Strain identifier
BacDive ID: 5415
Type strain:
Species: Peptoclostridium acidaminophilum
Strain Designation: al-2
Strain history: <- U. Zindel <- H. Lebertz <- F. Widdel, al-2
NCBI tax ID(s): 1286171 (strain), 1731 (species)
General
@ref: 1530
BacDive-ID: 5415
DSM-Number: 3953
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, motile, curved-shaped
description: Peptoclostridium acidaminophilum al-2 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from waste water ditch.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1286171 | strain |
1731 | species |
strain history
- @ref: 1530
- history: <- U. Zindel <- H. Lebertz <- F. Widdel, al-2
doi: 10.13145/bacdive5415.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Peptostreptococcaceae
- genus: Peptoclostridium
- species: Peptoclostridium acidaminophilum
- full scientific name: Peptoclostridium acidaminophilum (Zindel et al. 1989) Galperin et al. 2016
synonyms
- @ref: 20215
- synonym: Eubacterium acidaminophilum
@ref: 1530
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Peptostreptococcaceae
genus: Peptoclostridium
species: Peptoclostridium acidaminophilum
full scientific name: Peptoclostridium acidaminophilum (Zindel et al. 1989) Galperin et al. 2016
strain designation: al-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
25060 | positive | 2.0-8.0 µm | 0.5-1.5 µm | curved-shaped | yes | |
69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 1530
- name: EBA MEDIUM (DSMZ Medium 454)
- growth: yes
- link: https://mediadive.dsmz.de/medium/454
- composition: Name: EBA MEDIUM (DSMZ Medium 454) Composition: Glycine 2.09205 g/l NaCl 1.04603 g/l KCl 0.523013 g/l MgSO4 x 7 H2O 0.523013 g/l NH4Cl 0.261506 g/l KH2PO4 0.209205 g/l CaCl2 x 2 H2O 0.156904 g/l Na2SeO3 x 5 H2O 0.00263014 g/l HCl 0.00261506 g/l FeCl2 x 4 H2O 0.00156904 g/l Resazurin 0.00104603 g/l CoCl2 x 6 H2O 0.000198745 g/l MnCl2 x 4 H2O 0.000104603 g/l ZnCl2 7.32218e-05 g/l Na2MoO4 x 2 H2O 3.76569e-05 g/l NiCl2 x 6 H2O 2.51046e-05 g/l H3BO3 6.27615e-06 g/l CuCl2 x 2 H2O 2.09205e-06 g/l Biotin NaHCO3 Na2S Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1530 | positive | growth | 34 | mesophilic |
25060 | positive | growth | 15.0-40.0 | |
25060 | no | growth | 42 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
25060 | positive | growth | 6.5-8.4 |
25060 | positive | optimum | 7.1-7.4 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
1530 | anaerobe | |
25060 | obligate anaerobe | |
69480 | anaerobe | 99.438 |
spore formation
- @ref: 25060
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
25060 | NaCl | no | growth | 6 % |
25060 | NaCl | minimum | 0.001-0.002 M |
murein
- @ref: 1530
- murein short key: A31
- type: A1gamma m-Dpm-direct
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25060 | 17632 | nitrate | - | reduction |
25060 | 16189 | sulfate | - | reduction |
25060 | 16094 | thiosulfate | - | reduction |
25060 | 16856 | glutathione | + | assimilation |
25060 | 17201 | glycylglycine | + | assimilation |
25060 | 63961 | glycylglycylglycine | + | assimilation |
25060 | 27612 | hydantoin | + | assimilation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
25060 | catalase | - | 1.11.1.6 |
25060 | cytochrome oxidase | - | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
1530 | waste water ditch | near Konstanz | Germany | DEU | Europe |
25060 | anaerobic black mud from a waste water ditch | near Konstanz |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Mud (Sludge) |
#Condition | #Anoxic (anaerobic) | |
#Engineered | #Waste | #Wastewater |
taxonmaps
- @ref: 69479
- File name: preview.99_4467.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16294;96_2232;97_2703;98_3356;99_4467&stattab=map
- Last taxonomy: Peptoclostridium acidaminophilum subclade
- 16S sequence: AF071416
- Sequence Identity:
- Total samples: 2680
- soil counts: 102
- aquatic counts: 636
- animal counts: 1891
- plant counts: 51
Safety information
risk assessment
- @ref: 1530
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1530
- description: Clostridium acidaminophilum 16S ribosomal RNA gene, partial sequence
- accession: AF071416
- length: 1508
- database: ena
- NCBI tax ID: 1286171
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Peptoclostridium acidaminophilum DSM 3953 al-2 | GCA_000597865 | complete | ncbi | 1286171 |
66792 | Eubacterium acidaminophilum DSM 3953 | 1286171.3 | complete | patric | 1286171 |
66792 | Peptoclostridium acidaminophilum DSM 3953 strain al-2 | 1286171.8 | plasmid | patric | 1286171 |
66792 | Peptoclostridium acidaminophilum al-2 | 2562617038 | complete | img | 1286171 |
GC content
@ref | GC-content |
---|---|
1530 | 44.0 |
25060 | 44 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 88 | no |
motile | yes | 75.022 | no |
flagellated | no | 70.464 | no |
gram-positive | yes | 62.143 | no |
anaerobic | yes | 99.637 | no |
halophile | no | 92.301 | no |
spore-forming | yes | 79.019 | no |
glucose-util | yes | 78.528 | no |
aerobic | no | 98.627 | yes |
thermophile | no | 75.586 | no |
glucose-ferment | yes | 54.03 | no |
External links
@ref: 1530
culture collection no.: DSM 3953, ATCC 49065
straininfo link
- @ref: 74904
- straininfo: 42275
literature
- topic: Genetics
- Pubmed-ID: 24926057
- title: Complete Genome Sequence of Amino Acid-Utilizing Eubacterium acidaminophilum al-2 (DSM 3953).
- authors: Poehlein A, Andreesen JR, Daniel R
- journal: Genome Announc
- DOI: 10.1128/genomeA.00573-14
- year: 2014
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1530 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3953) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3953 | |||
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 | |||
25060 | M. Y. B. Galperin, V.,Tolstoy, I.,Yutin, N. | 10.1099/ijsem.0.001548 | Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov | IJSEM 66: 5506-5513 2016 | 27902180 | |
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 | |
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) | |||
74904 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42275.1 | StrainInfo: A central database for resolving microbial strain identifiers |