Strain identifier

BacDive ID: 11304

Type strain: Yes

Species: Herminiimonas fonticola

Strain Designation: S-94

Strain history: CIP <- 2004, M. Costa, Coimbra Univ., Coimbra, Portugal: strain S-94

NCBI tax ID(s): 303380 (species)

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

@ref: 7587

BacDive-ID: 11304

DSM-Number: 18555

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Herminiimonas fonticola S-94 is an aerobe, mesophilic, motile bacterium that was isolated from bore hole of mineral water spring.

NCBI tax id

  • NCBI tax id: 303380
  • Matching level: species

strain history

@refhistory
7587<- CIP <- C. Fernandes, Univ. de Coimbra
119418CIP <- 2004, M. Costa, Coimbra Univ., Coimbra, Portugal: strain S-94

doi: 10.13145/bacdive11304.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Herminiimonas
  • species: Herminiimonas fonticola
  • full scientific name: Herminiimonas fonticola Fernandes et al. 2005

@ref: 7587

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herminiimonas

species: Herminiimonas fonticola

full scientific name: Herminiimonas fonticola Fernandes et al. 2005

strain designation: S-94

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.94
69480100negative
119418nonegativerod-shaped

colony morphology

@refincubation period
595743 days
119418

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7587HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)yeshttps://mediadive.dsmz.de/medium/428Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
7587R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
33957MEDIUM 584 - for Herminiimonas fonticolayesSolution A - M01006 (50.000 ml);Solution B - M01007 (850.000 ml);Solution C - M01008 (20.000 ml);Solution D - M01009 (30.000 ml);Solution E - M01010 (50.000 ml);Vitamins solution - M01011 (5.000 ml)
119418CIP Medium 584yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=584

culture temp

@refgrowthtypetemperaturerange
7587positivegrowth28mesophilic
7587positivegrowth30mesophilic
33957positivegrowth30mesophilic
59574positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59574aerobe
119418obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11941817632nitrate-reduction
11941816301nitrite-reduction

metabolite production

  • @ref: 119418
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119418oxidase+
119418alcohol dehydrogenase-1.1.1.1
119418catalase+1.11.1.6
119418lysine decarboxylase-4.1.1.18
119418ornithine decarboxylase-4.1.1.17
119418urease-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
119418--+--+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
7587bore hole of mineral water springPortugalPRTEurope
59574Water,borehole mineral waterPortugalPRTEurope1997Serra da Estrela
119418Environment, Mineral waterPortugalPRTEuropeSerra da Esrela1997

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_40323.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_2343;97_23298;98_29431;99_40323&stattab=map
  • Last taxonomy: Herminiimonas fonticola
  • 16S sequence: AB512142
  • Sequence Identity:
  • Total samples: 4
  • aquatic counts: 3
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75871Risk group (German classification)
1194181Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Herminiimonas fonticola gene for 16S rRNA, partial sequence, strain: da Costa S-94AB5121421485ena303380
7587Herminiimonas fonticola 16S ribosomal RNA gene, partial sequenceAY6764621426ena303380

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herminiimonas fonticola DSM 18555GCA_004361795contigncbi303380
66792Herminiimonas fonticola S-94GCA_003293745contigncbi303380
66792Herminiimonas fonticola strain DSM 18555303380.4wgspatric303380
66792Herminiimonas fonticola DSM 185552802429731draftimg303380

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.522no
anaerobicno98.725yes
halophileno93.88no
spore-formingno94.938no
glucose-utilno76.836no
motileyes85.14no
flagellatedyes66.749no
aerobicyes94.282yes
thermophileno98.739yes
glucose-fermentno92.391no

External links

@ref: 7587

culture collection no.: CCUG 52513, DSM 18555, CIP 108398, LMG 22527

straininfo link

  • @ref: 80537
  • straininfo: 131987

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16156117Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water.Fernandes C, Rainey FA, Nobre MF, Pinhal I, Folhas F, da Costa MSSyst Appl Microbiol10.1016/j.syapm.2005.03.0132005Base Sequence, Fatty Acids/analysis, Genes, rRNA, Mineral Waters/*microbiology, Molecular Sequence Data, Oxalobacteraceae/chemistry/*classification/*isolation & purification/physiology, Portugal, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny16902005Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium.Muller D, Simeonova DD, Riegel P, Mangenot S, Koechler S, Lievremont D, Bertin PN, Lett MCInt J Syst Evol Microbiol10.1099/ijs.0.64308-02006Aerobiosis, Arsenites/*metabolism, Catalase/metabolism, Culture Media, DNA, Bacterial/genetics, Fatty Acids/analysis, Genome, Bacterial, Molecular Sequence Data, Nitrates/metabolism, Nucleic Acid Hybridization, Oxalobacteraceae/chemistry/*classification/isolation & purification/physiology, Oxidation-Reduction, Oxidoreductases/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Species SpecificityMetabolism
Phylogeny17978229Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock.Lang E, Swiderski J, Stackebrandt E, Schumann P, Sproer C, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.65163-02007Bacterial Typing Techniques, *Calcium Carbonate, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Lichens/growth & development/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/chemistry/*classification/genetics/isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, TurkeyGenetics
Phylogeny22447701Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals.Kampfer P, P Glaeser S, Lodders N, Busse HJ, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.039073-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, *Drug Contamination, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7587Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18555)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18555
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
33957Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6015
59574Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52513)https://www.ccug.se/strain?id=52513
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)
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
80537Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131987.1StrainInfo: A central database for resolving microbial strain identifiers
119418Curators of the CIPCollection of Institut Pasteur (CIP 108398)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108398