Strain identifier
BacDive ID: 132345
Type strain:
Species: Bifidobacterium myosotis
Strain Designation: MRM_5.9
Strain history: P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; MRM_5.9.
NCBI tax ID(s): 1630166 (species)
General
@ref: 24134
BacDive-ID: 132345
DSM-Number: 100196
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-positive, rod-shaped, colony-forming
description: Bifidobacterium myosotis MRM_5.9 is an anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from faeces of baby common marmosets .
NCBI tax id
- NCBI tax id: 1630166
- Matching level: species
strain history
@ref | history |
---|---|
24134 | <- P. Mattarelli, Univ. Bologna, Italy; MRM_5.9 <- M. Modesto |
67770 | P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; MRM_5.9. |
doi: 10.13145/bacdive132345.20230509.8.1
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 myosotis
- full scientific name: Bifidobacterium myosotis Michelini et al. 2016
@ref: 24134
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium myosotis
full scientific name: Bifidobacterium myosotis Michelini et al. 2016
strain designation: MRM_5.9
type strain: yes
Morphology
cell morphology
- @ref: 43839
- gram stain: positive
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 43839
- type of hemolysis: gamma
- colony size: 1-2 mm
- colony color: White
- colony shape: circular
- incubation period: 3 days
- medium used: TPY agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43839 | TPY agar | yes | ||
24134 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43839 | positive | growth | 25-46 | |
43839 | positive | optimum | 40 | thermophilic |
24134 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
43839 | positive | growth | 4.5-8 |
43839 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 43839
- oxygen tolerance: anaerobe
spore formation
- @ref: 43839
- spore formation: no
murein
- @ref: 24134
- murein short key: A11.35
- type: A4alpha L-Lys-L-Ala-L-Glu
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43839 | 16808 | 2-dehydro-D-gluconate | - | builds acid from |
43839 | 58143 | 5-dehydro-D-gluconate | - | builds acid from |
43839 | 18305 | arbutin | - | builds acid from |
43839 | 15963 | ribitol | - | builds acid from |
43839 | 17108 | D-arabinose | - | builds acid from |
43839 | 18333 | D-arabitol | - | builds acid from |
43839 | 28847 | D-fucose | - | builds acid from |
43839 | 62318 | D-lyxose | - | builds acid from |
43839 | 16988 | D-ribose | - | builds acid from |
43839 | 17924 | D-sorbitol | - | builds acid from |
43839 | 16443 | D-tagatose | - | builds acid from |
43839 | 16813 | galactitol | - | builds acid from |
43839 | 17113 | erythritol | - | builds acid from |
43839 | 28066 | gentiobiose | - | builds acid from |
43839 | 24265 | gluconate | - | builds acid from |
43839 | 17754 | glycerol | - | builds acid from |
43839 | 28087 | glycogen | - | builds acid from |
43839 | 17268 | myo-inositol | - | builds acid from |
43839 | 15443 | inulin | - | builds acid from |
43839 | 18403 | L-arabitol | - | builds acid from |
43839 | 62345 | L-rhamnose | - | builds acid from |
43839 | 17266 | L-sorbose | - | builds acid from |
43839 | 65328 | L-xylose | - | builds acid from |
43839 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
43839 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
43839 | 506227 | N-acetylglucosamine | - | builds acid from |
43839 | 28017 | starch | - | builds acid from |
43839 | 27082 | trehalose | - | builds acid from |
43839 | 17151 | xylitol | - | builds acid from |
43839 | 17632 | nitrate | - | reduction |
43839 | 17057 | cellobiose | + | builds acid from |
43839 | 17634 | D-glucose | + | builds acid from |
43839 | 65327 | D-xylose | + | builds acid from |
43839 | 30849 | L-arabinose | + | builds acid from |
43839 | 17716 | lactose | + | builds acid from |
43839 | 17306 | maltose | + | builds acid from |
43839 | 28053 | melibiose | + | builds acid from |
43839 | 17814 | salicin | + | builds acid from |
43839 | 17992 | sucrose | + | builds acid from |
43839 | 27082 | trehalose | + | builds acid from |
43839 | 4853 | esculin | + | hydrolysis |
43839 | 27613 | amygdalin | +/- | builds acid from |
43839 | 15824 | D-fructose | +/- | builds acid from |
43839 | 12936 | D-galactose | +/- | builds acid from |
43839 | 16899 | D-mannitol | +/- | builds acid from |
43839 | 16024 | D-mannose | +/- | builds acid from |
43839 | 28066 | gentiobiose | +/- | builds acid from |
43839 | 6731 | melezitose | +/- | builds acid from |
43839 | 74863 | methyl beta-D-xylopyranoside | +/- | builds acid from |
43839 | 32528 | turanose | +/- | builds acid from |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | + | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | + | builds acid from |
68371 | 28066 | gentiobiose | + | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | + | builds acid from |
68371 | 28017 | starch | + | builds acid from |
68371 | 16634 | raffinose | + | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | + | builds acid from |
68371 | 17716 | lactose | + | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
metabolite production
- @ref: 43839
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
43839 | catalase | - | 1.11.1.6 |
43839 | cytochrome oxidase | - | 1.9.3.1 |
43839 | urease | + | 3.5.1.5 |
43839 | arginine dihydrolase | + | 3.5.3.6 |
