Strain identifier
BacDive ID: 2281
Type strain:
Species: Trichococcus flocculiformis
Strain Designation: Echt
Strain history: <- G. Scheff and F. Lingens, strain Echt <- O. Salcher
NCBI tax ID(s): 82803 (species)
General
@ref: 718
BacDive-ID: 2281
DSM-Number: 2094
keywords: genome sequence, 16S sequence, Bacteria
description: Trichococcus flocculiformis Echt is a bacterium that was isolated from sewage sludge, sewage plant.
NCBI tax id
- NCBI tax id: 82803
- Matching level: species
strain history
- @ref: 718
- history: <- G. Scheff and F. Lingens, strain Echt <- O. Salcher
doi: 10.13145/bacdive2281.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Carnobacteriaceae
- genus: Trichococcus
- species: Trichococcus flocculiformis
- full scientific name: Trichococcus flocculiformis Scheff et al. 1984
@ref: 718
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Carnobacteriaceae
genus: Trichococcus
species: Trichococcus flocculiformis
full scientific name: Trichococcus flocculiformis Scheff et al. 1984 emend. Liu et al. 2002
strain designation: Echt
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.117 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 718
- name: TRICHOCOCCUS MEDIUM (DSMZ Medium 183)
- growth: yes
- link: https://mediadive.dsmz.de/medium/183
- composition: Name: TRICHOCOCCUS MEDIUM (DSMZ Medium 183) Composition: Tryptone 10.0 g/l Na2SO4 4.0 g/l Glucose 3.0 g/l MgCl2 x 6 H2O 1.1 g/l KCl 0.7 g/l Distilled water
culture temp
- @ref: 718
- growth: positive
- type: growth
- temperature: 20-30
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.839
murein
- @ref: 718
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
Isolation, sampling and environmental information
isolation
- @ref: 718
- sample type: sewage sludge, sewage plant
- geographic location: Echterdingen
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Industrial | #Plant (Factory) |
#Engineered | #Waste | #Sewage sludge |
taxonmaps
- @ref: 69479
- File name: preview.99_24449.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_12252;97_14862;98_18388;99_24449&stattab=map
- Last taxonomy: Trichococcus
- 16S sequence: Y17301
- Sequence Identity:
- Total samples: 38677
- soil counts: 4890
- aquatic counts: 19650
- animal counts: 13208
- plant counts: 929
Safety information
risk assessment
- @ref: 718
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Trichococcus flocculiformis 16S rRNA gene, strain DSM 2094 | AJ306611 | 1438 | ena | 82803 |
718 | Trichococcus flocculiformis 16S rRNA gene | Y17301 | 1550 | ena | 82803 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Trichococcus flocculiformis DSM 2094 | GCA_900113645 | scaffold | ncbi | 82803 |
66792 | Trichococcus flocculiformis strain DSM 2094 | 82803.9 | wgs | patric | 82803 |
66792 | Trichococcus flocculiformis DSM 2094 | 2619618836 | draft | img | 82803 |
GC content
- @ref: 718
- GC-content: 46.8
- method: Buoyant density centrifugation (BD)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 52 | no |
motile | no | 94.042 | no |
flagellated | no | 93.041 | no |
gram-positive | yes | 91.77 | no |
anaerobic | no | 78.591 | no |
aerobic | no | 92.269 | no |
halophile | yes | 66.519 | no |
spore-forming | no | 87.879 | no |
glucose-ferment | yes | 77.94 | no |
thermophile | no | 99.607 | no |
glucose-util | yes | 89.446 | no |
External links
@ref: 718
culture collection no.: DSM 2094, ATCC 51221
straininfo link
- @ref: 71839
- straininfo: 42865
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12148615 | Emended description of the genus Trichococcus, description of Trichococcus collinsii sp. nov., and reclassification of Lactosphaera pasteurii as Trichococcus pasteurii comb. nov. and of Ruminococcus palustris as Trichococcus palustris comb. nov. in the low-G+C gram-positive bacteria. | Liu JR, Tanner RS, Schumann P, Weiss N, McKenzie CA, Janssen PH, Seviour EM, Lawson PA, Allen TD, Seviour RJ | Int J Syst Evol Microbiol | 10.1099/00207713-52-4-1113 | 2002 | Bacteria/*classification/genetics/metabolism/ultrastructure, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics | Genetics |
Phylogeny | 31914924 | Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. | Strepis N, Naranjo HD, Meier-Kolthoff J, Goker M, Shapiro N, Kyrpides N, Klenk HP, Schaap PJ, Stams AJM, Sousa DZ | BMC Genomics | 10.1186/s12864-019-6410-x | 2020 | Bacterial Typing Techniques, Carnobacteriaceae/*genetics/metabolism/*physiology, Phenotype, Phylogeny, Propylene Glycols/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
718 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2094) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2094 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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) | |||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
71839 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42865.1 | StrainInfo: A central database for resolving microbial strain identifiers |