Strain identifier
BacDive ID: 12515
Type strain:
Species: Dysgonomonas gadei
Strain history: CIP <- 2000, CCUG <- CDC group DF-3
NCBI tax ID(s): 742766 (strain), 156974 (species)
General
@ref: 16530
BacDive-ID: 12515
DSM-Number: 22811
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped, human pathogen
description: Dysgonomonas gadei DSM 22811 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from gall bladder .
NCBI tax id
NCBI tax id | Matching level |
---|---|
742766 | strain |
156974 | species |
strain history
@ref | history |
---|---|
16530 | <- CIP <- CCUG <- T. Hofstad |
67770 | CCUG 42882 <-- T. Hofstad 1145589. |
119501 | CIP <- 2000, CCUG <- CDC group DF-3 |
doi: 10.13145/bacdive12515.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Dysgonomonadaceae
- genus: Dysgonomonas
- species: Dysgonomonas gadei
- full scientific name: Dysgonomonas gadei Hofstad et al. 2000
@ref: 16530
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Dysgonomonadaceae
genus: Dysgonomonas
species: Dysgonomonas gadei
full scientific name: Dysgonomonas gadei Hofstad et al. 2000 emend. Hahnke et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 119501
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
@ref | incubation period |
---|---|
16530 | 2-3 days |
119501 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16530 | 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 |
16530 | 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 |
32967 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
119501 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16530 | positive | growth | 37 | mesophilic |
32967 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
119501 | positive | growth | 25-37 | mesophilic |
119501 | no | growth | 15 | psychrophilic |
119501 | no | growth | 41 | thermophilic |
119501 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
16530 | anaerobe |
16530 | microaerophile |
55590 | microaerophile |
119501 | facultative anaerobe |
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 | 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 | 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 |
68367 | L-rhamnose | + | builds acid from | 62345 |
68367 | sorbitol | - | builds acid from | 30911 |
68367 | raffinose | + | builds acid from | 16634 |
68367 | D-mannose | + | builds acid from | 16024 |
68367 | esculin | + | hydrolysis | 4853 |
68367 | gelatin | - | hydrolysis | 5291 |
68367 | L-arabinose | + | builds acid from | 30849 |
68367 | D-xylose | + | builds acid from | 65327 |
68367 | maltose | + | builds acid from | 17306 |
68367 | sucrose | + | builds acid from | 17992 |
68367 | D-mannitol | - | builds acid from | 16899 |
68367 | D-glucose | + | builds acid from | 17634 |
68367 | urea | - | hydrolysis | 16199 |
68367 | tryptophan | - | energy source | 27897 |
119501 | esculin | + | hydrolysis | 4853 |
119501 | hippurate | - | hydrolysis | 606565 |
119501 | nitrate | - | reduction | 17632 |
119501 | nitrite | - | reduction | 16301 |
119501 | nitrate | + | respiration | 17632 |
68377 | D-glucose | + | builds acid from | 17634 |
68377 | D-fructose | + | builds acid from | 15824 |
68377 | maltose | + | builds acid from | 17306 |
68377 | ornithine | - | degradation | 18257 |
68377 | tryptophan | - | energy source | 27897 |
68380 | urea | - | hydrolysis | 16199 |
68380 | D-mannose | + | fermentation | 16024 |
68380 | L-glutamate | - | degradation | 29985 |
68380 | nitrate | - | reduction | 17632 |
68380 | tryptophan | - | energy source | 27897 |
antibiotic resistance
- @ref: 119501
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68377 | 35581 | indole | no |
68367 | 35581 | indole | no |
119501 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | - |
68377 | 35581 | indole | - |
68367 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
16530 | catalase | + | 1.11.1.6 |
68380 | serine arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
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-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | urease | - | 3.5.1.5 |
68377 | tryptophan deaminase | - | 4.1.99.1 |
68377 | ornithine decarboxylase | - | 4.1.1.17 |
68367 | catalase | + | 1.11.1.6 |
68367 | beta-glucosidase | + | 3.2.1.21 |
68367 | gelatinase | - | |
68367 | urease | - | 3.5.1.5 |
119501 | oxidase | - | |
119501 | beta-galactosidase | + | 3.2.1.23 |
119501 | alcohol dehydrogenase | - | 1.1.1.1 |
119501 | catalase | + | 1.11.1.6 |
119501 | gamma-glutamyltransferase | - | 2.3.2.2 |
119501 | lysine decarboxylase | - | 4.1.1.18 |
119501 | ornithine decarboxylase | - | 4.1.1.17 |
119501 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | + | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119501 | - | + | + | + | - | - | - | - | + | + | + | + | - | - | - | + | + | + | - | + |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16530 | - | - | + | - | +/- | + | + | - | + | + | - | + | +/- | - | + | +/- | + | - | + | +/- | |
16530 | - | - | + | - | + | + | + | + | + | + | - | + | - | + | + | + | + | - | + | + | + |
API 50CHac
@ref | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119501 | + | - | + | + | - | + | - | - | - | + | + | + | + | - | + | - | - | - | - | +/- | +/- | + | + | + | + | + | +/- | + | + | + | + | + | + | + | + | + | + | - | + | + | - | - | - | + | - | - | - | - | - |
