Strain identifier
BacDive ID: 12498
Type strain:
Species: Parabacteroides johnsonii
Strain Designation: M-165
Strain history: CIP <- 2007, DSMZ <- M. Sakamoto, Bioresources Cent., Saitama, Japan: strain M-165
NCBI tax ID(s): 537006 (strain), 387661 (species)
General
@ref: 7499
BacDive-ID: 12498
DSM-Number: 18315
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Parabacteroides johnsonii M-165 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
537006 | strain |
387661 | species |
strain history
@ref | history |
---|---|
7499 | <- M. Sakamoto; M-165 <- M. Kitahara |
67770 | M. Sakamoto <-- M. Kitahara M-165. |
120361 | CIP <- 2007, DSMZ <- M. Sakamoto, Bioresources Cent., Saitama, Japan: strain M-165 |
doi: 10.13145/bacdive12498.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Tannerellaceae
- genus: Parabacteroides
- species: Parabacteroides johnsonii
- full scientific name: Parabacteroides johnsonii Sakamoto et al. 2007
@ref: 7499
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Tannerellaceae
genus: Parabacteroides
species: Parabacteroides johnsonii
full scientific name: Parabacteroides johnsonii Sakamoto et al. 2007 emend. Hahnke et al. 2016
strain designation: M-165
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
31881 | negative | 1.7-2.5 µm | 0.8 µm | rod-shaped | no |
120361 | negative | rod-shaped | no |
colony morphology
@ref | incubation period |
---|---|
7499 | 1-2 days |
60403 | 2 days |
pigmentation
- @ref: 31881
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7499 | 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 |
7499 | 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 |
34705 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml) | |
120361 | CIP Medium 137 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=137 | |
120361 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7499 | positive | growth | 37 | mesophilic |
34705 | positive | growth | 37 | mesophilic |
60403 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
7499 | anaerobe |
31881 | anaerobe |
60403 | anaerobe |
120361 | anaerobe |
spore formation
- @ref: 31881
- spore formation: no
observation
- @ref: 67770
- observation: quinones: MK-9, MK-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31881 | 22599 | arabinose | + | carbon source |
31881 | 17234 | glucose | + | carbon source |
31881 | 17716 | lactose | + | carbon source |
31881 | 17306 | maltose | + | carbon source |
31881 | 37684 | mannose | + | carbon source |
31881 | 16634 | raffinose | + | carbon source |
31881 | 26546 | rhamnose | + | carbon source |
31881 | 17992 | sucrose | + | carbon source |
31881 | 27082 | trehalose | + | carbon source |
31881 | 18222 | xylose | + | carbon source |
31881 | 4853 | esculin | + | hydrolysis |
68367 | 30911 | sorbitol | - | 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 | 17814 | salicin | - | 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 |
120361 | 17632 | nitrate | - | reduction |
120361 | 16301 | nitrite | - | reduction |
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 |
---|---|---|---|
120361 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
31881 | alkaline phosphatase | + | 3.1.3.1 |
31881 | alpha-galactosidase | + | 3.2.1.22 |
31881 | catalase | + | 1.11.1.6 |
68380 | histidine arylamidase | + | |
68380 | glycin arylamidase | + | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | leucine arylamidase | + | 3.4.11.1 |
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 | 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 |
120361 | oxidase | - | |
120361 | catalase | + | 1.11.1.6 |
120361 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120361 | - | + | - | - | - | + | - | - | - | + | + | - | + | + | - | - | - | + | - | - |
API 20A
@ref | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7499 | - | + | - | + | + | +/- | - | + | + | - | + | - | - | + | + | +/- | - | +/- | +/- |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7499 | - | - | + | + | - | + | + | + | +/- | + | + | + | + | - | - | - | + | + | - | + | +/- | + | - | +/- | + | + | + | +/- | +/- |
7499 | - | - | + | + | - | + | + | + | - | + | + | +/- | + | - | - | - | + | + | - | + | + | + | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
7499 | human faeces | Japan | JPN | Asia |
60403 | Human feces | |||
67770 | Human feces | |||
120361 | Human, Faeces | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_4981.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_972;97_1132;98_3725;99_4981&stattab=map
- Last taxonomy: Parabacteroides johnsonii subclade
- 16S sequence: AB261128
- Sequence Identity:
- Total samples: 70244
- soil counts: 461
- aquatic counts: 2276
- animal counts: 67348
- plant counts: 159
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7499 | 1 | Risk group (German classification) |
120361 | 2 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7499
- description: Parabacteroides johnsonii gene for 16S ribosomal RNA, partial sequence
- accession: AB261128
- length: 1492
- database: ena
- NCBI tax ID: 537006
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Parabacteroides johnsonii DSM 18315 | 537006.5 | wgs | patric | 537006 |
66792 | Parabacteroides johnsonii DSM 18315 | 642979358 | draft | img | 537006 |
67770 | Parabacteroides johnsonii DSM 18315 | GCA_000156495 | scaffold | ncbi | 537006 |
66792 | Parabacteroides johnsonii DSM 18315 | GCA_025151045 | complete | ncbi | 537006 |
66792 | Parabacteroides johnsonii DSM 18315 | 537006.36 | complete | patric | 537006 |
GC content
@ref | GC-content | method |
---|---|---|
7499 | 47.6 | |
7499 | 45.2 | sequence analysis |
67770 | 47.6 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 89.993 | no |
flagellated | no | 97.944 | no |
gram-positive | no | 96.914 | yes |
anaerobic | yes | 97.023 | yes |
aerobic | no | 95.696 | yes |
halophile | no | 86.777 | no |
spore-forming | no | 95.83 | yes |
glucose-ferment | yes | 60.426 | no |
thermophile | no | 98.088 | yes |
glucose-util | yes | 90.856 | no |
External links
@ref: 7499
culture collection no.: DSM 18315, CIP 109537, JCM 13406, CCUG 54943
straininfo link
- @ref: 81717
- straininfo: 293991
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17267966 | Parabacteroides johnsonii sp. nov., isolated from human faeces. | Sakamoto M, Kitahara M, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64588-0 | 2007 | Anaerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Feces/*microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid | Pathogenicity |
Phylogeny | 23563230 | Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces. | Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijs.0.050146-0 | 2013 | Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, Chaperonin 60/genetics, Chinchilla/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/microbiology, Genes, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis | Genetics |
Phylogeny | 30652964 | Parabacteroides acidifaciens sp. nov., isolated from human faeces. | Wang YJ, Xu XJ, Zhou N, Sun Y, Liu C, Liu SJ, You X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003230 | 2019 | Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Fermentation, Humans, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Pathogenicity |
30687968 | A 2.08 A resolution structure of HLB5, a novel cellulase from the anaerobic gut bacterium Parabacteroides johnsonii DSM 18315. | Chang C, Brooke C, Piao H, Mack J, Babnigg G, Joachimiak A, Hess M | Protein Sci | 10.1002/pro.3582 | 2019 | Bacterial Proteins/*chemistry, Bacteroidetes/*chemistry, Binding Sites, Cellulase/*chemistry, Crystallography, X-Ray, Hydrolysis, Models, Molecular, Protein Conformation |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7499 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18315) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18315 | |||
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 | |||
31881 | 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 | 28141 | 28776041 | |
34705 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7291 | ||||
60403 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54943) | https://www.ccug.se/strain?id=54943 | |||
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 | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
81717 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID293991.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120361 | Curators of the CIP | Collection of Institut Pasteur (CIP 109537) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109537 |