Strain identifier

BacDive ID: 140552

Type strain: Yes

Species: Parafilimonas rhizosphaerae

Strain Designation: T16E-198

Strain history: S.-W. Kwon; KACC, South Korea; T16E-198.

NCBI tax ID(s): 1864942 (species)

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General

@ref: 43296

BacDive-ID: 140552

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

description: Parafilimonas rhizosphaerae T16E-198 is an aerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from the rhizosphere of tomato plant collected from a farm on Buyeogun, Chungcheongnam-do, South Korea.

NCBI tax id

  • NCBI tax id: 1864942
  • Matching level: species

strain history

  • @ref: 67770
  • history: S.-W. Kwon; KACC, South Korea; T16E-198.

doi: 10.13145/bacdive140552.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Parafilimonas
  • species: Parafilimonas rhizosphaerae
  • full scientific name: Parafilimonas rhizosphaerae Cho et al. 2017

@ref: 43296

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Chitinophagales

family: Chitinophagaceae

genus: Parafilimonas

species: Parafilimonas rhizosphaerae

strain designation: T16E-198

type strain: yes

Morphology

cell morphology

  • @ref: 43296
  • gram stain: negative
  • cell length: 2-4 µm
  • cell width: 1.0-1.2 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43296
  • colony color: Yellow
  • colony shape: irregular
  • incubation period: 3 days
  • medium used: R2A agar medium

pigmentation

  • @ref: 43296
  • production: yes
  • name: Flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 43296
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43296positiveoptimum28-30mesophilic
43296positivegrowth15-45
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
43296positivegrowth5.5-8
43296positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43296
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43296
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43296NaClpositivegrowth0.5 %
43296NaClpositivegrowth0 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43296casein-hydrolysis
43296dna-hydrolysis16991
43296tween 80-hydrolysis53426
43296carboxymethylcellulose-hydrolysis85146
43296hypoxanthine-hydrolysis17368
43296starch-hydrolysis28017
43296urea-hydrolysis16199
43296xanthine-hydrolysis15318
43296gelatin+hydrolysis5291
43296tyrosine+hydrolysis18186
43296esculin+hydrolysis4853
43296D-glucose+assimilation17634
43296L-arabinose+assimilation30849
43296D-mannose+assimilation16024
43296N-acetylglucosamine+assimilation506227
43296maltose+assimilation17306
43296potassium gluconate+assimilation32032
43296L-rhamnose+assimilation62345
43296D-ribose+assimilation16988
43296sucrose+assimilation17992
43296glycogen+assimilation28087
43296salicin+assimilation17814
43296melibiose+assimilation28053
43296D-mannitol-assimilation16899
43296decanoate-assimilation27689
43296adipate-assimilation17128
43296malate-assimilation25115
43296phenylacetate-assimilation18401
43296myo-inositol-assimilation17268
43296itaconate-assimilation17240
43296suberic acid-assimilation9300
43296sodium malonate-assimilation62983
43296sodium acetate-assimilation32954
43296lactate-assimilation24996
43296L-alanine-assimilation16977
43296potassium 5-dehydro-D-gluconate-assimilation
432963-hydroxybenzoate-assimilation16193
43296L-serine-assimilation17115
43296L-fucose-assimilation18287
43296D-sorbitol-assimilation17924
43296propionate-assimilation17272
43296valerate-assimilation31011
43296L-histidine-assimilation15971
43296potassium 2-dehydro-D-gluconate-assimilation
432963-hydroxybutyrate-assimilation37054
432964-hydroxybenzoate-assimilation17879
43296L-proline-assimilation17203
43296nitrate-reduction17632
43296D-ribose+builds acid from16988
43296methyl beta-D-xylopyranoside-builds acid from74863
43296N-acetylglucosamine+builds acid from506227
43296arbutin+builds acid from18305
43296starch+builds acid from28017
43296glycogen+builds acid from28087
43296L-fucose-builds acid from18287
43296D-arabinose+builds acid from17108
43296L-arabinose+builds acid from30849
43296D-xylose+builds acid from65327
43296D-galactose+builds acid from12936
43296D-glucose+builds acid from17634
43296D-fructose+builds acid from15824
43296D-mannose+builds acid from16024
43296L-rhamnose+builds acid from62345
43296methyl alpha-D-glucopyranoside+builds acid from320061
43296esculin+builds acid from4853
43296salicin+builds acid from17814
43296cellobiose+builds acid from17057
43296maltose+builds acid from17306
43296lactose+builds acid from17716
43296melibiose+builds acid from28053
43296sucrose+builds acid from17992
43296trehalose+builds acid from27082
43296raffinose+builds acid from16634
43296gentiobiose+builds acid from28066
43296turanose+builds acid from32528
43296glycerol 3-phosphate-builds acid from15978
43296erythritol-builds acid from17113
43296L-xylose-builds acid from65328
43296ribitol-builds acid from15963
43296L-sorbose-builds acid from17266
43296galactitol-builds acid from16813
43296myo-inositol-builds acid from17268
43296D-mannitol-builds acid from16899
43296D-sorbitol-builds acid from17924
43296amygdalin-builds acid from27613
43296inulin-builds acid from15443
43296melezitose-builds acid from6731
43296xylitol-builds acid from17151
43296D-tagatose-builds acid from16443
43296D-fucose-builds acid from28847
43296D-arabitol-builds acid from18333
43296L-arabitol-builds acid from18403
43296potassium gluconate-builds acid from32032
43296potassium 2-dehydro-D-gluconate-builds acid from
43296potassium 5-dehydro-D-gluconate-builds acid from
43296methyl alpha-D-mannoside+builds acid from43943
43296glucose-fermentation17234
43296sodium citrate-assimilation53258

