Strain identifier

BacDive ID: 11751

Type strain: Yes

Species: Histophilus somni

Strain Designation: 8025

Strain history: CIP <- 2003, CCUG <- W. Mannheim, Philipps-Univ., Marburg, Germany <- L. Corboz: strain 8025

NCBI tax ID(s): 731 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17404

BacDive-ID: 11751

DSM-Number: 23850

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

description: Histophilus somni 8025 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from bovine brain with TME lesions.

NCBI tax id

  • NCBI tax id: 731
  • Matching level: species

strain history

@refhistory
17404<- CCUG; CCUG 36157 <- W. Mannheim, Univ. Marburg; <- L. Corboz, Univ. Zurich; <- R. M. Schultz; 8025
122676CIP <- 2003, CCUG <- W. Mannheim, Philipps-Univ., Marburg, Germany <- L. Corboz: strain 8025

doi: 10.13145/bacdive11751.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pasteurellales
  • family: Pasteurellaceae
  • genus: Histophilus
  • species: Histophilus somni
  • full scientific name: Histophilus somni Angen et al. 2003

@ref: 17404

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Histophilus

species: Histophilus somni

full scientific name: Histophilus somni Angen et al. 2003

strain designation: 8025

type strain: yes

Morphology

cell morphology

  • @ref: 122676
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

@reftype of hemolysishemolysis ability
17404alpha1
122676

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17404COLUMBIA 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
32889MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
122676CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
17404positivegrowth37mesophilic
32889positivegrowth37mesophilic
122676positivegrowth25-37mesophilic
122676nogrowth41thermophilic
122676nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17404microaerophile
53176microaerophile

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose-builds acid from15824
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122676esculin-hydrolysis4853
122676hippurate+hydrolysis606565
122676nitrate+reduction17632
122676nitrite-reduction16301
68377D-glucose+builds acid from17634
68377urea-hydrolysis16199

metabolite production

  • @ref: 122676
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
17404catalase-1.11.1.6
17404cytochrome-c oxidase+1.9.3.1
68377beta-galactosidase-3.2.1.23
68377urease-3.5.1.5
122676oxidase-
122676beta-galactosidase+3.2.1.23
122676alcohol dehydrogenase-1.1.1.1
122676catalase-1.11.1.6
122676gamma-glutamyltransferase-2.3.2.2
122676lysine decarboxylase+4.1.1.18
122676ornithine decarboxylase+4.1.1.17
122676urease-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
122676-----+--------+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122676----------+/--+/-----------------------------+/-------+/-

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
17404+++/-+/-+--+--++-
17404-+---+-------
17404-+++/-+/-+--+--++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122676---------+--+----------------------------+-------------+-----------------+------------+----+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17404bovine brain with TME lesionsWisconsinUSAUSANorth America
53176Bovine brain
122676Animal, Bovine brainZurichSwitzerlandCHEEurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Brain

taxonmaps

  • @ref: 69479
  • File name: preview.99_200.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_142;97_153;98_171;99_200&stattab=map
  • Last taxonomy: Histophilus somni subclade
  • 16S sequence: AF549387
  • Sequence Identity:
  • Total samples: 7878
  • soil counts: 129
  • aquatic counts: 313
  • animal counts: 7347
  • plant counts: 89

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
17404yes2Risk group (German classification)
1226761Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17404
  • description: Histophilus somni 8025 16S ribosomal RNA (rrn) gene, partial sequence
  • accession: AF549387
  • length: 1361
  • database: ena
  • NCBI tax ID: 731

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Histophilus somni DSM 23850GCA_014202395scaffoldncbi731
66792Histophilus somni strain DSM 23850731.218wgspatric731
66792Histophilus somni DSM 238502861509796draftimg731

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.792no
gram-positiveno98.697no
anaerobicno97.388yes
aerobicno93.901yes
halophileyes64.597no
spore-formingno98.668no
glucose-utilyes56.501no
thermophileno96.444yes
motileno90.446no
glucose-fermentyes56.54no

External links

@ref: 17404

culture collection no.: DSM 23850, ATCC 43625, CCUG 36157, MCCM 00728, CIP 108133, HIM 736-6

straininfo link

  • @ref: 80969
  • straininfo: 41945

literature

  • topic: Phylogeny
  • Pubmed-ID: 13130032
  • title: Proposal of Histophilus somni gen. nov., sp. nov. for the three species incertae sedis 'Haemophilus somnus', 'Haemophilus agni' and 'Histophilus ovis'.
  • authors: Angen O, Ahrens P, Kuhnert P, Christensen H, Mutters R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02637-0
  • year: 2003
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, DNA-Directed RNA Polymerases/genetics, Genes, Bacterial, Haemophilus/*classification/genetics/metabolism, Molecular Sequence Data, Pasteurellaceae/*classification/genetics/metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
17404Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23850)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23850
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
32889Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5722
53176Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 36157)https://www.ccug.se/strain?id=36157
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
80969Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41945.1StrainInfo: A central database for resolving microbial strain identifiers
122676Curators of the CIPCollection of Institut Pasteur (CIP 108133)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108133