Strain identifier

BacDive ID: 24013

Type strain: Yes

Species: Limibacter armeniacum

Strain Designation: YM11-185

Strain history: <- JW Yoon, Tokyo Univ., Japan

NCBI tax ID(s): 466084 (species)

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General

@ref: 21184

BacDive-ID: 24013

DSM-Number: 26026

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

description: Limibacter armeniacum YM11-185 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from shore sediment sample.

NCBI tax id

  • NCBI tax id: 466084
  • Matching level: species

strain history

@refhistory
21184<- KCTC; KCTC 22132
67771<- JW Yoon, Tokyo Univ., Japan

doi: 10.13145/bacdive24013.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Flammeovirgaceae
  • genus: Limibacter
  • species: Limibacter armeniacum
  • full scientific name: Limibacter armeniacum Yoon et al. 2008

@ref: 21184

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Flammeovirgaceae

genus: Limibacter

species: Limibacter armeniacum

full scientific name: Limibacter armeniacum Yoon et al. 2008

strain designation: YM11-185

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
32507negative27.5 µm0.4 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative

pigmentation

  • @ref: 32507
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21184
  • 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
21184positivegrowth28mesophilic
32507positivegrowth17-37
32507positiveoptimum28.5mesophilic
67771positivegrowth27-30mesophilic

culture pH

@refabilitytypepHPH range
32507positivegrowth07-09alkaliphile
32507positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32507aerobe
67771aerobe

spore formation

@refspore formation
32507no
67771no

halophily

  • @ref: 32507
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-6.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3250740585alpha-cyclodextrin+carbon source
3250722599arabinose+carbon source
3250717057cellobiose+carbon source
3250723652dextrin+carbon source
3250728260galactose+carbon source
3250728087glycogen+carbon source
3250717716lactose+carbon source
3250717306maltose+carbon source
3250737684mannose+carbon source
32507506227N-acetylglucosamine+carbon source
3250727082trehalose+carbon source

enzymes

@refvalueactivityec
32507acid phosphatase+3.1.3.2
32507alkaline phosphatase+3.1.3.1
32507catalase+1.11.1.6
32507gelatinase+
32507cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21184shore sediment sampleCarp Island (07° 05' 22.9'' N 134° 16' 46.4'' E)PalauPLWAustralia and Oceania
67771From marine sedimentPalauPLWAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_66544.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6541;96_28813;97_36316;98_46964;99_66544&stattab=map
  • Last taxonomy: Limibacter armeniacum subclade
  • 16S sequence: AB359907
  • Sequence Identity:
  • Total samples: 106
  • soil counts: 46
  • aquatic counts: 55
  • animal counts: 3
  • plant counts: 2

Safety information

risk assessment

  • @ref: 21184
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21184
  • description: Limibacter armeniacum gene for 16S rRNA, partial sequence, strain: YM11-185
  • accession: AB359907
  • length: 1467
  • database: ena
  • NCBI tax ID: 466084

GC content

@refGC-contentmethod
2118427.9high performance liquid chromatography (HPLC)
3250727.8-27.9
6777127.9

External links

@ref: 21184

culture collection no.: DSM 26026, KCTC 22132, MBIC 08286

straininfo link

  • @ref: 87987
  • straininfo: 405754

literature

  • topic: Phylogeny
  • Pubmed-ID: 18398206
  • title: Limibacter armeniacum gen. nov., sp. nov., a novel representative of the family 'Flammeovirgaceae' isolated from marine sediment.
  • authors: Yoon J, Matsuo Y, Kasai H, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65595-0
  • year: 2008
  • mesh: Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Genes, Bacterial, Geologic Sediments/microbiology, Molecular Sequence Data, Palau, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic, Vitamin K 2/metabolism
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21184Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26026Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26026)
32507Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172872728776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/
87987Reimer, 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-ID405754.1