Strain identifier

BacDive ID: 11875

Type strain: No

Species: Phyllobacterium myrsinacearum

Strain history: CIP <- 2004, CCUG <- 1995, LMG, Phyllobacterium rubiacearum <- 1973, D. Knösel

NCBI tax ID(s): 28101 (species)

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General

@ref: 2351

BacDive-ID: 11875

DSM-Number: 5893

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-negative

description: Phyllobacterium myrsinacearum DSM 5893 is an obligate aerobe, Gram-negative bacterium of the family Phyllobacteriaceae.

NCBI tax id

  • NCBI tax id: 28101
  • Matching level: species

strain history

@refhistory
2351<- ATCC <- NCIMB <- J. De Ley, LMG <- D. Knösel
67770IAM 13587 <-- LMG 1(t1) <-- D. Knösel.
121213CIP <- 2004, CCUG <- 1995, LMG, Phyllobacterium rubiacearum <- 1973, D. Knösel

doi: 10.13145/bacdive11875.20240916.9.1

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

@refgram staincell shapemotilityconfidence
121213negativerod-shapedyes
69480negative98

colony morphology

  • @ref: 121213

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2351NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
36708MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121213CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121213CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
2351positivegrowth26
36708positivegrowth25
67770positivegrowth30
121213positivegrowth25-30
121213nogrowth10
121213nogrowth37
121213nogrowth41
121213nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 121213
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
121213NaClpositivegrowth0-2 %
121213NaClnogrowth4 %
121213NaClnogrowth6 %
121213NaClnogrowth8 %
121213NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12121316947citrate+carbon source
1212134853esculin+hydrolysis
121213606565hippurate+hydrolysis
12121317632nitrate-reduction
12121316301nitrite-reduction
12121317632nitrate-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

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12121315688acetoin-
12121317234glucose-

enzymes

@refvalueactivityec
121213oxidase+
121213beta-galactosidase-3.2.1.23
121213alcohol dehydrogenase-1.1.1.1
121213gelatinase-
121213amylase-
121213DNase-
121213caseinase-3.4.21.50
121213catalase+1.11.1.6
121213tween esterase-
121213gamma-glutamyltransferase+2.3.2.2
121213lecithinase-
121213lipase-
121213lysine decarboxylase-4.1.1.18
121213ornithine decarboxylase-4.1.1.17
121213phenylalanine ammonia-lyase-4.3.1.24
121213tryptophan deaminase-
121213urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121213-+++-+--++++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121213+++++--+-++----++-+++++++-+-+++++++-++-+-+------++++-++++--++-+++-----++-+-----++++-+-+-++++-++--++

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
36708Stuttgart-HohenheimGermanyDEUEurope
67770Leaf nodule
121213Stuttgart HohenheimGermanyDEUEuropePlant, Leaf nodule, Pavetta zimmermanniana

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
23511Risk group (German classification)
1212131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Phyllobacterium myrsinacearum gene for 16S rRNA, strain: IAM 13587D127901430nuccore28101
124043Phyllobacterium myrsinacearum gene for 16S rRNA, partial sequence, strain: NBRC 100017.AB6811301410nuccore28101

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phyllobacterium myrsinacearum strain DSM 589328101.7wgspatric28101
66792Phyllobacterium rubiacearum DSM 58932799112214draftimg28101
67770Phyllobacterium myrsinacearum DSM 5893GCA_004216655scaffoldncbi28101

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.295yes
69480spore-formingspore-formingAbility to form endo- or exosporesno87.895no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.338yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.75no
69480flagellatedmotile2+Ability to perform flagellated movementno51.528no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361292Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend.Mergaert J, Cnockaert MC, Swings JInt J Syst Evol Microbiol10.1099/00207713-52-5-18212002Alphaproteobacteria/*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 TopicGenetics
35591989Third 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 LFront Microbiol10.3389/fmicb.2022.8426842022

Reference

@idauthorscataloguedoi/urltitle
2351Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5893)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5893
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
36708Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5835
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81092Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127101.1StrainInfo: A central database for resolving microbial strain identifiers
121213Curators of the CIPCollection of Institut Pasteur (CIP 108235)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108235
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy