Strain identifier
BacDive ID: 18007
Type strain: 
Species: Sedimentibacter hydroxybenzoicus
Strain Designation: JW/Z-1
Strain history: <- J. Wiegel, JW/Z-1
NCBI tax ID(s): 1123245 (strain), 29345 (species)
version 8.1 (current version)
General
@ref: 3112
BacDive-ID: 18007
DSM-Number: 7310
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive
description: Sedimentibacter hydroxybenzoicus JW/Z-1 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from freshwater pond.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 29345 | species |
| 1123245 | strain |
strain history
- @ref: 3112
- history: <- J. Wiegel, JW/Z-1
doi: 10.13145/bacdive18007.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Tissierellales
- family: Sedimentibacteraceae
- genus: Sedimentibacter
- species: Sedimentibacter hydroxybenzoicus
- full scientific name: Sedimentibacter hydroxybenzoicus (Zhang et al. 1994) Breitenstein et al. 2002
synonyms
- @ref: 20215
- synonym: Clostridium hydroxybenzoicum
@ref: 3112
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridia, not assigned to family
genus: Sedimentibacter
species: Sedimentibacter hydroxybenzoicus
full scientific name: Sedimentibacter hydroxybenzoicus (Zhang et al. 1994) Breitenstein et al. 2002
strain designation: JW/Z-1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 3112
- name: SEDIMENTIBACTER MEDIUM (DSMZ Medium 643)
- growth: yes
- link: https://mediadive.dsmz.de/medium/643
- composition: Name: SEDIMENTIBACTER MEDIUM (DSMZ Medium 643) Composition: Yeast extract 9.94036 g/l L-Arginine x HCl 2.08748 g/l L-Lysine HCl 1.78926 g/l Glycine 0.745527 g/l NH4Cl 0.497018 g/l Na2S x 9 H2O 0.397614 g/l L-Cysteine HCl x H2O 0.397614 g/l MgCl2 x 7 H2O 0.0994036 g/l MgSO4 x 7 H2O 0.0149105 g/l Nitrilotriacetic acid 0.00745527 g/l NaCl 0.00497018 g/l MnSO4 x H2O 0.00248509 g/l ZnSO4 x 7 H2O 0.000894632 g/l CoSO4 x 7 H2O 0.000894632 g/l Sodium resazurin 0.000497018 g/l CaCl2 x 2 H2O 0.000497018 g/l FeSO4 x 7 H2O 0.000497018 g/l NiCl2 x 6 H2O 0.000149105 g/l AlK(SO4)2 x 12 H2O 9.94036e-05 g/l Pyridoxine hydrochloride 9.94036e-05 g/l Calcium D-(+)-pantothenate 4.97018e-05 g/l p-Aminobenzoic acid 4.97018e-05 g/l (DL)-alpha-Lipoic acid 4.97018e-05 g/l Nicotinic acid 4.97018e-05 g/l CuSO4 x 5 H2O 4.97018e-05 g/l H3BO3 4.97018e-05 g/l Thiamine HCl 4.97018e-05 g/l Riboflavin 4.97018e-05 g/l Na2MoO4 x 2 H2O 4.97018e-05 g/l Folic acid 1.98807e-05 g/l Biotin 1.98807e-05 g/l Na2WO4 x 2 H2O 1.98807e-06 g/l Na2SeO3 x 5 H2O 1.49105e-06 g/l Vitamin B12 9.94036e-07 g/l Sodium Potassium phosphate buffer Distilled water
culture temp
- @ref: 3112
- growth: positive
- type: growth
- temperature: 35
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 3112 | anaerobe | |
| 69480 | anaerobe | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 3112
- sample type: freshwater pond
- geographic location: Athens
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Pond (small) |
Safety information
risk assessment
- @ref: 3112
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3112
- description: Sedimentibacter hydroxybenzoicus strain JW/Z-1 16S ribosomal RNA gene, partial sequence
- accession: L11305
- length: 1457
- database: ena
- NCBI tax ID: 29345
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sedimentibacter hydroxybenzoicus DSM 7310 | GCA_013403245 | contig | ncbi | 1123245 |
| 66792 | Sedimentibacter hydroxybenzoicus DSM 7310 | 1123245.3 | wgs | patric | 1123245 |
GC content
- @ref: 3112
- GC-content: 35.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 85 | no |
| motile | yes | 85.273 | no |
| flagellated | no | 62.4 | no |
| gram-positive | yes | 52.065 | no |
| anaerobic | yes | 99.343 | yes |
| aerobic | no | 97.726 | no |
| halophile | no | 89.135 | no |
| spore-forming | yes | 85.531 | no |
| glucose-util | yes | 78.903 | no |
| thermophile | no | 99.756 | no |
| glucose-ferment | no | 57.177 | no |
External links
@ref: 3112
culture collection no.: DSM 7310, ATCC 51151
straininfo link
- @ref: 86994
- straininfo: 45271
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 7744052 | Purification and characterization of an oxygen-sensitive reversible 4-hydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum. | He Z, Wiegel J | Eur J Biochem | 10.1111/j.1432-1033.1995.tb20440.x | 1995 | Amino Acid Sequence, Carboxy-Lyases/chemistry/*isolation & purification/metabolism, Clostridium/*enzymology, Enzyme Activation, Molecular Sequence Data, Oxygen/metabolism, Sequence Alignment, Substrate Specificity | Metabolism |
| Phylogeny | 8186087 | Clostridium hydroxybenzoicum sp. nov., an amino acid-utilizing, hydroxybenzoate-decarboxylating bacterium isolated from methanogenic freshwater pond sediment. | Zhang X, Mandelco L, Wiegel J | Int J Syst Bacteriol | 10.1099/00207713-44-2-214 | 1994 | Amino Acids/*metabolism, Clostridium/*classification/isolation & purification/*metabolism/ultrastructure, Decarboxylation, Fatty Acids/biosynthesis, Fresh Water, Hydroxybenzoates/*metabolism, Methane/metabolism, Parabens/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, RNA, Water Microbiology | Metabolism |
| Enzymology | 8655551 | Purification and characterization of an oxygen-sensitive, reversible 3,4-dihydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum. | He Z, Wiegel J | J Bacteriol | 10.1128/jb.178.12.3539-3543.1996 | 1996 | Amino Acid Sequence, Carboxy-Lyases/*isolation & purification/metabolism, Catechols/metabolism, Clostridium/*enzymology, Hydrogen-Ion Concentration, Molecular Sequence Data, Molecular Weight, Oxygen/metabolism, Substrate Specificity, Temperature | Metabolism |
| Enzymology | 10438791 | Cloning, characterization, and expression of a novel gene encoding a reversible 4-hydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum. | Huang J, He Z, Wiegel J | J Bacteriol | 10.1128/JB.181.16.5119-5122.1999 | 1999 | Base Sequence, Carboxy-Lyases/*genetics/metabolism, Cloning, Molecular, Clostridium/*enzymology/*genetics, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Molecular Sequence Data, Promoter Regions, Genetic/genetics, Sequence Homology, Amino Acid | Genetics |
| Phylogeny | 12054241 | Reclassification of Clostridium hydroxybenzoicum as Sedimentibacter hydroxybenzoicus gen. nov., comb. nov., and description of Sedimentibacter saalensis sp. nov.. | Breitenstein A, Wiegel J, Haertig C, Weiss N, Andreesen JR, Lechner U | Int J Syst Evol Microbiol | 10.1099/00207713-52-3-801 | 2002 | Bacterial Typing Techniques, Base Composition, Clostridium/*classification/genetics/growth & development/metabolism, Culture Media, DNA, Ribosomal/analysis, Fresh Water/microbiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Cultivation |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 3112 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7310) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7310 | |
| 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) | |
| 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) | |
| 86994 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45271.1 | StrainInfo: A central database for resolving microbial strain identifiers |