Strain identifier
BacDive ID: 140730
Type strain:
Species: Amylibacter cionae
Strain Designation: H-12
NCBI tax ID(s): 2035344 (species)
General
@ref: 43509
BacDive-ID: 140730
keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoautolithotroph, Gram-negative, rod-shaped, colony-forming
description: Amylibacter cionae H-12 is an aerobe, chemoautolithotroph, Gram-negative bacterium that forms circular colonies and was isolated from inner content of a sea squirt.
NCBI tax id
- NCBI tax id: 2035344
- Matching level: species
doi: 10.13145/bacdive140730.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Amylibacter
- species: Amylibacter cionae
- full scientific name: Amylibacter cionae Wang et al. 2017
@ref: 43509
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Amylibacter
species: Amylibacter cionae
strain designation: H-12
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43509 | negative | 1.5-2.2 µm | 0.6-1.1 µm | rod-shaped | no | |
69480 | negative | 99.996 |
colony morphology
- @ref: 43509
- colony color: light yellow
- colony shape: circular
- incubation period: 4 days
- medium used: MA agar
Culture and growth conditions
culture medium
- @ref: 43509
- name: Marine agar (MA)
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43509 | positive | growth | 10-35 | |
43509 | positive | optimum | 25-30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43509 | positive | growth | 6-9 | alkaliphile |
43509 | positive | optimum | 7-8 |
Physiology and metabolism
oxygen tolerance
- @ref: 43509
- oxygen tolerance: aerobe
nutrition type
- @ref: 43509
- type: chemoautolithotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43509 | NaCl | positive | growth | 1-6 %(w/v) |
43509 | NaCl | positive | optimum | 3-4 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43509 | 17128 | adipate | - | assimilation |
43509 | 27689 | decanoate | - | assimilation |
43509 | 16899 | D-mannitol | - | assimilation |
43509 | 16024 | D-mannose | - | assimilation |
43509 | 25115 | malate | - | assimilation |
43509 | 17234 | glucose | - | assimilation |
43509 | 30849 | L-arabinose | - | assimilation |
43509 | 17306 | maltose | - | assimilation |
43509 | 506227 | N-acetylglucosamine | - | assimilation |
43509 | 18401 | phenylacetate | - | assimilation |
43509 | 32032 | potassium gluconate | - | assimilation |
43509 | 53258 | sodium citrate | - | assimilation |
43509 | 16763 | 2-oxobutanoate | - | carbon source |
43509 | 73918 | 3-O-methyl-D-glucose | - | carbon source |
43509 | 18101 | 4-hydroxyphenylacetic acid | - | carbon source |
43509 | 30089 | acetate | - | carbon source |
43509 | 13705 | acetoacetate | - | carbon source |
43509 | 17925 | alpha-D-glucose | - | carbon source |
43509 | 36219 | alpha-lactose | - | carbon source |
43509 | 73706 | bromosuccinate | - | carbon source |
43509 | 17057 | cellobiose | - | carbon source |
43509 | 18333 | D-arabitol | - | carbon source |
43509 | 29990 | D-aspartate | - | carbon source |
43509 | 15824 | D-fructose | - | carbon source |
43509 | 28847 | D-fucose | - | carbon source |
43509 | 12936 | D-galactose | - | carbon source |
43509 | 18024 | D-galacturonic acid | - | carbon source |
43509 | 8391 | D-gluconate | - | carbon source |
43509 | 14314 | D-glucose 6-phosphate | - | carbon source |
43509 | 15748 | D-glucuronate | - | carbon source |
43509 | 16899 | D-mannitol | - | carbon source |
43509 | 16024 | D-mannose | - | carbon source |
43509 | 33801 | D-saccharate | - | carbon source |
43509 | 16523 | D-serine | - | carbon source |
43509 | 17924 | D-sorbitol | - | carbon source |
43509 | 23652 | dextrin | - | carbon source |
43509 | 15740 | formate | - | carbon source |
43509 | 16537 | galactarate | - | carbon source |
43509 | 16865 | gamma-aminobutyric acid | - | carbon source |
43509 | 5291 | gelatin | - | carbon source |
43509 | 28066 | gentiobiose | - | carbon source |
43509 | 17754 | glycerol | - | carbon source |
43509 | 70744 | glycine-proline | - | carbon source |
43509 | 17596 | inosine | - | carbon source |
43509 | 16467 | L-arginine | - | carbon source |
43509 | 29991 | L-aspartate | - | carbon source |
43509 | 18287 | L-fucose | - | carbon source |
43509 | 17464 | L-galactonic acid gamma-lactone | - | carbon source |
43509 | 18183 | L-pyroglutamic acid | - | carbon source |
43509 | 62345 | L-rhamnose | - | carbon source |
43509 | 17115 | L-serine | - | carbon source |
43509 | 25115 | malate | - | carbon source |
43509 | 17306 | maltose | - | carbon source |
43509 | 28053 | melibiose | - | carbon source |
43509 | 74611 | methyl (R)-lactate | - | carbon source |
43509 | 37657 | methyl D-glucoside | - | carbon source |
43509 | 51850 | methyl pyruvate | - | carbon source |
43509 | 17268 | myo-inositol | - | carbon source |
43509 | 63154 | N-acetyl-beta-D-mannosamine | - | carbon source |
