Strain identifier
BacDive ID: 1607
Type strain:
Species: Phocaeicola plebeius
Strain Designation: M12
Strain history: M. Kitahara M12.
NCBI tax ID(s): 484018 (strain), 310297 (species)
General
@ref: 6782
BacDive-ID: 1607
DSM-Number: 17135
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Phocaeicola plebeius M12 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human feces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
484018 | strain |
310297 | species |
strain history
@ref | history |
---|---|
6782 | <- Maki Kitahara, M12 |
67770 | M. Kitahara M12. |
doi: 10.13145/bacdive1607.20230509.8.1
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 plebeius
- full scientific name: Phocaeicola plebeius (Kitahara et al. 2005) García-López et al. 2020
synonyms
- @ref: 20215
- synonym: Bacteroides plebeius
@ref: 6782
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Phocaeicola
species: Phocaeicola plebeius
full scientific name: Phocaeicola plebeius (Kitahara et al. 2005) García-López et al. 2020
strain designation: M12
type strain: yes
Morphology
cell morphology
- @ref: 31548
- gram stain: negative
- cell length: 3 µm
- cell width: 0.8 µm
- cell shape: rod-shaped
- motility: no
colony morphology
@ref | incubation period |
---|---|
6782 | 3-7 days |
60271 | 2 days |
pigmentation
- @ref: 31548
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6782 | 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 |
6782 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) Yeast extract 5.0 g/l K2HPO4 5.0 g/l Pectin 0.5 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6782 | positive | growth | 37 | mesophilic |
31548 | positive | optimum | 37 | mesophilic |
60271 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6782 | anaerobe |
31548 | anaerobe |
60271 | anaerobe |
spore formation
- @ref: 31548
- spore formation: no
observation
@ref | observation |
---|---|
31548 | aggregates in clumps |
67770 | quinones: MK-10, MK-11 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31548 | 22599 | arabinose | + | carbon source |
31548 | 17057 | cellobiose | + | carbon source |
31548 | 17234 | glucose | + | carbon source |
31548 | 17716 | lactose | + | carbon source |
31548 | 17306 | maltose | + | carbon source |
31548 | 37684 | mannose | + | carbon source |
31548 | 16634 | raffinose | + | carbon source |
31548 | 26546 | rhamnose | + | carbon source |
31548 | 17992 | sucrose | + | carbon source |
31548 | 18222 | xylose | + | carbon source |
31548 | 4853 | esculin | + | hydrolysis |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
31548 | alkaline phosphatase | + | 3.1.3.1 |
31548 | alpha-galactosidase | + | 3.2.1.22 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68380 | serine arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
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 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
60271 | - | + | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
60271 | - | - | + | + | - | - | + | + | - | + | - | - | - | - | - | - | + | + | - | + | - | + | - | - | + | + | - | - | - |
6782 | - | +/- | + | + | - | +/- | +/- | +/- | - | + | - | - | - | - | - | - | + | + | - | + | - | + | - | - | + | + | +/- | + | - |
6782 | - | - | + | + | - | +/- | - | +/- | - | + | +/- | +/- | - | - | - | - | + | + | - | + | + | + | - | + | + | + | + | + | - |
6782 | - | +/- | + | + | - | + | + | + | - | + | +/- | + | - | + | - | - | + | + | + | + | + | - | +/- | + | + | + | + | - | |
6782 | - | - | + | + | - | - | - | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
6782 | human feces | Japan | JPN | Asia |
60271 | Human faeces | Japan | JPN | Asia |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_12193.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_258;96_4788;97_5805;98_7283;99_12193&stattab=map
- Last taxonomy: Phocaeicola plebeius subclade
- 16S sequence: AB200217
- Sequence Identity:
- Total samples: 37805
- soil counts: 244
- aquatic counts: 1112
- animal counts: 36355
- plant counts: 94
Safety information
risk assessment
- @ref: 6782
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6782
- description: Bacteroides plebeius gene for 16S rRNA, partial sequence, strain: M12
- accession: AB200217
- length: 1490
- database: ena
- NCBI tax ID: 484018
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides plebeius DSM 17135 | 484018.6 | wgs | patric | 484018 |
66792 | Bacteroides plebeius M12, DSM 17135 | 642979351 | draft | img | 484018 |
67770 | Phocaeicola plebeius DSM 17135 | GCA_000187895 | scaffold | ncbi | 484018 |
GC content
@ref | GC-content | method |
---|---|---|
6782 | 43.9 | |
67770 | 43.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 97.027 | yes |
anaerobic | yes | 99.04 | yes |
halophile | no | 84.007 | no |
spore-forming | no | 96.153 | yes |
glucose-util | yes | 89.06 | yes |
aerobic | no | 98.083 | yes |
thermophile | no | 96.88 | yes |
motile | no | 93.011 | yes |
flagellated | no | 97.406 | yes |
glucose-ferment | yes | 69.439 | no |
External links
@ref: 6782
culture collection no.: CCUG 54634, DSM 17135, JCM 12973
straininfo link
- @ref: 71252
- straininfo: 231847
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16166722 | Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. | Kitahara M, Sakamoto M, Ike M, Sakata S, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.63788-0 | 2005 | Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification/physiology, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Feces/*microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Pathogenicity |
Phylogeny | 17158987 | Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum. | Lan PTN, Sakamoto M, Sakata S, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64517-0 | 2006 | Animals, Bacterial Typing Techniques, Bacteroides/chemistry/*classification/genetics/isolation & purification, Cecum/*microbiology, Chickens/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis | Genetics |
Enzymology | 30110640 | Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal. | Kearney SM, Gibbons SM, Erdman SE, Alm EJ | Cell Rep | 10.1016/j.celrep.2018.07.032 | 2018 | Animals, Bacterial Load, Bacteroides/isolation & purification/*physiology, Diet/*methods, Eating/physiology, Feces/microbiology, Female, Gastrointestinal Microbiome/*physiology, Mice, Mice, Inbred C57BL, Seaweed/*chemistry, Symbiosis/*physiology, Verrucomicrobia/isolation & purification/physiology | Phylogeny |
Pathogenicity | 36058421 | Altered gut microbiota correlates with behavioral problems but not gastrointestinal symptoms in individuals with autism. | Chen YC, Lin HY, Chien Y, Tung YH, Ni YH, Gau SS | Brain Behav Immun | 10.1016/j.bbi.2022.08.015 | 2022 | *Autism Spectrum Disorder/metabolism, *Autistic Disorder, Biomarkers, *Gastrointestinal Diseases/complications, *Gastrointestinal Microbiome/genetics, Humans, *Problem Behavior | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6782 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17135) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17135 | |||
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 | |||
31548 | 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 | 27839 | 28776041 | |
60271 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54634) | https://www.ccug.se/strain?id=54634 | |||
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/ | ||||
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 | |||
71252 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID231847.1 | StrainInfo: A central database for resolving microbial strain identifiers |