Strain identifier
BacDive ID: 1726
Type strain:
Species: Bifidobacterium merycicum
Strain Designation: Ru915B
Strain history: B. Biavati Ru915B.
NCBI tax ID(s): 1410646 (strain), 78345 (species)
General
@ref: 2697
BacDive-ID: 1726
DSM-Number: 6492
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped, colony-forming
description: Bifidobacterium merycicum Ru915B is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from rumen of cattle.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1410646 | strain |
78345 | species |
strain history
@ref | history |
---|---|
2697 | <- B. Biavati, Ru915B |
67770 | B. Biavati Ru915B. |
doi: 10.13145/bacdive1726.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Bifidobacteriales
- family: Bifidobacteriaceae
- genus: Bifidobacterium
- species: Bifidobacterium merycicum
- full scientific name: Bifidobacterium merycicum Biavati and Mattarelli 1991
@ref: 2697
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium merycicum
full scientific name: Bifidobacterium merycicum Biavati and Mattarelli 1991 emend. Nouioui et al. 2018
strain designation: Ru915B
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell shape | motility | confidence |
---|---|---|---|---|---|
23364 | positive | 2.0-5.0 µm | rod-shaped | no | |
69480 | no | 91.529 | |||
69480 | positive | 99.999 |
colony morphology
- @ref: 23364
- colony color: cream to white
- colony shape: circular
- medium used: Trypticase-Phytone-yeast extract agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2697 | BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) | yes | https://mediadive.dsmz.de/medium/58 | Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water |
23364 | Trypticase-Phytone-yeast extract agar | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2697 | positive | growth | 37 | mesophilic |
23364 | no | growth | 25 | mesophilic |
23364 | no | growth | >45 | thermophilic |
23364 | positive | optimum | 38-42 | |
52428 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
23364 | positive | optimum | 6.5-6.9 |
23364 | no | growth | 4.5 |
23364 | no | growth | 8.0 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
2697 | anaerobe | |
23364 | anaerobe | |
52428 | anaerobe | |
69480 | anaerobe | 99.35 |
spore formation
@ref | spore formation | confidence |
---|---|---|
23364 | no | |
69481 | no | 100 |
69480 | no | 100 |
murein
- @ref: 2697
- murein short key: A11.32
- type: A4alpha L-Lys(L-Orn)-D-Asp
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23364 | 24265 | gluconate | - | builds acid from |
23364 | 29864 | mannitol | - | builds acid from |
23364 | 6731 | melezitose | - | builds acid from |
23364 | 24265 | gluconate | - | fermentation |
23364 | 17754 | glycerol | - | fermentation |
23364 | 24996 | lactate | - | fermentation |
23364 | 29864 | mannitol | - | fermentation |
23364 | 37684 | mannose | - | fermentation |
23364 | 6731 | melezitose | - | fermentation |
23364 | 26546 | rhamnose | - | fermentation |
23364 | 30911 | sorbitol | - | fermentation |
23364 | 27082 | trehalose | - | fermentation |
23364 | 17632 | nitrate | - | reduction |
23364 | 35581 | indole | - | |
23364 | 17272 | propionate | - | |
23364 | 17057 | cellobiose | + | builds acid from |
23364 | 16988 | D-ribose | + | builds acid from |
23364 | 65327 | D-xylose | + | builds acid from |
23364 | 30849 | L-arabinose | + | builds acid from |
23364 | 22599 | arabinose | + | fermentation |
23364 | 23652 | dextrin | + | fermentation |
23364 | 28260 | galactose | + | fermentation |
23364 | 17234 | glucose | + | fermentation |
23364 | 17716 | lactose | + | fermentation |
23364 | 17306 | maltose | + | fermentation |
23364 | 28053 | melibiose | + | fermentation |
23364 | 16634 | raffinose | + | fermentation |
23364 | 33942 | ribose | + | fermentation |
23364 | 28017 | starch | + | fermentation |
23364 | 17992 | sucrose | + | fermentation |
23364 | 18222 | xylose | + | fermentation |
23364 | 15443 | inulin | +/- | builds acid from |
23364 | 17814 | salicin | +/- | builds acid from |
23364 | 17057 | cellobiose | +/- | fermentation |
23364 | 28757 | fructose | +/- | fermentation |
23364 | 15443 | inulin | +/- | fermentation |
23364 | 17814 | salicin | +/- | fermentation |
enzymes
- @ref: 23364
- value: catalase
- activity: -
- ec: 1.11.1.6
