Strain identifier
BacDive ID: 17767
Type strain: 
Species: Aminobacterium colombiense
Strain Designation: ALA-1
Strain history: <- J.-L. Garcia, Université de Provence, Marseille, France; ALA-1 <- S. Baena {1996}
NCBI tax ID(s): 572547 (strain), 81468 (species)
version 8.1 (current version)
General
@ref: 4661
BacDive-ID: 17767
DSM-Number: 12261
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Aminobacterium colombiense ALA-1 is an anaerobe, mesophilic bacterium that was isolated from anaerobic lagoon of dairy wastewater treatment plant.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 81468 | species |
| 572547 | strain |
strain history
- @ref: 4661
- history: <- J.-L. Garcia, Université de Provence, Marseille, France; ALA-1 <- S. Baena {1996}
doi: 10.13145/bacdive17767.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/synergistota
- domain: Bacteria
- phylum: Synergistota
- class: Synergistia
- order: Synergistales
- family: Synergistaceae
- genus: Aminobacterium
- species: Aminobacterium colombiense
- full scientific name: Aminobacterium colombiense Baena et al. 1999
@ref: 4661
domain: Bacteria
phylum: Synergistetes
class: Synergistia
order: Synergistales
family: Synergistaceae
genus: Aminobacterium
species: Aminobacterium colombiense
full scientific name: Aminobacterium colombiense Baena et al. 1999
strain designation: ALA-1
type strain: yes
Morphology
multimedia
- @ref: 66793
- multimedia content: EM_DSM_12261_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 4661
- name: AMINOMONAS MEDIUM (DSMZ Medium 846)
- growth: yes
- link: https://mediadive.dsmz.de/medium/846
- composition: Name: AMINOMONAS MEDIUM (DSMZ Medium 846) Composition: Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l L-Serine 1.04686 g/l NaCl 0.997009 g/l Na2S x 9 H2O 0.498504 g/l KCl 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l KH2PO4 0.299103 g/l NH4Cl 0.299103 g/l K2HPO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
- @ref: 4661
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 4661
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 4661
- sample type: anaerobic lagoon of dairy wastewater treatment plant
- country: Colombia
- origin.country: COL
- continent: Middle and South America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Dairy product |
| #Engineered | #Waste | #Water treatment plant |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_62276.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_365;96_1576;97_2432;98_3009;99_62276&stattab=map
- Last taxonomy: Aminobacterium colombiense subclade
- 16S sequence: AF069287
- Sequence Identity:
- Total samples: 119
- soil counts: 6
- aquatic counts: 111
- animal counts: 1
- plant counts: 1
Safety information
risk assessment
- @ref: 4661
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4661
- description: Aminobacterium colombiense 16S ribosomal RNA gene, partial sequence
- accession: AF069287
- length: 1519
- database: ena
- NCBI tax ID: 572547
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Aminobacterium colombiense DSM 12261 | GCA_000025885 | complete | ncbi | 572547 |
| 66792 | Aminobacterium colombiense DSM 12261 | 572547.3 | complete | patric | 572547 |
| 66792 | Aminobacterium colombiense ALA-1, DSM 12261 | 646564503 | complete | img | 572547 |
GC content
- @ref: 4661
- GC-content: 46
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 88.944 | no |
| flagellated | no | 98.949 | no |
| gram-positive | no | 98.62 | no |
| anaerobic | yes | 99.734 | yes |
| aerobic | no | 98.721 | yes |
| halophile | no | 81.921 | no |
| spore-forming | no | 94.763 | no |
| thermophile | yes | 55.543 | yes |
| glucose-util | yes | 66.748 | no |
| glucose-ferment | no | 64.382 | no |
External links
@ref: 4661
culture collection no.: DSM 12261
straininfo link
- @ref: 86758
- straininfo: 49260
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year |
|---|---|---|---|---|---|---|
| Phylogeny | 16887649 | Aminobacterium colombiensegen. nov. sp. nov., an amino acid-degrading anaerobe isolated from anaerobic sludge. | Baena S, Fardeau ML, Labat M, Ollivier B, Thomas P, Garcia JL, Patel BK | Anaerobe | 10.1006/anae.1998.0170 | 1998 |
| Genetics | 21304712 | Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). | Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP | Stand Genomic Sci | 10.4056/sigs.902116 | 2010 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4661 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12261) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12261 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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 | |||
| 86758 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49260.1 | StrainInfo: A central database for resolving microbial strain identifiers |