Strain identifier

BacDive ID: 12663

Type strain: Yes

Species: Propionimicrobium lymphophilum

Strain history: CIP <- 2003, JCM <- ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 7625B

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General

@ref: 1870

BacDive-ID: 12663

DSM-Number: 4903

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped

description: Propionimicrobium lymphophilum CCUG 27816 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from submaxillary tissue.

NCBI tax id

NCBI tax idMatching level
33012species
1123001strain

strain history

@refhistory
1870<- ATCC <- W.E.C. Moore, VPI 7625B
67770ATCC 27520 <-- W. E. C. Moore VPI 7625 B.
120724CIP <- 2003, JCM <- ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 7625B

doi: 10.13145/bacdive12663.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Propionimicrobium
  • species: Propionimicrobium lymphophilum
  • full scientific name: Propionimicrobium lymphophilum (Torrey 1916) Stackebrandt et al. 2002
  • synonyms

    @refsynonym
    20215Propionibacterium lymphophilum
    20215Bacillus lymphophilus

@ref: 1870

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Propionimicrobium

species: Propionimicrobium lymphophilum

full scientific name: Propionimicrobium lymphophilum (Torrey 1916) Stackebrandt et al. 2002

type strain: yes

Morphology

cell morphology

  • @ref: 120724
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 120724

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_4903_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_4903_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_4903_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_4903_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_4903_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1870PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
37134MEDIUM 26 - for Gardnerella and Propionibacterium lymphophilumyesDistilled water make up to (1000.000 ml);Horse serum (200.000 ml);Brainheart infusion (37.000 g);Maltose 10 % solution - M0173 (200.000 ml)
120724CIP Medium 26yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=26
120724CIP Medium 433yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=433

culture temp

@refgrowthtypetemperaturerange
1870positivegrowth37mesophilic
37134positivegrowth37mesophilic
48963positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
1870anaerobe
48963anaerobe
120724anaerobe

murein

  • @ref: 1870
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12072417108D-arabinose-degradation
12072415824D-fructose+degradation
12072417634D-glucose+degradation
12072465327D-xylose-degradation
12072417057cellobiose-degradation
12072417716lactose-degradation
12072417306maltose+degradation
12072417814salicin-degradation
12072417992sucrose-degradation
1207244853esculin-hydrolysis
12072417632nitrate-reduction
12072416301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
12072435581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase+3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
120724oxidase-
120724beta-galactosidase-3.2.1.23
120724gelatinase-
120724amylase-
120724DNase-
120724caseinase-3.4.21.50
120724catalase-1.11.1.6
120724tween esterase-
120724lecithinase-
120724lipase-
120724protease-
120724urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1870--------+--------------------

Isolation, sampling and environmental information

isolation

@refsample type
1870submaxillary tissue
48963Human submaxillary tissue
67770Submaxillary tissue
120724Human, Submaxillary tissue

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Mouth

taxonmaps

  • @ref: 69479
  • File name: preview.99_2335.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_1261;97_1496;98_1822;99_2335&stattab=map
  • Last taxonomy: Propionimicrobium lymphophilum subclade
  • 16S sequence: AJ003056
  • Sequence Identity:
  • Total samples: 9509
  • soil counts: 283
  • aquatic counts: 1384
  • animal counts: 7765
  • plant counts: 77

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
18702Risk group (German classification)
1207241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Propionibacterium lymphophilum ATCC 27520 16S rRNA gene, partial sequenceU02907388ena33012
20218Propionibacterium lymphophilum DSM 4903 16S rRNA geneAJ0030561502ena33012
20218Propionimicrobium lymphophilum gene for 16S ribosomal RNA, partial sequence, strain: JCM 5829AB7290701482ena33012

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propionimicrobium lymphophilum DSM 49031123001.3wgspatric1123001
66792Propionimicrobium lymphophilum DSM 49032523533555draftimg1123001
67770Propionimicrobium lymphophilum DSM 4903GCA_000423485scaffoldncbi1123001

GC content

@refGC-contentmethod
187054.0
6777056high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.858no
flagellatedno97.516no
gram-positiveyes90.089no
anaerobicyes90.534yes
aerobicno93.677yes
halophileno78.275no
spore-formingno93.85no
glucose-utilyes84.281no
thermophileno92.036yes
glucose-fermentyes70.598no

External links

@ref: 1870

culture collection no.: CCUG 27816, NCTC 11866, LMG 16728, DSM 4903, ATCC 27520, JCM 5829, VPI 7625B, CIP 103263, NCIMB 702587, NCDO 2587

straininfo link

  • @ref: 81875
  • straininfo: 8646

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1870Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4903)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4903
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37134Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15041
48963Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27816)https://www.ccug.se/strain?id=27816
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
81875Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8646.1StrainInfo: A central database for resolving microbial strain identifiers
120724Curators of the CIPCollection of Institut Pasteur (CIP 103263)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103263