Strain identifier
BacDive ID: 2282
Type strain:
Species: Trichococcus palustris
Strain Designation: Z-7189
Strain history: CIP <- 1997, DSM <- T.N. Zhilina: strain Z-7189
NCBI tax ID(s): 140314 (species)
General
@ref: 3503
BacDive-ID: 2282
DSM-Number: 9172
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, oval-shaped
description: Trichococcus palustris Z-7189 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from swamp.
NCBI tax id
- NCBI tax id: 140314
- Matching level: species
strain history
@ref | history |
---|---|
3503 | <- T.N. Zhilina, Z-7189 |
121521 | CIP <- 1997, DSM <- T.N. Zhilina: strain Z-7189 |
doi: 10.13145/bacdive2282.20230509.8.1
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 palustris
- full scientific name: Trichococcus palustris (Zhilina et al. 1997) Liu et al. 2002
synonyms
- @ref: 20215
- synonym: Ruminococcus palustris
@ref: 3503
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Carnobacteriaceae
genus: Trichococcus
species: Trichococcus palustris
full scientific name: Trichococcus palustris (Zhilina et al. 1997) Liu et al. 2002
strain designation: Z-7189
type strain: yes
Morphology
cell morphology
- @ref: 121521
- gram stain: positive
- cell shape: oval-shaped
- motility: no
colony morphology
- @ref: 121521
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3503 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | 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 |
39276 | MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicola | yes | Distilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g) | |
121521 | CIP Medium 118-b | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b | |
121521 | CIP Medium 187 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=187 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3503 | positive | growth | 30 | mesophilic |
39276 | positive | growth | 30 | mesophilic |
121521 | positive | growth | 5-30 | |
121521 | no | growth | 37 | mesophilic |
121521 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
3503 | microaerophile |
121521 | facultative anaerobe |
murein
- @ref: 3503
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | + | builds acid from | 16634 |
68371 | melezitose | + | builds acid from | 6731 |
68371 | inulin | + | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | + | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | + | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | + | builds acid from | 18305 |
68371 | amygdalin | + | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | + | builds acid from | 17924 |
68371 | D-mannitol | + | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
121521 | esculin | + | hydrolysis | 4853 |
121521 | hippurate | + | hydrolysis | 606565 |
121521 | nitrate | - | reduction | 17632 |
121521 | nitrite | - | reduction | 16301 |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
121521 | oxidase | - | |
121521 | beta-galactosidase | + | 3.2.1.23 |
121521 | alcohol dehydrogenase | - | 1.1.1.1 |
121521 | gelatinase | - | |
121521 | amylase | - | |
121521 | DNase | - | |
121521 | caseinase | - | 3.4.21.50 |
121521 | catalase | - | 1.11.1.6 |
121521 | tween esterase | - | |
121521 | gamma-glutamyltransferase | - | 2.3.2.2 |
121521 | lecithinase | - | |
121521 | lipase | - | |
121521 | lysine decarboxylase | - | 4.1.1.18 |
121521 | ornithine decarboxylase | - | 4.1.1.17 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121521 | - | - | + | + | - | - | - | - | - | - | + | + | + | - | + | - | + | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121521 | - | - | - | - | + | - | - | - | - | + | + | + | + | - | - | - | - | + | + | - | - | + | + | + | + | + | + | + | + | + | + | - | + | + | + | - | - | - | + | +/- | - | +/- | - | - | - | - | +/- | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
3503 | swamp | Russia, near Abramtsevo settlement | Russia | RUS | Europe |
121521 | Swamp | Russian Federation | RUS | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Wetland (Swamp)
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: AJ296179
- Sequence Identity:
- Total samples: 38677
- soil counts: 4890
- aquatic counts: 19650
- animal counts: 13208
- plant counts: 929
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3503 | 1 | Risk group (German classification) |
121521 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 3503
- description: Ruminococcus palustris 16S rRNA gene, strain DSM 9172T
- accession: AJ296179
- length: 1520
- database: ena
- NCBI tax ID: 140314
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Trichococcus palustris DSM 9172 | GCA_900114465 | scaffold | ncbi | 140314 |
66792 | Trichococcus palustris strain DSM 9172 | 140314.8 | wgs | patric | 140314 |
66792 | Trichococcus palustris DSM 9172 | 2619618822 | draft | img | 140314 |
GC content
- @ref: 3503
- GC-content: 47.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 58.486 | no |
flagellated | no | 77.364 | no |
gram-positive | yes | 82.253 | no |
anaerobic | no | 70.073 | no |
aerobic | no | 96.508 | no |
halophile | no | 55.261 | no |
spore-forming | no | 77.161 | no |
glucose-ferment | yes | 79.771 | no |
thermophile | no | 99.378 | yes |
glucose-util | yes | 87.43 | no |
External links
@ref: 3503
culture collection no.: DSM 9172, CIP 105359
straininfo link
- @ref: 71840
- straininfo: 48588
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 |
Metabolism | 24126154 | Enhanced start-up of anaerobic facultatively autotrophic biocathodes in bioelectrochemical systems. | Zaybak Z, Pisciotta JM, Tokash JC, Logan BE | J Biotechnol | 10.1016/j.jbiotec.2013.10.001 | 2013 | Anaerobiosis/genetics, *Autotrophic Processes, Bacteria, Anaerobic/classification/genetics/*metabolism, Bioelectric Energy Sources/microbiology, Carbon Cycle, Carbon Dioxide/*metabolism, Electrodes, Electrons, Fresh Water/*microbiology, Geologic Sediments/microbiology, Hydrogen/metabolism, RNA, Ribosomal, 16S/genetics | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3503 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9172) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9172 | |||
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 | |||
39276 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17370 | ||||
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 | |
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
71840 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48588.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121521 | Curators of the CIP | Collection of Institut Pasteur (CIP 105359) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105359 |