Strain identifier

BacDive ID: 3796

Type strain: Yes

Species: Hymenobacter roseosalivarius

Strain Designation: AA-718

Strain history: CIP <- 2000, P. Hirsch, Kiel Univ., Kiel, Germany: strain AA-718

NCBI tax ID(s): 645990 (strain), 89967 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4243

BacDive-ID: 3796

DSM-Number: 11622

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative

description: Hymenobacter roseosalivarius AA-718 is a psychrophilic, Gram-negative bacterium that was isolated from soil sample.

NCBI tax id

NCBI tax idMatching level
89967species
645990strain

strain history

@refhistory
4243<- P. Hirsch; AA-718
122259CIP <- 2000, P. Hirsch, Kiel Univ., Kiel, Germany: strain AA-718

doi: 10.13145/bacdive3796.20230509.8.1

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 roseosalivarius
  • full scientific name: Hymenobacter roseosalivarius Hirsch et al. 1999

@ref: 4243

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter roseosalivarius

full scientific name: Hymenobacter roseosalivarius Hirsch et al. 1999 emend. Hahnke et al. 2016

strain designation: AA-718

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.99
122259negativerod-shapedno

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_11622_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 4243
  • name: PYGV AGAR (DSMZ Medium 621)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/621
  • composition: Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water

culture temp

@refgrowthtypetemperaturerange
4243positivegrowth9psychrophilic
122259positivegrowth22-25psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no96
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1222594853esculin+hydrolysis
122259606565hippurate-hydrolysis
12225917632nitrate+reduction
12225916301nitrite-reduction
12225935020tributyrin-hydrolysis
12225915792malonate-assimilation

metabolite production

  • @ref: 122259
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12225915688acetoin-
12225917234glucose-

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
122259oxidase-
122259beta-galactosidase-3.2.1.23
122259alcohol dehydrogenase-1.1.1.1
122259gelatinase+
122259catalase+1.11.1.6
122259gamma-glutamyltransferase-2.3.2.2
122259lysine decarboxylase-4.1.1.18
122259ornithine decarboxylase-4.1.1.17
122259phenylalanine ammonia-lyase-4.3.1.24
122259tryptophan deaminase-
122259urease-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
122259-++++++++-++---+-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122259---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
4243soil sampleDry Valleys of South Victoria LandAustralia and Oceania
122259Environment, Sandstone and soilsDry ValleyAntarcticaAntarcticaATA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6473.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_263;96_3062;97_3761;98_4775;99_6473&stattab=map
  • Last taxonomy: Hymenobacter roseosalivarius
  • 16S sequence: NR_029359
  • Sequence Identity:
  • Total samples: 728
  • soil counts: 218
  • aquatic counts: 128
  • animal counts: 318
  • plant counts: 64

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42431Risk group (German classification)
1222591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Hymenobacter roseosalivarius 16S rRNA gene, strain AA718Y188331508ena645990
4243Hymenobacter roseosalivarius DSM 11622 strain AA-718 16S ribosomal RNA, partial sequenceNR_0293591496nuccore645990

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter roseosalivarius DSM 11622GCA_900176135contigncbi645990
66792Hymenobacter roseosalivarius DSM 11622 strain DSM 11622645990.3wgspatric645990
66792Hymenobacter roseosalivarius AA-718, DSM 116222502422321draftimg645990

GC content

  • @ref: 4243
  • GC-content: 56.4
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
gram-positiveno96.844no
anaerobicno99.397no
halophileno91.955no
spore-formingno94.909no
glucose-utilyes80.858no
flagellatedno97.519no
aerobicyes88.227no
thermophileno95.527yes
motileno94.384no
glucose-fermentno89.736no

External links

@ref: 4243

culture collection no.: DSM 11622, CIP 106397

straininfo link

  • @ref: 73308
  • straininfo: 68852

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9841127Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent.Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B, Gallikowski CASyst Appl Microbiol10.1016/s0723-2020(98)80047-71998Antarctic Regions, Bacterial Typing Techniques, Bacteroides/classification/genetics, Base Composition, Culture Media, Cytophaga/classification/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacterium/classification/genetics, Gram-Negative Aerobic Rods and Cocci/*classification/growth & development/*isolation & purification/ultrastructure, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Terminology as TopicCultivation
Phylogeny16825654Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family "Flexibacteraceae".Suresh K, Mayilraj S, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.64144-02006Aerobiosis, Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cytophagaceae/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Water MicrobiologyMetabolism
Phylogeny25242537Hymenobacter roseus sp. nov., isolated from sand.Subhash Y, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.066225-02014Bacterial Typing Techniques, Base Composition, Carotenoids/chemistry, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Triterpenes/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4243Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11622)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11622
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
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
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
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
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
73308Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID68852.1StrainInfo: A central database for resolving microbial strain identifiers
122259Curators of the CIPCollection of Institut Pasteur (CIP 106397)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106397