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 52428 C10:0 3 10 52428 C12:0 11.3 12 52428 C14:0 16.3 14 52428 C16:0 17.3 16 52428 C18:0 2.7 18 52428 C13:0 3OH/C15:1 i I/H 2.3 14.469 52428 C13:1 at 12-13 0.6 12.931 52428 C16:0 3OH 0.6 17.52 52428 C16:1 ω9c 10.4 15.774 52428 C17:1 ω5c ISO 0.7 16.461 52428 C17:1 ω9c 0.9 16.773 52428 C18:1 ω9c 22.2 17.769 52428 C18:2 ω6,9c/C18:0 ANTE 4.7 17.724 52428 Unidentified 0.6 12.472 52428 Unidentified 1 13.768 52428 Unidentified 4.7 18.225 52428 Unidentified 0.7 19.297 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
2697 | rumen of cattle |
52428 | Cattle rumen |
67770 | Bovine rumen |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Bovinae (Cow, Cattle) |
#Host Body-Site | #Organ | #Rumen |
Safety information
risk assessment
- @ref: 2697
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bifidobacterium merycicum strain DSM 6492 16S ribosomal RNA gene, partial sequence | GQ487639 | 137 | ena | 78345 |
20218 | Bifidobacterium merycicum gene for 16S rRNA, partial sequence, strain: JCM 8219 | AB116324 | 435 | ena | 78345 |
20218 | Bifidobacterium merycicum gene for 16S rRNA, partial sequence, strain: JCM 8219 | AB507128 | 840 | ena | 78345 |
20218 | Bifidobacterium merycicum gene for 16S rRNA, partial sequence, strain: JCM 8219 | D86192 | 1435 | ena | 78345 |
20218 | Bifidobacterium merycicum strain KCTC 3369 16S ribosomal RNA gene, partial sequence | GU361825 | 1480 | ena | 78345 |
67770 | Bifidobacterium merycicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 8219 | LC071847 | 1392 | ena | 78345 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bifidobacterium merycicum DSM 6492 | 1410646.3 | wgs | patric | 1410646 |
66792 | Bifidobacterium merycicum DSM 6492 | 1410646.5 | wgs | patric | 1410646 |
66792 | Bifidobacterium merycicum strain LMG 11341 | 78345.3 | wgs | patric | 78345 |
66792 | Bifidobacterium merycicum DSM 6492 | 2660238375 | draft | img | 1410646 |
66792 | Bifidobacterium merycicum DSM 6492 | 2563366502 | draft | img | 1410646 |
66792 | Bifidobacterium merycicum LMG 11341 | 2600254980 | draft | img | 78345 |
67770 | Bifidobacterium merycicum DSM 6492 | GCA_900129045 | contig | ncbi | 1410646 |
67770 | Bifidobacterium merycicum DSM 6492 | GCA_000770945 | contig | ncbi | 1410646 |
67770 | Bifidobacterium merycicum LMG 11341 | GCA_000741615 | contig | ncbi | 78345 |
GC content
@ref | GC-content | method |
---|---|---|
2697 | 59.0 | thermal denaturation, midpoint method (Tm) |
23364 | 59.0 | Thermal denaturation, fluorometry |
67770 | 59 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 90.029 | no |
gram-positive | yes | 90.743 | yes |
anaerobic | yes | 99.318 | no |
halophile | no | 69.967 | no |
spore-forming | no | 95.258 | yes |
thermophile | no | 95.963 | no |
glucose-util | yes | 87.146 | no |
aerobic | no | 97.851 | no |
flagellated | no | 95.569 | yes |
glucose-ferment | yes | 83.68 | no |
External links
@ref: 2697
culture collection no.: DSM 6492, ATCC 49391, CCUG 34976, JCM 8219, CGMCC 1.2273, KCTC 3369, KCTC 3423, LMG 11341
straininfo link
- @ref: 71373
- straininfo: 14148
literature
- topic: Phylogeny
- Pubmed-ID: 1995032
- title: Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle.
- authors: Biavati B, Mattarelli P
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-41-1-163
- year: 1991
- mesh: Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/cytology/isolation & purification/physiology, Cattle/*microbiology, DNA, Bacterial/analysis/genetics, Nucleic Acid Hybridization, Rumen/*microbiology, Sequence Homology, Nucleic Acid, Terminology as Topic
- topic2: Enzymology
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2697 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6492) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6492 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
23364 | B. BIAVATI, P. MATTARELLI | 10.1099/00207713-41-1-163 | Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the Rumens of Cattle | IJSEM 41: 163-168 1991 | 1995032 | |
52428 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 34976) | https://www.ccug.se/strain?id=34976 | |||
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/ | ||||
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) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
71373 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID14148.1 | StrainInfo: A central database for resolving microbial strain identifiers |