Strain identifier

BacDive ID: 3803

Type strain: Yes

Species: Hymenobacter actinosclerus

Strain Designation: Collins 1187, IFR 1187

Strain history: CIP <- 2000, CCUG <- 1998, M. D. Collins, IFR, Reading, UK, Deinobacter-like

NCBI tax ID(s): 82805 (species)

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General

@ref: 5839

BacDive-ID: 3803

DSM-Number: 15310

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

description: Hymenobacter actinosclerus Collins 1187 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from pork chops irradiated to a dose of 1.75 kGy.

NCBI tax id

  • NCBI tax id: 82805
  • Matching level: species

strain history

@refhistory
5839<- CCUG <- M. D. Collins, Dept. Food Sci. and Technol., Univ. Reading, UK
116034CIP <- 2000, CCUG <- 1998, M. D. Collins, IFR, Reading, UK, Deinobacter-like

doi: 10.13145/bacdive3803.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter actinosclerus
  • full scientific name: Hymenobacter actinosclerus Collins et al. 2000

@ref: 5839

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter actinosclerus

full scientific name: Hymenobacter actinosclerus Collins et al. 2000

strain designation: Collins 1187, IFR 1187

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
116034negativerod-shapedno

colony morphology

@refincubation period
54859>1 day
116034

pigmentation

  • @ref: 116034
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5839OXOID NUTRIENT BROTH (DSMZ Medium 948)yeshttps://mediadive.dsmz.de/medium/948Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
5839NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605)yeshttps://mediadive.dsmz.de/medium/605Name: NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l Distilled water
32998MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116034CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
5839positivegrowth30mesophilic
32998positivegrowth30mesophilic
54859positivegrowth30mesophilic
116034positivegrowth15-30
116034nogrowth5psychrophilic
116034nogrowth37mesophilic
116034nogrowth41thermophilic
116034nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 54859
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
116034NaClpositivegrowth0 %
116034NaClnogrowth2 %
116034NaClnogrowth4 %
116034NaClnogrowth6 %
116034NaClnogrowth8 %
116034NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1160344853esculin-hydrolysis
116034606565hippurate-hydrolysis
11603417632nitrate-reduction
11603416301nitrite-reduction
11603415792malonate-assimilation

antibiotic resistance

  • @ref: 116034
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116034
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11603415688acetoin-
11603417234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116034beta-galactosidase-3.2.1.23
116034alcohol dehydrogenase-1.1.1.1
116034gelatinase-
116034catalase+1.11.1.6
116034gamma-glutamyltransferase-2.3.2.2
116034lysine decarboxylase-4.1.1.18
116034ornithine decarboxylase-4.1.1.17
116034phenylalanine ammonia-lyase-4.3.1.24
116034tryptophan deaminase-
116034urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116034-+++-+++--++--------

Isolation, sampling and environmental information

isolation

@refsample type
5839pork chops irradiated to a dose of 1.75 kGy
54859Pork chops,irradiated to a dose of 1.75 kGy
116034Food, Pork chops, irradiated to a dose of 1.75 kGY

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Meat
#Host#Mammals#Suidae (Pig,Swine)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58391Risk group (German classification)
1160341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5839
  • description: Hymenobacter actinosclerus 16S rRNA gene
  • accession: Y17356
  • length: 1445
  • database: ena
  • NCBI tax ID: 82805

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter actinosclerus DSM 15310GCA_900111515scaffoldncbi82805
66792Hymenobacter actinosclerus strain DSM 1531082805.3wgspatric82805
66792Hymenobacter actinosclerus DSM 153102622736539draftimg82805

GC content

  • @ref: 5839
  • GC-content: 62.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno93.023no
flagellatedno97.419no
gram-positiveno97.81no
anaerobicno99.142yes
aerobicyes86.487no
halophileno92.448no
spore-formingno94.538no
glucose-fermentno90.902no
thermophileno97.374yes
glucose-utilyes76.998no

External links

@ref: 5839

culture collection no.: DSM 15310, CCUG 39621, CIP 106628, KACC 17382

straininfo link

  • @ref: 73315
  • straininfo: 68851

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10758882Phylogenetic characterization of a novel radiation-resistant bacterium from irradiated pork: description of Hymenobacter actinosclerus sp. nov.Collins MD, Hutson RA, Grant IR, Patterson MFInt J Syst Evol Microbiol10.1099/00207713-50-2-7312000Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Food Irradiation, Genes, rRNA, Gram-Negative Aerobic Bacteria/*classification/*isolation & purification/physiology/radiation effects, Meat/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Sequence Analysis, DNA, SwineGenetics
Phylogeny29148363Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility.Kang JW, Choi S, Choe HN, Seong CNInt J Syst Evol Microbiol10.1099/ijsem.0.0024972017Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Tibet, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiologyTranscriptome
Phylogeny29458543Hymenobacter profundi sp. nov., isolated from deep-sea water.Sun J, Xing M, Wang W, Dai F, Liu J, Hao JInt J Syst Evol Microbiol10.1099/ijsem.0.0026212018
Phylogeny35061583Hymenobacter piscis sp. nov., isolated from a fish pond.Sheu SY, Yang CC, Kwon SW, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0051942022Animals, Bacterial Typing Techniques, Base Composition, *Cytophagaceae/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fishes, Phospholipids/chemistry, *Phylogeny, *Ponds/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TaiwanTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5839Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15310)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15310
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
32998Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18780
54859Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39621)https://www.ccug.se/strain?id=39621
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
73315Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID68851.1StrainInfo: A central database for resolving microbial strain identifiers
116034Curators of the CIPCollection of Institut Pasteur (CIP 106628)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106628