Strain identifier
BacDive ID: 11875
Type strain:
Species: Phyllobacterium myrsinacearum
Strain history: CIP <- 2004, CCUG <- 1995, LMG, Phyllobacterium rubiacearum <- 1973, D. Knösel
NCBI tax ID(s): 28101 (species)
General
@ref: 2351
BacDive-ID: 11875
DSM-Number: 5893
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile
description: Phyllobacterium myrsinacearum DSM 5893 is an obligate aerobe, mesophilic, motile bacterium of the family Phyllobacteriaceae.
NCBI tax id
- NCBI tax id: 28101
- Matching level: species
strain history
@ref | history |
---|---|
2351 | <- ATCC <- NCIMB <- J. De Ley, LMG <- D. Knösel |
67770 | IAM 13587 <-- LMG 1(t1) <-- D. Knösel. |
121213 | CIP <- 2004, CCUG <- 1995, LMG, Phyllobacterium rubiacearum <- 1973, D. Knösel |
doi: 10.13145/bacdive11875.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Phyllobacteriaceae
- genus: Phyllobacterium
- species: Phyllobacterium myrsinacearum
- full scientific name: Phyllobacterium myrsinacearum (ex Knösel 1962) Knösel 1984
synonyms
- @ref: 20215
- synonym: Phyllobacterium rubiacearum
@ref: 2351
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Phyllobacteriaceae
genus: Phyllobacterium
species: Phyllobacterium myrsinacearum
full scientific name: Phyllobacterium myrsinacearum (ex Knösel 1962) Knösel 1984 emend. Mergaert et al. 2002 emend. Hameed et al. 2015
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 93.585 | ||
69480 | 99.984 | negative | ||
121213 | yes | negative | rod-shaped |
colony morphology
- @ref: 121213
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2351 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
36708 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121213 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
121213 | CIP Medium 328 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2351 | positive | growth | 26 | mesophilic |
36708 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
121213 | positive | growth | 25-30 | mesophilic |
121213 | no | growth | 10 | psychrophilic |
121213 | no | growth | 37 | mesophilic |
121213 | no | growth | 41 | thermophilic |
121213 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 121213
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.994 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121213 | NaCl | positive | growth | 0-2 % |
121213 | NaCl | no | growth | 4 % |
121213 | NaCl | no | growth | 6 % |
121213 | NaCl | no | growth | 8 % |
121213 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
121213 | 16947 | citrate | + | carbon source |
121213 | 4853 | esculin | + | hydrolysis |
121213 | 606565 | hippurate | + | hydrolysis |
121213 | 17632 | nitrate | - | reduction |
121213 | 16301 | nitrite | - | reduction |
121213 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 121213
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 121213
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
121213 | 15688 | acetoin | - | |
121213 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
121213 | oxidase | + | |
121213 | beta-galactosidase | - | 3.2.1.23 |
121213 | alcohol dehydrogenase | - | 1.1.1.1 |
121213 | gelatinase | - | |
121213 | amylase | - | |
121213 | DNase | - | |
121213 | caseinase | - | 3.4.21.50 |
121213 | catalase | + | 1.11.1.6 |
121213 | tween esterase | - | |
121213 | gamma-glutamyltransferase | + | 2.3.2.2 |
121213 | lecithinase | - | |
121213 | lipase | - | |
121213 | lysine decarboxylase | - | 4.1.1.18 |
121213 | ornithine decarboxylase | - | 4.1.1.17 |
121213 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121213 | tryptophan deaminase | - | |
121213 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121213 | - | + | + | + | - | + | - | - | + | + | + | + | - | - | - | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121213 | + | + | + | + | + | - | - | + | - | + | + | - | - | - | - | + | + | - | + | + | + | + | + | + | + | - | + | - | + | + | + | + | + | + | + | - | + | + | - | + | - | + | - | - | - | - | - | - | + | + | + | + | - | + | + | + | + | - | - | + | + | - | + | + | + | - | - | - | - | - | + | + | - | + | - | - | - | - | - | + | + | + | + | - | + | - | + | - | + | + | + | + | - | + | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | geographic location | country | origin.country | continent | sample type |
---|---|---|---|---|---|
36708 | Stuttgart-Hohenheim | Germany | DEU | Europe | |
67770 | Leaf nodule | ||||
121213 | Stuttgart Hohenheim | Germany | DEU | Europe | Plant, Leaf nodule, Pavetta zimmermanniana |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
2351 | 1 | Risk group (German classification) |
121213 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 67770
- description: Phyllobacterium myrsinacearum gene for 16S rRNA, strain: IAM 13587
- accession: D12790
- length: 1430
- database: ena
- NCBI tax ID: 28101
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Phyllobacterium myrsinacearum strain DSM 5893 | 28101.7 | wgs | patric | 28101 |
66792 | Phyllobacterium rubiacearum DSM 5893 | 2799112214 | draft | img | 28101 |
67770 | Phyllobacterium myrsinacearum DSM 5893 | GCA_004216655 | scaffold | ncbi | 28101 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 89.321 | no |
gram-positive | no | 97.776 | no |
anaerobic | no | 99.159 | no |
halophile | no | 93.083 | no |
spore-forming | no | 96.036 | no |
glucose-util | yes | 89.673 | no |
flagellated | no | 79.254 | no |
aerobic | yes | 95.054 | no |
thermophile | no | 98.904 | yes |
glucose-ferment | no | 87.015 | no |
External links
@ref: 2351
culture collection no.: DSM 5893, ATCC 43591, LMG 1t1, NCIMB 12128, JCM 20934, CCUG 34964, CIP 108235, HAMBI 1991, HAMBI 2264, IAM 13587, LMG 1.1, NBRC 100017
straininfo link
- @ref: 81092
- straininfo: 127101
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12361292 | Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend. | Mergaert J, Cnockaert MC, Swings J | Int J Syst Evol Microbiol | 10.1099/00207713-52-5-1821 | 2002 | Alphaproteobacteria/*classification/genetics/isolation & purification/metabolism, Beta vulgaris/microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic | Genetics |
35591989 | Third Generation Genome Sequencing Reveals That Endobacteria in Nematophagous Fungi Esteya vermicola Contain Multiple Genes Encoding for Nematicidal Proteins. | Wang R, Dong L, Chen Y, Wang S, Qu L | Front Microbiol | 10.3389/fmicb.2022.842684 | 2022 |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
2351 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5893) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5893 | |
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 | |
36708 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5835 | ||
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/ | ||
68382 | Automatically annotated from API zym | |||
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 | |
81092 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127101.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
121213 | Curators of the CIP | Collection of Institut Pasteur (CIP 108235) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108235 |