Strain identifier

BacDive ID: 1102

Type strain: Yes

Species: Heyndrickxia oleronia

Strain Designation: RT 10

Strain history: CIP <- 1996, DSMZ <- H. König, Gutenberg Univ., Mainz, Germany: strain Rt 10

NCBI tax ID(s): 38875 (species)

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General

@ref: 3476

BacDive-ID: 1102

DSM-Number: 9356

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

description: Heyndrickxia oleronia RT 10 is an aerobe, spore-forming, mesophilic bacterium that was isolated from gut of the termite Reticulitermes santonensis .

NCBI tax id

  • NCBI tax id: 38875
  • Matching level: species

strain history

@refhistory
3476<- H. König, Univ. Ulm; RT 10
121413CIP <- 1996, DSMZ <- H. König, Gutenberg Univ., Mainz, Germany: strain Rt 10

doi: 10.13145/bacdive1102.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Heyndrickxia
  • species: Heyndrickxia oleronia
  • full scientific name: Heyndrickxia oleronia (Kuhnigk et al. 1996) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus oleronius

@ref: 3476

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Heyndrickxia

species: Heyndrickxia oleronia

full scientific name: Heyndrickxia oleronia (Kuhnigk et al. 1996) Gupta et al. 2020

strain designation: RT 10

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29921negativerod-shapedno
69480yes97.867
69480positive100
121413negativerod-shapedyes

colony morphology

  • @ref: 121413

pigmentation

  • @ref: 29921
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3476NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38523MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121413CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3476positivegrowth30mesophilic
29921positivegrowth30-50
29921positiveoptimum37mesophilic
38523positivegrowth30mesophilic
121413positivegrowth22-45
121413nogrowth10psychrophilic
121413nogrowth55thermophilic

culture pH

@refabilitytypepH
29921positivegrowth5.7-6.8
121413positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29921aerobe
121413obligate aerobe

spore formation

@refspore formationconfidence
29921yes
69481yes100
69480yes100
121413yes

halophily

@refsaltgrowthtested relationconcentration
29921NaClpositivegrowth<7 %
121413NaClpositivegrowth0-6 %
121413NaClnogrowth8 %
121413NaClnogrowth10 %

observation

  • @ref: 29921
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2992117057cellobiose+carbon source
2992128757fructose+carbon source
2992128260galactose+carbon source
2992117234glucose+carbon source
2992117754glycerol+carbon source
2992117306maltose+carbon source
2992129864mannitol+carbon source
2992137684mannose+carbon source
2992133942ribose+carbon source
2992117814salicin+carbon source
2992127082trehalose+carbon source
299214853esculin+hydrolysis
2992117632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-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
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+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
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+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
6837117754glycerol+builds acid from
12141316947citrate-carbon source
1214134853esculin-hydrolysis
121413606565hippurate+hydrolysis
12141317632nitrate+reduction
12141316301nitrite-reduction
12141317632nitrate-respiration

metabolite production

  • @ref: 121413
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12141315688acetoin+
12141317234glucose-

enzymes

@refvalueactivityec
29921catalase+1.11.1.6
29921gelatinase+
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
121413oxidase+
121413beta-galactosidase+3.2.1.23
121413alcohol dehydrogenase-1.1.1.1
121413gelatinase-
121413amylase-
121413DNase-
121413caseinase-3.4.21.50
121413catalase+1.11.1.6
121413tween esterase-
121413gamma-glutamyltransferase-2.3.2.2
121413lecithinase-
121413lipase-
121413lysine decarboxylase-4.1.1.18
121413ornithine decarboxylase-4.1.1.17
121413urease-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
121413--++-+----++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121413+---+----+/-++-----+---+----+/-+---+---+/------+----+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121413------------------+-------------------+-----------------+++---+-----------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
3476gut of the termite Reticulitermes santonensis (Feytaud)Reticulitermes santonensisîle d'OleronFranceFRAEurope
121413Animal, Termite gutOléron IslandFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_3283.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1672;97_2002;98_2518;99_3283&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: X82492
  • Sequence Identity:
  • Total samples: 802
  • soil counts: 374
  • aquatic counts: 65
  • animal counts: 331
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34761Risk group (German classification)
1214131Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3476
  • description: Bacillus oleronius 16S rRNA gene, strain DSM 9356
  • accession: X82492
  • length: 1519
  • database: ena
  • NCBI tax ID: 38875

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Heyndrickxia oleronia DSM 9356GCA_017809215completencbi38875
66792Heyndrickxia oleronia DSM 9356GCA_002009555scaffoldncbi38875
66792Bacillus oleronius strain DSM 935638875.4wgspatric38875
66792Bacillus oleronius strain DSM 935638875.15completepatric38875
66792Bacillus oleronius strain DSM 935638875.5wgspatric38875
66792Heyndrickxia oleronia DSM 9356GCA_025263665completencbi38875
66792Heyndrickxia oleronia strain DSM 935638875.25completepatric38875

GC content

@refGC-contentmethod
347635.2high performance liquid chromatography (HPLC)
2992135.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes68.418yes
gram-positiveyes70.109yes
anaerobicno98.738yes
aerobicyes90.482yes
halophileyes56.018yes
spore-formingyes97.371yes
thermophileno96.549yes
glucose-utilyes87.831yes
motileyes88.256yes
glucose-fermentno87.898no

External links

@ref: 3476

culture collection no.: DSM 9356, CIP 104972, LMG 17952

straininfo link

  • @ref: 70774
  • straininfo: 10541

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7553453Bacillus oleronius sp.nov., a member of the hindgut flora of the termite Reticulitermes santonensis (Feytaud).Kuhnigk T, Borst EM, Breunig A, Konig H, Collins MD, Hutson RA, Kampfer PCan J Microbiol10.1139/m95-0961995Animals, Bacillus/classification/*genetics/*isolation & purification, Base Composition, Base Sequence, Cell Wall/chemistry, DNA, Bacterial/chemistry, Digestive System/microbiology, Insecta/*microbiology, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as TopicGenetics
Phylogeny16166720Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin.Albert RA, Archambault J, Rossello-Mora R, Tindall BJ, Matheny MInt J Syst Evol Microbiol10.1099/ijs.0.02337-02005Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, *Soil Microbiology, Sphagnopsida/*metabolism, *Water MicrobiologyGenetics
Phylogeny27055557Bacillus vini sp. nov. isolated from alcohol fermentation pit mud.Ma K, Chen X, Guo X, Wang Y, Wang H, Zhou S, Song J, Kong D, Zhu J, Dong W, He M, Hu G, Zhao B, Ruan ZArch Microbiol10.1007/s00203-016-1218-42016Alcohols/*metabolism, *Bacillus/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/metabolism, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Fermentation, Glycolipids/analysis, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylethanolamines/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil MicrobiologyMetabolism
Genetics28386530Draft genome sequence of Bacillus oleronius DSM 9356 isolated from the termite Reticulitermes santonensis.Owusu-Darko R, Allam M, Mtshali S, Ismail A, Buys EMGenom Data10.1016/j.gdata.2017.03.0052017

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
3476Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9356)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9356
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
29921Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2629228776041
38523Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16939
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)
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
70774Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10541.1StrainInfo: A central database for resolving microbial strain identifiers
121413Curators of the CIPCollection of Institut Pasteur (CIP 104972)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104972