Strain identifier
BacDive ID: 23102
Type strain: 
Species: Microbacterium lacus
Strain Designation: SDZ, SDZm4
Strain history: <- W. Tappe, Forschungszentrum Jülich (IGB), Germany; SDZm4 <- W. Tappe and S. Kummer
NCBI tax ID(s): 415217 (species)
version 9.3 (current version)
General
@ref: 19076
BacDive-ID: 23102
DSM-Number: 26765
keywords: genome sequence, Bacteria, mesophilic
description: Microbacterium lacus SDZ is a mesophilic bacterium that was isolated from typic Hapludalf soil.
NCBI tax id
- NCBI tax id: 415217
- Matching level: species
strain history
- @ref: 19076
- history: <- W. Tappe, Forschungszentrum Jülich (IGB), Germany; SDZm4 <- W. Tappe and S. Kummer
doi: 10.13145/bacdive23102.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Microbacterium
- species: Microbacterium lacus
- full scientific name: Microbacterium lacus Kageyama et al. 2008
@ref: 19076
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium lacus
full scientific name: Microbacterium lacus Kageyama et al. 2008
strain designation: SDZ, SDZm4
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | no | 92.875 | |
| 125438 | 90.45 | positive | |
| 125439 | 95.1 | positive |
Culture and growth conditions
culture medium
- @ref: 19076
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
- @ref: 19076
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.7
Isolation, sampling and environmental information
isolation
- @ref: 19076
- sample type: typic Hapludalf soil
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 19076
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microbacterium lacus SDZm4 | GCA_002812805 | contig | ncbi | 415217 |
| 66792 | Microbacterium lacus strain SDZm4 | 415217.3 | wgs | patric | 415217 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 90.45 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.916 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 74.695 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.146 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.429 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 92.875 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 74.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 75.7 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 95.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.7 |
External links
@ref: 19076
culture collection no.: DSM 26765
straininfo link
- @ref: 87339
- straininfo: 397793
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 23396336 | Degradation of sulfadiazine by Microbacterium lacus strain SDZm4, isolated from lysimeters previously manured with slurry from sulfadiazine-medicated pigs. | Tappe W, Herbst M, Hofmann D, Koeppchen S, Kummer S, Thiele B, Groeneweg J | Appl Environ Microbiol | 10.1128/AEM.03636-12 | 2013 | Animals, Bacterial Typing Techniques, Carbon Radioisotopes, Manure/microbiology, Molecular Sequence Data, Mycobacterium/genetics/isolation & purification/*metabolism, Pyrimidines, Soil Microbiology, Sulfadiazine/chemistry/*metabolism/therapeutic use, Swine | Genetics |
| Metabolism | 25715827 | A novel isolated Terrabacter-like bacterium can mineralize 2-aminopyrimidine, the principal metabolite of microbial sulfadiazine degradation. | Tappe W, Hofmann D, Disko U, Koeppchen S, Kummer S, Vereecken H | Biodegradation | 10.1007/s10532-015-9722-9 | 2015 | Biodegradation, Environmental, Carbon Dioxide/metabolism, Carbon Radioisotopes, Gas Chromatography-Mass Spectrometry, *Genes, Bacterial, Humans, Micrococcaceae/*metabolism, Phylogeny, Pyrimidines/*metabolism, RNA, Ribosomal, 16S/*genetics, Soil Pollutants/*metabolism, Sulfadiazine/*metabolism | Phylogeny |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 19076 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26765) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26765 | |
| 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 | |
| 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) | |
| 87339 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397793.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |