Strain identifier
BacDive ID: 6377
Type strain: 
Species: Lachnoanaerobaculum umeaense
Strain Designation: CD3:22, CD3 : 22
Strain history: <- M. Hedberg, Umea University, Institution of Clinical Microbiology, Div. of Immunology; CD3 : 22 <- M. Hedberg {2007}
NCBI tax ID(s): 617123 (species)
version 8.1 (current version)
General
@ref: 17229
BacDive-ID: 6377
DSM-Number: 23576
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, rod-shaped, human pathogen
description: Lachnoanaerobaculum umeaense CD3:22 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from biopsy from the small intestine of a child with coeliac disease.
NCBI tax id
- NCBI tax id: 617123
- Matching level: species
strain history
- @ref: 17229
- history: <- M. Hedberg, Umea University, Institution of Clinical Microbiology, Div. of Immunology; CD3 : 22 <- M. Hedberg {2007}
doi: 10.13145/bacdive6377.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Lachnoanaerobaculum
- species: Lachnoanaerobaculum umeaense
- full scientific name: Lachnoanaerobaculum umeaense Hedberg et al. 2012
@ref: 17229
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Lachnoanaerobaculum
species: Lachnoanaerobaculum umeaense
full scientific name: Lachnoanaerobaculum umeaense Hedberg et al. 2012
strain designation: CD3:22, CD3 : 22
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell shape | confidence |
|---|---|---|---|---|
| 30331 | positive | 15 µm | rod-shaped | |
| 69480 | positive | 100 |
colony morphology
- @ref: 61755
- incubation period: 1 day
Culture and growth conditions
culture medium
- @ref: 17229
- name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104c
- composition: Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17229 | positive | growth | 37 | mesophilic |
| 30331 | positive | growth | 37 | mesophilic |
| 61755 | positive | growth | 37 | mesophilic |
culture pH
- @ref: 30331
- ability: positive
- type: optimum
- pH: 6.75
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 17229 | anaerobe | |
| 30331 | anaerobe | |
| 61755 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30331 | yes | |
| 69481 | yes | 92 |
| 69480 | no | 99.925 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30331 | 22599 | arabinose | + | carbon source |
| 30331 | 37684 | mannose | + | carbon source |
| 30331 | 16634 | raffinose | + | carbon source |
enzymes
- @ref: 30331
- value: alpha-galactosidase
- activity: +
- ec: 3.2.1.22
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 17229 | biopsy from the small intestine of a child with coeliac disease | Umea, Umea University Hospital, Department of Paediatrics | Sweden | SWE | Europe | |
| 61755 | Jejunal biopsy,celiac disease patient | Umeå | Sweden | SWE | Europe | 2007-11-11 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | #Biopsy |
| #Infection | #Patient | |
| #Host Body-Site | #Gastrointestinal tract | #Small intestine |
| #Host | #Human | #Child |
taxonmaps
- @ref: 69479
- File name: preview.99_169864.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_353;96_1513;97_1805;98_2208;99_169864&stattab=map
- Last taxonomy: Lachnoanaerobaculum umeaense
- 16S sequence: FJ796700
- Sequence Identity:
- Total samples: 1453
- soil counts: 4
- aquatic counts: 8
- animal counts: 1437
- plant counts: 4
Safety information
risk assessment
- @ref: 17229
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17229
- description: Lachnoanaerobaculum umeaense strain CD3: 22 16S ribosomal RNA gene, partial sequence
- accession: FJ796700
- length: 1594
- database: ena
- NCBI tax ID: 617123
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Lachnoanaerobaculum umeaense DSM 23576 = CCUG 58757 | GCA_003589745 | complete | ncbi | 617123 |
| 66792 | Lachnoanaerobaculum umeaense DSM 23576 | GCA_003254255 | scaffold | ncbi | 617123 |
| 66792 | Lachnoanaerobaculum umeaense strain DSM 23576 | 617123.3 | wgs | patric | 617123 |
| 66792 | Lachnoanaerobaculum umeaense strain DSM 23576 = CCUG 58757 | 617123.56 | complete | patric | 617123 |
| 66792 | Lachnoanaerobaculum umeaense DSM 23576 | 2754412935 | draft | img | 617123 |
| 66792 | Lachnoanaerobaculum umeaense DSM 23576 | 2832953387 | complete | img | 617123 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17229 | 35 | high performance liquid chromatography (HPLC) |
| 30331 | 35 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 92 | no |
| motile | no | 90.23 | no |
| flagellated | no | 95.622 | no |
| gram-positive | yes | 90.624 | no |
| anaerobic | yes | 99.259 | no |
| aerobic | no | 99.03 | no |
| halophile | no | 82.725 | no |
| spore-forming | no | 50 | yes |
| glucose-util | yes | 90.347 | no |
| thermophile | no | 96.008 | no |
| glucose-ferment | yes | 75.491 | no |
External links
@ref: 17229
culture collection no.: DSM 23576, CCUG 58757
straininfo link
- @ref: 75850
- straininfo: 406142
literature
- topic: Phylogeny
- Pubmed-ID: 22228654
- title: Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prevot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.
- authors: Hedberg ME, Moore ERB, Svensson-Stadler L, Horstedt P, Baranov V, Hernell O, Wai SN, Hammarstrom S, Hammarstrom ML
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.033613-0
- year: 2012
- mesh: Adult, Bacterial Typing Techniques, Celiac Disease/microbiology, Child, DNA, Bacterial/genetics, Eubacterium/*classification/genetics/isolation & purification, Fatty Acids/analysis, Female, Humans, Intestine, Small/*microbiology, Male, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saliva/*microbiology, Sequence Analysis, DNA
- topic2: Pathogenicity
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17229 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23576) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23576 | |||
| 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 | |||
| 30331 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26672 | 28776041 | |
| 61755 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58757) | https://www.ccug.se/strain?id=58757 | |||
| 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) | |||
| 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 | |||
| 75850 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406142.1 | StrainInfo: A central database for resolving microbial strain identifiers |