Strain identifier

BacDive ID: 1260

Type strain: Yes

Species: Bacillus alveayuensis

Strain Designation: TM1

Strain history: CIP <- 2005, JCM <- 2004, S. J. Kim: strain TM1

NCBI tax ID(s): 279215 (species)

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General

@ref: 7883

BacDive-ID: 1260

DSM-Number: 19092

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive, motile, rod-shaped

description: Bacillus alveayuensis TM1 is an aerobe, spore-forming, thermophilic bacterium that was isolated from deep sea sediment.

NCBI tax id

  • NCBI tax id: 279215
  • Matching level: species

strain history

@refhistory
7883<- JCM <-S.-J. Kim, strain TM1
67770S.-J. Kim TM1.
116270CIP <- 2005, JCM <- 2004, S. J. Kim: strain TM1

doi: 10.13145/bacdive1260.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 7883

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus alveayuensis

full scientific name: Bacillus alveayuensis Bae et al. 2005

strain designation: TM1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31374positive3.8 µm0.75 µmrod-shapedyes
116270positiverod-shapedyes

colony morphology

  • @ref: 116270
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7883BACTO 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
38310Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116270CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116270CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7883positivegrowth55thermophilic
31374positivegrowth40-65thermophilic
31374positiveoptimum55thermophilic
38310positivegrowth55thermophilic
67770positivegrowth55thermophilic

culture pH

@refabilitytypepHPH range
31374positivegrowth6.5-9.0alkaliphile
31374positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31374aerobe
116270obligate aerobe

spore formation

@refspore formation
31374yes
116270yes

halophily

@refsaltgrowthtested relationconcentration
31374NaClpositivegrowth3.0-4.0 %
31374NaClpositiveoptimum3 %

observation

  • @ref: 31374
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31374581435-dehydro-D-gluconate+carbon source
3137428757fructose+carbon source
3137417754glycerol+carbon source
3137417306maltose+carbon source
3137437684mannose+carbon source
3137417992sucrose+carbon source
3137427082trehalose+carbon source
313744853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
11627017632nitrate-reduction
11627016301nitrite-reduction

enzymes

@refvalueactivityec
31374catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116270oxidase+
116270alcohol dehydrogenase-1.1.1.1
116270catalase+1.11.1.6
116270lysine decarboxylase-4.1.1.18
116270ornithine decarboxylase-4.1.1.17
116270urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116270-+++-------+---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116270+/----------+/-+/-+/---------------+/---+/-+/--------+/--+/-------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
7883deep sea sedimentAyu Trough
67770Deep sea sediment of the Ayu Trough (4000 m below sea level) in the western Pacific Ocean
116270Environment, Deep-sea sediments of the Ayu TroughPacific Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_89288.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1802;97_27076;98_61624;99_89288&stattab=map
  • Last taxonomy: Bacillus alveayuensis subclade
  • 16S sequence: AY605232
  • Sequence Identity:
  • Total samples: 366
  • soil counts: 104
  • aquatic counts: 116
  • animal counts: 122
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78831Risk group (German classification)
1162701Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7883
  • description: Bacillus alveayuensis strain TM1 16S ribosomal RNA gene, partial sequence
  • accession: AY605232
  • length: 1532
  • database: ena
  • NCBI tax ID: 279215

Genome sequences

  • @ref: 66792
  • description: Bacillus alveayuensis DSM 19092
  • accession: 2926480455
  • assembly level: draft
  • database: img
  • NCBI tax ID: 279215

GC content

@refGC-contentmethod
788338.7
6777038.7thermal denaturation, midpoint method (Tm)

External links

@ref: 7883

culture collection no.: DSM 19092, CIP 108784, JCM 12523, KCTC 10634

straininfo link

  • @ref: 70916
  • straininfo: 138968

literature

  • topic: Phylogeny
  • Pubmed-ID: 15879257
  • title: Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough.
  • authors: Bae SS, Lee JH, Kim SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63424-0
  • year: 2005
  • mesh: Bacillus/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Geologic Sediments/*microbiology, Growth Inhibitors/pharmacology, Hot Temperature, Molecular Sequence Data, Movement, Pacific Ocean, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Spores, Bacterial/cytology, Water Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7883Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19092)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19092
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
31374Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2768728776041
38310Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6451
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/
68371Automatically annotated from API 50CH acid
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
70916Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138968.1StrainInfo: A central database for resolving microbial strain identifiers
116270Curators of the CIPCollection of Institut Pasteur (CIP 108784)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108784