Strain identifier
BacDive ID: 1610
Type strain:
Species: Bacteroides finegoldii
Strain Designation: 199
Strain history: M. Kitahara 199 <-- M. Matsumoto.
NCBI tax ID(s): 483215 (strain), 338188 (species)
General
@ref: 6977
BacDive-ID: 1610
DSM-Number: 17565
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Bacteroides finegoldii 199 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human feces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
338188 | species |
483215 | strain |
strain history
@ref | history |
---|---|
6977 | <- M. Sakamoto <- M. Matsumoto; 199 |
67770 | M. Kitahara 199 <-- M. Matsumoto. |
doi: 10.13145/bacdive1610.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Bacteroidaceae
- genus: Bacteroides
- species: Bacteroides finegoldii
- full scientific name: Bacteroides finegoldii Bakir et al. 2006
@ref: 6977
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Bacteroides
species: Bacteroides finegoldii
full scientific name: Bacteroides finegoldii Bakir et al. 2006
strain designation: 199
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31702 | negative | 1.5-4.5 µm | 0.8 µm | rod-shaped | no | |
69480 | no | 93.58 | ||||
69480 | negative | 99.993 |
colony morphology
@ref | incubation period |
---|---|
6977 | 1-2 days |
60059 | 2 days |
pigmentation
- @ref: 31702
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6977 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
6977 | 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 |
---|---|---|---|---|
6977 | positive | growth | 37 | mesophilic |
31702 | positive | growth | 20-40 | |
31702 | positive | optimum | 37 | mesophilic |
60059 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31702 | positive | growth | 7 |
31702 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
6977 | anaerobe | |
31702 | anaerobe | |
60059 | anaerobe | |
69480 | anaerobe | 99.114 |
spore formation
@ref | spore formation | confidence |
---|---|---|
31702 | no | |
69481 | no | 100 |
69480 | no | 99.997 |
observation
- @ref: 31702
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31702 | 22599 | arabinose | + | carbon source |
31702 | 17057 | cellobiose | + | carbon source |
31702 | 17234 | glucose | + | carbon source |
31702 | 17716 | lactose | + | carbon source |
31702 | 17306 | maltose | + | carbon source |
31702 | 37684 | mannose | + | carbon source |
31702 | 16634 | raffinose | + | carbon source |
31702 | 26546 | rhamnose | + | carbon source |
31702 | 17814 | salicin | + | carbon source |
31702 | 17992 | sucrose | + | carbon source |
31702 | 4853 | esculin | + | hydrolysis |
68367 | 27082 | trehalose | - | builds acid from |
68367 | 62345 | L-rhamnose | + | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 16634 | raffinose | + | builds acid from |
68367 | 6731 | melezitose | - | builds acid from |
68367 | 16024 | D-mannose | + | builds acid from |
68367 | 17057 | cellobiose | + | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 4853 | esculin | + | hydrolysis |
68367 | 5291 | gelatin | - | hydrolysis |
68367 | 30849 | L-arabinose | + | builds acid from |
68367 | 65327 | D-xylose | + | 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 | 16024 | D-mannose | + | fermentation |
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 | histidine arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
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 | alpha-fucosidase | - | 3.2.1.51 |
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-arabinosidase | + | 3.2.1.55 |
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 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | beta-glucosidase | + | 3.2.1.21 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6977 | - | - | + | - | + | + | + | - | + | + | - | + | - | + | + | - | + | - | + | - |
6977 | - | - | + | - | + | + | + | +/- | + | + | - | + | - | + | + | - | + | - | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6977 | - | - | + | + | - | + | + | + | - | + | + | + | + | - | - | - | + | - | - | + | - | - | - | + | + | + | - | + | - |
6977 | - | - | + | + | - | + | + | + | - | + | + | + | + | - | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
6977 | - | - | + | + | - | + | + | + | - | + | + | +/- | + | - | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
6977 | human feces | Japan | JPN | Asia |
60059 | Human feces | |||
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
Safety information
risk assessment
- @ref: 6977
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6977
- description: Bacteroides finegoldii gene for 16S rRNA, partial sequence, strain:JCM 13345
- accession: AB222699
- length: 1485
- database: ena
- NCBI tax ID: 483215
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides finegoldii DSM 17565 | 483215.6 | wgs | patric | 483215 |
66792 | Bacteroides finegoldii DSM 17565 | 2562617142 | draft | img | 483215 |
67770 | Bacteroides finegoldii DSM 17565 | GCA_000156195 | scaffold | ncbi | 483215 |
GC content
@ref | GC-content | method |
---|---|---|
6977 | 42.4-43 | |
31702 | 42.4-43.0 | |
67770 | 42 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.303 | no |
anaerobic | yes | 98.767 | yes |
halophile | no | 90.486 | no |
spore-forming | no | 95.045 | yes |
glucose-util | yes | 88.943 | no |
aerobic | no | 97.27 | yes |
thermophile | no | 99.206 | yes |
motile | no | 92.725 | yes |
flagellated | no | 97.457 | yes |
glucose-ferment | yes | 74.606 | no |
External links
@ref: 6977
culture collection no.: DSM 17565, JCM 13345, CCUG 53890
straininfo link
- @ref: 71255
- straininfo: 291124
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16627634 | Bacteroides finegoldii sp. nov., isolated from human faeces. | Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64084-0 | 2006 | Adult, Bacteroides/*classification/genetics/isolation & purification/physiology, Bacteroides Infections/microbiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, Humans, Male, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Pathogenicity |
Phylogeny | 20008108 | Bacteroides faecis sp. nov., isolated from human faeces. | Kim MS, Roh SW, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijs.0.020024-0 | 2009 | Adult, Bacteroides/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Feces/*microbiology, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 33881983 | Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces. | Ge Y, Zhang G, Yang J, Lai XH, Jin D, Lu S, Pu J, Huang Y, Luo X, Zheng H, Zhang X, Xu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004772 | 2021 | Bacterial Typing Techniques, Bacteroides/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
6977 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17565) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17565 | ||||
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 | ||||
31702 | 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 | 27979 | 28776041 | ||
60059 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53890) | https://www.ccug.se/strain?id=53890 | ||||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68367 | Automatically annotated from API 20A | ||||||
68380 | Automatically annotated from API rID32A | ||||||
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 | ||||
71255 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID291124.1 | StrainInfo: A central database for resolving microbial strain identifiers |