Strain identifier

BacDive ID: 159735

Type strain: Yes

Species: Amylibacter kogurei

Strain Designation: 4G11

Strain history: <- Wong Shu Kuan, The Univ. of Tokyo

NCBI tax ID(s): 1889778 (species)

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General

@ref: 66644

BacDive-ID: 159735

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

description: Amylibacter kogurei 4G11 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from SML water sample.

NCBI tax id

  • NCBI tax id: 1889778
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Wong Shu Kuan, The Univ. of Tokyo

doi: 10.13145/bacdive159735.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Amylibacter
  • species: Amylibacter kogurei
  • full scientific name: Amylibacter kogurei Wong et al. 2018

@ref: 66644

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Amylibacter

species: Amylibacter kogurei

strain designation: 4G11

type strain: yes

Morphology

cell morphology

  • @ref: 66644
  • gram stain: negative
  • cell length: 0.76-2.47 µm
  • cell width: 0.39-0.7 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 66644
  • colony color: white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: 1/2-strength marine agar

Culture and growth conditions

culture medium

  • @ref: 66644
  • name: 1/2-strength marine agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66644positiveoptimum15-30
66644positivegrowth5-30
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
66644positivegrowth4-12alkaliphile
66644positiveoptimum7-10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66644aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
66644NaClpositivegrowth1-7 %(w/v)
66644NaClpositiveoptimum5-7 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
666446731melezitose+builds acid from
6664415443inulin+builds acid from
6664415824D-fructose+builds acid from
6664416024D-mannose+builds acid from
6664416634raffinose+builds acid from
6664417057cellobiose+builds acid from
6664417151xylitol+builds acid from
6664417268myo-inositol+builds acid from
6664417634D-glucose+builds acid from
6664417716lactose+builds acid from
6664417814salicin+builds acid from
6664417992sucrose+builds acid from
6664418305arbutin+builds acid from
6664427082trehalose+builds acid from
6664427613amygdalin+builds acid from
6664428017starch+builds acid from
6664428087glycogen+builds acid from
6664430849L-arabinose+builds acid from
6664433942ribose+builds acid from
66644581435-dehydro-D-gluconate+builds acid from
6664459640N-acetylglucosamine+builds acid from
6664462345L-rhamnose+builds acid from
66644320061methyl alpha-D-glucopyranoside+builds acid from
666445291gelatin-hydrolysis
6664485146carboxymethylcellulose-hydrolysis
66644crab shell chitin-hydrolysis
666444853esculin+hydrolysis
6664416199urea+hydrolysis
6664416991dna+hydrolysis
6664428017starch+hydrolysis
6664417632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6664415688acetoinyes
6664435581indoleno

enzymes

@refvalueactivityec
66644acid phosphatase-3.1.3.2
66644alpha-chymotrypsin-3.4.21.1
66644alpha-fucosidase-3.2.1.51
66644alpha-galactosidase-3.2.1.22
66644alpha-mannosidase-3.2.1.24
66644beta-galactosidase-3.2.1.23
66644beta-glucosidase-3.2.1.21
66644beta-glucuronidase-3.2.1.31
66644N-acetyl-beta-glucosaminidase-3.2.1.52
66644trypsin-3.4.21.4
66644alkaline phosphatase+3.1.3.1
66644alpha-glucosidase+3.2.1.20
66644catalase+1.11.1.6
66644cystine arylamidase+3.4.11.3
66644cytochrome oxidase+1.9.3.1
66644esterase (C 4)+
66644esterase Lipase (C 8)+
66644leucine arylamidase+3.4.11.1
66644lipase (C 14)+
66644naphthol-AS-BI-phosphohydrolase+
66644valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66644C18:01.1
    66644C12:11.6
    66644C18:26.7
    66644C16:08.7
    66644C18:181.9
  • type of FA analysis: whole cell analysis
  • incubation medium: 1/2-strength marine agar
  • incubation temperature: 25
  • incubation time: 3
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
66644SML water samplenear the pier of the University of Tokyo's Misaki Marine Biological Station at Misaki, Kanagawa PrefectureJapanJPNAsia35.1583139.6081/10-strength ZoBell agar medium(0.5 g peptone, 0.1 g yeast extract, 15 g agar in 800 ml natural seawater aged for at least 1 year and 200 ml distilled water)4 days20Aliquots of 100 µl seawater from the SML were plated onto 1/10-strength ZoBell agar medium. Initial incubation was carried out at 20°C for 4 days.
67771From seawater, surface microlayercoastal waterJapanJPNAsia35.1577139.612

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Sequence information

16S sequences

  • @ref: 66644
  • description: Amylibacter sp. strain 4G11 16S ribosomal RNA gene, partial sequence
  • accession: KY463497
  • length: 1282
  • database: ena
  • NCBI tax ID: 1889778

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amylibacter kogurei 4G11GCA_002742285contigncbi1889778
66792Amylibacter kogurei 4G112788500138draftimg1889778

GC content

  • @ref: 66644
  • GC-content: 50
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 66644

culture collection no.: KY 463497, KCTC 52506, NBRC 112428

literature

  • topic: Phylogeny
  • Pubmed-ID: 30016227
  • title: Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet.
  • authors: Wong SK, Yoshizawa S, Nakajima Y, Cuadra MJ, Nogi Y, Nakamura K, Takami H, Ogura Y, Hayashi T, Chiura HX, Hamasaki K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002911
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Bays, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/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
66644Shu-Kuan Wong, Susumu Yoshizawa, Yu Nakajima, Marie Johanna Cuadra, Yuichi Nogi, Keiji Nakamura, Hideto Takami, Yoshitoshi Ogura, Tetsuya Hayashi, Hiroshi Xavier Chiura, Koji HamasakiAmylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet10.1099/ijsem.0.002911IJSEM 68: 2872-2877 201830016227
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc