Strain identifier

BacDive ID: 158705

Type strain: Yes

Species: Hymenobacter rivuli

Strain Designation: TAPP3

Strain history: <- Wen-Ming Chen, National Kaohsiung Marine Univ..

NCBI tax ID(s): 1815561 (species)

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General

@ref: 65447

BacDive-ID: 158705

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

description: Hymenobacter rivuli TAPP3 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from a surface water sample .

NCBI tax id

  • NCBI tax id: 1815561
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Wen-Ming Chen, National Kaohsiung Marine Univ..

doi: 10.13145/bacdive158705.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter rivuli
  • full scientific name: Hymenobacter rivuli Sheu et al. 2018

@ref: 65447

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter rivuli

strain designation: TAPP3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
65447negative1.7-3.6 µm0.6-0.8 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative

colony morphology

  • @ref: 65447
  • colony size: 1.5-2.5 mm
  • colony color: bright red
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Reasoner's 2A agar

Culture and growth conditions

culture medium

  • @ref: 65447
  • name: Reasoner's 2A agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65447positivegrowth20-35
65447positiveoptimum25-30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
65447positivegrowth6.5-7.5
65447positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65447aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
65447NaClpositivegrowth0-1 %
65447NaClpositiveoptimum0 %

observation

@refobservation
65447rods that were covered by large capsules
65447the predominant respiratory quinone is MK-7
65447the polar lipid profile consists of phosphatidylethanolamine, six uncharacterized aminophospholipids and four uncharacterized lipids
65447homospermidine is the major polyamine
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65447168082-dehydro-D-gluconate-builds acid from
65447581435-dehydro-D-gluconate+builds acid from
6544717128adipate+assimilation
6544715963ribitol+aerobic growth
6544717925alpha-D-glucose-aerobic growth
6544727613amygdalin-builds acid from
6544722599arabinose+assimilation
6544718305arbutin-builds acid from
6544727689decanoate+assimilation
6544785146carboxymethylcellulose-hydrolysis
65447casein+hydrolysis
6544717057cellobiose-builds acid from
6544717057cellobiose+aerobic growth
6544717029chitin-hydrolysis
6544715963ribitol-builds acid from
6544717108D-arabinose-builds acid from
6544718333D-arabitol-builds acid from
6544715824D-fructose-aerobic growth
6544715824D-fructose+builds acid from
6544728847D-fucose-builds acid from
6544712936D-galactose-aerobic growth
6544712936D-galactose+builds acid from
6544717634D-glucose-builds acid from
6544762318D-lyxose-builds acid from
6544716899D-mannitol-aerobic growth
6544716899D-mannitol-builds acid from
6544716024D-mannose-aerobic growth
6544716024D-mannose+builds acid from
6544716988D-ribose-builds acid from
6544717924D-sorbitol-aerobic growth
6544717924D-sorbitol-builds acid from
6544716443D-tagatose-builds acid from
6544765327D-xylose+builds acid from
6544716991dna+hydrolysis
6544716813galactitol-builds acid from
6544717113erythritol-builds acid from
65447esculin ferric citrate-hydrolysis
65447esculin ferric citrate+builds acid from
65447495056gamma-cyclodextrin+aerobic growth
654475291gelatin+hydrolysis
6544728066gentiobiose-builds acid from
6544724265gluconate-builds acid from
6544724265gluconate+assimilation
6544717234glucose+assimilation
6544717754glycerol-builds acid from
6544728087glycogen+builds acid from
6544715443inulin-builds acid from
6544730849L-arabinose+builds acid from
65447L-arabito-builds acid from
6544718287L-fucose-builds acid from
6544762345L-rhamnose-builds acid from
6544762345L-rhamnose+aerobic growth
6544717266L-sorbose-builds acid from
6544765328L-xylose-builds acid from
6544717716lactose+builds acid from
6544761995lecithin-hydrolysis
6544725115malate+assimilation
6544717306maltose-aerobic growth
6544717306maltose-builds acid from
6544717306maltose+assimilation
6544729864mannitol+assimilation
6544737684mannose+assimilation
654476731melezitose-builds acid from
6544728053melibiose+builds acid from
6544743943methyl alpha-D-mannoside-builds acid from
6544774863methyl beta-D-xylopyranoside-builds acid from
6544737657methyl D-glucoside-builds acid from
6544717268myo-inositol-builds acid from
65447506227N-acetylglucosamine-builds acid from
65447506227N-acetylglucosamine+assimilation
6544717632nitrate-reduction
6544718401phenylacetate+assimilation
6544716634raffinose-aerobic growth
6544716634raffinose-builds acid from
6544717814salicin-builds acid from
6544753311sodium alginate-hydrolysis
6544753258sodium citrate+assimilation
6544728017starch+builds acid from
6544728017starch+hydrolysis
6544717992sucrose+aerobic growth
6544717992sucrose+builds acid from
6544727082trehalose-aerobic growth
6544727082trehalose-builds acid from
6544732528turanose-builds acid from
6544753424tween 20-hydrolysis
6544753424tween 20+aerobic growth
6544753423tween 40+aerobic growth
6544753423tween 40+hydrolysis
6544753425tween 60+aerobic growth
6544753425tween 60+hydrolysis
6544753426tween 80+aerobic growth
6544753426tween 80+hydrolysis
6544717151xylitol-builds acid from

