Strain identifier
BacDive ID: 159628
Type strain:
Species: Suipraeoptans intestinalis
Strain Designation: 68-1-5
Strain history: B. Abt; DSMZ, Germany; DSM 104945 (=68-1-5) <-- T. Looft; ARS, USDA, USA.
NCBI tax ID(s): 2606628 (species)
General
@ref: 66464
BacDive-ID: 159628
DSM-Number: 104945
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Suipraeoptans intestinalis 68-1-5 is an anaerobe, mesophilic bacterium that was isolated from intestinal tract of a three month-old healthy pig.
NCBI tax id
- NCBI tax id: 2606628
- Matching level: species
strain history
@ref | history |
---|---|
66464 | <- T. Looft, USDA-ARS-NADC; 68-1-5 |
67770 | B. Abt; DSMZ, Germany; DSM 104945 (=68-1-5) <-- T. Looft; ARS, USDA, USA. |
doi: 10.13145/bacdive159628.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Suipraeoptans
- species: Suipraeoptans intestinalis
- full scientific name: Suipraeoptans intestinalis corrig. Wylensek et al. 2021
synonyms
- @ref: 20215
- synonym: Suipraoptans intestinalis
@ref: 66464
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Lachnospiraceae
genus: Suipraeoptans
species: Suipraeoptans intestinalis
full scientific name: Suipraeoptans intestinalis
strain designation: 68-1-5
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell length | cell shape |
---|---|---|---|---|---|
69480 | no | 91.181 | |||
69480 | 100 | positive | |||
69645 | positive | 0.5 µm | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
66464 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water |
66464 | 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 |
69645 | Hog gastric mucin medium | yes | ||
69645 | Brain Heart Infusion (Oxoid, ref. CM1135) | yes | ||
69645 | Wilkins-Chalgren Anaerobe broth | yes | supplemented with L-cysteine and DTT (0.05% and 0.02% (w/v), respectively) |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
66464 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
69645 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
69480 | anaerobe | 99.998 |
69645 | anaerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.997
observation
- @ref: 69645
- observation: Cells grow as single cells or in pairs
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
69645 | 17234 | glucose | + | assimilation |
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 | Chebi-ID | metabolite | production |
---|---|---|---|
69645 | 30089 | acetate | yes |
69645 | 15740 | formate | yes |
68380 | 35581 | indole | 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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
66464 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | + | - | - | - | - | - | - | - | - | - | - |
66464 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | + | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | latitude | longitude | geographic location | enrichment culture | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|
66464 | intestinal tract (ileal contents) of a three month-old healthy pig | USA | USA | North America | 42.0308 | -93.6319 | |||||
67770 | Ileal content of a pig in Ames | USA | USA | North America | Iowa | ||||||
69645 | Ileal content of a pig | USA | USA | North America | Ames, Iowa | Hog gastric mucin medium | 3-5 days | 37 | anaerobic |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Suidae (Pig,Swine) |
#Host Body-Site | #Gastrointestinal tract |
Sequence information
16S sequences
- @ref: 66464
- description: Lachnospiraceae bacterium DSM 104945 16S ribosomal RNA gene, partial sequence
- accession: MN537470
- length: 1380
- database: ena
- NCBI tax ID: 2652301
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridiaceae bacterium 68-1-5 | 2606628.3 | wgs | patric | 2606628 |
66792 | Suipraeoptans intestinalis 68-1-5 | GCA_009696485 | contig | ncbi | 2606628 |
69645 | Whole genome shotgun | VULY00000000 | ncbi | 2606628 |
GC content
- @ref: 67770
- GC-content: 47.7
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 55 | no |
motile | no | 89.786 | no |
gram-positive | yes | 92.207 | no |
anaerobic | yes | 99.697 | no |
aerobic | no | 99.101 | no |
halophile | no | 75.474 | no |
spore-forming | no | 75.524 | no |
glucose-util | yes | 88.988 | no |
flagellated | no | 96.556 | no |
thermophile | no | 97.417 | yes |
glucose-ferment | yes | 83.126 | no |
External links
@ref: 66464
culture collection no.: DSM 104945, JCM 34387
straininfo link
- @ref: 112102
- straininfo: 399464
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
66464 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104945 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104945) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68380 | Automatically annotated from API rID32A | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
69645 | David Wylensek, Thomas C. A. Hitch, Thomas Riedel, Afrizal Afrizal, Neeraj Kumar, Esther Wortmann, Tianzhe Liu, Saravanan Devendran, Till R. Lesker, Sara B. Hernández, Viktoria Heine, Eva M. Buhl, Paul M. D'Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R. Parreira, Birte Abt, Heidi L. Doden, Lindsey Ly, João M. P. Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P. Neumann, Garret Suen, Tomas de Wouters, Sascha Rohn, Ilias Lagkouvardos, Emma Allen-Vercoe, Cathrin Spröer, Boyke Bunk, Anja J. Taverne-Thiele, Marcel Giesbers, Jerry M. Wells, Klaus Neuhaus, Angelika Schnieke, Felipe Cava, Nicola Segata, Lothar Elling, Till Strowig, Jason M. Ridlon, Tobias A. M. Gulder, Jörg Overmann, Thomas Clavel | A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity | 10.1038/s41467-020-19929-w | |
112102 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID399464.1 |