Strain identifier

BacDive ID: 140769

Type strain: Yes

Species: Limibaculum halophilum

Strain history: <- Wonyong Kim, Chung-Ang Univ.

NCBI tax ID(s): 1902428 (species)

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General

@ref: 64912

BacDive-ID: 140769

DSM-Number: 108279

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

description: Limibaculum halophilum KCTC 52187 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from reclaimed land mud.

NCBI tax id

  • NCBI tax id: 1902428
  • Matching level: species

strain history

@refhistory
64912<- Y. Muramatsu, NBRC; NBRC 112522 <- W. Kim, Chung-Ang Univ., Seoul, Republic of Korea; CAU 1123
67771<- Wonyong Kim, Chung-Ang Univ.

doi: 10.13145/bacdive140769.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Limibaculum
  • species: Limibaculum halophilum
  • full scientific name: Limibaculum halophilum Shin et al. 2017

@ref: 64912

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Limibaculum

species: Limibaculum halophilum

full scientific name: Limibaculum halophilum Shin et al. 2017

type strain: yes

Morphology

cell morphology

  • @ref: 43547
  • gram stain: negative
  • cell length: 1.2-1.9 µm
  • cell width: 0.6-1.3 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43547
  • colony size: 0.2-0.3 mm
  • colony color: cream coloured
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43547Marine agar (MA)yes
64912BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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

@refgrowthtypetemperature
43547positivegrowth20-40
43547positiveoptimum37
64912positivegrowth30
67771positivegrowth37

culture pH

@refabilitytypepHPH range
43547positivegrowth6.5-9alkaliphile
43547positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43547aerobe
67771aerobe

spore formation

  • @ref: 43547
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43547NaClpositivegrowth0-7 %(w/v)
43547NaClpositiveoptimum2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4354717128adipate-assimilation
4354727689decanoate-assimilation
4354716899D-mannitol-assimilation
4354716024D-mannose-assimilation
4354730849L-arabinose-assimilation
4354725115malate-assimilation
4354717306maltose-assimilation
43547506227N-acetylglucosamine-assimilation
4354718401phenylacetate-assimilation
4354732032potassium gluconate-assimilation
4354715824D-fructose-carbon source
4354712936D-galactose-carbon source
4354717634D-glucose-carbon source
4354716899D-mannitol-carbon source
4354716988D-ribose-carbon source
4354765327D-xylose-carbon source
4354730849L-arabinose-carbon source
4354717716lactose-carbon source
4354715824D-fructose-energy source
4354712936D-galactose-energy source
4354717634D-glucose-energy source
4354716899D-mannitol-energy source
4354716988D-ribose-energy source
4354765327D-xylose-energy source
4354730849L-arabinose-energy source
4354717716lactose-energy source
43547casein-hydrolysis
4354750144sodium pyruvate-hydrolysis
4354728017starch-hydrolysis
4354716199urea-hydrolysis
4354753258sodium citrate+assimilation
4354718333D-arabitol+carbon source
4354716443D-tagatose+carbon source
4354718287L-fucose+carbon source
43547potassium 5-dehydro-D-gluconate+carbon source
4354717151xylitol+carbon source
4354718333D-arabitol+energy source
4354716443D-tagatose+energy source
4354718287L-fucose+energy source
43547potassium 5-dehydro-D-gluconate+energy source
4354717151xylitol+energy source
4354716947citrate+hydrolysis
435474853esculin+hydrolysis
435475291gelatin+hydrolysis
4354717632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
43547esterase (C 4)+
43547esterase Lipase (C 8)+
43547leucine arylamidase+3.4.11.1
43547valine arylamidase+
43547cystine arylamidase+3.4.11.3
43547acid phosphatase+3.1.3.2
43547naphthol-AS-BI-phosphohydrolase+
43547N-acetyl-beta-glucosaminidase+3.2.1.52
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43547C10:0 3OH1.7
    43547C12:1 3OH3.4
    43547C16:06.5
    43547C16:1ω7c / C16:1ω6c1.2
    43547C18:01.9
    43547C18:1ω7c73.6
    4354711-methyl C18:1ω7c8.7
    43547C18:1ω9c0.7
    43547unknown 18.846 / C19:1ω6c / cyclo-C19:1.1
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • agar/liquid: agar
  • incubation temperature: 37
  • incubation time: 3
  • incubation_oxygen: aerobic
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64912-----++/--------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64912+----+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43547reclaimed land mudModoRepublic of KoreaKORAsia37.536126.414
64912Soil of reclaimed landModo (37° 32' 12.28'' N, 126° 24' 51.47'' E)Republic of KoreaKORAsia37.5367126.414
67771From soil of reclaim landModo, IncheonRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_54571.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_866;96_24368;97_30491;98_39007;99_54571&stattab=map
  • Last taxonomy: Limibaculum halophilum subclade
  • 16S sequence: KX774334
  • Sequence Identity:
  • Total samples: 365
  • soil counts: 131
  • aquatic counts: 201
  • animal counts: 33

Safety information

risk assessment

  • @ref: 64912
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64912
  • description: Limibaculum halophilum strain CAU 1123 16S ribosomal RNA gene, partial sequence
  • accession: KX774334
  • length: 1403
  • database: nuccore
  • NCBI tax ID: 1902428

GC content

  • @ref: 43547
  • GC-content: 71.1
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64912

culture collection no.: KCTC 52187, NBRC 112522, DSM 108279, CAU 1123

straininfo link

  • @ref: 96786
  • straininfo: 403089

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28879850Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae.Shin YH, Kim JH, Suckhoom A, Kantachote D, Kim WInt J Syst Evol Microbiol10.1099/ijsem.0.0022002017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny34424448Thermohalobaculum xanthum gen. nov., sp. nov., a moderately thermophilic bacterium isolated from mangrove sediment.Pan X, Li Z, Li F, Huang Y, Wang Q, Huang S, Hu W, Jiang MAntonie Van Leeuwenhoek10.1007/s10482-021-01641-42021Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis, *Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae, Sequence Analysis, DNA, UbiquinoneTranscriptome
Phylogeny35439113Algiphilus acroporae sp. nov. and Coraliihabitans acroporae gen. nov. sp. nov., isolated from scleractinian coral Acropora digitifera.Sun H, Zheng H, Liao B, Chen B, Li A, Xiao BInt J Syst Evol Microbiol10.1099/ijsem.0.0053212022Animals, *Anthozoa/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylglycerols/analysis, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Ubiquinone/chemistryTranscriptome
Phylogeny36269565Limibaculum sediminis sp. nov., isolated from mangrove sediment.Huang Y, Liu L, Li J, Pan J, Li MInt J Syst Evol Microbiol10.1099/ijsem.0.0055802022RNA, Ribosomal, 16S/genetics, Phylogeny, *Sodium Chloride, Base Composition, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Sequence Analysis, DNA, Phospholipids/chemistry, Glycolipids/chemistry, Phosphatidylglycerols, Quinones, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43547Yong Ho Shin, Jong-Hwa Kim, Ampaitip Suckhoom, Duangporn Kantachote, Wonyong KimLimibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae10.1099/ijsem.0.002200IJSEM 67: 3812-3818 201728879850
64912Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108279Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108279)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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/
96786Reimer, 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-ID403089.1