Strain identifier
BacDive ID: 23707
Type strain:
Species: Halalkalibacter nanhaiisediminis
Strain Designation: NH3
Strain history: J. Zhang NH3.
NCBI tax ID(s): 688079 (species)
General
@ref: 20435
BacDive-ID: 23707
DSM-Number: 27953
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Halalkalibacter nanhaiisediminis NH3 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediment.
NCBI tax id
- NCBI tax id: 688079
- Matching level: species
strain history
@ref | history |
---|---|
20435 | <- JCM <- J. Zhang; NH3 |
67770 | J. Zhang NH3. |
doi: 10.13145/bacdive23707.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Halalkalibacter
- species: Halalkalibacter nanhaiisediminis
- full scientific name: Halalkalibacter nanhaiisediminis (Zhang et al. 2011) Joshi et al. 2022
synonyms
@ref synonym 20215 Alkalihalobacillus nanhaiisediminis 20215 Bacillus nanhaiisediminis
@ref: 20435
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Bacillaceae
genus: Halalkalibacter
species: Halalkalibacter nanhaiisediminis
full scientific name: Halalkalibacter nanhaiisediminis (Zhang et al. 2011) Joshi et al. 2022
strain designation: NH3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29877 | positive | 1.9 µm | 0.6 µm | rod-shaped | yes | |
69480 | yes | 96.892 | ||||
69480 | positive | 100 |
pigmentation
- @ref: 29877
- production: yes
Culture and growth conditions
culture medium
- @ref: 20435
- name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
- growth: yes
- link: https://mediadive.dsmz.de/medium/220
- composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20435 | positive | growth | 30 | mesophilic |
29877 | positive | growth | 10-43 | |
29877 | positive | optimum | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29877 | positive | growth | 6.5-10 | alkaliphile |
29877 | positive | optimum | 9 |
Physiology and metabolism
oxygen tolerance
- @ref: 29877
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
29877 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
halophily
- @ref: 29877
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-11 %
observation
@ref | observation |
---|---|
29877 | aggregates in clumps |
67770 | quinones: MK-7 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29877 | 30089 | acetate | + | carbon source |
29877 | 22599 | arabinose | + | carbon source |
29877 | 17057 | cellobiose | + | carbon source |
29877 | 28260 | galactose | + | carbon source |
29877 | 5417 | glucosamine | + | carbon source |
29877 | 17234 | glucose | + | carbon source |
29877 | 17754 | glycerol | + | carbon source |
29877 | 17306 | maltose | + | carbon source |
29877 | 29864 | mannitol | + | carbon source |
29877 | 37684 | mannose | + | carbon source |
29877 | 28053 | melibiose | + | carbon source |
29877 | 15361 | pyruvate | + | carbon source |
29877 | 16634 | raffinose | + | carbon source |
29877 | 26546 | rhamnose | + | carbon source |
29877 | 30911 | sorbitol | + | carbon source |
29877 | 30031 | succinate | + | carbon source |
29877 | 27082 | trehalose | + | carbon source |
29877 | 16199 | urea | + | carbon source |
29877 | 17151 | xylitol | + | carbon source |
29877 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 29877
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 29877
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
29877 | catalase | + | 1.11.1.6 |
29877 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent |
---|---|---|---|
20435 | sediment | South China Sea | Asia |
67770 | Sediment sample collected from the South China Sea |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Sediment |
#Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_60426.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2523;97_33372;98_42890;99_60426&stattab=map
- Last taxonomy: Alkalihalobacillus nanhaiisediminis subclade
- 16S sequence: GQ292773
- Sequence Identity:
- Total samples: 1840
- soil counts: 517
- aquatic counts: 594
- animal counts: 650
- plant counts: 79
Safety information
risk assessment
- @ref: 20435
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20435
- description: Bacillus nanhaiisediminis 16S ribosomal RNA gene, partial sequence
- accession: GQ292773
- length: 1419
- database: ena
- NCBI tax ID: 688079
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halalkalibacter nanhaiisediminis CGMCC 1.10116 | GCA_007830185 | scaffold | ncbi | 688079 |
66792 | Bacillus nanhaiisediminis strain CGMCC 1.10116 | 688079.3 | wgs | patric | 688079 |
66792 | Bacillus nanhaiisediminis CGMCC 1.10116 | 2596583586 | draft | img | 688079 |
GC content
@ref | GC-content | method |
---|---|---|
20435 | 40.3 | thermal denaturation, midpoint method (Tm) |
29877 | 40.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 91.491 | yes |
flagellated | yes | 86.909 | no |
gram-positive | yes | 89.146 | yes |
anaerobic | no | 98.136 | no |
aerobic | yes | 90.227 | no |
halophile | yes | 67.065 | no |
spore-forming | yes | 94.279 | yes |
thermophile | no | 97.91 | no |
glucose-util | yes | 89.811 | yes |
glucose-ferment | no | 93.938 | no |
External links
@ref: 20435
culture collection no.: DSM 27953, CGMCC 1.10116, JCM 16507
straininfo link
- @ref: 87753
- straininfo: 401112
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20525818 | Bacillus nanhaiisediminis sp. nov., an alkalitolerant member of Bacillus rRNA group 6. | Zhang J, Wang J, Song F, Fang C, Xin Y, Zhang Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.023671-0 | 2010 | Alkalies/*metabolism, Bacillus/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/*genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Metabolism |
Phylogeny | 24554634 | Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea. | Zhu D, Tanabe SH, Xie C, Honda D, Sun J, Ai L | Int J Syst Evol Microbiol | 10.1099/ijs.0.058610-0 | 2014 | Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology | Genetics |
Phylogeny | 26604103 | Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils. | Dou G, Liu H, He W, Ma Y | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0616-y | 2015 | Bacillus/*classification/genetics/*isolation & purification/metabolism, Base Sequence, Cell Wall/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/metabolism, Fatty Acids/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/metabolism, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism/pharmacology, Soil/chemistry, *Soil Microbiology | Metabolism |
Phylogeny | 26971318 | Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye. | Hirota K, Aino K, Yumoto I | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001015 | 2016 | Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Indigo Carmine/*chemistry, Nucleic Acid Hybridization, *Phylogeny, Polygonum/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||||
20435 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27953 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27953) | ||||
29877 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26251 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
87753 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID401112.1 |