43839 | proline-arylamidase | + | 3.4.11.5 |
43839 | leucyl glycin arylamidase | + | 3.4.11.1 |
43839 | phenylalanine arylamidase | + | |
43839 | leucine arylamidase | + | 3.4.11.1 |
43839 | tyrosine arylamidase | + | |
43839 | alanine arylamidase | + | 3.4.11.2 |
43839 | glycin arylamidase | + | |
43839 | histidine arylamidase | + | |
43839 | serine arylamidase | + | |
43839 | alkaline phosphatase | - | 3.1.3.1 |
43839 | esterase Lipase (C 8) | - | |
43839 | valine arylamidase | - | |
43839 | cystine arylamidase | - | 3.4.11.3 |
43839 | trypsin | - | 3.4.21.4 |
43839 | alpha-chymotrypsin | - | 3.4.21.1 |
43839 | beta-glucuronidase | - | 3.2.1.31 |
43839 | alpha-mannosidase | - | 3.2.1.24 |
43839 | alpha-fucosidase | - | 3.2.1.51 |
43839 | alpha-galactosidase | - | 3.2.1.22 |
43839 | 6-phospho-beta-galactosidase | - | 3.2.1.85 |
43839 | alpha-glucosidase | - | 3.2.1.20 |
43839 | beta-glucosidase | - | 3.2.1.21 |
43839 | alpha-arabinosidase | - | 3.2.1.55 |
43839 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24134 | - | - | - | - | + | - | + | - | - | - | + | + | + | - | - | - | - | - | - | - | - | + | - | + | + | + | + | + | + | + | + | + | - | - | - | + | + | + | - | + | + | - | - | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
24134 | faeces of baby common marmosets (Callithrix jacchus L.) | Callithrix jacchus | Verona | Italy | ITA | Europe |
43839 | The feaces of common marmosets (Callithrix jacchus L.) | |||||
67770 | Feces of a common marmosets |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Primates |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_116632.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_46219;97_59316;98_78788;99_116632&stattab=map
- Last taxonomy: Bifidobacterium myosotis subclade
- 16S sequence: KP718941
- Sequence Identity:
- Total samples: 3583
- soil counts: 22
- aquatic counts: 51
- animal counts: 3510
Safety information
risk assessment
- @ref: 24134
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24134
- description: Bifidobacterium myosotis strain MRM_5.9 16S ribosomal RNA gene, partial sequence
- accession: KP718941
- length: 1423
- database: ena
- NCBI tax ID: 1630166
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bifidobacterium myosotis DSM 100196 | GCA_002259745 | contig | ncbi | 1630166 |
66792 | Bifidobacterium myosotis strain DSM 100196 | 1630166.3 | wgs | patric | 1630166 |
66792 | Bifidobacterium myosotis DSM 100196 | 2791355235 | draft | img | 1630166 |
GC content
- @ref: 24134
- GC-content: 65.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 94.315 | yes |
gram-positive | yes | 91.192 | no |
anaerobic | yes | 97.689 | yes |
aerobic | no | 96.354 | yes |
halophile | no | 80.925 | no |
spore-forming | no | 95.136 | no |
glucose-util | yes | 85.417 | no |
flagellated | no | 97.071 | yes |
thermophile | no | 92.432 | no |
glucose-ferment | yes | 81.418 | no |
External links
@ref: 24134
culture collection no.: DSM 100196, JCM 30796, MRM 5.9, KCTC 15589
straininfo link
- @ref: 90691
- straininfo: 404288
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26515885 | Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.). | Michelini S, Oki K, Yanokura E, Shimakawa Y, Modesto M, Mattarelli P, Biavati B, Watanabe K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000708 | 2015 | Aldehyde-Lyases/metabolism, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Bifidobacterium/classification/genetics/isolation & purification, Callithrix/*microbiology, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Heat-Shock Proteins/genetics, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 31180316 | Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus). | Modesto M, Watanabe K, Arita M, Satti M, Oki K, Sciavilla P, Patavino C, Camma C, Michelini S, Sgorbati B, Mattarelli P | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003518 | 2019 | Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/isolation & purification, Callithrix/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Phylogeny | 31585749 | Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov. | Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang CH, Liou JS, Miyashita M, Tamura T, Saito S, Mori K, Huang L, Sciavilla P, Sandri C, Spiezio C, Vitali F, Cavalieri D, Perpetuini G, Tofalo R, Bonetti A, Arita M, Mattarelli P | Syst Appl Microbiol | 10.1016/j.syapm.2019.126017 | 2019 | Amino Acids/analysis, Animals, Base Composition, Bifidobacterium/chemistry/*classification/genetics/growth & development, Chiroptera/*microbiology, DNA, Bacterial/genetics, Egypt, Fatty Acids/analysis, Feces/*microbiology, Genes, Essential/genetics, Genetic Variation, Genome, Bacterial/genetics, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | |||
24134 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100196 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100196) | |||
43839 | Samanta Michelini, Kaihei Oki, Emiko Yanokura, Yasuhisa Shimakawa, Monica Modesto, Paola Mattarelli, Bruno Biavati, Koichi Watanabe | Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.) | 10.1099/ijsem.0.000708 | IJSEM 66: 255-265 2016 | 26515885 | |
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 | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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/ | |||
90691 | 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-ID404288.1 |