metabolite production

  • @ref: 65447
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65447cytochrome oxidase+1.9.3.1
65447catalase+1.11.1.6
65447lipase-
65447arginine dihydrolase-3.5.3.6
65447urease-3.5.1.5
65447alkaline phosphatase+3.1.3.1
65447esterase (C 4)+
65447esterase Lipase (C 8)+
65447lipase (C 14)+
65447leucine arylamidase+3.4.11.1
65447valine arylamidase+
65447cystine arylamidase+3.4.11.3
65447acid phosphatase+3.1.3.2
65447naphthol-AS-BI-phosphohydrolase+
65447alpha-galactosidase+3.2.1.22
65447beta-galactosidase+3.2.1.23
65447alpha-glucosidase+3.2.1.20
65447N-acetyl-beta-glucosaminidase+3.2.1.52
65447trypsin-3.4.21.4
65447alpha-chymotrypsin-3.4.21.1
65447beta-glucuronidase-3.2.1.31
65447beta-glucosidase-3.2.1.21
65447alpha-mannosidase-3.2.1.24
65447alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65447C14:02.8
    65447C16:03.4
    65447C18:01.7
    65447C14:0 anteiso2.2
    65447C15:0 iso33
    65447C15:0 anteiso6.6
    65447C17:0 iso1.1
    65447C16:0 3OH2.4
    65447C15:0 iso 3OH1.3
    65447C16:1ω5c15.4
    65447C18:1ω9c1.7
    65447C16:1ω7c and/or C16:1ω6c22.6
    65447iso-C17:1 I and/or ante-iso-C17:1 B1.7
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65447a surface water sample (28 C, pH 7, 0 % NaCl)Wanan Creek in the vicinity of Pingtung CountyTaiwanTWNAsiaR2A agar3 days25collected and then was plated on R2A agar (BD Difco) by using the standard dilution plating method
67771From freshwater, riverthe Wanan Creek, the vicinity of Pingtung CountyTaiwanTWNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Surface water

Sequence information

16S sequences

  • @ref: 65447
  • description: 16S rRNA gene sequence
  • accession: LT223127
  • database: nuccore

GC content

@refGC-contentmethod
6544762.8high performance liquid chromatography (HPLC)
6777162.8

External links

@ref: 65447

culture collection no.: BCRC 80979, LMG 29559, KCTC 52236

literature

  • topic: Phylogeny
  • Pubmed-ID: 29504928
  • title: Hymenobacter rivuli sp. nov., isolated from a freshwater creek.
  • authors: Sheu SY, Hsieh TY, Kwon SW, Chen WM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002657
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology
  • 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
65447Shih-Yi Sheu, Tsai-Ying Hsieh, Soon-Wo Kwon, Wen-Ming ChenHymenobacter rivuli sp. nov., isolated from a freshwater creek10.1099/ijsem.0.002657IJSEM 68: 1220-1226 201829504928
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc