Strain identifier
BacDive ID: 158916
Type strain: 
Species: Clostridium sp.
Strain Designation: HV4-5-A1G
Strain history: <- S. Hahnke; HV4-5-A1G (Clostridium luticellarii) <- T. Langer
NCBI tax ID(s): 1506 (species)
version 9.3 (current version)
General
@ref: 65738
BacDive-ID: 158916
DSM-Number: 104276
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Clostridium sp. HV4-5-A1G is an anaerobe, mesophilic bacterium that was isolated from Process fluid from a laboratory-scale fermenter treating grass cutting.
NCBI tax id
- NCBI tax id: 1506
- Matching level: species
strain history
- @ref: 65738
- history: <- S. Hahnke; HV4-5-A1G (Clostridium luticellarii) <- T. Langer
doi: 10.13145/bacdive158916.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Clostridium
- species: Clostridium sp.
- full scientific name: Clostridium Prazmowski 1880 (Approved Lists 1980)
synonyms
@ref synonym 20215 Anaerobacter 20215 Inflabilis 20215 Tyzzerella 20215 Pseudoclostridium 20215 Lachnoclostridium
@ref: 65738
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Clostridiaceae
genus: Clostridium
species: Clostridium sp.
full scientific name: Clostridium sp.
strain designation: HV4-5-A1G
type strain: no
Culture and growth conditions
culture medium
- @ref: 65738
- name: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/110a
- composition: Name: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Yeast extract 5.0 g/l K2HPO4 5.0 g/l D-Glucose 4.0 g/l Na2CO3 1.5 g/l Cellobiose 1.0 g/l Maltose 1.0 g/l Starch 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l NaOH Distilled water
culture temp
- @ref: 65738
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | anaerobe | 94.309 |
| 125439 | anaerobe | 99.6 |
Isolation, sampling and environmental information
isolation
- @ref: 65738
- sample type: Process fluid from a laboratory-scale fermenter treating grass cutting
- geographic location: Jena
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Engineered | #Laboratory | #Lab enrichment |
| #Engineered | #Bioreactor |
Sequence information
16S sequences
- @ref: 65738
- description: Clostridium sp. HV4-5-A1G, whole genome shotgun sequencing project
- accession: VXJK00000000
- length: 287
- database: nuccore
- NCBI tax ID: 2004595
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium sp. HV4-5-A1G | GCA_008692765 | contig | ncbi | 2004595 |
| 66792 | Clostridium sp. HV4-5-A1G HV4-6-A5C | GCA_900184915 | contig | ncbi | 2004595 |
| 66792 | Clostridium sp. HV4-5-A1G | 2004595.3 | wgs | patric | 2004595 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 61.589 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 94.309 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 74.358 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 97.628 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 88.074 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 74.366 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 82.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 79.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 79.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 99.6 |
External links
@ref: 65738
culture collection no.: DSM 104276
straininfo link
- @ref: 111435
- straininfo: 406798
literature
- topic: Genetics
- Pubmed-ID: 31948972
- title: Complete Genome Sequence of a New Clostridium sp. Isolated from Anaerobic Digestion and Biomethanation.
- authors: Hahnke S, Abendroth C, Pascual J, Langer T, Ramm P, Klocke M, Luschnig O, Porcar M
- journal: Microbiol Resour Announc
- DOI: 10.1128/MRA.01472-19
- year: 2020
- topic2: Phylogeny
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 65738 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104276 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104276) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 111435 | 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-ID406798.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |