Strain identifier
BacDive ID: 11307
Type strain:
Species: Herminiimonas glaciei
Strain Designation: UMB49
Strain history: <- J. Loveland-Curtze, Pennsylvania University <- V. I. Miteva, Pennsylvania University
NCBI tax ID(s): 523788 (species)
General
@ref: 15563
BacDive-ID: 11307
DSM-Number: 21140
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Herminiimonas glaciei UMB49 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from ice core of Greenland Glacier at 3042 m depth.
NCBI tax id
- NCBI tax id: 523788
- Matching level: species
strain history
- @ref: 15563
- history: <- J. Loveland-Curtze, Pennsylvania University <- V. I. Miteva, Pennsylvania University
doi: 10.13145/bacdive11307.20230509.8.1
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 glaciei
- full scientific name: Herminiimonas glaciei Loveland-Curtze et al. 2009
@ref: 15563
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Herminiimonas
species: Herminiimonas glaciei
full scientific name: Herminiimonas glaciei Loveland-Curtze et al. 2009
strain designation: UMB49
type strain: yes
Morphology
cell morphology
- @ref: 28924
- gram stain: negative
- cell length: 0.7 µm
- cell width: 0.35 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 28924
- production: yes
Culture and growth conditions
culture medium
- @ref: 15563
- name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1a
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15563 | positive | growth | 28 | mesophilic |
28924 | positive | growth | 01-35 | |
28924 | positive | optimum | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 28924
- oxygen tolerance: aerobe
spore formation
- @ref: 28924
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
28924 | 16449 | alanine | + | carbon source |
28924 | 22599 | arabinose | + | carbon source |
28924 | 16947 | citrate | + | carbon source |
28924 | 33984 | fucose | + | carbon source |
28924 | 28260 | galactose | + | carbon source |
28924 | 24996 | lactate | + | carbon source |
28924 | 25115 | malate | + | carbon source |
28924 | 33942 | ribose | + | carbon source |
28924 | 30031 | succinate | + | carbon source |
28924 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
28924 | catalase | + | 1.11.1.6 |
28924 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
15563 | ice core of Greenland Glacier at 3042 m depth | Greenland | GRL | North America |
62136 | Ice core of Greenland glacier at 3042 m depth | Greenland | GRL | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Glacier |
#Environmental | #Aquatic | #Ice |
#Environmental | #Terrestrial | #Core sample |
taxonmaps
- @ref: 69479
- File name: preview.99_5056.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_2343;97_2853;98_3549;99_5056&stattab=map
- Last taxonomy: Herminiimonas
- 16S sequence: EU489741
- Sequence Identity:
- Total samples: 2485
- soil counts: 780
- aquatic counts: 491
- animal counts: 395
- plant counts: 819
Safety information
risk assessment
- @ref: 15563
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15563
- description: Herminiimonas glaciei strain UMB49 16S ribosomal RNA gene, partial sequence
- accession: EU489741
- length: 1434
- database: ena
- NCBI tax ID: 523788
GC content
@ref | GC-content | method |
---|---|---|
15563 | 59.0 | thermal denaturation, midpoint method (Tm) |
28924 | 59 |
External links
@ref: 15563
culture collection no.: DSM 21140, ATCC BAA 1623, CCUG 59859
straininfo link
- @ref: 80540
- straininfo: 408231
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19502300 | Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice. | Loveland-Curtze J, Miteva VI, Brenchley JE | Int J Syst Evol Microbiol | 10.1099/ijs.0.001685-0 | 2009 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genotype, Greenland, *Ice, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 20370834 | Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of Oxalicibacterium solurbis sp. nov. | Sahin N, Gonzalez JM, Iizuka T, Hill JE | FEMS Microbiol Lett | 10.1111/j.1574-6968.2010.01954.x | 2010 | Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Chaperones/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | 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 |
Phylogeny | 29101383 | Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans. | Koh HW, Hur M, Kang MS, Ku YB, Ghai R, Park SJ | Sci Rep | 10.1038/s41598-017-15164-4 | 2017 | Bacterial Typing Techniques, DNA, Bacterial/*genetics, Oxalobacteraceae/genetics/*physiology, *Phylogeny, *RNA, Ribosomal, 16S |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15563 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21140) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21140 | |||
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 | |||
28924 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25363 | 28776041 | |
62136 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 59859) | https://www.ccug.se/strain?id=59859 | |||
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 | |||
80540 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408231.1 | StrainInfo: A central database for resolving microbial strain identifiers |