Strain identifier
BacDive ID: 1699
Type strain:
Species: Bifidobacterium choerinum
Strain Designation: SU806
Strain history: CIP <- 2019, DSMZ <- 1990, DSMZ <- ATCC <- V. Scardovi <- D. Matteuzzi: strain SU806
NCBI tax ID(s): 1121107 (strain), 35760 (species)
General
@ref: 8810
BacDive-ID: 1699
DSM-Number: 20434
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped
description: Bifidobacterium choerinum SU806 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from piglet faeces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
35760 | species |
1121107 | strain |
strain history
@ref | history |
---|---|
8810 | <- ATCC <- V. Scardovi, SU806 |
67770 | ATCC 27686 <-- V. Scardovi <-- D. Matteuzzi SU 806. |
118249 | CIP <- 2019, DSMZ <- 1990, DSMZ <- ATCC <- V. Scardovi <- D. Matteuzzi: strain SU806 |
doi: 10.13145/bacdive1699.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Bifidobacteriales
- family: Bifidobacteriaceae
- genus: Bifidobacterium
- species: Bifidobacterium choerinum
- full scientific name: Bifidobacterium choerinum Scardovi et al. 1979 (Approved Lists 1980)
@ref: 8810
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium choerinum
full scientific name: Bifidobacterium choerinum Scardovi et al. 1979
strain designation: SU806
type strain: yes
Morphology
cell morphology
- @ref: 118249
- gram stain: positive
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8810 | BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) | yes | https://mediadive.dsmz.de/medium/58 | Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 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 Tween 80 Resazurin Distilled water |
118249 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8810 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 8810
- oxygen tolerance: anaerobe
murein
- @ref: 8810
- murein short key: A11.21
- type: A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala2
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | + | builds acid from | 28087 |
68371 | starch | + | builds acid from | 28017 |
68371 | raffinose | + | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | + | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | + | builds acid from | 65327 |
68371 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8810 | - | - | - | - | - | + | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date |
---|---|---|
8810 | piglet faeces | |
47994 | Swine feces | 1989-05-02 |
67770 | Pig feces | |
118249 | Animal, Piglet, feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Suidae (Pig,Swine) |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_5739.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_259;97_3388;98_4273;99_5739&stattab=map
- Last taxonomy: Bifidobacterium
- 16S sequence: LC071800
- Sequence Identity:
- Total samples: 42281
- soil counts: 410
- aquatic counts: 231
- animal counts: 41508
- plant counts: 132
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8810 | 1 | Risk group (German classification) |
118249 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bifidobacterium choerinum gene for 16S rRNA, partial sequence, strain: ATCC 27686 | D86186 | 1530 | ena | 35760 |
20218 | Bifidobacterium choerinum 16S-23S rRNA intergenic spacer region | L36968 | 552 | ena | 35760 |
20218 | Bifidobacterium choerinum strain DSM 20434 16S ribosomal RNA gene, partial sequence | GQ487638 | 148 | ena | 35760 |
20218 | Bifidobacterium choerinum gene for 16S rRNA, partial sequence, strain: JCM 1212 | AB116296 | 489 | ena | 35760 |
20218 | Bifidobacterium choerinum gene for 16S rRNA, partial sequence, strain: JCM 1212 | AB507092 | 658 | ena | 35760 |
20218 | Bifidobacterium choerinum strain KCTC 3275 16S ribosomal RNA gene, partial sequence | GU361817 | 1494 | ena | 35760 |
67770 | Bifidobacterium choerinum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1212 | LC071800 | 1466 | ena | 35760 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bifidobacterium choerinum DSM 20434 | 1121107.3 | wgs | patric | 1121107 |
66792 | Bifidobacterium choerinum DSM 20434 | 1121107.4 | wgs | patric | 1121107 |
66792 | Bifidobacterium choerinum strain LMG 10510 | 35760.3 | wgs | patric | 35760 |
66792 | Bifidobacterium choerinum DSM 20434 | 2529292584 | draft | img | 1121107 |
66792 | Bifidobacterium choerinum LMG 10510 | 2597490261 | draft | img | 35760 |
66792 | Bifidobacterium choerinum DSM 20434 | 2660238656 | draft | img | 1121107 |
67770 | Bifidobacterium choerinum DSM 20434 | GCA_000484675 | contig | ncbi | 1121107 |
67770 | Bifidobacterium choerinum DSM 20434 | GCA_000771425 | contig | ncbi | 1121107 |
67770 | Bifidobacterium choerinum LMG 10510 | GCA_000741135 | contig | ncbi | 35760 |
GC content
- @ref: 8810
- GC-content: 66.3
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 94.54 | no |
flagellated | no | 97.228 | no |
gram-positive | yes | 88.994 | no |
anaerobic | yes | 98.495 | yes |
aerobic | no | 97.759 | yes |
halophile | no | 70.184 | no |
spore-forming | no | 96.69 | no |
thermophile | no | 95.533 | yes |
glucose-util | yes | 83.511 | no |
glucose-ferment | yes | 79.585 | no |
External links
@ref: 8810
culture collection no.: DSM 20434, ATCC 27686, CCUG 24609, JCM 1212, CGMCC 1.2276, CIP 103378, KCTC 3275, LMG 10510
straininfo link
- @ref: 71346
- straininfo: 13594
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 29395537 | Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov. | Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M | Syst Appl Microbiol | 10.1016/j.syapm.2018.01.002 | 2018 | Animals, Bacterial Typing Techniques, Base Sequence, Bifidobacterium/*classification/genetics, Callithrix/microbiology, Cricetinae/microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/*microbiology, Geese/microbiology, High-Throughput Nucleotide Sequencing, Italy, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rabbits/microbiology, Saguinus/microbiology, Sequence Analysis, DNA | Transcriptome |
Phylogeny | 30789326 | Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov. | Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003306 | 2019 | Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification, Callithrix/*microbiology, DNA, Bacterial/genetics, Feces/microbiology, Genes, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rodentia/*microbiology, Saimiri/*microbiology, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8810 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20434) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20434 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
47994 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 24609) | https://www.ccug.se/strain?id=24609 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
71346 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13594.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118249 | Curators of the CIP | Collection of Institut Pasteur (CIP 103378) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103378 |