Strain identifier
BacDive ID: 141038
Type strain: 
Species: Halobacterium litoreum
Strain Designation: ZS-54-S2
Strain history: H.-L. Cui ZS-54-S2.
NCBI tax ID(s): 2039234 (species)
version 8.1 (current version)
General
@ref: 43918
BacDive-ID: 141038
keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Halobacterium litoreum ZS-54-S2 is a mesophilic, Gram-negative, motile archaeon that forms circular colonies and was isolated from sediment of Zhoushan marine solar saltern, Zhejiang Province, China.
NCBI tax id
- NCBI tax id: 2039234
- Matching level: species
strain history
- @ref: 67770
- history: H.-L. Cui ZS-54-S2.
doi: 10.13145/bacdive141038.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Halobacteriales
- family: Halobacteriaceae
- genus: Halobacterium
- species: Halobacterium litoreum
- full scientific name: Halobacterium litoreum Lü et al. 2017
@ref: 43918
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halobacteriaceae
genus: Halobacterium
species: Halobacterium litoreum
strain designation: ZS-54-S2
type strain: yes
Morphology
cell morphology
- @ref: 43918
- gram stain: negative
- cell length: 0.8-2.0 µm
- cell width: 0.4-0.5 µm
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 43918
- colony color: red
- colony shape: circular
- medium used: Neutral haloarchaeal medium
Culture and growth conditions
culture medium
- @ref: 43918
- name: Neutral haloarchaeal medium
- growth: yes
- composition: supplemented with 3.9 M NaCl, yeast extract 0.05 g/L, fish peptone 0.25 g/L, sodium pyruvate 1.0 g/L, KCl 5.4 g/L, K2HPO4 0.3 g/L, CaCl2 0.29 g/L, NH4Cl 0.27 g/L, MgSO4.7H2O 26.8 g/L, MgCl2.6H2O 23.0 g/L, NaCl 184.0 g/L, pH 7.0–7.2
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 43918 | positive | optimum | 35 | mesophilic |
| 43918 | positive | growth | 20-50 | |
| 67770 | positive | growth | 37 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 43918 | positive | optimum | 7 | |
| 43918 | positive | growth | 5.0-9.5 | alkaliphile |
Physiology and metabolism
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 43918 | NaCl | positive | optimum | 3.9 M |
| 43918 | NaCl | positive | growth | 1.7-4.8 M |
| 43918 | MgCl2 | positive | optimum | 0.05 M |
| 43918 | MgCl2 | positive | growth | 0.005-1 M |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43918 | 16947 | citrate | - | carbon source |
| 43918 | 15824 | D-fructose | - | carbon source |
| 43918 | 12936 | D-galactose | - | carbon source |
| 43918 | 17634 | D-glucose | - | carbon source |
| 43918 | 16899 | D-mannitol | - | carbon source |
| 43918 | 16024 | D-mannose | - | carbon source |
| 43918 | 16988 | D-ribose | - | carbon source |
| 43918 | 17924 | D-sorbitol | - | carbon source |
| 43918 | 65327 | D-xylose | - | carbon source |
| 43918 | 24996 | lactate | - | carbon source |
| 43918 | 15428 | glycine | - | carbon source |
| 43918 | 16977 | L-alanine | - | carbon source |
| 43918 | 16467 | L-arginine | - | carbon source |
| 43918 | 29991 | L-aspartate | - | carbon source |
| 43918 | 29985 | L-glutamate | - | carbon source |
| 43918 | 18019 | L-lysine | - | carbon source |
| 43918 | 15589 | L-malate | - | carbon source |
| 43918 | 15729 | L-ornithine | - | carbon source |
| 43918 | 17266 | L-sorbose | - | carbon source |
| 43918 | 17716 | lactose | - | carbon source |
| 43918 | 17306 | maltose | - | carbon source |
| 43918 | 28017 | starch | - | carbon source |
| 43918 | 30031 | succinate | - | carbon source |
| 43918 | casein | - | hydrolysis | |
| 43918 | 28017 | starch | - | hydrolysis |
| 43918 | 53426 | tween 80 | - | hydrolysis |
| 43918 | 17632 | nitrate | + | builds gas from |
| 43918 | 30089 | acetate | + | carbon source |
| 43918 | 29806 | fumarate | + | carbon source |
| 43918 | 17754 | glycerol | + | carbon source |
| 43918 | 15361 | pyruvate | + | carbon source |
| 43918 | 17992 | sucrose | + | carbon source |
| 43918 | 5291 | gelatin | + | hydrolysis |
| 43918 | 17632 | nitrate | + | reduction |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
|---|---|---|---|---|---|---|---|
