Strain identifier
BacDive ID: 1627
Type strain:
Species: Phocaeicola sartorii
Strain Designation: A-C2-0, AC20
Strain history: CCUG 57211 <-- A. Saalfrank A-C2-0.
NCBI tax ID(s): 671267 (species)
General
@ref: 16058
BacDive-ID: 1627
DSM-Number: 21941
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Phocaeicola sartorii A-C2-0 is an anaerobe, mesophilic bacterium that was isolated from caecum of a 5-week-old male heterozygous TNFdeltaARE C57BL/6 mouse.
NCBI tax id
- NCBI tax id: 671267
- Matching level: species
strain history
@ref | history |
---|---|
16058 | <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; A-C2-0 <- A. Saalfrank |
67770 | CCUG 57211 <-- A. Saalfrank A-C2-0. |
doi: 10.13145/bacdive1627.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Bacteroidaceae
- genus: Phocaeicola
- species: Phocaeicola sartorii
- full scientific name: Phocaeicola sartorii (Clavel et al. 2010) García-López et al. 2020
synonyms
@ref synonym 20215 Bacteroides chinchillae 20215 Phocaeicola chinchillae 20215 Bacteroides sartorii
@ref: 16058
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Phocaeicola
species: Phocaeicola sartorii
full scientific name: Phocaeicola sartorii (Clavel et al. 2010) García-López et al. 2020
strain designation: A-C2-0, AC20
type strain: yes
Morphology
colony morphology
- @ref: 61243
- incubation period: 1-2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16058 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
16058 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16058 | positive | growth | 37 | mesophilic |
61243 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
16058 | anaerobe |
61243 | anaerobe |
observation
- @ref: 67770
- observation: quinones: MK-9, MK-10, MK-9
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68367 | 27082 | trehalose | - | builds acid from |
68367 | 62345 | L-rhamnose | + | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 6731 | melezitose | - | builds acid from |
68367 | 16024 | D-mannose | + | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 5291 | gelatin | - | hydrolysis |
68367 | 30849 | L-arabinose | + | builds acid from |
68367 | 65327 | D-xylose | + | builds acid from |
68367 | 17814 | salicin | - | builds acid from |
68367 | 17306 | maltose | + | builds acid from |
68367 | 17992 | sucrose | - | builds acid from |
68367 | 17716 | lactose | + | builds acid from |
68367 | 16899 | D-mannitol | - | builds acid from |
68367 | 17634 | D-glucose | + | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | - | energy source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 29985 | L-glutamate | + | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68367 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | - |
68367 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | alkaline phosphatase | + | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | glutamate decarboxylase | + | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | gelatinase | - | |
68367 | urease | - | 3.5.1.5 |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16058 | - | - | + | - | + | - | + | - | + | + | - | +/- | - | +/- | + | - | +/- | - | + | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16058 | - | - | + | + | - | + | +/- | + | - | + | + | - | + | + | - | - | + | + | - | + | - | + | - | - | + | + | - | - | - |
16058 | - | - | +/- | + | - | + | - | - | - | + | - | +/- | + | +/- | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
16058 | - | - | + | + | - | + | + | + | - | + | +/- | +/- | + | + | - | - | + | +/- | - | + | - | +/- | - | - | + | +/- | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16058 | caecum of a 5-week-old male heterozygous TNFdeltaARE C57BL/6 mouse | Freising | Germany | DEU | Europe |
61243 | Mouse intestine | Freising | Germany | DEU | Europe |
67770 | Mouse cecal samples |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Muridae (Mouse/Rat) |
#Host Body-Site | #Gastrointestinal tract | #Large intestine |
taxonmaps
- @ref: 69479
- File name: preview.99_7372.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_3450;97_4233;98_5406;99_7372&stattab=map
- Last taxonomy: Phocaeicola sartorii subclade
- 16S sequence: GQ456204
- Sequence Identity:
- Total samples: 121989
- soil counts: 1570
- aquatic counts: 3072
- animal counts: 116898
- plant counts: 449
Safety information
risk assessment
- @ref: 16058
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bacteroides sartorii gene for 16S ribosomal RNA, partial sequence | AB572597 | 1490 | ena | 1236515 |
16058 | Bacteroides sartorii JCM 17136 = DSM 21941 strain A-C2-0 16S ribosomal RNA gene, partial sequence | GQ456204 | 1468 | ena | 1236515 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides sartorii JCM 17136 = DSM 21941 | 1236515.3 | wgs | patric | 1236515 |
66792 | Bacteroides sartorii JCM 17136, DSM 21941 | 2585427920 | draft | img | 1236515 |
67770 | Phocaeicola sartorii JCM 17136 = DSM 21941 | GCA_000614185 | contig | ncbi | 1236515 |
66792 | Phocaeicola sartorii DSM 21941 | GCA_024622025 | contig | ncbi | 671267 |
GC content
@ref | GC-content | method |
---|---|---|
16058 | 41.5 | high performance liquid chromatography (HPLC) |
67770 | 43.8 | genome sequence analysis |
67770 | 45.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 91.822 | no |
gram-positive | no | 97.122 | no |
anaerobic | yes | 98.049 | no |
aerobic | no | 97.57 | yes |
halophile | no | 88.652 | no |
spore-forming | no | 94.23 | no |
glucose-util | yes | 89.487 | no |
flagellated | no | 96.759 | no |
thermophile | no | 98.1 | yes |
glucose-ferment | yes | 78.708 | no |
External links
@ref: 16058
culture collection no.: DSM 21941, CCUG 57211, JCM 17136
straininfo link
- @ref: 71273
- straininfo: 404753
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20369227 | Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov. | Clavel T, Saalfrank A, Charrier C, Haller D | Arch Microbiol | 10.1007/s00203-010-0568-6 | 2010 | Animals, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, Cecum/*microbiology, Culture Media, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Genes, Bacterial, Genes, rRNA, Genotype, Male, Mice, Mice, Inbred C57BL, Phenotype, Phylogeny, Sequence Analysis, DNA | Cultivation |
Phylogeny | 21764984 | Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority. | Sakamoto M, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijs.0.035659-0 | 2011 | Bacterial Proteins/genetics, Bacteroides/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16058 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21941) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21941 | |||
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 | |
61243 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 57211) | https://www.ccug.se/strain?id=57211 | |||
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/ | ||||
68367 | Automatically annotated from API 20A | |||||
68380 | Automatically annotated from API rID32A | |||||
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 | |||
71273 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404753.1 | StrainInfo: A central database for resolving microbial strain identifiers |