Strain identifier

BacDive ID: 141062

Type strain: Yes

Species: Shewanella gelidii

Strain Designation: RZB5-4

Strain history: Y. Wang; Sch. of Life Sci. & Technol., Xin Xiang Med. Univ., China; RZB5-4.

NCBI tax ID(s): 1642821 (species)

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General

@ref: 43941

BacDive-ID: 141062

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Shewanella gelidii RZB5-4 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from red algae Gelidium amansii collected from the coastal region of Rizhao, Yellow Sea, PR China.

NCBI tax id

  • NCBI tax id: 1642821
  • Matching level: species

strain history

  • @ref: 67770
  • history: Y. Wang; Sch. of Life Sci. & Technol., Xin Xiang Med. Univ., China; RZB5-4.

doi: 10.13145/bacdive141062.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Shewanellaceae
  • genus: Shewanella
  • species: Shewanella gelidii
  • full scientific name: Shewanella gelidii Wang et al. 2016

@ref: 43941

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella gelidii

strain designation: RZB5-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43941negative1.5-2.5 µm0.5-1.0 µmrod-shapedyespolar
69480yes96.711
69480negative99.971

colony morphology

  • @ref: 43941
  • colony size: 1.0-2.0 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 1 day
  • medium used: Marine ahar 2216

Culture and growth conditions

culture medium

  • @ref: 43941
  • name: Marine ahar 2216
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43941positivegrowth4-32
43941positiveoptimum24-28
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43941positivegrowth6.0-10.0alkaliphile
43941positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43941
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
43941no
69481no100
69480no99.962

halophily

@refsaltgrowthtested relationconcentration
43941NaClpositivegrowth1-5 %(w/v)
43941NaClpositiveoptimum2-3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4394117634D-glucose-builds acid from
4394117992sucrose-builds acid from
4394130089acetate-carbon source
4394116150benzoate-carbon source
4394117057cellobiose-carbon source
4394116947citrate-carbon source
4394112936D-galactose-carbon source
4394117634D-glucose-carbon source
4394116024D-mannose-carbon source
4394165327D-xylose-carbon source
4394116449dl-alanine-carbon source
4394128757fructose-carbon source
4394117754glycerol-carbon source
4394115978glycerol 3-phosphate-carbon source
4394117268myo-inositol-carbon source
4394115971L-histidine-carbon source
4394117295L-phenylalanine-carbon source
4394117203L-proline-carbon source
4394117716lactose-carbon source
4394117306maltose-carbon source
4394144337N-acetyl-L-glutamate-carbon source
43941506227N-acetylglucosamine-carbon source
4394117992sucrose-carbon source
4394117029chitin-hydrolysis
4394128017starch-hydrolysis
4394153426tween 80-hydrolysis
4394116199urea-hydrolysis
4394124996lactate+carbon source
4394115603L-leucine+carbon source
4394115729L-ornithine+carbon source
4394125094lysine+carbon source
4394153424tween 20+carbon source
4394153423tween 40+carbon source
4394153425tween 60+carbon source
4394153426tween 80+carbon source
43941casein+hydrolysis
4394116991dna+hydrolysis
439414853esculin+hydrolysis
439415291gelatin+hydrolysis
4394153424tween 20+hydrolysis
4394153423tween 40+hydrolysis
4394153425tween 60+hydrolysis
4394117632nitrate+reduction
4394153424tween 20+/-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4394128971ampicillinyesyes10 µg (disc)
439413393carbenicillinyesyes100 µg (disc)
439413493cefoperazoneyesyes75 µg (disc)
4394148923erythromycinyesyes15 µg (disc)
4394131845midecamycinyesyes30 µg (disc)
43941100246norfloxacinyesyes10 µg (disc)
439417731ofloxacinyesyes5 µg (disc)
43941100241ciprofloxacinyesyes5 µg (disc)
4394117698chloramphenicolyesyes30 µg (disc)
439413508ceftazidimeyesyes30 µg (disc)
439413534cephalexinyesyes30 µg (disc)
439413770co-trimoxazoleyesyes25 µg (disc)
4394117334penicillinyesyes10 µg (disc)
439417809oxacillinyesyes1 µg (disc)
439418232piperacillinyesyes100 µg (disc)
439413547cephradineyesyes30 µg (disc)
439412637amikacinyesyes30 µg (disc)
4394117833gentamicinyesyes10 µg (disc)
439416104kanamycinyesyes30 µg (disc)
4394127902tetracyclineyesyes30 µg (disc)
439417507neomycinyesyes30 µg (disc)
4394150845doxycyclineyesyes30 µg (disc)
4394128001vancomycinyesyes30 µg (disc)
439418309polymyxin byesyes300 µg (disc)
4394150694minocyclineyesyes30 µg (disc)
439413745clindamycinyesyes2 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4394135581indoleno
4394116136hydrogen sulfideyes

