Strain identifier
BacDive ID: 143604
Type strain:
Species: Eubacterium sulci
Strain history: <- CCUG <- G Sundqvist, Umea, Sweden <- ATCC <- EP Cato <- WEC Moore
NCBI tax ID(s): 888727 (strain), 143393 (species)
version 9.1 (current version)
General
@ref: 47154
BacDive-ID: 143604
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, rod-shaped
description: Eubacterium sulci CCUG 20560 is an anaerobe, rod-shaped bacterium that was isolated from Human gingival sulcus.
NCBI tax id
NCBI tax id | Matching level |
---|---|
143393 | species |
888727 | strain |
strain history
- @ref: 67771
- history: <- CCUG <- G Sundqvist, Umea, Sweden <- ATCC <- EP Cato <- WEC Moore
doi: 10.13145/bacdive143604.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Eubacteriaceae
- genus: Eubacterium
- species: Eubacterium sulci
- full scientific name: Eubacterium sulci (Cato et al. 1985) Jalava and Eerola 1999
synonyms
- @ref: 20215
- synonym: Fusobacterium sulci
@ref: 47154
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Eubacteriaceae
genus: Eubacterium
species: Eubacterium sulci
type strain: yes
Morphology
cell morphology
@ref | cell shape | motility | gram stain | confidence |
---|---|---|---|---|
67771 | rod-shaped | no | ||
67771 | negative | |||
69480 | no | 91.471 |
colony morphology
- @ref: 47154
- incubation period: 3 days
Culture and growth conditions
culture temp
- @ref: 67771
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
47154 | anaerobe | |
67771 | anaerobe | |
69480 | anaerobe | 91.932 |
spore formation
- @ref: 67771
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
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 |
68381 | 29016 | arginine | - | hydrolysis |
68381 | 16988 | D-ribose | - | builds acid from |
68381 | 16899 | D-mannitol | - | builds acid from |
68381 | 30911 | sorbitol | - | builds acid from |
68381 | 17716 | lactose | - | builds acid from |
68381 | 27082 | trehalose | - | builds acid from |
68381 | 16634 | raffinose | - | builds acid from |
68381 | 17992 | sucrose | - | builds acid from |
68381 | 30849 | L-arabinose | - | builds acid from |
68381 | 18333 | D-arabitol | - | builds acid from |
68381 | 40585 | alpha-cyclodextrin | - | builds acid from |
68381 | 606565 | hippurate | - | hydrolysis |
68381 | 28087 | glycogen | - | builds acid from |
68381 | 27941 | pullulan | - | builds acid from |
68381 | 17306 | maltose | - | builds acid from |
68381 | 28053 | melibiose | - | builds acid from |
68381 | 6731 | melezitose | - | builds acid from |
68381 | 320055 | methyl beta-D-glucopyranoside | - | builds acid from |
68381 | 16443 | D-tagatose | - | builds acid from |
68381 | 16199 | urea | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68380 | 35581 | indole | no |
68381 | 15688 | acetoin | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68381 | 15688 | acetoin | - | |
68380 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68381 | urease | - | 3.5.1.5 |
68381 | beta-mannosidase | - | 3.2.1.25 |
68381 | glycyl tryptophan arylamidase | - | |
68381 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68381 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68381 | beta-galactosidase | - | 3.2.1.23 |
68381 | Alanyl-Phenylalanyl-Proline arylamidase | - | |
68381 | alkaline phosphatase | - | 3.1.3.1 |
68381 | alpha-galactosidase | - | 3.2.1.22 |
68381 | beta-glucuronidase | - | 3.2.1.31 |
68381 | beta-glucosidase | - | 3.2.1.21 |
68381 | arginine dihydrolase | - | 3.5.3.6 |
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 |
fatty acid profile
@ref fatty acid percentage ECL 47154 C14:0 4.2 14 47154 C16:0 14 16 47154 C18:0 1.3 18 47154 C13:0 3OH/C15:1 i I/H 0.7 14.469 47154 C14:0 2OH 0.7 15.205 47154 C14:0 ISO 3OH 5.3 15.117 47154 C15:0 ANTEISO 6.7 14.711 47154 C15:0 ISO 31.9 14.621 47154 C17:0 anteiso 1.5 16.722 47154 C17:0 iso 3.2 16.629 47154 C17:1 ISO I/C16:0 DMA 9.7 16.481 47154 C18:1 ω7c DMA 3 18.282 47154 C18:1 ω9c 2 17.769 47154 C18:2 ω6,9c/C18:0 ANTE 5.4 17.724 47154 Unidentified 1.5 17.105 47154 unknown 13.566 1.8 13.566 47154 unknown 14.966 3.9 14.966 47154 unknown 18.177 3.3 18.177 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
@ref fatty acid percentage ECL 47154 C14:0 4.4 14 47154 C16:0 19.8 16 47154 C15:0 ANTEISO 8.4 14.711 47154 C15:0 ISO 51.3 14.621 47154 C17:0 iso 7.8 16.629 47154 C17:1 ISO I/C16:0 DMA 3 16.481 47154 C18:2 ω6,9c/C18:0 ANTE 5.4 17.724 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
