Strain identifier
BacDive ID: 1229
Type strain: 
Species: Alkalihalobacillus macyae
Strain Designation: JMM-4
Strain history: <- J. M. Santini, La Trobe University, Victoria, Australia; JMM-4
NCBI tax ID(s): 157733 (species)
version 8.1 (current version)
General
@ref: 6397
BacDive-ID: 1229
DSM-Number: 16346
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Alkalihalobacillus macyae JMM-4 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from arsenic-contaminated mud.
NCBI tax id
- NCBI tax id: 157733
- Matching level: species
strain history
- @ref: 6397
- history: <- J. M. Santini, La Trobe University, Victoria, Australia; JMM-4
doi: 10.13145/bacdive1229.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Alkalihalobacillus
- species: Alkalihalobacillus macyae
- full scientific name: Alkalihalobacillus macyae (Santini et al. 2004) Patel and Gupta 2020
synonyms
@ref synonym 20215 Pseudalkalibacillus macyae 20215 Anaerobacillus macyae 20215 Bacillus macyae
@ref: 6397
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Alkalihalobacillus
species: Alkalihalobacillus macyae
full scientific name: Alkalihalobacillus macyae (Santini et al. 2004) Patel and Gupta 2020
strain designation: JMM-4
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31214 | positive | 2.75 µm | 0.6 µm | rod-shaped | yes | |
| 69480 | yes | 94.262 | ||||
| 69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 6397
- name: CHRYSIOGENES MEDIUM (DSMZ Medium 818)
- growth: yes
- link: https://mediadive.dsmz.de/medium/818
- composition: Name: CHRYSIOGENES MEDIUM (DSMZ Medium 818; with strain-specific modifications) Composition: NaCl 1.19641 g/l Na-(L)-lactate 1.09671 g/l Yeast extract 0.797607 g/l NaHCO3 0.598205 g/l KNO3 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l NH4Cl 0.299103 g/l KCl 0.299103 g/l Na2SO4 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l Na2-EDTA x 2 H2O 0.00518445 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l Nicotinic acid 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Calcium pantothenate 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6397 | positive | growth | 30 | mesophilic |
| 31214 | positive | growth | 28-37 | mesophilic |
| 31214 | positive | optimum | 32.5 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31214 | positive | growth | 7-8.4 |
| 31214 | positive | optimum | 7.8 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 6397 | anaerobe |
| 31214 | anaerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31214 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 100 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31214 | NaCl | positive | growth | 1.2-30 % |
| 31214 | NaCl | positive | optimum | 1.2 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31214 | 30089 | acetate | + | carbon source |
| 31214 | 29987 | glutamate | + | carbon source |
| 31214 | 24996 | lactate | + | carbon source |
| 31214 | 15361 | pyruvate | + | carbon source |
| 31214 | 30031 | succinate | + | carbon source |
| 31214 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 31214
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 6397
- sample type: arsenic-contaminated mud
- geographic location: Bendigo, Victoria
- country: Australia
- origin.country: AUS
- continent: Australia and Oceania
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Heavy metal |
| #Environmental | #Terrestrial | #Mud (Sludge) |
Safety information
risk assessment
- @ref: 6397
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6397
- description: Bacillus macyae strain JMM-4 16S ribosomal RNA gene, partial sequence
- accession: AY032601
- length: 1512
- database: ena
- NCBI tax ID: 157733
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Alkalihalobacillus macyae DSM 16346 | GCA_001039475 | scaffold | ncbi | 157733 |
| 66792 | Anaerobacillus macyae strain DSM 16346 | 157733.5 | wgs | patric | 157733 |
| 66792 | Anaerobacillus macyae DSM 16346 | 2630968384 | draft | img | 157733 |
GC content
- @ref: 6397
- GC-content: 37
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 79.818 | no |
| flagellated | no | 55.208 | no |
| gram-positive | yes | 81.411 | no |
| anaerobic | no | 98.282 | yes |
| aerobic | yes | 92.664 | no |
| halophile | yes | 82.563 | no |
| spore-forming | yes | 92.166 | no |
| glucose-util | yes | 91.486 | no |
| thermophile | no | 97.926 | no |
| glucose-ferment | no | 93.108 | no |
External links
@ref: 6397
culture collection no.: DSM 16346, CIP 108766, JCM 12340
straininfo link
- @ref: 70885
- straininfo: 134415
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15545465 | Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine. | Santini JM, Streimann ICA, Hoven RNV | Int J Syst Evol Microbiol | 10.1099/ijs.0.63059-0 | 2004 | Acetates/metabolism, Anaerobiosis, Arsenates/*metabolism, Arsenite Transporting ATPases, Arsenites/metabolism, Australia, Bacillus/*classification/cytology/*isolation & purification/metabolism, Bacterial Proteins/isolation & purification/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Enzyme Induction, Enzyme Stability, Genes, rRNA, Gentian Violet, Gold, Hydrogen-Ion Concentration, Ion Pumps/metabolism, Membrane Proteins/metabolism, *Mining, Molecular Sequence Data, Molecular Weight, Movement, Multienzyme Complexes/metabolism, Nitrates/metabolism, Nucleic Acid Hybridization, Oxidation-Reduction, Phenazines, Phylogeny, Protein Subunits/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Metabolism |
| Genetics | 26272580 | Genome Sequence of Anaerobacillus macyae JMM-4T (DSM 16346), the First Genomic Information of the Newly Established Genus Anaerobacillus. | Wang JP, Liu B, Liu GH, Ge CB, Chen QQ, Zhu YJ, Chen Z | Genome Announc | 10.1128/genomeA.00922-15 | 2015 | ||
| Phylogeny | 29580368 | Anaerobacillus isosaccharinicus sp. nov., an alkaliphilic bacterium which degrades isosaccharinic acid. | Bassil NM, Lloyd JR | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002721 | 2019 | Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sugar Acids/*metabolism | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 6397 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16346) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16346 | ||||
| 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 | ||||
| 31214 | 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 | 27540 | 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 | ||
| 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 | ||||
| 70885 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134415.1 | StrainInfo: A central database for resolving microbial strain identifiers |