Strain identifier

BacDive ID: 24311

Type strain: Yes

Species: Pseudohoeflea suaedae

Strain Designation: YC6898

Strain history: <- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6898 <- F. Bibi

NCBI tax ID(s): 877384 (species)

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General

@ref: 20608

BacDive-ID: 24311

DSM-Number: 23348

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

description: Pseudohoeflea suaedae YC6898 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-sterilized root of the halophyte Suaeda maritima.

NCBI tax id

  • NCBI tax id: 877384
  • Matching level: species

strain history

  • @ref: 20608
  • history: <- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6898 <- F. Bibi

doi: 10.13145/bacdive24311.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Pseudohoeflea
  • species: Pseudohoeflea suaedae
  • full scientific name: Pseudohoeflea suaedae (Chung et al. 2013) Hyeon et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Hoeflea suaedae

@ref: 20608

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Pseudohoeflea

species: Pseudohoeflea suaedae

full scientific name: Pseudohoeflea suaedae (Chung et al. 2013) Hyeon et al. 2017

strain designation: YC6898

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityflagellum arrangementcell lengthcell width
25207negativerod-shapedyesmonotrichous, polar
30830negativerod-shapedyes1.35 µm0.4 µm

pigmentation

  • @ref: 30830
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20608
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20608positivegrowth28mesophilic
30830positivegrowth10-42
30830positiveoptimum33.5mesophilic

culture pH

  • @ref: 30830
  • ability: positive
  • type: growth
  • pH: 5.0-10.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25207aerobe
30830aerobe

spore formation

  • @ref: 30830
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30830NaClpositivegrowth0-9.5 %
30830NaClpositiveoptimum3.5 %

observation

  • @ref: 30830
  • observation: aggregates in clumps

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
25207casein-hydrolysis
25207gelatin-hydrolysis5291
25207N-acetylglucosamine-assimilation506227
25207starch-hydrolysis28017
25207tween 20-hydrolysis53424
25207tween 80-hydrolysis53426
25207tyrosine-hydrolysis18186
25207D-glucose+assimilation17634
25207D-mannitol+assimilation16899
25207D-mannose+assimilation16024
25207esculin+hydrolysis4853
25207L-arabinose+assimilation30849
25207malate+assimilation25115
25207maltose+assimilation17306
25207phenylacetate+assimilation18401
25207potassium gluconate+assimilation32032
25207sodium citrate+assimilation53258
25207urea+hydrolysis16199
308305-dehydro-D-gluconate+carbon source58143
30830arabinose+carbon source22599
30830L-arabitol+carbon source18403
30830fucose+carbon source33984
30830glucose+carbon source17234
30830glycerol+carbon source17754
30830malate+carbon source25115
30830N-acetylglucosamine+carbon source506227
30830ribose+carbon source33942
30830salicin+carbon source17814
30830xylose+carbon source18222
30830esculin+hydrolysis4853

enzymes

@refvalueactivityec
25207acid phosphatase+3.1.3.2
25207alkaline phosphatase+3.1.3.1
25207alpha-chymotrypsin-3.4.21.1
25207alpha-fucosidase-3.2.1.51
25207alpha-galactosidase-3.2.1.22
25207alpha-glucosidase+3.2.1.20
25207alpha-mannosidase-3.2.1.24
25207arginine dihydrolase-3.5.3.6
25207beta-galactosidase-3.2.1.23
25207beta-glucosidase+3.2.1.21
25207beta-glucuronidase-3.2.1.31
25207cystine arylamidase+3.4.11.3
25207esterase (C 4)+
25207esterase Lipase (C 8)+
25207leucine arylamidase+3.4.11.1
25207lipase (C 14)+
25207N-acetyl-beta-glucosaminidase-3.2.1.52
25207naphthol-AS-BI-phosphohydrolase+
25207trypsin+3.4.21.4
25207valine arylamidase+
30830acid phosphatase+3.1.3.2
30830alkaline phosphatase+3.1.3.1
30830catalase+1.11.1.6
30830gelatinase+
30830cytochrome oxidase+1.9.3.1
30830urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    2520711-Methyl C18:1ω7c11.6
    25207C16:014.1
    25207C16:1ω7c / C16:1ω6c7.8
    25207C18:03.3
    25207C18:1ω7c / C18:1ω6c41.4
    25207Cyclo C19:0ω8c17.1
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine Agar (MA)
  • agar/liquid: agar
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 20608
  • sample type: surface-sterilized root of the halophyte Suaeda maritima
  • host species: Suaeda maritima
  • geographic location: tidal flat of Namhae Island
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_32753.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2317;97_19414;98_24237;99_32753&stattab=map
  • Last taxonomy: Pseudohoeflea suaedae subclade
  • 16S sequence: HM800935
  • Sequence Identity:
  • Total samples: 482
  • soil counts: 95
  • aquatic counts: 260
  • animal counts: 70
  • plant counts: 57

Safety information

risk assessment

  • @ref: 20608
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20608
  • description: Hoeflea suaedae strain YC6898 16S ribosomal RNA gene, partial sequence
  • accession: HM800935
  • length: 1449
  • database: ena
  • NCBI tax ID: 877384

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudohoeflea suaedae YC6898GCA_004354915contigncbi877384
66792Pseudohoeflea suaedae YC68982837651117draftimg877384

GC content

@refGC-contentmethod
2060853.7high performance liquid chromatography (HPLC)
3083053.7

External links

@ref: 20608

culture collection no.: DSM 23348, KACC 14911, NBRC 107700

straininfo link

  • @ref: 88244
  • straininfo: 396609

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23159752Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima.Chung EJ, Park JA, Pramanik P, Bibi F, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.045484-02012Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny27902230Roseitalea porphyridii gen. nov., sp. nov., isolated from a red alga, and reclassification of Hoeflea suaedae Chung et al. 2013 as Pseudohoeflea suaedae gen. nov., comb. nov.Hyeon JW, Jeong SE, Baek K, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0016332017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodophyta/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmedID_cross_reference
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
20608Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-23348Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23348)
25207J. W. J. Hyeon, S. E.,Baek, K.,Jeon, C. O.Roseitalea porphyridii gen. nov., sp. nov., isolated from a red alga, and reclassification of Hoeflea suaedae Chung et al. 2013 as Pseudohoeflea suaedae gen. nov., comb. nov10.1099/ijsem.0.001633IJSEM 67: 362-368 201727902230
30830Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127160
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/
88244Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID396609.1