Strain identifier
BacDive ID: 3935
Type strain:
Species: Barrientosiimonas humi
Strain Designation: 39
Strain history: CGMCC 4.6864 <-- L.-H. Lee 39.
NCBI tax ID(s): 999931 (species)
General
@ref: 17717
BacDive-ID: 3935
DSM-Number: 24617
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped
description: Barrientosiimonas humi 39 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Antarctic soil, upper top soil layer.
NCBI tax id
- NCBI tax id: 999931
- Matching level: species
strain history
@ref | history |
---|---|
17717 | <- L.-H. Lee, Universiti Putra Malaysia, Dept. Biomedical Science, Faculty Medicine and Health Scs.; strain 39 |
67770 | CGMCC 4.6864 <-- L.-H. Lee 39. |
doi: 10.13145/bacdive3935.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Dermacoccaceae
- genus: Barrientosiimonas
- species: Barrientosiimonas humi
- full scientific name: Barrientosiimonas humi Lee et al. 2013
@ref: 17717
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Dermacoccaceae
genus: Barrientosiimonas
species: Barrientosiimonas humi
full scientific name: Barrientosiimonas humi Lee et al. 2013
strain designation: 39
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30533 | positive | 1.25 µm | 0.315 µm | coccus-shaped | no | |
69480 | no | 97.517 | ||||
69480 | positive | 100 |
pigmentation
- @ref: 30533
- production: yes
Culture and growth conditions
culture medium
- @ref: 17717
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17717 | positive | growth | 28 | mesophilic |
30533 | positive | growth | 24-40 | |
30533 | positive | optimum | 32 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30533 | positive | growth | 06-10 | alkaliphile |
30533 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 30533
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30533 | no | |
69480 | no | 99.967 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30533 | NaCl | positive | growth | 0-14 % |
30533 | NaCl | positive | optimum | 2 % |
murein
- @ref: 17717
- murein short key: A11.36
- type: A4alpha L-Lys-L-Ser-D-Asp
observation
@ref | observation |
---|---|
30533 | aggregates in chains |
67770 | quinones: MK-8(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30533 | 30089 | acetate | + | carbon source |
30533 | 16449 | alanine | + | carbon source |
30533 | 22599 | arabinose | + | carbon source |
30533 | 29016 | arginine | + | carbon source |
30533 | 23652 | dextrin | + | carbon source |
30533 | 28757 | fructose | + | carbon source |
30533 | 28260 | galactose | + | carbon source |
30533 | 24265 | gluconate | + | carbon source |
30533 | 17234 | glucose | + | carbon source |
30533 | 29987 | glutamate | + | carbon source |
30533 | 17754 | glycerol | + | carbon source |
30533 | 27570 | histidine | + | carbon source |
30533 | 17306 | maltose | + | carbon source |
30533 | 37684 | mannose | + | carbon source |
30533 | 28053 | melibiose | + | carbon source |
30533 | 28044 | phenylalanine | + | carbon source |
30533 | 51850 | methyl pyruvate | + | carbon source |
30533 | 16634 | raffinose | + | carbon source |
30533 | 33942 | ribose | + | carbon source |
30533 | 17814 | salicin | + | carbon source |
30533 | 17822 | serine | + | carbon source |
30533 | 17992 | sucrose | + | carbon source |
30533 | 16296 | D-tryptophan | + | carbon source |
30533 | 53423 | tween 40 | + | carbon source |
30533 | 53426 | tween 80 | + | carbon source |
30533 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30533 | catalase | + | 1.11.1.6 |
30533 | gelatinase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent | latitude | longitude |
---|---|---|---|---|---|
17717 | Antarctic soil, upper top soil layer | Barrientos Island (62°24' 26.0'' S 59° 44' 49.1'' W) | Australia and Oceania | -62.4072 | -59.747 |
67770 | Soil from Barrientos Island in the Antarctic |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Condition | #Psychrophilic (<10°C) | |
#Climate | #Cold | #Polar |
taxonmaps
- @ref: 69479
- File name: preview.99_11725.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_844;97_986;98_8794;99_11725&stattab=map
- Last taxonomy: Barrientosiimonas
- 16S sequence: JF346171
- Sequence Identity:
- Total samples: 1666
- soil counts: 161
- aquatic counts: 155
- animal counts: 1304
- plant counts: 46
Safety information
risk assessment
- @ref: 17717
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17717
- description: Barrientosiimonas humi strain 39 16S ribosomal RNA gene, partial sequence
- accession: JF346171
- length: 1495
- database: ena
- NCBI tax ID: 999931
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Barrientosiimonas humi strain DSM 24617 | 999931.3 | wgs | patric | 999931 |
66792 | Barrientosiimonas humi DSM 24617 | 2814122977 | draft | img | 999931 |
67770 | Barrientosiimonas humi DSM 24617 | GCA_006716095 | contig | ncbi | 999931 |
GC content
@ref | GC-content | method |
---|---|---|
17717 | 68.4 | high performance liquid chromatography (HPLC) |
30533 | 68.4 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 57 | no |
motile | no | 94.402 | yes |
flagellated | no | 97.427 | yes |
gram-positive | yes | 91.538 | yes |
anaerobic | no | 98.852 | no |
halophile | no | 88.842 | no |
spore-forming | no | 84.953 | yes |
thermophile | no | 98.064 | no |
glucose-util | yes | 88.86 | yes |
aerobic | yes | 93.763 | no |
glucose-ferment | no | 89.62 | no |
External links
@ref: 17717
culture collection no.: DSM 24617, CGMCC 4.6864, JCM 19663
straininfo link
- @ref: 73444
- straininfo: 401745
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22389286 | Barrientosiimonas humi gen. nov., sp. nov., an actinobacterium of the family Dermacoccaceae. | Lee LH, Cheah YK, Sidik SM, Xie QY, Tang YL, Lin HP, Mutalib NA, Hong K | Int J Syst Evol Microbiol | 10.1099/ijs.0.038232-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Phylogeny | 26060216 | Barrientosiimonas endolithica sp. nov., isolated from pebbles, reclassification of the only species of the genus Tamlicoccus, Tamlicoccus marinus Lee 2013, as Barrientosiimonas marina comb. nov. and emended description of the genus Barrientosiimonas. | Parag B, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijs.0.000374 | 2015 | *Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Lysine, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17717 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24617) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24617 | ||||
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 | ||||
30533 | 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 | 26865 | 28776041 | ||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
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) | ||||
73444 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401745.1 | StrainInfo: A central database for resolving microbial strain identifiers |