Strain identifier
BacDive ID: 11304
Type strain:
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)
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
@ref | history |
---|---|
7587 | <- CIP <- C. Fernandes, Univ. de Coimbra |
119418 | CIP <- 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 96.94 | ||
69480 | 100 | negative | ||
119418 | no | negative | rod-shaped |
colony morphology
@ref | incubation period |
---|---|
59574 | 3 days |
119418 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7587 | HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) | yes | https://mediadive.dsmz.de/medium/428 | Name: 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 |
7587 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
33957 | MEDIUM 584 - for Herminiimonas fonticola | yes | Solution 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) | |
119418 | CIP Medium 584 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=584 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7587 | positive | growth | 28 | mesophilic |
7587 | positive | growth | 30 | mesophilic |
33957 | positive | growth | 30 | mesophilic |
59574 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
59574 | aerobe |
119418 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 100 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
119418 | 17632 | nitrate | - | reduction |
119418 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 119418
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
119418 | oxidase | + | |
119418 | alcohol dehydrogenase | - | 1.1.1.1 |
119418 | catalase | + | 1.11.1.6 |
119418 | lysine decarboxylase | - | 4.1.1.18 |
119418 | ornithine decarboxylase | - | 4.1.1.17 |
119418 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119418 | - | - | + | - | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date | geographic location | isolation date |
---|---|---|---|---|---|---|---|
7587 | bore hole of mineral water spring | Portugal | PRT | Europe | |||
59574 | Water,borehole mineral water | Portugal | PRT | Europe | 1997 | Serra da Estrela | |
119418 | Environment, Mineral water | Portugal | PRT | Europe | Serra da Esrela | 1997 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
7587 | 1 | Risk group (German classification) |
119418 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Herminiimonas fonticola gene for 16S rRNA, partial sequence, strain: da Costa S-94 | AB512142 | 1485 | ena | 303380 |
7587 | Herminiimonas fonticola 16S ribosomal RNA gene, partial sequence | AY676462 | 1426 | ena | 303380 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Herminiimonas fonticola DSM 18555 | GCA_004361795 | contig | ncbi | 303380 |
66792 | Herminiimonas fonticola S-94 | GCA_003293745 | contig | ncbi | 303380 |
66792 | Herminiimonas fonticola strain DSM 18555 | 303380.4 | wgs | patric | 303380 |
66792 | Herminiimonas fonticola DSM 18555 | 2802429731 | draft | img | 303380 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.522 | no |
anaerobic | no | 98.725 | yes |
halophile | no | 93.88 | no |
spore-forming | no | 94.938 | no |
glucose-util | no | 76.836 | no |
motile | yes | 85.14 | no |
flagellated | yes | 66.749 | no |
aerobic | yes | 94.282 | yes |
thermophile | no | 98.739 | yes |
glucose-ferment | no | 92.391 | no |
External links
@ref: 7587
culture collection no.: CCUG 52513, DSM 18555, CIP 108398, LMG 22527
straininfo link
- @ref: 80537
- straininfo: 131987
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16156117 | Herminiimonas 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 MS | Syst Appl Microbiol | 10.1016/j.syapm.2005.03.013 | 2005 | Base Sequence, Fatty Acids/analysis, Genes, rRNA, Mineral Waters/*microbiology, Molecular Sequence Data, Oxalobacteraceae/chemistry/*classification/*isolation & purification/physiology, Portugal, RNA, Ribosomal, 16S/genetics | Genetics |
Phylogeny | 16902005 | Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium. | Muller D, Simeonova DD, Riegel P, Mangenot S, Koechler S, Lievremont D, Bertin PN, Lett MC | Int J Syst Evol Microbiol | 10.1099/ijs.0.64308-0 | 2006 | Aerobiosis, 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 Specificity | Metabolism |
Phylogeny | 17978229 | Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock. | Lang E, Swiderski J, Stackebrandt E, Schumann P, Sproer C, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.65163-0 | 2007 | Bacterial 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, Turkey | Genetics |
Phylogeny | 22447701 | Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals. | Kampfer P, P Glaeser S, Lodders N, Busse HJ, Falsen E | Int J Syst Evol Microbiol | 10.1099/ijs.0.039073-0 | 2012 | Bacterial 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/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7587 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18555) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18555 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
33957 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6015 | ||||
59574 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 52513) | https://www.ccug.se/strain?id=52513 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
80537 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131987.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119418 | Curators of the CIP | Collection of Institut Pasteur (CIP 108398) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108398 |