metabolite production

  • @ref: 43296
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
43296catalase+1.11.1.6
43296cytochrome oxidase+1.9.3.1
43296arginine dihydrolase-3.5.3.6
43296alkaline phosphatase+3.1.3.1
43296esterase (C 4)+
43296esterase Lipase (C 8)+
43296leucine arylamidase+3.4.11.1
43296valine arylamidase+
43296cystine arylamidase+3.4.11.3
43296acid phosphatase+3.1.3.2
43296naphthol-AS-BI-phosphohydrolase+
43296alpha-galactosidase+3.2.1.22
432966-phospho-beta-galactosidase+3.2.1.85
43296alpha-glucosidase+3.2.1.20
43296beta-glucosidase+3.2.1.21
43296N-acetyl-beta-glucosaminidase+3.2.1.52
43296alpha-mannosidase+3.2.1.24
43296alpha-fucosidase+3.2.1.51
43296lipase (C 14)-
43296trypsin-3.4.21.4
43296alpha-chymotrypsin-3.4.21.1
43296beta-glucuronidase-3.2.1.31

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43296C15:1 iso G19.7
    43296C15:0 iso33.6
    43296C16:04.1
    43296iso-C15:03-OH4.1
    43296C16:0 3OH3.6
    43296C17:0 iso 3OH27.2
    43296C16:1ω7c / iso15:02-OH6.7
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • incubation_oxygen: aerobic
  • software version: Sherlock 5.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43296the rhizosphere of tomato plant collected from a farm on Buyeogun, Chungcheongnam-do, South KoreaBuyeo-gun, Chungcheongnam-doRepublic of KoreaKORAsia36126
67770Rhizosphere of tomato plant collected from a farm on Buyeo-gunChungcheongnam-doRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_94526.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_19043;97_23605;98_64965;99_94526&stattab=map
  • Last taxonomy: Parafilimonas rhizosphaerae
  • 16S sequence: KX417300
  • Sequence Identity:
  • Total samples: 2873
  • soil counts: 1763
  • aquatic counts: 200
  • animal counts: 252
  • plant counts: 658

Sequence information

16S sequences

  • @ref: 43296
  • description: 16s rRNA
  • accession: KX417300
  • database: nuccore

GC content

@refGC-contentmethod
4329641.2real time PCR (RTD-PCR)
6777041.2thermal denaturation, midpoint method (Tm)

External links

@ref: 43296

culture collection no.: KACC 18786, JCM 31601

literature

  • topic: Phylogeny
  • Pubmed-ID: 28693664
  • title: Parafilimonas rhizosphaerae sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.).
  • authors: Cho H, Ahn JH, Weon HY, Joa JH, Hong SB, Seok SJ, Kim JS, Kwon SW, Kim SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001945
  • year: 2017
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, 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
43296Hayoung Cho, Jae-Hyung Ahn, Hang-Yeon Weon, Jae-Ho Joa, Seung-Beom Hong, Soon-Ja Seok, Jeong-Seon Kim, Soon-Wo Kwon, Soo-Jin KimParafilimonas rhizosphaerae sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.)10.1099/ijsem.0.001945IJSEM 67: 2279-2283 201728693664
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/