Strain identifier

BacDive ID: 133027

Type strain: Yes

Species: Saccharibacillus endophyticus

Strain Designation: JM-1350

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-1350

NCBI tax ID(s): 2060666 (species)

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General

@ref: 24815

BacDive-ID: 133027

DSM-Number: 103533

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, Gram-positive, rod-shaped, colony-forming

description: Saccharibacillus endophyticus JM-1350 is a spore-forming, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from inner tissues of field grown cotton .

NCBI tax id

  • NCBI tax id: 2060666
  • Matching level: species

strain history

@refhistory
24815<- P. Kämpfer, Justus-Liebig-Universität Gießen, Germany; JM-1350 <- John A. McInroy
119031CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-1350

doi: 10.13145/bacdive133027.20230509.8.1

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 endophyticus
  • full scientific name: Saccharibacillus endophyticus Kämpfer et al. 2016

@ref: 24815

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Saccharibacillus

species: Saccharibacillus endophyticus

full scientific name: Saccharibacillus endophyticus Kämpfer et al. 2016

strain designation: JM-1350

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25105positive4.0-6.5 µm0.8-1.3 µmrod-shapedno
69480yes96.97
69480positive100
119031positiverod-shapedyes

colony morphology

  • @ref: 25105
  • colony size: 2.0-3.0 mm
  • colony color: beige
  • colony shape: circular
  • incubation period: 2 days
  • medium used: TSA

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25105Trypticase Soy Agar (TSA)yes
42167MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
24815CASO AGAR (MERCK 105458) (DSMZ Medium 220)yesName: 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 waterhttps://mediadive.dsmz.de/medium/220
119031CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
25105positivegrowth10-36
25105positiveoptimum28-30mesophilic
25105nogrowth4psychrophilic
25105nogrowth45thermophilic
42167positivegrowth25mesophilic
24815positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
25105positivegrowth5.5-9.5alkaliphile
25105positiveoptimum7.0-8.0

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
25105oval, formed in a terminal position in a swollen sporangiumendosporeyes
69481yes100
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
25105NaClpositivegrowth1.0-7.0 %
25105NaClnogrowth9 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25105309162-oxoglutarate-carbon source
2510516865gamma-aminobutyric acid-carbon source
2510530089acetate-carbon source
2510517128adipate-carbon source
2510578208azelaate-carbon source
25105casein-hydrolysis
2510517057cellobiose-builds acid from
2510516383cis-aconitate-carbon source
2510516947citrate-carbon source
2510515963ribitol-builds acid from
2510515963ribitol-carbon source
2510518333D-arabitol-builds acid from
2510516899D-mannitol-builds acid from
2510516024D-mannose-builds acid from
2510516024D-mannose-assimilation
2510565327D-xylose-builds acid from
2510517113erythritol-builds acid from
2510516813galactitol-builds acid from
251055291gelatin-hydrolysis
2510524265gluconate-carbon source
2510517240itaconate-carbon source
2510530849L-arabinose-assimilation
2510562345L-rhamnose-builds acid from
2510562345L-rhamnose-carbon source
2510517716lactose-builds acid from
2510525115malate-carbon source
2510525115malate-assimilation
2510517306maltose-builds acid from
2510517306maltose-assimilation
2510528053melibiose-builds acid from
2510528053melibiose-carbon source
2510536986mesaconate-carbon source
25105506227N-acetylglucosamine-carbon source
25105506227N-acetylglucosamine-assimilation
2510532032potassium gluconate-assimilation
2510517272propionate-carbon source
2510517148putrescine-carbon source
2510515361pyruvate-carbon source
2510516634raffinose-builds acid from
2510533942ribose-carbon source
2510517814salicin-builds acid from
2510553258sodium citrate-assimilation
2510528017starch-hydrolysis
2510517992sucrose-builds acid from
2510515708trans-aconitate-carbon source
2510527082trehalose-builds acid from
2510527897tryptophan-energy source
251054-nitrophenyl beta-D-galactopyranoside hydrolysate+hydrolysis
2510518305arbutin+carbon source
2510517057cellobiose+carbon source
2510515824D-fructose+carbon source
2510512936D-galactose+carbon source
2510517634D-glucose+builds acid from
2510517634D-glucose+carbon source
2510516899D-mannitol+carbon source
2510516024D-mannose+carbon source
2510517924D-sorbitol+builds acid from
2510517924D-sorbitol+carbon source
2510565327D-xylose+carbon source
251054853esculin+hydrolysis
2510517268myo-inositol+carbon source
25105L-alanine 4-nitroanilide+hydrolysis
2510530849L-arabinose+builds acid from
2510530849L-arabinose+carbon source
2510568428maltitol+carbon source
2510517306maltose+carbon source
2510517632nitrate+reduction
2510517814salicin+carbon source
2510517992sucrose+carbon source
2510527082trehalose+carbon source

