Strain identifier
BacDive ID: 132644
Type strain: 
Species: Harryflintia acetispora
Strain Designation: V20-281a
Strain history: <- D. Petzoldt, Lohmann Animal Health GmbH, Hannover, Germany; V20-281a <- D. Petzoldt {2014}
NCBI tax ID(s): 1849041 (species)
version 8.1 (current version)
General
@ref: 24433
BacDive-ID: 132644
DSM-Number: 100433
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, Gram-negative, rod-shaped, colony-forming
description: Harryflintia acetispora V20-281a is an anaerobe, spore-forming, Gram-negative bacterium that forms circular colonies and was isolated from cecum of commercial broiler chicken.
NCBI tax id
- NCBI tax id: 1849041
- Matching level: species
strain history
- @ref: 24433
- history: <- D. Petzoldt, Lohmann Animal Health GmbH, Hannover, Germany; V20-281a <- D. Petzoldt {2014}
doi: 10.13145/bacdive132644.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Harryflintia
- species: Harryflintia acetispora
- full scientific name: Harryflintia acetispora Petzoldt et al. 2016
@ref: 24433
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridia, not assigned to order
family: Oscillospiraceae
genus: Harryflintia
species: Harryflintia acetispora
full scientific name: Harryflintia acetispora Petzoldt et al. 2016
strain designation: V20-281a
type strain: yes
Morphology
cell morphology
- @ref: 24927
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 24927
- colony size: 1-3 mm
- colony shape: circular
- incubation period: 3 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 24433 | RCM MEDIUM (DSMZ Medium 634) | yes | https://mediadive.dsmz.de/medium/634 | Name: RCM MEDIUM (DSMZ Medium 634) Composition: Sodium resazurin 0.0005 g/l dehydrated RCM medium |
| 24433 | WILKINS-CHALGREN ANAEROBE BROTH (N2/CO2) (DSMZ Medium 339a) | yes | https://mediadive.dsmz.de/medium/339a | Name: WILKINS-CHALGREN ANAEROBE BROTH (N2/CO2) (DSMZ Medium 339a) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l D-Glucose 5.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 24927 | positive | growth | 20-25 | |
| 24927 | positive | optimum | 37-41 | |
| 24433 | positive | growth | 37 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 24927 | positive | growth | 4.0-9.0 | alkaliphile |
| 24927 | positive | optimum | 7.0-8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 24927
- oxygen tolerance: anaerobe
spore formation
- @ref: 24927
- type of spore: endospore
- spore formation: yes
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 24927 | 22599 | arabinose | - | builds acid from |
| 24927 | 4853 | esculin | - | hydrolysis |
| 24927 | 15443 | inulin | - | builds acid from |
| 24927 | 29864 | mannitol | - | builds acid from |
| 24927 | 16634 | raffinose | - | builds acid from |
| 24927 | 17814 | salicin | - | builds acid from |
| 24927 | 17992 | sucrose | - | builds acid from |
| 24927 | 16199 | urea | - | hydrolysis |
| 24927 | 28757 | fructose | + | builds acid from |
| 24927 | 28260 | galactose | + | builds acid from |
| 24927 | 17306 | maltose | + | builds acid from |
| 24927 | 27082 | trehalose | + | builds acid from |
enzymes
- @ref: 24927
- value: cytochrome oxidase
- activity: -
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
- @ref: 24433
- sample type: cecum of commercial broiler chicken
- geographic location: Lower Saxony
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Birds | #Chicken |
| #Host Body-Site | #Gastrointestinal tract | #Large intestine |
taxonmaps
- @ref: 69479
- File name: preview.99_5810.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_154;96_2784;97_3422;98_4322;99_5810&stattab=map
- Last taxonomy: Oscillospiraceae
- 16S sequence: KU999999
- Sequence Identity:
- Total samples: 40963
- soil counts: 178
- aquatic counts: 386
- animal counts: 40300
- plant counts: 99
Safety information
risk assessment
- @ref: 24433
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24433
- description: Harryflintia acetispora strain V20-281a 16S ribosomal RNA gene, partial sequence
- accession: KU999999
- length: 1363
- database: ena
- NCBI tax ID: 1849041
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Harryflintia acetispora strain DSM 100433 | 1849041.17 | wgs | patric | 1849041 |
| 66792 | Harryflintia acetispora DSM 100433 | 2788499847 | draft | img | 1849041 |
GC content
- @ref: 24433
- GC-content: 62.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 91.365 | yes |
| gram-positive | yes | 88.754 | no |
| anaerobic | yes | 99.606 | yes |
| aerobic | no | 98.637 | yes |
| halophile | no | 87.693 | no |
| spore-forming | no | 76.72 | no |
| glucose-util | yes | 86.13 | no |
| flagellated | no | 97.379 | yes |
| thermophile | no | 96.07 | yes |
| glucose-ferment | yes | 74.298 | no |
External links
@ref: 24433
culture collection no.: DSM 100433, CECT 8892
straininfo link
- @ref: 90957
- straininfo: 405230
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 27432404 | Harryflintia acetispora gen. nov., sp. nov., isolated from chicken caecum. | Petzoldt D, Breves G, Rautenschlein S, Taras D | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001317 | 2016 | Animals, Bacterial Typing Techniques, Base Composition, Cecum/*microbiology, Chickens/*microbiology, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
| Phylogeny | 28901896 | Paludicola psychrotolerans gen. nov., sp. nov., a novel psychrotolerant chitinolytic anaerobe of the family Ruminococcaceae. | Li Y, Zhang LL, Liu L, Tian YQ, Liu XF, Li WJ, Dai YM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002260 | 2017 | Bacterial Typing Techniques, Base Composition, China, Chitin/metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Wetlands | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 24433 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100433 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100433) | |||
| 24927 | D. B. Petzoldt, Gerhard,Rautenschlein, Silke,Taras, David | Harryflintia acetispora gen. nov., sp. nov., isolated from chicken caecum | 10.1099/ijsem.0.001317 | IJSEM 66: 4099-4104 2016 | 27432404 | |
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 90957 | 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-ID405230.1 |