Strain identifier

BacDive ID: 11725

Type strain: Yes

Species: Mannheimia varigena

Strain Designation: 177

Strain history: CIP <- 1999, CCUG <- Ö. Angen, SVS, Copenhagen, Denmark: strain 177

NCBI tax ID(s): 85404 (species)

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General

@ref: 7946

BacDive-ID: 11725

DSM-Number: 19166

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped, animal pathogen

description: Mannheimia varigena 177 is an obligate aerobe, mesophilic, Gram-negative animal pathogen that was isolated from cattle.

NCBI tax id

  • NCBI tax id: 85404
  • Matching level: species

strain history

@refhistory
7946<- CIP <- CCUG <- Ö. Angen; 177
123802CIP <- 1999, CCUG <- Ö. Angen, SVS, Copenhagen, Denmark: strain 177

doi: 10.13145/bacdive11725.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pasteurellales
  • family: Pasteurellaceae
  • genus: Mannheimia
  • species: Mannheimia varigena
  • full scientific name: Mannheimia varigena Angen et al. 1999

@ref: 7946

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Mannheimia

species: Mannheimia varigena

full scientific name: Mannheimia varigena Angen et al. 1999

strain designation: 177

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123802negativerod-shapedno
125438no92.988
125438negative97.5

colony morphology

  • @ref: 123802
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7946COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
7946BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
40150MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicolayesDistilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g)
123802CIP Medium 118-byeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b

culture temp

@refgrowthtypetemperature
7946positivegrowth37
40150positivegrowth37
123802positivegrowth30-41
123802nogrowth15

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
123802obligate aerobe
125439obligate aerobe95.3

spore formation

@refspore formationconfidence
125438no91.019
125439no94.8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837727897tryptophan-energy source
6837716199urea-hydrolysis
6837717634D-glucose+builds acid from
12380216947citrate-carbon source
1238024853esculin-hydrolysis
12380217234glucose+fermentation
123802606565hippurate+hydrolysis
12380217716lactose-fermentation
12380217632nitrate+reduction
12380216301nitrite-reduction
123802132112sodium thiosulfate-builds gas from
12380217234glucose+degradation
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837718257ornithine-degradation
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from

antibiotic resistance

  • @ref: 123802
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
12380235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837735581indole-
12380215688acetoin-
12380217234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
123802oxidase+
123802beta-galactosidase+3.2.1.23
123802alcohol dehydrogenase-1.1.1.1
123802catalase+1.11.1.6
123802lysine decarboxylase-4.1.1.18
123802ornithine decarboxylase+4.1.1.17
123802phenylalanine ammonia-lyase-4.3.1.24
123802tryptophan deaminase-
123802urease-3.5.1.5
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase-3.4.11.5
68377alkaline phosphatase+3.1.3.1
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123802-+---+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123802+--+++---+++--+-++---+--------+------------+--+--

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
7946++-+---++----
7946-++-+---++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7946cattleGermanyDEUEurope
54269Bovine pneumoniaGermanyDEUEuropeWest
123802Animal, Bovine, pneumoniaGermanyDEUEuropeWest

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Bovinae (Cow, Cattle)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4027.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_125;97_2470;98_3052;99_4027&stattab=map
  • Last taxonomy: Mannheimia varigena subclade
  • 16S sequence: AF053893
  • Sequence Identity:
  • Total samples: 1771
  • soil counts: 19
  • aquatic counts: 55
  • animal counts: 1694
  • plant counts: 3

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
7946yes2Risk group (German classification)
1238021Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7946
  • description: Mannheimia varigena strain 177; CCUG 38462 16S ribosomal RNA gene, partial sequence
  • accession: AF053893
  • length: 1504
  • database: nuccore
  • NCBI tax ID: 85404

Genome sequences

  • @ref: 66792
  • description: Mannheimia varigena 177
  • accession: GCA_013377235
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 85404

GC content

  • @ref: 7946
  • GC-content: 41.7

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.581no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no62.98yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.019no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5no
125438motile2+flagellatedAbility to perform flagellated movementno92.988no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.8
125439BacteriaNetmotilityAbility to perform movementno64.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative70.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.3

External links

@ref: 7946

culture collection no.: DSM 19166, CCUG 38462, CIP 106064

straininfo link

  • @ref: 80944
  • straininfo: 69232

literature

  • topic: Phylogeny
  • Pubmed-ID: 10028248
  • title: Taxonomic relationships of the [Pasteurella] haemolytica complex as evaluated by DNA-DNA hybridizations and 16S rRNA sequencing with proposal of Mannheimia haemolytica gen. nov., comb. nov., Mannheimia granulomatis comb. nov., Mannheimia glucosida sp. nov., Mannheimia ruminalis sp. nov. and Mannheimia varigena sp. nov.
  • authors: Angen O, Mutters R, Caugant DA, Olsen JE, Bisgaard M
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-1-67
  • year: 1999
  • mesh: Base Composition, Base Sequence, DNA, Bacterial/*analysis, Mannheimia haemolytica/*classification/genetics, *Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*chemistry

Reference

@idauthorscataloguedoi/urltitle
7946Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19166)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19166
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
40150Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18152
54269Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38462)https://www.ccug.se/strain?id=38462
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)
68371Automatically annotated from API 50CH acid
68377Automatically annotated from API NH
68382Automatically annotated from API zym
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
80944Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID69232.1StrainInfo: A central database for resolving microbial strain identifiers
123802Curators of the CIPCollection of Institut Pasteur (CIP 106064)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106064
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1