Strain identifier
BacDive ID: 6365
Type strain: 
Species: Pseudobutyrivibrio xylanivorans
Strain Designation: Mz 5, Mz5
Strain history: CIP <- 2003, M. Zorec, Domzale, Slovenia: strain Mz5
NCBI tax ID(s): 1123012 (strain), 185007 (species)
version 8.1 (current version)
General
@ref: 5556
BacDive-ID: 6365
DSM-Number: 14809
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, rod-shaped
description: Pseudobutyrivibrio xylanivorans Mz 5 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from rumen fluid of cow.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123012 | strain |
| 185007 | species |
strain history
| @ref | history |
|---|---|
| 5556 | <- J. Kopecny, Czech Academy of Sciences, Prague, Czech Republic; Mz 5 <- M. Zorec {1997} |
| 39960 | 2003, M. Zorec, Domzale, Slovenia: strain Mz5 |
| 123997 | CIP <- 2003, M. Zorec, Domzale, Slovenia: strain Mz5 |
doi: 10.13145/bacdive6365.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Pseudobutyrivibrio
- species: Pseudobutyrivibrio xylanivorans
- full scientific name: Pseudobutyrivibrio xylanivorans Kopecný et al. 2003
@ref: 5556
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Pseudobutyrivibrio
species: Pseudobutyrivibrio xylanivorans
full scientific name: Pseudobutyrivibrio xylanivorans Kopecný et al. 2003
strain designation: Mz 5, Mz5
type strain: yes
Morphology
cell morphology
- @ref: 123997
- gram stain: negative
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 5556 | RUMEN BACTERIA MEDIUM (DSMZ Medium 330) | yes | https://mediadive.dsmz.de/medium/330 | Name: RUMEN BACTERIA MEDIUM (DSMZ Medium 330) Composition: Na2CO3 4.0 g/l Trypticase peptone 2.0 g/l D-Glucose 0.5 g/l Yeast extract 0.5 g/l Maltose 0.5 g/l Cellobiose 0.5 g/l Starch 0.5 g/l Glycerol 0.5 g/l NaCl 0.456 g/l K2HPO4 0.3 g/l L-Cysteine HCl x H2O 0.25 g/l Na2S x 9 H2O 0.25 g/l (NH4)2SO4 0.228 g/l KH2PO4 0.228 g/l MgSO4 x 7 H2O 0.095 g/l CaCl2 x 2 H2O 0.0608 g/l Hemin 0.001 g/l Sodium resazurin 0.0005 g/l NaOH None Distilled water |
| 39960 | MEDIUM 224 - for anaerobic bacteria TGV | yes | Distilled water make up to (1000.000 ml);Glucose (10.000 g);Yeast extract (20.000 g);Resazurin (2.000 mg);Trypto casein soy broth (30.000 g);L-Cysteine (0.500 g);Hemin solution - M00149 (25.000 ml);Vitamins solution - M00850 (10.000 ml) | |
| 123997 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 5556 | positive | growth | 40 | thermophilic |
| 39960 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 5556
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 5556 | rumen fluid of cow | Donzale | Slovenia | SVN | Europe |
| 123997 | Animal, Cow, rumen fluid | Domzale | Slovenia | SVN | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
| #Host Body-Site | #Organ | #Rumen |
| #Host Body Product | #Fluids | #Rumen fluid |
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 5556 | 1 | Risk group (German classification) |
| 123997 | 2 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5556
- description: Pseudobutyrivibrio xylanovorans partial 16S rRNA gene, strain Mz 5
- accession: AJ428548
- length: 1442
- database: ena
- NCBI tax ID: 185007
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudobutyrivibrio xylanivorans DSM 14809 | GCA_900141825 | scaffold | ncbi | 1123012 |
| 66792 | Pseudobutyrivibrio xylanivorans DSM 14809 | 1123012.3 | wgs | patric | 1123012 |
| 66792 | Pseudobutyrivibrio xylanivorans DSM 14809 | 2585428087 | draft | img | 1123012 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 78.746 | no |
| flagellated | no | 55.568 | no |
| gram-positive | yes | 56.427 | no |
| anaerobic | yes | 99.545 | yes |
| aerobic | no | 98.949 | yes |
| halophile | no | 92.107 | no |
| spore-forming | yes | 63.712 | no |
| thermophile | no | 90.724 | no |
| glucose-util | yes | 88.769 | no |
| glucose-ferment | yes | 78.611 | no |
External links
@ref: 5556
culture collection no.: DSM 14809, ATCC BAA 455, CIP 107891
straininfo link
- @ref: 75838
- straininfo: 100879
literature
- topic: Phylogeny
- Pubmed-ID: 12656174
- title: Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen.
- authors: Kopecny J, Zorec M, Mrazek J, Kobayashi Y, Marinsek-Logar R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02345-0
- year: 2003
- mesh: Animals, Base Composition, Base Sequence, Butyrates/*metabolism, Cattle, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fermentation, Genetic Variation, Genotype, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/isolation & purification/*metabolism, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rumen/microbiology, Sheep
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5556 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14809) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14809 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 39960 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5452 | ||||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 75838 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100879.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 123997 | Curators of the CIP | Collection of Institut Pasteur (CIP 107891) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107891 |