Strain identifier

BacDive ID: 1222

Type strain: Yes

Species: Caldalkalibacillus mannanilyticus

Strain Designation: AM-001

Strain history: CIP <- 2005, JCM <- 1999, K. Horikoshi, Japan Ag. Marine-Earth Science Technol., Yokosuka, Japan: strain AM-001

NCBI tax ID(s): 1236954 (strain), 1418 (species)

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General

@ref: 6305

BacDive-ID: 1222

DSM-Number: 16130

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

description: Caldalkalibacillus mannanilyticus AM-001 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1236954strain
1418species

strain history

@refhistory
6305<- Y. Nogi <- T. Akino and N. Nakamura; AM-001
67770K. Horikoshi AM-001.
120779CIP <- 2005, JCM <- 1999, K. Horikoshi, Japan Ag. Marine-Earth Science Technol., Yokosuka, Japan: strain AM-001

doi: 10.13145/bacdive1222.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Caldalkalibacillus
  • species: Caldalkalibacillus mannanilyticus
  • full scientific name: Caldalkalibacillus mannanilyticus (Nogi et al. 2005) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus mannanilyticus

@ref: 6305

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Caldalkalibacillus

species: Caldalkalibacillus mannanilyticus

full scientific name: Caldalkalibacillus mannanilyticus (Nogi et al. 2005) Gupta et al. 2020

strain designation: AM-001

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31483variable4.5 µm0.7 µmrod-shapedyes
69480yes95.534
69480positive100
120779positiverod-shapedyes

colony morphology

  • @ref: 120779

pigmentation

  • @ref: 31483
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6305ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
36776MEDIUM 648 - for Bacillus oshimensisyesDistilled water make up to (900.000 ml);Sodium chloride (10.000 g);Magnesium sulphate heptahydrate (0.200 g);Agar (15.000 g);Glucose (10.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.000 g);Polypeptone (5.000 g);Sodium carbonate soluti
120779CIP Medium 648yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=648

culture temp

@refgrowthtypetemperaturerange
6305positivegrowth30mesophilic
31483positivegrowth20-45
31483positiveoptimum37mesophilic
36776positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31483positivegrowth08-10alkaliphile
31483positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31483aerobe
120779obligate aerobe

spore formation

@refspore formationconfidence
31483yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
31483NaClpositivegrowth0-4 %
31483NaClpositiveoptimum2 %

observation

@refobservation
31483aggregates in clumps
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3148328757fructose+carbon source
3148328260galactose+carbon source
3148317234glucose+carbon source
3148317754glycerol+carbon source
3148317716lactose+carbon source
3148317306maltose+carbon source
3148329864mannitol+carbon source
3148337684mannose+carbon source
3148316634raffinose+carbon source
3148330911sorbitol+carbon source
3148317992sucrose+carbon source
3148327082trehalose+carbon source
3148353424tween 20+carbon source
3148353423tween 40+carbon source
3148353425tween 60+carbon source
3148318222xylose+carbon source
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
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-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
6837116024D-mannose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12077917632nitrate+reduction
12077916301nitrite-reduction

metabolite production

  • @ref: 120779
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31483catalase+1.11.1.6
31483gelatinase+
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
67770beta-mannosidase3.2.1.25
120779oxidase+
120779alcohol dehydrogenase-1.1.1.1
120779catalase+1.11.1.6
120779lysine decarboxylase-4.1.1.18
120779ornithine decarboxylase-4.1.1.17
120779urease-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
120779--+---------+--+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120779----+/-+/-----+/-+/-------+/--+/------+/-+/---+/-+/---+/-+/-+/------------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6305soilTokyoJapanJPNAsia
67770SoilKunitachi, TokyoJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5334.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2581;97_3163;98_3975;99_5334&stattab=map
  • Last taxonomy: Bacillus mannanilyticus subclade
  • 16S sequence: AB043864
  • Sequence Identity:
  • Total samples: 619
  • soil counts: 313
  • aquatic counts: 106
  • animal counts: 181
  • plant counts: 19

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63051Risk group (German classification)
1207791Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31483
  • description: Bacillus mannanilyticus gene for 16S rRNA
  • accession: AB043864
  • length: 1547
  • database: nuccore
  • NCBI tax ID: 1418

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus mannanilyticus JCM 105961236954.3wgspatric1236954
66792Bacillus mannanilyticus JCM 105962565956590draftimg1236954
67770Caldalkalibacillus mannanilyticus JCM 10596GCA_000615945contigncbi1236954

GC content

@refGC-contentmethod
3148337.4
6777037.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes91.395no
gram-positiveyes77.307no
anaerobicno95.79yes
aerobicyes73.505no
halophileno87.678no
spore-formingyes95.206yes
glucose-utilyes90.079no
flagellatedyes81.338no
thermophileno96.454yes
glucose-fermentno88.279no

External links

@ref: 6305

culture collection no.: DSM 16130, JCM 10596, CIP 109019

straininfo link

  • @ref: 70878
  • straininfo: 281442

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280488Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species.Nogi Y, Takami H, Horikoshi KInt J Syst Evol Microbiol10.1099/ijs.0.63649-02005Bacillus/*classification/genetics/isolation & purification, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, *Industrial Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/geneticsGenetics
Phylogeny35174423Caldalkalibacillus salinus sp. nov., isolated from a salt lake in Xinjiang, northwest China.Ouyang TH, Peng M, Zhang Z, Chunyu WX, Wang LM, Zhou EM, Gao XH, Tang SKArch Microbiol10.1007/s00203-022-02789-x2022*Bacillaceae, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Lakes/microbiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6305Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16130)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16130
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
31483Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2778128776041
36776Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6714
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70878Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281442.1StrainInfo: A central database for resolving microbial strain identifiers
120779Curators of the CIPCollection of Institut Pasteur (CIP 109019)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109019