Strain identifier
BacDive ID: 4141
Type strain: 
Species: Humidesulfovibrio mexicanus
Strain history: DSM 13116 <-- J.-L. Garcia Lup1.
NCBI tax ID(s): 1121458 (strain), 147047 (species)
version 8.1 (current version)
General
@ref: 4908
BacDive-ID: 4141
DSM-Number: 13116
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Humidesulfovibrio mexicanus DSM 13116 is an anaerobe, mesophilic, motile bacterium that was isolated from upflow anaerobic sludge blanket reactor.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1121458 | strain |
| 147047 | species |
strain history
| @ref | history |
|---|---|
| 4908 | <- J.-L. Garcia, Universités de Provence et de la Méditerranée, ESIL, Marseille, France; Lup1 <- G. Hernandez-Eugenio {1998} |
| 67770 | DSM 13116 <-- J.-L. Garcia Lup1. |
doi: 10.13145/bacdive4141.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfovibrionaceae
- genus: Humidesulfovibrio
- species: Humidesulfovibrio mexicanus
- full scientific name: Humidesulfovibrio mexicanus (Hernandez-Eugenio et al. 2001) Waite et al. 2020
synonyms
- @ref: 20215
- synonym: Desulfovibrio mexicanus
@ref: 4908
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfovibrionaceae
genus: Humidesulfovibrio
species: Humidesulfovibrio mexicanus
full scientific name: Humidesulfovibrio mexicanus (Hernandez-Eugenio et al. 2001) Waite et al. 2020
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.11 | |
| 69480 | 99.992 | negative |
Culture and growth conditions
culture medium
- @ref: 4908
- name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)
- growth: yes
- link: https://mediadive.dsmz.de/medium/641
- composition: Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) Composition: Na-DL-lactate 2.49252 g/l Na2SO4 1.99402 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l Na2S2O3 x 5 H2O 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 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 | growth | type | temperature | range |
|---|---|---|---|---|
| 4908 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4908 | anaerobe | |
| 69480 | anaerobe | 99.726 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.534 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 4908 | upflow anaerobic sludge blanket reactor | Mexico | MEX | North America |
| 67770 | Mexican UASB digester treating cheese factory wastewater |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | #Anaerobic digestor |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_43868.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15811;96_18053;97_25106;98_31834;99_43868&stattab=map
- Last taxonomy: Desulfovibrio mexicanus subclade
- 16S sequence: AF227984
- Sequence Identity:
- Total samples: 246
- soil counts: 11
- aquatic counts: 205
- animal counts: 6
- plant counts: 24
Safety information
risk assessment
- @ref: 4908
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4908
- description: Desulfovibrio mexicoense 16S ribosomal RNA gene, partial sequence
- accession: AF227984
- length: 1500
- database: ena
- NCBI tax ID: 147047
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfovibrio mexicanus strain DSM 13116 | 147047.3 | wgs | patric | 147047 |
| 66792 | Desulfovibrio mexicanus DSM 13116 | 2622736540 | draft | img | 1121458 |
| 67770 | Humidesulfovibrio mexicanus DSM 13116 | GCA_900188225 | scaffold | ncbi | 147047 |
GC content
- @ref: 4908
- GC-content: 66
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
- trait: spore-forming
- prediction: no
- confidence: 100
- training_data: no
External links
@ref: 4908
culture collection no.: DSM 13116, JCM 15822, Lup 1
straininfo link
- @ref: 73644
- straininfo: 49406
literature
- topic: Phylogeny
- Pubmed-ID: 21317277
- title: Desulfovibrio arcticus sp. nov., a psychrotolerant sulfate-reducing bacterium from a cryopeg.
- authors: Pecheritsyna SA, Rivkina EM, Akimov VN, Shcherbakova VA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.021451-0
- year: 2011
- mesh: Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desulfovibrio/*classification/genetics/*isolation & purification/physiology, *Environmental Microbiology, Flagella/physiology, Hydrogensulfite Reductase/analysis, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Sulfates/*metabolism, Temperature
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4908 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13116) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13116 | |||
| 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) | |||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 73644 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49406.1 | StrainInfo: A central database for resolving microbial strain identifiers |