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Strain identifier

BacDive ID: 23756

Type strain: Yes

Species: Ureibacillus massiliensis

Strain Designation: 4400831

Strain history: <- CIP <- 2004, R. Roux, La Timone Hosp., Marseille, France, strain 4400831

NCBI tax ID(s): 292806 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20433

BacDive-ID: 23756

DSM-Number: 27596

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

description: Ureibacillus massiliensis 4400831 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from Human cephalorachidial liquid,54-yr-old man.

NCBI tax id

  • NCBI tax id: 292806
  • Matching level: species

strain history

doi: 10.13145/bacdive23756.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Ureibacillus
  • species: Ureibacillus massiliensis
  • full scientific name: Ureibacillus massiliensis (Glazunova et al. 2006) Gupta and Patel 2020
  • synonyms

    @refsynonym
    20215Bacillus massiliensis
    20215Lysinibacillus massiliensis

@ref: 20433

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Ureibacillus

species: Ureibacillus massiliensis

full scientific name: Ureibacillus massiliensis (Glazunova et al. 2006) Gupta and Patel 2020

strain designation: 4400831

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31658negative1.5-4 µm0.3-0.5 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771positive
69480yes58.062
69480positive94.415

pigmentation

  • @ref: 31658
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20433CASO 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
37295MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
20433positivegrowth37mesophilic
31658positivegrowth25-45
31658positiveoptimum30-37mesophilic
37295positivegrowth37mesophilic
58599positivegrowth30-37mesophilic
67771positivegrowth30-37mesophilic

culture pH

@refabilitytypepH
31658positivegrowth7
31658positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31658aerobe
58599aerobe
67771aerobe

spore formation

@refspore formationtype of sporeconfidence
31658yes
67771yesendospore
69480yes96.691

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
31658NaClpositivegrowth5 %
31658NaClpositiveoptimum5 %
69480non-halophilic90.678

observation

  • @ref: 31658
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3165830089acetate+carbon source
3165816947citrate+carbon source
3165851850methyl pyruvate+carbon source
3165815361pyruvate+carbon source

enzymes

@refvalueactivityec
31658catalase+1.11.1.6
31658cytochrome oxidase+1.9.3.1
31658urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
58599Human cephalorachidial liquid,54-yr-old man2004-03-01Marseille,Timone hospitalFranceFRAEurope
20433cerebrospinal fluid, humanMarseilleFranceFRAEurope
67771From Rachidian liquidMarseilleFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Cerebrospinal fluid
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_86864.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3452;97_5123;98_60080;99_86864&stattab=map
  • Last taxonomy: Lysinibacillus
  • 16S sequence: AY677116
  • Sequence Identity:
  • Total samples: 17
  • soil counts: 6
  • animal counts: 11

Safety information

risk assessment

  • @ref: 20433
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20433
  • description: Bacillus massiliensis 16S ribosomal RNA gene, partial sequence
  • accession: AY677116
  • length: 1472
  • database: ena
  • NCBI tax ID: 1211035

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ureibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 4400831GCA_002200855contigncbi1211035
66792Ureibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 CCUG 49529GCA_000772965contigncbi1211035
66792Lysinibacillus massiliensis 4400831 = CIP 108448 = CCUG 495291211035.3wgspatric1211035
66792Lysinibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 strain 44008311211035.4wgspatric1211035
66792Lysinibacillus massiliensis 4400831 = CIP 108448 = CCUG 495292627853741draftimg1211035
66792uncultured Prevotella sp. HGM04976GCA_900765035contigpatric159272
66792uncultured Ruminococcus sp. SRR11489790_bin.4_metaWRAP_v1.3_MAGGCA_945932805contigpatric165186

External links

@ref: 20433

culture collection no.: DSM 27596, CCUG 49529, CIP 108446, KCTC 13178

straininfo link

@refpassport
20218http://www.straininfo.net/strains/689519
20218http://www.straininfo.net/strains/689520
20218http://www.straininfo.net/strains/857362

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825616Bacillus massiliensis sp. nov., isolated from cerebrospinal fluid.Glazunova OO, Raoult D, Roux VInt J Syst Evol Microbiol10.1099/ijs.0.63982-02006Bacillaceae Infections/cerebrospinal fluid/*microbiology, Bacillus/chemistry/*classification/cytology/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cerebrospinal Fluid/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/chemistry/isolation & purification, Genes, rRNA, Gentian Violet, Humans, Male, Middle Aged, Molecular Sequence Data, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidEnzymology
Phylogeny22140163Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended description of the genus Lysinibacillus.Jung MY, Kim JS, Paek WK, Styrak I, Park IS, Sin Y, Paek J, Park KA, Kim H, Kim HL, Chang YHInt J Syst Evol Microbiol10.1099/ijs.0.033837-02011Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/*analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny23584285Lysinibacillus manganicus sp. nov., isolated from manganese mining soil.Liu H, Song Y, Chen F, Zheng S, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.050492-02013Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Manganese, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny23812821Lysinibacillus chungkukjangi sp. nov., isolated from Chungkukjang, Korean fermented soybean food.Kim SJ, Jang YH, Hamada M, Ahn JH, Weon HY, Suzuki K, Whang KS, Kwon SWJ Microbiol10.1007/s12275-013-2664-12013Bacillaceae/classification/genetics/*metabolism, Cardiolipins/metabolism, Fermentation, Phosphatidylethanolamines/metabolism, Phosphatidylglycerols/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SoybeansMetabolism
Phylogeny26762029[Microbiological characteristics of a Lysinibacillus strain isolated from Populous euphratica].Anwar N, Erkin R, Mamtimin H, Hamood B, Ismayi N, Abdukerim M, Rahman EWei Sheng Wu Xue Bao2015Bacillaceae/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Populus/*microbiology, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny31124045Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean.Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang QJ Microbiol10.1007/s12275-019-8709-32019Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques/methods, Geologic Sediments/*microbiology, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology

Reference

@idauthorstitledoi/urljournalpubmedcatalogueID_cross_reference
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
20433Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27596Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27596)
2793910.1099/ijs.0.63982-016825616
31658Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127939
37295Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6069
58599Curators of the CCUGhttps://www.ccug.se/strain?id=49529Culture Collection University of Gothenburg (CCUG) (CCUG 49529)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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