts: 176
  • aquatic counts: 47
  • animal counts: 125
  • plant counts: 163

Sequence information

16S sequences

  • @ref: 43973
  • description: 16S rRNA gene sequence
  • accession: KM073965
  • database: nuccore

GC content

  • @ref: 43973
  • GC-content: 45.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43973

culture collection no.: KCTC 42735, CCTCC AB 2015293, THG S15-2

literature

  • topic: Phylogeny
  • Pubmed-ID: 27032079
  • title: Pedobacter humi sp. nov., isolated from a playground soil.
  • authors: Trinh H, Yi TH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001032
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, 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
43973Huan Trinh, Tae-Hoo YiPedobacter humi sp. nov., isolated from a playground soil10.1099/ijsem.0.001032IJSEM 66: 2382-2388 201627032079
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/