enzymes

@refvalueactivityec
43941cytochrome oxidase+1.9.3.1
43941catalase+1.11.1.6
43941alkaline phosphatase+3.1.3.1
43941esterase (C 4)+
43941esterase Lipase (C 8)+
43941leucine arylamidase+3.4.11.1
43941alpha-chymotrypsin+3.4.21.1
43941acid phosphatase+3.1.3.2
43941naphthol-AS-BI-phosphohydrolase+
43941lipase (C 14)-
43941trypsin-3.4.21.4
43941valine arylamidase-
43941cystine arylamidase-3.4.11.3
43941alpha-galactosidase-3.2.1.22
43941beta-galactosidase-3.2.1.23
43941beta-glucuronidase-3.2.1.31
43941alpha-glucosidase-3.2.1.20
43941beta-glucosidase-3.2.1.21
43941N-acetyl-beta-glucosaminidase-3.2.1.52
43941alpha-mannosidase-3.2.1.24
43941alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43941C15:0 anteiso1
    43941C10:01.8
    43941C11:0 3OH1.5
    43941C12:0 3OH1.7
    43941C14:02.6
    43941C15:1ω8c0.8
    43941C16:020.2
    43941C16:1ω7c / C16:1ω6c23.3
    43941C17:02.9
    43941C17:1ω8c7.4
    43941C18:01.2
    43941C18:1ω7c / C18:1ω6c2
    43941C18:1ω9c0.9
    43941C11:0 iso 3OH3.3
    43941C13:0 iso1.2
    43941C13:0 iso 3OH1
    43941C14:0 iso0.9
    43941C15:0 iso18.9
    43941C16:0 iso1.8
    43941C17:0 iso1.7
    43941C17:1 iso I /C17:1 anteiso B3.7
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 25
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6 6.10
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture temperaturehost species
43941red algae Gelidium amansii collected from the coastal region of Rizhao, Yellow Sea, PR China2014-11Rizhao, Yellow SeaChinaCHNAsia35.517119.625Marine agar 221625
67770Red algae Gelidium amansii from the coastal region of RizhaoChinaCHNAsiaGelidium amansii

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Aquatic#Marine
#Host#Algae#Red algae

Sequence information

16S sequences

  • @ref: 43941
  • description: partial 16S rRNA gene sequence
  • accession: KR080702
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella gelidii JCM 30804GCA_014647855scaffoldncbi1642821
66792Shewanella gelidii strain JCM 308041642821.3wgspatric1642821
66792Shewanella gelidii KCTC 42663GCA_023283645contigncbi1642821

GC content

  • @ref: 67770
  • GC-content: 47
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes91.589yes
gram-positiveno98.866no
anaerobicno95.329yes
aerobicno74.1yes
halophileyes60.362no
spore-formingno96.454no
thermophileno99.359yes
glucose-utilyes84.08yes
motileyes91.692yes
glucose-fermentno56.64no

External links

@ref: 43941

culture collection no.: JCM 30804, KCTC 42663, MCCC 1K00697

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27064664Shewanella gelidii sp. nov., isolated from the red algae Gelidium amansii, and emended description of Shewanella waksmanii.Wang Y, Chen H, Liu Z, Ming H, Zhou C, Zhu X, Zhang P, Jing C, Feng HInt J Syst Evol Microbiol10.1099/ijsem.0.0010752016Bacterial Typing Techniques, Base Composition, China, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodophyta/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31778351Shewanella maritima sp. nov., a facultative anaerobic marine bacterium isolated from seawater, and emended description of Shewanella intestini.Bae SS, Jung YH, Baek KInt J Syst Evol Microbiol10.1099/ijsem.0.0039162020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/isolation & purificationTranscriptome

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
43941Yan Wang, Hongli Chen, Zhenhua Liu, Hong Ming, Chenyan Zhou, Xinshu Zhu, Peng Zhang, Changqin Jing, Huigen FengShewanella gelidii sp. nov., isolated from the red algae Gelidium amansii, and emended description of Shewanella waksmanii10.1099/ijsem.0.001075IJSEM 66: 2899-2905 201627064664
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1