Strain identifier
BacDive ID: 23756
Type strain:
Species: Ureibacillus massiliensis
Strain Designation: 4400831
Strain history: CIP <- 2004, V. Roux, Timone Hosp., Marseille, France: strain 4400831
NCBI tax ID(s): 292806 (species)
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
@ref | history |
---|---|
20433 | <- KCTC; KCTC 13178 |
37295 | 2004, R. Roux, La Timone Hosp., Marseille, France: strain 4400831 |
67771 | <- CIP <- 2004, R. Roux, La Timone Hosp., Marseille, France, strain 4400831 |
120852 | CIP <- 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
@ref synonym 20215 Bacillus massiliensis 20215 Lysinibacillus 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
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
31658 | negative | 1.5-4 µm | 0.3-0.5 µm | rod-shaped | yes | ||
67771 | rod-shaped | yes | peritrichous | ||||
67771 | positive | ||||||
69480 | yes | 95.528 | |||||
69480 | positive | 100 | |||||
120852 | positive | rod-shaped | no |
colony morphology
- @ref: 120852
pigmentation
- @ref: 31658
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
20433 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: 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 |
37295 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120852 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20433 | positive | growth | 37 | mesophilic |
31658 | positive | growth | 25-45 | |
31658 | positive | optimum | 30-37 | mesophilic |
37295 | positive | growth | 37 | mesophilic |
58599 | positive | growth | 30-37 | mesophilic |
67771 | positive | growth | 30-37 | mesophilic |
120852 | positive | growth | 22-37 | |
120852 | no | growth | 10 | psychrophilic |
120852 | no | growth | 45 | thermophilic |
120852 | no | growth | 55 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31658 | positive | growth | 7 |
31658 | positive | optimum | 7 |
120852 | positive | growth | 6 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31658 | aerobe |
58599 | aerobe |
67771 | aerobe |
120852 | obligate aerobe |
spore formation
@ref | spore formation | type of spore | confidence |
---|---|---|---|
31658 | yes | ||
67771 | yes | endospore | |
69481 | yes | 100 | |
69480 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31658 | NaCl | positive | growth | 5 % |
31658 | NaCl | positive | optimum | 5 % |
120852 | NaCl | positive | growth | 2-4 % |
120852 | NaCl | no | growth | 0 % |
120852 | NaCl | no | growth | 6 % |
120852 | NaCl | no | growth | 8 % |
120852 | NaCl | no | growth | 10 % |
observation
- @ref: 31658
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31658 | 30089 | acetate | + | carbon source |
31658 | 16947 | citrate | + | carbon source |
31658 | 51850 | methyl pyruvate | + | carbon source |
31658 | 15361 | pyruvate | + | carbon source |
120852 | 16947 | citrate | - | carbon source |
120852 | 4853 | esculin | - | hydrolysis |
120852 | 606565 | hippurate | - | hydrolysis |
120852 | 17632 | nitrate | - | reduction |
120852 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 120852
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
120852 | 15688 | acetoin | - | |
120852 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31658 | catalase | + | 1.11.1.6 |
31658 | cytochrome oxidase | + | 1.9.3.1 |
31658 | urease | + | 3.5.1.5 |
120852 | oxidase | + | |
120852 | beta-galactosidase | - | 3.2.1.23 |
120852 | alcohol dehydrogenase | + | 1.1.1.1 |
120852 | gelatinase | - | |
120852 | amylase | - | |
120852 | DNase | - | |
120852 | caseinase | - | 3.4.21.50 |
120852 | catalase | + | 1.11.1.6 |
120852 | tween esterase | - | |
120852 | gamma-glutamyltransferase | - | 2.3.2.2 |
120852 | lecithinase | - | |
120852 | lipase | - | |
120852 | lysine decarboxylase | + | 4.1.1.18 |
120852 | ornithine decarboxylase | + | 4.1.1.17 |
120852 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120852 | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|---|
58599 | Human cephalorachidial liquid,54-yr-old man | 2004-03-01 | Marseille,Timone hospital | France | FRA | Europe | |
20433 | cerebrospinal fluid, human | Marseille | France | FRA | Europe | ||
67771 | From Rachidian liquid | Marseille | France | FRA | Europe | ||
120852 | Human, Rachidian liquid | Marseille | France | FRA | Europe | 2004 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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 | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
20433 | yes, in single cases | 1 | Risk group (German classification) |
120852 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Ureibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 | GCA_002200855 | contig | ncbi | 1211035 |
66792 | Ureibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 | GCA_000772965 | contig | ncbi | 1211035 |
66792 | Lysinibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 | 1211035.3 | wgs | patric | 1211035 |
66792 | Lysinibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 strain 4400831 | 1211035.4 | wgs | patric | 1211035 |
66792 | Lysinibacillus massiliensis 4400831 = CIP 108448 = CCUG 49529 | 2627853741 | draft | img | 1211035 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 86.556 | yes |
gram-positive | yes | 84.97 | no |
anaerobic | no | 98.112 | no |
aerobic | yes | 89.379 | yes |
halophile | no | 76.649 | no |
spore-forming | yes | 94.995 | yes |
thermophile | no | 98.86 | yes |
glucose-util | yes | 83.889 | no |
flagellated | yes | 91.255 | yes |
glucose-ferment | no | 90.041 | no |
External links
@ref: 20433
culture collection no.: DSM 27596, CCUG 49529, CIP 108446, KCTC 13178
straininfo link
- @ref: 87792
- straininfo: 297131
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16825616 | Bacillus massiliensis sp. nov., isolated from cerebrospinal fluid. | Glazunova OO, Raoult D, Roux V | Int J Syst Evol Microbiol | 10.1099/ijs.0.63982-0 | 2006 | Bacillaceae 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 Acid | Enzymology |
Phylogeny | 22140163 | Description 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 YH | Int J Syst Evol Microbiol | 10.1099/ijs.0.033837-0 | 2011 | Bacillaceae/*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 Microbiology | Genetics |
Phylogeny | 23584285 | Lysinibacillus manganicus sp. nov., isolated from manganese mining soil. | Liu H, Song Y, Chen F, Zheng S, Wang G | Int J Syst Evol Microbiol | 10.1099/ijs.0.050492-0 | 2013 | Bacillaceae/*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/analysis | Genetics |
Phylogeny | 23812821 | Lysinibacillus 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 SW | J Microbiol | 10.1007/s12275-013-2664-1 | 2013 | Bacillaceae/classification/genetics/*metabolism, Cardiolipins/metabolism, Fermentation, Phosphatidylethanolamines/metabolism, Phosphatidylglycerols/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soybeans | Metabolism |
Phylogeny | 26762029 | [Microbiological characteristics of a Lysinibacillus strain isolated from Populous euphratica]. | Anwar N, Erkin R, Mamtimin H, Hamood B, Ismayi N, Abdukerim M, Rahman E | Wei Sheng Wu Xue Bao | 2015 | Bacillaceae/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/genetics | Metabolism | |
Phylogeny | 31124045 | Isolation 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 Q | J Microbiol | 10.1007/s12275-019-8709-3 | 2019 | Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques/methods, Geologic Sediments/*microbiology, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics | Enzymology |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||||
20433 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27596 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27596) | ||||
31658 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27939 | 28776041 | ||
37295 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6069 | |||||
58599 | Curators of the CCUG | https://www.ccug.se/strain?id=49529 | Culture Collection University of Gothenburg (CCUG) (CCUG 49529) | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
87792 | Reimer, 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 identifiers | 10.60712/SI-ID297131.1 | ||||
120852 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108446 | Collection of Institut Pasteur (CIP 108446) |