Strain identifier

BacDive ID: 1357

Type strain: Yes

Species: Halolactibacillus halophilus

Strain Designation: M2-2

Strain history: IAM 15242 <-- M. Ishikawa and K. Yamasato M2-2.

NCBI tax ID(s): 306540 (species)

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General

@ref: 6740

BacDive-ID: 1357

DSM-Number: 17073

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, motile, rod-shaped

description: Halolactibacillus halophilus M2-2 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from living sponge.

NCBI tax id

  • NCBI tax id: 306540
  • Matching level: species

strain history

@refhistory
6740<- M. Ishikawa, M2-2
67770IAM 15242 <-- M. Ishikawa and K. Yamasato M2-2.

doi: 10.13145/bacdive1357.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halolactibacillus
  • species: Halolactibacillus halophilus
  • full scientific name: Halolactibacillus halophilus Ishikawa et al. 2005

@ref: 6740

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Halolactibacillus

species: Halolactibacillus halophilus

full scientific name: Halolactibacillus halophilus Ishikawa et al. 2005

strain designation: M2-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
22995positive3.6-4.5 µm0.6-0.9 µmrod-shapedyesperitrichous
69480yes90.757
69480positive100

Culture and growth conditions

culture medium

  • @ref: 6740
  • name: BOGORIELLA MEDIUM (DSMZ Medium 785)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/785
  • composition: Name: BOGORIELLA MEDIUM (DSMZ Medium 785) Composition: NaCl 40.0 g/l Glucose 10.0 g/l Na2CO3 10.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6740positivegrowth30mesophilic
22995positivegrowth10.0-40.0
22995positiveoptimum30.0-37.0mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
22995positiveoptimum8.0-9.0alkaliphile
22995positivegrowth6.5-9.5

Physiology and metabolism

oxygen tolerance

  • @ref: 6740
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
22995no
69480no98.804

halophily

@refsalttested relationconcentrationgrowthhalophily level
22995NaCloptimum2.0-3.0 %
22995NaClgrowth0.0-24.0 %positive
22995slightly halophilic
22995halotolerant

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2299515963ribitol-fermentation
2299517108D-arabinose-fermentation
229956731melezitose-fermentation
2299563150D-rhamnose-fermentation
2299517924D-sorbitol-fermentation
2299565327D-xylose-fermentation
2299516813galactitol-fermentation
2299515443inulin-fermentation
2299530849L-arabinose-fermentation
2299517268myo-inositol-fermentation
22995casein-hydrolysis
2299317632nitrate-reduction
2299517057cellobiose+fermentation
2299515824D-fructose+fermentation
2299512936D-galactose+fermentation
2299517634D-glucose+fermentation
2299516899D-mannitol+fermentation
2299516024D-mannose+fermentation
2299516634raffinose+fermentation
2299516988D-ribose+fermentation
2299516551D-trehalose+fermentation
2299517754glycerol+fermentation
2299517716lactose+fermentation
2299517306maltose+fermentation
2299528053melibiose+fermentation
22995320061methyl alpha-D-glucopyranoside+fermentation
2299517814salicin+fermentation
2299528017starch+fermentation
2299517992sucrose+fermentation

enzymes

@refvalueactivityec
22995catalase-1.11.1.6
22995cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
22995living spongeOura beach,Miura Peninsula,Kanagawa PrefectureJapanJPNAsia35.1333139.667
6740decaying marine algaOura beach, Miura Peninsula, Kanagawa PrefectureJapanJPNAsia
67770Decaying marine alga at Oura beachMiura Peninsula, Kanagawa Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Porifera (Sponges)

taxonmaps

  • @ref: 69479
  • File name: preview.99_36487.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3777;97_4656;98_26886;99_36487&stattab=map
  • Last taxonomy: Halolactibacillus halophilus subclade
  • 16S sequence: AB362694
  • Sequence Identity:
  • Total samples: 542
  • soil counts: 44
  • aquatic counts: 180
  • animal counts: 307
  • plant counts: 11

Safety information

risk assessment

  • @ref: 6740
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halolactibacillus halophilus gene for 16S rRNA, partial sequence, strain: NRIC 0628AB3626941558ena306540
20218Halolactibacillus halophilus gene for 16S rRNA, partial sequence, strain: NBRC 100868AB6812731489ena306540
6740Halolactibacillus halophilus gene for 16S rRNA, partial sequenceAB1967831491ena306540

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halolactibacillus halophilus strain DSM 17073306540.4wgspatric306540
66792Halolactibacillus halophilus strain NBRC 100868306540.5wgspatric306540
66792Halolactibacillus halophilus DSM 170732675903232draftimg306540
67770Halolactibacillus halophilus NBRC 100868GCA_007990285contigncbi306540
67770Halolactibacillus halophilus DSM 17073GCA_900115605scaffoldncbi306540

GC content

@refGC-contentmethod
674040.2
6777040.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes58no
gram-positiveyes90.575yes
anaerobicno91.908no
halophileyes87.394no
spore-formingno63.366no
glucose-utilyes88.211no
motileyes84.472yes
flagellatedyes61.24yes
aerobicno93.369no
thermophileno93.609no
glucose-fermentyes64.935yes

External links

@ref: 6740

culture collection no.: DSM 17073, IAM 15242, NBRC 100868, NRIC 0628, JCM 21694

straininfo link

  • @ref: 71008
  • straininfo: 281447

literature

  • topic: Phylogeny
  • Pubmed-ID: 16280507
  • title: Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1.
  • authors: Ishikawa M, Nakajima K, Itamiya Y, Furukawa S, Yamamoto Y, Yamasato K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63713-0
  • year: 2005
  • mesh: Animals, Bacillaceae/*classification/genetics/isolation & purification, Bacillus/*classification/genetics, Base Composition, DNA, Ribosomal/analysis, Hydrogen-Ion Concentration, Lactic Acid/metabolism, *Marine Biology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6740Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17073)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17073
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
22993Yi-Guang Chen,Yu-Qin Zhang,Zhu-Xiang Liu,Da-Chun Zhuang,Hans-Peter Klenk,Shu-Kun Tang,Xiao-Long Cui,Wen-Jun Li10.1099/ijs.0.010801-0Halobacillus salsuginis sp. nov., a moderately halophilic bacterium from a subterranean brineIJSEM 59: 2505-2509 200919622644
22995Morio Ishikawa,Kazuyuki Nakajima,Yuko Itamiya,Sayumi Furukawa,Yasushi Yamamoto,Kazuhide Yamasato10.1099/ijs.0.63713-0Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1IJSEM 55: 2427-2439 200516280507
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
71008Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281447.1StrainInfo: A central database for resolving microbial strain identifiers