Strain identifier
BacDive ID: 160513
Type strain: 
Species: Botrimarina mediterranea
Strain Designation: Spa11
Strain history: <- M. Jogler, Leibniz-Institut DSMZ GmbH, Braunschweig, Germany; Spa11 <- A. Stieler
NCBI tax ID(s): 2528022 (species)
version 8.1 (current version)
General
@ref: 67421
BacDive-ID: 160513
DSM-Number: 100745
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, other
description: Botrimarina mediterranea Spa11 is a mesophilic, Gram-negative, other bacterium that was isolated from seawater 10 meter depth.
NCBI tax id
- NCBI tax id: 2528022
- Matching level: species
strain history
- @ref: 67421
- history: <- M. Jogler, Leibniz-Institut DSMZ GmbH, Braunschweig, Germany; Spa11 <- A. Stieler
doi: 10.13145/bacdive160513.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/planctomycetota
- domain: Bacteria
- phylum: Planctomycetota
- class: Planctomycetia
- order: Pirellulales
- family: Lacipirellulaceae
- genus: Botrimarina
- species: Botrimarina mediterranea
- full scientific name: Botrimarina mediterranea Wiegand et al. 2021
@ref: 67421
domain: Bacteria
phylum: Planctomycetes
class: Planctomycetia
order: Pirellulales
family: Lacipirellulaceae
genus: Botrimarina
species: Botrimarina mediterranea
full scientific name: Botrimarina mediterranea Wiegand et al. 2020
strain designation: Spa11
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | confidence |
|---|---|---|---|---|---|
| 68355 | negative | 1-1.4 µm | 0.5-0.7 µm | other | |
| 69480 | negative | 99.974 |
colony morphology
- @ref: 68355
- colony color: white
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 67421 | https://www.dsmz.de/microorganisms/photos/DSM_100745.jpg | Micrograph of DSM 100745. Scale bar represents 1 um. | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH |
| 67421 | https://www.dsmz.de/microorganisms/photos/DSM_100745-1.jpg | DSM 100745 Botrimarina mediterranea culture on agar plate | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH |
| 67421 | https://www.dsmz.de/microorganisms/photos/DSM_100745-2.jpg | DSM 100745 Botrimarina mediterranea in liquid culture | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH |
Culture and growth conditions
culture medium
- @ref: 67421
- name: PLANCTOMYCES MEDIUM (DSMZ Medium 1560)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1560
- composition: Name: MARINES PLANCTOMYCES MEDIUM (DSMZ Medium 1560) Composition: Agar 15.0 g/l NaCl 11.735 g/l MgCl2 x 6 H2O 5.32 g/l HEPES 2.38 g/l Na2SO4 1.96 g/l N-Acetylglucosamine 0.8 g/l CaCl2 0.715 g/l MgSO4 x 7 H2O 0.594 g/l KCl 0.345 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.2 g/l NaHCO3 0.095 g/l CaCl2 x 2 H2O 0.0668 g/l KBr 0.048 g/l SrCl2 0.02 g/l H3BO3 0.013 g/l Na-Nitrilotriacetat 0.0015 g/l NaF 0.0015 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l MnSO4 x H2O 0.0005 g/l Na2MoO7O4 x 2 H2O 0.0002534 g/l Na-EDTA 0.00025 g/l Pyridoxine hydrochloride 0.0001 g/l Fe SO4 x 7 H2O 0.0001 g/l Co(NO3)2 x 6 H2O 0.0001 g/l ZnCl2 0.0001 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l NiCl2 x 6 H2O 5e-05 g/l H2SeO3 5e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l CuSO4 x 5 H2O 1e-05 g/l AlK(SO4)2 x 12 H2O 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l Na2WO4 x 2 H2O 1e-05 g/l Vitamin B12 1e-06 g/l Double distilled water Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 67421 | positive | growth | 28 | mesophilic |
| 68355 | positive | growth | 10-36 | |
| 68355 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 68355 | positive | growth | 5-9.5 | alkaliphile |
| 68355 | positive | optimum | 6.5 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.996 |
| 69481 | no | 100 |
observation
| @ref | observation |
|---|---|
| 68355 | form loose aggregates |
| 68355 | divide by budding |
| 68355 | feature a dimorphic life cycle |
| 68355 | Cells have ?agella, crateriform structures and ?bres covering only one pole. On the opposite side to the latter, a holdfast structure is located |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture |
|---|---|---|---|---|---|---|---|---|
| 67421 | seawater 10 meter depth | Costa Brava | Spain | ESP | Europe | 41.6667 | 2.9167 | |
| 68355 | costal seawater | Costa Brava | Spain | ESP | Europe | M1H NAG ASW medium |
Sequence information
16S sequences
- @ref: 68355
- description: Botrimarina mediterranea strain Spa11 16S ribosomal RNA gene, partial sequence
- accession: MK554534
- length: 1523
- database: ena
- NCBI tax ID: 2528022
Genome sequences
- @ref: 68355
- description: Botrimarina mediterranea Spa11
- accession: GCA_007753265
- assembly level: chromosome
- database: ncbi
- NCBI tax ID: 2528022
GC content
- @ref: 68355
- GC-content: 64.1
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 87.686 | no |
| flagellated | no | 75.974 | no |
| gram-positive | no | 96.767 | yes |
| anaerobic | no | 97.636 | no |
| aerobic | yes | 84.9 | no |
| halophile | no | 56.18 | no |
| spore-forming | no | 90.598 | no |
| glucose-util | yes | 91.286 | no |
| thermophile | no | 92.132 | yes |
| glucose-ferment | no | 87.713 | no |
External links
@ref: 67421
culture collection no.: DSM 100745, LMG 31350, CECT 9852, VKM B-3431
straininfo link
- @ref: 112756
- straininfo: 404251
literature
- topic: Phylogeny
- Pubmed-ID: 33151460
- title: Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana.
- authors: Wiegand S, Jogler M, Boedeker C, Heuer A, Peeters SH, Kallscheuer N, Jetten MSM, Kaster AK, Rohde M, Jogler C
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-020-01486-3
- year: 2020
- mesh: *Bacteria/genetics, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue | 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 | ||
| 67421 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100745 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100745) | ||
| 68355 | Sandra Wiegand, Mareike Jogler, Christian Boedeker, Anja Heuer, Stijn H. Peeters, Nicolai Kallscheuer, Mike S. M. Jetten, Anne-Kristin Kaster, Manfred Rohde & Christian Jogler | Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana | 10.1007/s10482-020-01486-3 | Antonie Van Leeuwenhoek 113: 1979-1997 2020 | |
| 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 | ||
| 112756 | 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-ID404251.1 |