| 43918 | 28368 | novobiocin | yes | yes | 30 µg (disc) | ||
| 43918 | 28669 | bacitracin | yes | yes | 0.04 Unit (disc) | ||
| 43918 | 7660 | nystatin | yes | yes | 100 µg (disc) | ||
| 43918 | 28077 | rifampicin | yes | yes | 5 µg (disc) | ||
| 43918 | 71415 | nitrofurantoin | yes | yes | 300 µg (disc) | ||
| 43918 | 45924 | trimethoprim | yes | yes | 5 µg (disc) | ||
| 43918 | 48923 | erythromycin | yes | yes | 15 µg (disc) | ||
| 43918 | 18208 | penicillin g | yes | yes | 10 Unit (disc) | ||
| 43918 | 28971 | ampicillin | yes | yes | 10 µg (disc) | ||
| 43918 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | ||
| 43918 | 7507 | neomycin | yes | yes | 30 µg (disc) | ||
| 43918 | 100246 | norfloxacin | yes | yes | 10 µg (disc) | ||
| 43918 | 100241 | ciprofloxacin | yes | yes | 5 µg (disc) | ||
| 43918 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
| 43918 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
| 43918 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
| 43918 | 28001 | vancomycin | yes | yes | 30 µg (disc) | ||
| 43918 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
| 43918 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) |
metabolite production
| @ref | Chebi-ID | metabolite | production |
|---|---|---|---|
| 43918 | 16136 | hydrogen sulfide | yes |
| 43918 | 35581 | indole | yes |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 43918 | catalase | + | 1.11.1.6 |
| 43918 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
|---|---|---|---|---|---|---|---|---|---|
| 43918 | sediment of Zhoushan marine solar saltern, Zhejiang Province, China | Zhejiang Province | China | CHN | Asia | Neutral haloarchaeal medium | yeast extract 0.05 g/L, fish peptone 0.25 g/L, sodium pyruvate 1.0 g/L, KCl 5.4 g/L, K2HPO4 0.3 g/L, CaCl2 0.29 g/L, NH4Cl 0.27 g/L, MgSO4.7H2O 26.8 g/L, MgCl2.6H2O 23.0 g/L, NaCl 184.0 g/L, pH 7.0–7.2 | 4 weeks | 37 |
| 67770 | Sediment of Zhoushan marine solar saltern | Zhejiang Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Condition | #Saline | |
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_189164.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17654;96_69406;97_90647;98_123200;99_189164&stattab=map
- Last taxonomy: Halobacterium
- 16S sequence: KC918831
- Sequence Identity:
- Total samples: 66
- soil counts: 4
- aquatic counts: 60
- animal counts: 2
Sequence information
16S sequences
- @ref: 43918
- description: 16S rRNA gene sequence
- accession: KC918831
- database: nuccore
Genome sequences
- @ref: 66792
- description: Halobacterium litoreum ZS-54-S2
- accession: GCA_021233415
- assembly level: complete
- database: ncbi
- NCBI tax ID: 2039234
GC content
- @ref: 67770
- GC-content: 66.7
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 95.701 | no |
| gram-positive | no | 96.441 | yes |
| anaerobic | no | 96.271 | no |
| aerobic | yes | 86.143 | no |
| halophile | yes | 90.978 | no |
| spore-forming | no | 95.11 | no |
| motile | no | 61.008 | yes |
| thermophile | no | 86.92 | yes |
| glucose-util | yes | 86.126 | no |
| glucose-ferment | no | 87.554 | no |
External links
@ref: 43918
culture collection no.: CGMCC 1.12562, JCM 30038
literature
- topic: Phylogeny
- Pubmed-ID: 28901903
- title: Halobacterium litoreum sp. nov., isolated from a marine solar saltern.
- authors: Lu ZZ, Li Y, Zhou Y, Cui HL, Li ZR
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002259
- year: 2017
- mesh: Base Composition, China, DNA, Archaeal/genetics, Genes, Archaeal, Glycolipids/analysis, Halobacterium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, *Water Microbiology
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | journal | pubmed |
|---|---|---|---|---|---|
| 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 | ||
| 43918 | Zhen-Zhen Lü, Yang Li, Yao Zhou, Heng-Lin Cui, Zheng-Rong Li | Halobacterium litoreum sp. nov., isolated from a marine solar saltern | 10.1099/ijsem.0.002259 | IJSEM 67: 4095-4099 2017 | 28901903 |
| 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 | ||
| 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/ |