Strain identifier

BacDive ID: 23756

Type strain: Yes

Species: Ureibacillus massiliensis

Strain Designation: 4400831

Strain history: CIP <- 2004, V. Roux, 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

@refhistory
20433<- KCTC; KCTC 13178
372952004, R. Roux, La Timone Hosp., Marseille, France: strain 4400831
67771<- CIP <- 2004, R. Roux, La Timone Hosp., Marseille, France, strain 4400831
120852CIP <- 2004, V. Roux, Timone Hosp., Marseille, France: strain 4400831

doi: 10.13145/bacdive23756.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: 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
69480yes95.528
69480positive100
120852positiverod-shapedno

colony morphology

  • @ref: 120852

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)
120852CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20433positivegrowth37mesophilic
31658positivegrowth25-45
31658positiveoptimum30-37mesophilic
37295positivegrowth37mesophilic
58599positivegrowth30-37mesophilic
67771positivegrowth30-37mesophilic
120852positivegrowth22-37
120852nogrowth10psychrophilic
120852nogrowth45thermophilic
120852nogrowth55thermophilic

culture pH

@refabilitytypepH
31658positivegrowth7
31658positiveoptimum7
120852positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31658aerobe
58599aerobe
67771aerobe
120852obligate aerobe

spore formation

@refspore formationtype of sporeconfidence
31658yes
67771yesendospore
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
31658NaClpositivegrowth5 %
31658NaClpositiveoptimum5 %
120852NaClpositivegrowth2-4 %
120852NaClnogrowth0 %
120852NaClnogrowth6 %
120852NaClnogrowth8 %
120852NaClnogrowth10 %

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
12085216947citrate-carbon source
1208524853esculin-hydrolysis
120852606565hippurate-hydrolysis
12085217632nitrate-reduction
12085216301nitrite-reduction

metabolite production

  • @ref: 120852
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12085215688acetoin-
12085217234glucose-

enzymes

@refvalueactivityec
31658catalase+1.11.1.6
31658cytochrome oxidase+1.9.3.1
31658urease+3.5.1.5
120852oxidase+
120852beta-galactosidase-3.2.1.23
120852alcohol dehydrogenase+1.1.1.1
120852gelatinase-
120852amylase-
120852DNase-
120852caseinase-3.4.21.50
120852catalase+1.11.1.6
120852tween esterase-
120852gamma-glutamyltransferase-2.3.2.2
120852lecithinase-
120852lipase-
120852lysine decarboxylase+4.1.1.18
120852ornithine decarboxylase+4.1.1.17
120852urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120852-++-----------------

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentisolation date
58599Human cephalorachidial liquid,54-yr-old man2004-03-01Marseille,Timone hospitalFranceFRAEurope
20433cerebrospinal fluid, humanMarseilleFranceFRAEurope
67771From Rachidian liquidMarseilleFranceFRAEurope
120852Human, Rachidian liquidMarseilleFranceFRAEurope2004

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

@refpathogenicity humanbiosafety levelbiosafety level comment
20433yes, in single cases1Risk group (German classification)
1208521Risk group (French 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 49529GCA_002200855contigncbi1211035
66792Ureibacillus massiliensis 4400831 = CIP 108448 = 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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes86.556yes
gram-positiveyes84.97no
anaerobicno98.112no
aerobicyes89.379yes
halophileno76.649no
spore-formingyes94.995yes
thermophileno98.86yes
glucose-utilyes83.889no
flagellatedyes91.255yes
glucose-fermentno90.041no

External links

@ref: 20433

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

straininfo link

  • @ref: 87792
  • straininfo: 297131

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/urlcatalogueID_cross_referencepubmedjournal
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
20433Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27596Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27596)
31658Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172793928776041
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/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.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
87792Reimer, 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-ID297131.1
120852Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108446Collection of Institut Pasteur (CIP 108446)