47154 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
API rID32STR
@ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
47154 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
47154 | Human gingival sulcus |
67771 | From human gingival sulcus |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body-Site | #Oral cavity and airways | #Gingiva |
#Infection | #Patient | |
#Host Body-Site | #Other | #Wound |
taxonmaps
- @ref: 69479
- File name: preview.99_4005.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_184;96_2034;97_2452;98_3034;99_4005&stattab=map
- Last taxonomy: Clostridiales Family XIII. Incertae Sedis
- 16S sequence: NR_025289
- Sequence Identity:
- Total samples: 83120
- soil counts: 945
- aquatic counts: 1208
- animal counts: 80513
- plant counts: 454
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
67771 | Fusobacterium sulci 16S ribosomal RNA, partial | AJ006963 | 1453 | nuccore | 888727 |
67771 | Eubacterium sulci ATCC 35585 16S ribosomal RNA, partial sequence | NR_025289 | 1453 | nuccore | 888727 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Eubacterium sulci ATCC 35585 | GCA_000526055 | contig | ncbi | 888727 |
66792 | Eubacterium sulci ATCC 35585 | 888727.210 | complete | patric | 888727 |
66792 | Eubacterium sulci ATCC 35585 | 888727.3 | wgs | patric | 888727 |
66792 | Eubacterium sulci ATCC 35585 | 2558860286 | draft | img | 888727 |
66792 | Eubacterium sulci ATCC 35585 | 2687453170 | complete | img | 888727 |
66792 | Eubacterium sulci ATCC 35585 | GCA_001189495 | complete | ncbi | 888727 |
GC content
- @ref: 67771
- GC-content: 39.0
Genome-based predictions
predictions
@ref | trait | model | description | prediction | confidence | training_data |
---|---|---|---|---|---|---|
69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 70 | no |
69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 57.904 | yes |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 91.932 | yes |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 97.16 | yes |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 69.645 | yes |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 89.03 | yes |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 91.471 | yes |
External links
@ref: 47154
culture collection no.: CCUG 20560, ATCC 35585, KCTC 15025, VPI D45A.29A
straininfo link
- @ref: 98949
- straininfo: 41173
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10555315 | Phylogenetic analysis of Fusobacterium alocis and Fusobacterium sulci based on 16S rRNA gene sequences: proposal of Filifactor alocis (Cato, Moore and Moore) comb. nov. and Eubacterium sulci (Cato, Moore and Moore) comb. nov. | Jalava J, Eerola E | Int J Syst Bacteriol | 10.1099/00207713-49-4-1375 | 1999 | Animals, Cats, DNA, Ribosomal/genetics, Eubacterium/*classification/genetics, Fusobacterium/*classification/*genetics, Fusobacterium Infections/microbiology, *Genes, rRNA, Humans, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA, Terminology as Topic | Pathogenicity |
Enzymology | 22405584 | Antimicrobial activity of Streptococcus salivarius K12 on bacteria involved in oral malodour. | Masdea L, Kulik EM, Hauser-Gerspach I, Ramseier AM, Filippi A, Waltimo T | Arch Oral Biol | 10.1016/j.archoralbio.2012.02.011 | 2012 | Actinobacteria/*growth & development/isolation & purification, Administration, Oral, Bacterial Proteins/pharmacology, Bacteriocins/pharmacology, Eubacterium/growth & development/isolation & purification, Gram-Positive Bacteria/growth & development/isolation & purification, Halitosis/*microbiology/*prevention & control, Humans, In Vitro Techniques, Linear Models, Microbial Sensitivity Tests, Probiotics/*pharmacology, Streptococcus/*physiology | Phylogeny |
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 | |
47154 | Curators of the CCUG | https://www.ccug.se/strain?id=20560 | Culture Collection University of Gothenburg (CCUG) (CCUG 20560) | |
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 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
68380 | Automatically annotated from API rID32A | |||
68381 | Automatically annotated from API rID32STR | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
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 | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
98949 | 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-ID41173.1 |