Strain identifier
BacDive ID: 2872
Type strain:
Species: Proteiniclasticum ruminis
Strain Designation: D3RC-2
Strain history: X. Dong D3RC-2.
NCBI tax ID(s): 1410668 (strain), 398199 (species)
General
@ref: 17757
BacDive-ID: 2872
DSM-Number: 24773
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Proteiniclasticum ruminis D3RC-2 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Yak rumen.
NCBI tax id
NCBI tax id | Matching level |
---|---|
398199 | species |
1410668 | strain |
strain history
@ref | history |
---|---|
17757 | <- JCM <- X. Dong; D3RC-2 |
67770 | X. Dong D3RC-2. |
doi: 10.13145/bacdive2872.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Proteiniclasticum
- species: Proteiniclasticum ruminis
- full scientific name: Proteiniclasticum ruminis Zhang et al. 2010
@ref: 17757
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Proteiniclasticum
species: Proteiniclasticum ruminis
full scientific name: Proteiniclasticum ruminis Zhang et al. 2010
strain designation: D3RC-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29371 | negative | 0.6-2 µm | 0.5-0.8 µm | rod-shaped | no | |
69480 | positive | 99.726 |
pigmentation
- @ref: 29371
- production: no
Culture and growth conditions
culture medium
- @ref: 17757
- name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
- growth: yes
- link: https://mediadive.dsmz.de/medium/339
- composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17757 | positive | growth | 37 | mesophilic |
29371 | positive | growth | 24-46 | |
29371 | positive | optimum | 38-39 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29371 | positive | growth | 5.6-8.7 | alkaliphile |
29371 | positive | optimum | 7-7.3 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
17757 | anaerobe | |
29371 | anaerobe | |
69480 | anaerobe | 98.287 |
spore formation
@ref | spore formation | confidence |
---|---|---|
29371 | no | |
69480 | no | 98.817 |
observation
- @ref: 29371
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29371 | 27570 | histidine | + | carbon source |
29371 | 25017 | leucine | + | carbon source |
29371 | 28044 | phenylalanine | + | carbon source |
29371 | 17822 | serine | + | carbon source |
29371 | 26986 | threonine | + | carbon source |
29371 | 4853 | esculin | + | hydrolysis |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
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 |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate 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 | 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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
17757 | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
17757 | Yak rumen | China | CHN | Asia |
67770 | Yak rumen |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Bovinae (Cow, Cattle) |
#Host Body-Site | #Organ | #Rumen |
taxonmaps
- @ref: 69479
- File name: preview.99_693.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_428;97_487;98_558;99_693&stattab=map
- Last taxonomy: Proteiniclasticum ruminis subclade
- 16S sequence: DQ852338
- Sequence Identity:
- Total samples: 2227
- soil counts: 211
- aquatic counts: 1488
- animal counts: 424
- plant counts: 104
Safety information
risk assessment
- @ref: 17757
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17757
- description: Clostridium sp. D3RC-2 16S ribosomal RNA gene, partial sequence
- accession: DQ852338
- length: 1516
- database: ena
- NCBI tax ID: 1410668
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Proteiniclasticum ruminis DSM 24773 | 1410668.3 | wgs | patric | 1410668 |
66792 | Proteiniclasticum ruminis strain CGMCC 1.5058 | 398199.5 | wgs | patric | 398199 |
66792 | Proteiniclasticum ruminis DSM 24773 | 2561511080 | draft | img | 1410668 |
66792 | Proteiniclasticum ruminis CGMCC 1.5058 | 2675903137 | draft | img | 398199 |
67770 | Proteiniclasticum ruminis CGMCC 1.5058 | GCA_900099635 | scaffold | ncbi | 398199 |
67770 | Proteiniclasticum ruminis DSM 24773 | GCA_000701905 | scaffold | ncbi | 1410668 |
GC content
@ref | GC-content | method |
---|---|---|
17757 | 41.0 | high performance liquid chromatography (HPLC) |
29371 | 41 | |
67770 | 41 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 74 | no |
motile | yes | 65.014 | yes |
gram-positive | yes | 52.909 | yes |
anaerobic | yes | 98.149 | yes |
halophile | no | 59.757 | no |
spore-forming | no | 64.912 | yes |
glucose-util | yes | 91.52 | no |
thermophile | no | 84.828 | yes |
aerobic | no | 96.789 | yes |
flagellated | no | 64.487 | no |
glucose-ferment | yes | 69.217 | no |
External links
@ref: 17757
culture collection no.: DSM 24773, CGMCC 1.5058, JCM 14817, KCTC 15188
straininfo link
- @ref: 72396
- straininfo: 407543
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19915115 | Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen. | Zhang K, Song L, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.011759-0 | 2009 | Animals, Bacteria, Anaerobic/*classification/genetics/*isolation & purification/metabolism, Cattle/*microbiology, Cellulose/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sodium Chloride/*metabolism | Metabolism |
Phylogeny | 24048874 | Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov. | Lawson PA, Wawrik B, Allen TD, Johnson CN, Marks CR, Tanner RS, Harriman BH, Strapoc D, Callaghan AV | Int J Syst Evol Microbiol | 10.1099/ijs.0.053728-0 | 2013 | Alaska, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/isolation & purification, Molecular Sequence Data, Natural Gas/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water/*analysis, Water Microbiology | Genetics |
Phylogeny | 34401954 | Proteiniclasticum sediminis sp. nov., an obligate anaerobic bacterium isolated from anaerobic sludge. | Liu J, Bao Y, Zhang X, Zhang K, Chen S, Wu H, He J | Antonie Van Leeuwenhoek | 10.1007/s10482-021-01620-9 | 2021 | Anaerobiosis, Bacterial Typing Techniques, Base Composition, Clostridiaceae, DNA, Bacterial/genetics, *Fatty Acids, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sewage | Transcriptome |
Phylogeny | 35394905 | Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis. | Namirimu T, Yang JA, Yang SH, Yu J, Kim YJ, Kwon KK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005275 | 2022 | Bacteria, Anaerobic/genetics, Bacterial Typing Techniques, Base Composition, Clostridiaceae, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Seawater/microbiology, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17757 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24773) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24773 | ||||
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 | ||||
29371 | 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 | 25780 | 28776041 | ||
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/ | |||||
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 | ||||
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) | ||||
72396 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407543.1 | StrainInfo: A central database for resolving microbial strain identifiers |