Strain identifier
BacDive ID: 131473
Type strain: 
Species: Paenibacillus physcomitrellae
Strain Designation: XB
Strain history: <- Y. H. Li, College of Life Sci., Capital Normal Univ., Beijing , PR China; XB
NCBI tax ID(s): 1619311 (species)
version 9.3 (current version)
General
@ref: 22700
BacDive-ID: 131473
DSM-Number: 29851
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Paenibacillus physcomitrellae XB is a spore-forming, mesophilic bacterium that was isolated from moss Physcomitrella patens.
NCBI tax id
- NCBI tax id: 1619311
- Matching level: species
strain history
- @ref: 22700
- history: <- Y. H. Li, College of Life Sci., Capital Normal Univ., Beijing , PR China; XB
doi: 10.13145/bacdive131473.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus physcomitrellae
- full scientific name: Paenibacillus physcomitrellae Zhou et al. 2015
@ref: 22700
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus physcomitrellae
full scientific name: Paenibacillus physcomitrellae Zhou et al. 2015
strain designation: XB
type strain: yes
Morphology
cell morphology
- @ref: 125439
- motility: yes
- confidence: 92
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 22700 | 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 |
| 22700 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | yes | https://mediadive.dsmz.de/medium/545 | Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water |
culture temp
- @ref: 22700
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 92.6
spore formation
- @ref: 125439
- spore formation: yes
- confidence: 97.2
Isolation, sampling and environmental information
isolation
- @ref: 22700
- sample type: moss Physcomitrella patens
- host species: Physcomitrella patens
- geographic location: Beijing
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Moss
Safety information
risk assessment
- @ref: 22700
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22700
- description: Paenibacillus physcomitrellae strain XB 16S ribosomal RNA gene, partial sequence
- accession: KP334123
- length: 1519
- database: nuccore
- NCBI tax ID: 1619311
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paenibacillus physcomitrellae XB | GCA_002240225 | chromosome | ncbi | 1619311 |
| 66792 | Paenibacillus physcomitrellae CGMCC 1.15044 | GCA_014640575 | contig | ncbi | 1619311 |
| 66792 | Paenibacillus physcomitrellae strain CGMCC 1.15044 | 1619311.4 | wgs | patric | 1619311 |
| 66792 | Paenibacillus physcomitrellae XB | 2765235940 | complete | img | 1619311 |
GC content
- @ref: 22700
- GC-content: 53.3
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence |
|---|---|---|---|---|---|
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 97.2 |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 92 |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 84.6 |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 92.6 |
External links
@ref: 22700
culture collection no.: DSM 29851, CGMCC 1.15044
straininfo link
- @ref: 89890
- straininfo: 401272
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26296580 | Paenibacillus physcomitrellae sp. nov., isolated from the moss Physcomitrella patens. | Zhou X, Nan Guo G, Qi Wang L, Lan Bai S, Li Li C, Yu R, Hong Li Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000428 | 2015 | Bacterial Typing Techniques, Base Composition, Beijing, Bryopsida/*microbiology, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 29458522 | Paenibacillus mobilis sp. nov., a Gram-stain-negative bacterium isolated from soil. | Yang D, Cha S, Choi J, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002643 | 2018 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22700 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29851 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29851) | |
| 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 | |
| 89890 | 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-ID401272.1 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |