Strain identifier

BacDive ID: 11667

Type strain: Yes

Species: Saccharibacillus sacchari

Strain Designation: GR21

Strain history: <- E. Velazquez; GR21

NCBI tax ID(s): 915437 (strain), 456493 (species)

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General

@ref: 7987

BacDive-ID: 11667

DSM-Number: 19268

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

description: Saccharibacillus sacchari GR21 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from inner tissues of Saccharum officinarum.

NCBI tax id

NCBI tax idMatching level
456493species
915437strain

strain history

  • @ref: 7987
  • history: <- E. Velazquez; GR21

doi: 10.13145/bacdive11667.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Saccharibacillus
  • species: Saccharibacillus sacchari
  • full scientific name: Saccharibacillus sacchari Rivas et al. 2008

@ref: 7987

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Saccharibacillus

species: Saccharibacillus sacchari

full scientific name: Saccharibacillus sacchari Rivas et al. 2008

strain designation: GR21

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32438variable03-04 µm0.8-1 µmrod-shapedyes
28660variable3-4 µm0.8-1 µmrod-shapedyes
69480yes94.776
69480positive100

colony morphology

  • @ref: 28660
  • colony size: 1-2 mm
  • colony color: pale pink
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Tryptic Soy Agar

pigmentation

  • @ref: 32438
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7987CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
28660Tryptic Soy Agaryes

culture temp

@refgrowthtypetemperaturerange
7987positivegrowth30mesophilic
32438positivegrowth08-40
32438positiveoptimum28mesophilic
28660positivegrowth8-40
28660positiveoptimum28mesophilic

culture pH

@refabilitytypepH
32438positivegrowth5.7-7
32438positiveoptimum7
28660positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32438facultative anaerobe
28660anaerobe

spore formation

@refspore formationspore descriptiontype of sporeconfidence
32438yes
28660yesfrom non-swollen sporangiaendospore
69481yes100
69480yes99.356

halophily

  • @ref: 28660
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 2 %

observation

  • @ref: 32438
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3243824265gluconate+carbon source
3243817234glucose+carbon source
3243817306maltose+carbon source
3243829864mannitol+carbon source
3243837684mannose+carbon source
324384853esculin+hydrolysis
3243817632nitrate+reduction
2866017634D-glucose+carbon source
286604853esculin+hydrolysis
2866017234glucose-builds gas from
2866017234glucose+builds acid from
2866030849L-arabinose-assimilation
2866017632nitrate+reduction
2866027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
2866015688acetoinyes
2866035581indoleno
2866016136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2866015688acetoin+
2866035581indole-

enzymes

@refvalueactivityec
32438catalase+1.11.1.6
28660cellulase+3.2.1.4
28660endo-1,4-beta-xylanase3.2.1.8
28660beta-galactosidase3.2.1.23
28660catalase-1.11.1.6
28660cytochrome oxidase1.9.3.1
28660amylase
28660gelatinase
28660caseinase3.4.21.50
28660arginine dihydrolase3.5.3.6
28660lysine decarboxylase4.1.1.18
28660ornithine decarboxylase4.1.1.17
28660tryptophan deaminase-4.1.99.1
28660urease3.5.1.5
28660phenylalanine deaminase4.3.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
7987inner tissues of Saccharum officinarumSaccharum officinarumGranadaSpainESPEurope
28660inner tissures of Saccharum officinarumGranadaSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6208.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2956;97_3637;98_4603;99_6208&stattab=map
  • Last taxonomy: Saccharibacillus sacchari
  • 16S sequence: EU014873
  • Sequence Identity:
  • Total samples: 916
  • soil counts: 91
  • aquatic counts: 83
  • animal counts: 637
  • plant counts: 105

Safety information

risk assessment

  • @ref: 7987
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7987
  • description: Saccharibacillus sacchari strain GR21 16S ribosomal RNA gene, partial sequence
  • accession: EU014873
  • length: 1491
  • database: ena
  • NCBI tax ID: 915437

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharibacillus sacchari DSM 19268GCA_000585395scaffoldncbi915437
66792Saccharibacillus sacchari DSM 19268915437.3wgspatric915437
66792Saccharibacillus sacchari DSM 192682512875015draftimg915437

GC content

@refGC-contentmethod
798757.8
2866057.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes87.828no
flagellatedyes78.872no
gram-positiveyes88.601yes
anaerobicno97.973no
halophileno85.128no
spore-formingyes90.662no
glucose-utilyes89.379yes
aerobicyes68.635yes
thermophileno99.891yes
glucose-fermentno64.225no

External links

@ref: 7987

culture collection no.: DSM 19268, LMG 24085

straininfo link

  • @ref: 80888
  • straininfo: 302804

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18676467Saccharibacillus sacchari gen. nov., sp. nov., isolated from sugar cane.Rivas R, Garcia-Fraile P, Zurdo-Pineiro JL, Mateos PF, Martinez-Molina E, Bedmar EJ, Sanchez-Raya J, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.65499-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Rods/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharum/*microbiology, Species SpecificityGenetics
Phylogeny19406774Saccharibacillus kuerlensis sp. nov., isolated from a desert soil.Yang SY, Liu H, Liu R, Zhang KY, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.005199-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Desert Climate, Fatty Acids/analysis, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny33913068Polyphasic characterization of and genomic insights into a haloalkali-tolerant Saccharibacillus alkalitolerans sp. nov., that produces three cellulase isozymes and several antimicrobial compounds.Darji H, Verma N, Lugani Y, Mehrotra P, Sindhu DK, Vemuluri VRAntonie Van Leeuwenhoek10.1007/s10482-021-01575-x2021*Anti-Infective Agents, Bacillales, Bacterial Typing Techniques, Base Composition, *Cellulases, DNA, Bacterial/genetics, Fatty Acids/analysis, Genomics, Isoenzymes, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlepubmedID_cross_reference
7987Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19268)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19268
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
2866010.1099/ijs.0.65499-018676467
32438Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128660
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)
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
80888Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302804.1StrainInfo: A central database for resolving microbial strain identifiers