metabolite production

  • @ref: 25105
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetaboliteindole testcitrate test
2510535581indole-
2510516947citrate-

enzymes

@refvalueactivityec
25105arginine dihydrolase-3.5.3.6
25105beta-galactosidase+3.2.1.23
25105catalase-1.11.1.6
25105cytochrome oxidase-1.9.3.1
25105gelatinase-
25105lysine decarboxylase-4.1.1.18
25105ornithine decarboxylase-4.1.1.17
25105tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
24815inner tissues of field grown cotton (Gossypium hirsutum, cultivar 'DES-119')Gossypium hirsutumAlabama, TallasseeUSAUSANorth America
25105healthy inner stem tissue of a field-grown cotton plant (Gossypium hirsutum, cultivar ‘DES-119’)
119031Tissues of field grown cotton, Gossypium hirsutumTallassee, Alabama, USAUnited States of AmericaUSANorth America1990-01-02

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_135605.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_11033;97_67628;98_90473;99_135605&stattab=map
  • Last taxonomy: Saccharibacillus endophyticus subclade
  • 16S sequence: KX523193
  • Sequence Identity:
  • Total samples: 519
  • soil counts: 74
  • aquatic counts: 74
  • animal counts: 101
  • plant counts: 270

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
248151Risk group (German classification)
1190311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24815
  • description: Saccharibacillus endophyticus strain JM-1350 16S ribosomal RNA gene, partial sequence
  • accession: KX523193
  • length: 1454
  • database: ena
  • NCBI tax ID: 2060666

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharibacillus endophyticus CCM 8702GCA_013185185contigncbi2060666
66792Saccharibacillus endophyticus CCM 8702GCA_014635605scaffoldncbi2060666
66792Saccharibacillus endophyticus strain CCM 87022060666.4wgspatric2060666
66792Saccharibacillus endophyticus strain CCM 87022060666.5wgspatric2060666
66792Saccharibacillus endophyticus CCM 87022910409337draftimg2060666

GC content

@refGC-contentmethod
2510555.2Thermal denaturation, fluorometry
2481555.2fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes75.802no
gram-positiveyes90.12yes
anaerobicno97.609no
aerobicyes71.443no
halophileno86.939no
spore-formingyes93.341yes
thermophileno99.872no
glucose-utilyes89.092yes
motileyes87.637no
glucose-fermentno66.236no

External links

@ref: 24815

culture collection no.: DSM 103533, CCM 8702, LMG 29710, CIP 111111

straininfo link

  • @ref: 91297
  • straininfo: 401753

literature

  • topic: Phylogeny
  • Pubmed-ID: 27613514
  • title: Saccharibacillus endophyticus sp. nov., an endophyte of cotton.
  • authors: Kampfer P, Busse HJ, Kleinhagauer T, McInroy JA, Glaeser SP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001484
  • year: 2016
  • mesh: Alabama, Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, *Endophytes, Fatty Acids/chemistry, Glycolipids/chemistry, Gossypium/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24815Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103533Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103533)
25105P. B. Kämpfer, H. J.,Kleinhagauer, T.,McInroy, J. A.,Glaeser, S. P.Saccharibacillus endophyticus sp. nov., an endophyte of cotton10.1099/ijsem.0.001484IJSEM 66: 5134-5139 201627613514
42167Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34936
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91297Reimer, 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-ID401753.1
119031Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111111Collection of Institut Pasteur (CIP 111111)