API NH
@ref | PEN | GLU | FRU | MAL | SAC | ODC | URE | LIP | PAL | beta GAL | ProA | GGT | IND |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16530 | + | + | + | + | - | - | + | + | + | - | + | - | - |
16530 | + | + | + | + | - | - | + | +/- | + | - | + | - | - |
16530 | - | + | + | + | + | - | - | + | + | + | - | + | - |
16530 | - | + | + | + | + | - | - | + | +/- | + | - | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16530 | - | - | + | + | - | + | + | +/- | - | + | + | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | +/- | - |
16530 | - | + | + | + | - | + | + | + | + | + | + | + | - | + | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16530 | gall bladder (68-year-old male patient) | Bergen | Norway | NOR | Europe |
55590 | Human gall bladder,68-yr-old man | Bergen | Norway | NOR | Europe |
67770 | Human infected gall bladder | ||||
119501 | Human, Gall bladder | Bergen | Norway | NOR | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Patient | |
#Host Body-Site | #Gastrointestinal tract | |
#Host | #Human | #Male |
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
16530 | yes, in single cases | 1 | Risk group (German classification) |
119501 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
16530 | Dysgonomonas gadei gene for 16S ribosomal RNA, partial sequence, strin: JCM 16698 | AB548675 | 1488 | ena | 742766 |
67770 | Dysgonomonas gadei strain 1145589 16S rRNA gene | Y18530 | 1464 | ena | 742766 |
Genome sequences
- @ref: 67770
- description: Dysgonomonas gadei ATCC BAA-286
- accession: GCA_000213555
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 742766
GC content
- @ref: 16530
- GC-content: 39.6
- method: sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 88.419 | no |
flagellated | no | 97.376 | no |
gram-positive | no | 94.35 | no |
anaerobic | yes | 90.23 | no |
aerobic | no | 93.167 | yes |
halophile | no | 95.293 | no |
spore-forming | no | 92.482 | no |
thermophile | no | 99.492 | no |
glucose-util | yes | 88.772 | no |
glucose-ferment | yes | 65.059 | no |
External links
@ref: 16530
culture collection no.: DSM 22811, ATCC BAA 286, CCUG 42882, CIP 106420, JCM 16698
straininfo link
- @ref: 81734
- straininfo: 44343
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11155996 | Dysgonomonas gen. nov. to accommodate Dysgonomonas gadei sp. nov., an organism isolated from a human gall bladder, and Dysgonomonas capnocytophagoides (formerly CDC group DF-3). | Hofstad T, Olsen I, Eribe ER, Falsen E, Collins MD, Lawson PA | Int J Syst Evol Microbiol | 10.1099/00207713-50-6-2189 | 2000 | Aged, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/analysis, Culture Media, Fatty Acids/analysis, Gallbladder/*microbiology, Gallbladder Diseases/*microbiology, Genes, rRNA, Gram-Negative Anaerobic Bacteria/*classification/drug effects/genetics/*isolation & purification/physiology, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Pathogenicity |
Phylogeny | 24899656 | Dysgonomonas macrotermitis sp. nov., isolated from the hindgut of a fungus-growing termite. | Yang YJ, Zhang N, Ji SQ, Lan X, Zhang KD, Shen YL, Li FL, Ni JF | Int J Syst Evol Microbiol | 10.1099/ijs.0.061739-0 | 2014 | Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Digestive System/microbiology, Fatty Acids/chemistry, Isoptera/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 25428419 | Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus. | Pramono AK, Sakamoto M, Iino T, Hongoh Y, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijs.0.070391-0 | 2014 | Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Isoptera/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 30656513 | Dysgonomonas massiliensis sp. nov., a new species isolated from the human gut and its taxonogenomic description. | Bilen M, Fonkou MDM, Dubourg G, Tomei E, Richez M, Delerce J, Levasseur A, Daoud Z, Raoult D, Cadoret F | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01227-1 | 2019 | Adult, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Feces/*microbiology, Gastrointestinal Microbiome, Humans, Male, Phylogeny, RNA, Ribosomal, 16S/genetics | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
16530 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22811) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22811 | |
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 | |
32967 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18549 | ||
55590 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 42882) | https://www.ccug.se/strain?id=42882 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68367 | Automatically annotated from API 20A | |||
68371 | Automatically annotated from API 50CH acid | |||
68377 | Automatically annotated from API NH | |||
68380 | Automatically annotated from API rID32A | |||
68382 | Automatically annotated from API zym | |||
81734 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44343.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
119501 | Curators of the CIP | Collection of Institut Pasteur (CIP 106420) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106420 |