Strain identifier
BacDive ID: 2797
Type strain:
Species: Anaerocolumna xylanovorans
Strain Designation: HESP1
Strain history: DSM 12503 <-- J. L. Garcia; HESP1.
NCBI tax ID(s): 1121345 (strain), 100134 (species)
General
@ref: 4749
BacDive-ID: 2797
DSM-Number: 12503
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Anaerocolumna xylanovorans HESP1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from anaerobic digester fed with olive mill wastewater.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121345 | strain |
100134 | species |
strain history
@ref | history |
---|---|
4749 | <- J. L. Garcia, Université de Provence, Marseille, France; HESP1 <- T. Mechichi {1998} |
67770 | DSM 12503 <-- J. L. Garcia; HESP1. |
doi: 10.13145/bacdive2797.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Anaerocolumna
- species: Anaerocolumna xylanovorans
- full scientific name: Anaerocolumna xylanovorans (Mechichi et al. 2000) Ueki et al. 2016
synonyms
- @ref: 20215
- synonym: Clostridium xylanovorans
@ref: 4749
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Anaerocolumna
species: Anaerocolumna xylanovorans
full scientific name: Anaerocolumna xylanovorans (Mechichi et al. 2000) Ueki et al. 2016
strain designation: HESP1
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 90.35 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 4749
- name: ANAEROCOLUMNA MEDIUM (DSMZ Medium 860)
- growth: yes
- link: https://mediadive.dsmz.de/medium/860
- composition: Name: ANAEROCOLUMNA MEDIUM (DSMZ Medium 860) Composition: D-Fructose 3.99202 g/l Na2CO3 1.49701 g/l NH4Cl 0.998004 g/l Yeast extract 0.998004 g/l NaCl 0.598802 g/l L-Cysteine HCl x H2O 0.499002 g/l K2HPO4 0.299401 g/l KH2PO4 0.299401 g/l Na2S x 9 H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l CaCl2 x 2 H2O 0.0998004 g/l KCl 0.0998004 g/l HCl 0.00374251 g/l FeCl2 x 4 H2O 0.00224551 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000284431 g/l MnCl2 x 4 H2O 0.000149701 g/l ZnCl2 0.00010479 g/l Na2MoO4 x 2 H2O 5.38922e-05 g/l NiCl2 x 6 H2O 3.59281e-05 g/l H3BO3 8.98204e-06 g/l CuCl2 x 2 H2O 2.99401e-06 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4749 | positive | growth | 35 | mesophilic |
67770 | positive | growth | 35 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
4749 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 91 |
69480 | yes | 99.447 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4749 | anaerobic digester fed with olive mill wastewater | Sfax | Tunisia | TUN | Africa |
67770 | Methanogenic digester |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Biodegradation | #Anaerobic digestor |
#Engineered | #Industrial | |
#Engineered | #Waste | #Industrial wastewater |
#Condition | #Anoxic (anaerobic) |
Safety information
risk assessment
- @ref: 4749
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4749
- description: Clostridium xylanovorans 16S ribosomal RNA gene, partial sequence
- accession: AF116920
- length: 1533
- database: ena
- NCBI tax ID: 100134
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Anaerocolumna cellulosilytica strain SN021 | 433286.4 | complete | patric | 433286 |
66792 | Anaerocolumna xylanovorans DSM 12503 | 1121345.3 | wgs | patric | 1121345 |
66792 | Anaerocolumna xylanovorans DSM 12503 | 2582580727 | draft | img | 1121345 |
67770 | Anaerocolumna xylanovorans DSM 12503 | GCA_900143645 | scaffold | ncbi | 1121345 |
GC content
@ref | GC-content | method |
---|---|---|
4749 | 40.0 | high performance liquid chromatography (HPLC) |
67770 | 40 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 91 | no |
gram-positive | yes | 87.637 | no |
anaerobic | yes | 98.102 | yes |
halophile | no | 95.799 | no |
spore-forming | yes | 93.903 | no |
glucose-util | yes | 88.836 | no |
aerobic | no | 97.386 | yes |
flagellated | yes | 61.811 | no |
thermophile | no | 98.431 | yes |
motile | yes | 82.494 | no |
glucose-ferment | yes | 64.848 | no |
External links
@ref: 4749
culture collection no.: DSM 12503, JCM 31057
straininfo link
- @ref: 72323
- straininfo: 49306
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10553289 | Characterization of a new xylanolytic bacterium, Clostridium xylanovorans sp. nov. | Mechichi T, Labat M, Garcia JL, Thomas P, Patel BK | Syst Appl Microbiol | 10.1016/S0723-2020(99)80044-7 | 1999 | Base Sequence, Biodegradation, Environmental, Carbohydrate Metabolism, Chromatography, High Pressure Liquid, Clostridium/*classification/cytology/physiology, Fermentation, Fumarates/metabolism, Methanol/metabolism, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial/chemistry, RNA, Ribosomal, 16S/chemistry, Xylans/*metabolism | Metabolism |
Phylogeny | 27126251 | Descriptions of Anaerotaenia torta gen. nov., sp. nov. and Anaerocolumna cellulosilytica gen. nov., sp. nov. isolated from a methanogenic reactor of cattle waste and reclassification of Clostridium aminovalericum, Clostridium jejuense and Clostridium xylanovorans as Anaerocolumna species. | Ueki A, Ohtaki Y, Kaku N, Ueki K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001123 | 2016 | Animals, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Cattle, Cellulose/metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Manure/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4749 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12503) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12503 | |||
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/ | ||||
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 | |||
72323 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49306.1 | StrainInfo: A central database for resolving microbial strain identifiers |