43509 | 28037 | N-acetylgalactosamine | - | carbon source |
43509 | 506227 | N-acetylglucosamine | - | carbon source |
43509 | 35418 | n-acetylneuraminate | - | carbon source |
43509 | 17309 | pectin | - | carbon source |
43509 | 17272 | propionate | - | carbon source |
43509 | 26490 | quinate | - | carbon source |
43509 | 16634 | raffinose | - | carbon source |
43509 | 17814 | salicin | - | carbon source |
43509 | 17164 | stachyose | - | carbon source |
43509 | 17992 | sucrose | - | carbon source |
43509 | 27082 | trehalose | - | carbon source |
43509 | 32528 | turanose | - | carbon source |
43509 | 53423 | tween 40 | - | carbon source |
43509 | 16763 | 2-oxobutanoate | - | energy source |
43509 | 73918 | 3-O-methyl-D-glucose | - | energy source |
43509 | 18101 | 4-hydroxyphenylacetic acid | - | energy source |
43509 | 30089 | acetate | - | energy source |
43509 | 13705 | acetoacetate | - | energy source |
43509 | 17925 | alpha-D-glucose | - | energy source |
43509 | 36219 | alpha-lactose | - | energy source |
43509 | 73706 | bromosuccinate | - | energy source |
43509 | 17057 | cellobiose | - | energy source |
43509 | 18333 | D-arabitol | - | energy source |
43509 | 29990 | D-aspartate | - | energy source |
43509 | 15824 | D-fructose | - | energy source |
43509 | 28847 | D-fucose | - | energy source |
43509 | 12936 | D-galactose | - | energy source |
43509 | 18024 | D-galacturonic acid | - | energy source |
43509 | 8391 | D-gluconate | - | energy source |
43509 | 14314 | D-glucose 6-phosphate | - | energy source |
43509 | 15748 | D-glucuronate | - | energy source |
43509 | 16899 | D-mannitol | - | energy source |
43509 | 16024 | D-mannose | - | energy source |
43509 | 33801 | D-saccharate | - | energy source |
43509 | 16523 | D-serine | - | energy source |
43509 | 17924 | D-sorbitol | - | energy source |
43509 | 23652 | dextrin | - | energy source |
43509 | 15740 | formate | - | energy source |
43509 | 16537 | galactarate | - | energy source |
43509 | 16865 | gamma-aminobutyric acid | - | energy source |
43509 | 5291 | gelatin | - | energy source |
43509 | 28066 | gentiobiose | - | energy source |
43509 | 17754 | glycerol | - | energy source |
43509 | 70744 | glycine-proline | - | energy source |
43509 | 17596 | inosine | - | energy source |
43509 | 16467 | L-arginine | - | energy source |
43509 | 29991 | L-aspartate | - | energy source |
43509 | 18287 | L-fucose | - | energy source |
43509 | 17464 | L-galactonic acid gamma-lactone | - | energy source |
43509 | 18183 | L-pyroglutamic acid | - | energy source |
43509 | 62345 | L-rhamnose | - | energy source |
43509 | 17115 | L-serine | - | energy source |
43509 | 25115 | malate | - | energy source |
43509 | 17306 | maltose | - | energy source |
43509 | 28053 | melibiose | - | energy source |
43509 | 74611 | methyl (R)-lactate | - | energy source |
43509 | 37657 | methyl D-glucoside | - | energy source |
43509 | 51850 | methyl pyruvate | - | energy source |
43509 | 17268 | myo-inositol | - | energy source |
43509 | 63154 | N-acetyl-beta-D-mannosamine | - | energy source |
43509 | 28037 | N-acetylgalactosamine | - | energy source |
43509 | 506227 | N-acetylglucosamine | - | energy source |
43509 | 35418 | n-acetylneuraminate | - | energy source |
43509 | 17309 | pectin | - | energy source |
43509 | 17272 | propionate | - | energy source |
43509 | 26490 | quinate | - | energy source |
43509 | 16634 | raffinose | - | energy source |
43509 | 17814 | salicin | - | energy source |
43509 | 17164 | stachyose | - | energy source |
43509 | 17992 | sucrose | - | energy source |
43509 | 27082 | trehalose | - | energy source |
43509 | 32528 | turanose | - | energy source |
43509 | 53423 | tween 40 | - | energy source |
43509 | 17234 | glucose | - | fermentation |
43509 | casein | - | hydrolysis | |
43509 | 16991 | dna | - | hydrolysis |
43509 | 17895 | L-tyrosine | - | hydrolysis |
43509 | 28017 | starch | - | hydrolysis |
43509 | 53426 | tween 80 | - | hydrolysis |
43509 | 16199 | urea | - | hydrolysis |
43509 | 17632 | nitrate | - | reduction |
43509 | 64552 | 2-hydroxybutyrate | + | carbon source |
43509 | 30916 | 2-oxoglutarate | + | carbon source |
43509 | 37054 | 3-hydroxybutyrate | + | carbon source |
43509 | 16947 | citrate | + | carbon source |
43509 | 78697 | D-fructose 6-phosphate | + | carbon source |
43509 | 32323 | glucuronamide | + | carbon source |
43509 | 15971 | L-histidine | + | carbon source |
43509 | 24996 | lactate | + | carbon source |
43509 | 25115 | malate | + | carbon source |
43509 | 64552 | 2-hydroxybutyrate | + | energy source |
43509 | 30916 | 2-oxoglutarate | + | energy source |
43509 | 37054 | 3-hydroxybutyrate | + | energy source |
43509 | 16947 | citrate | + | energy source |
43509 | 78697 | D-fructose 6-phosphate | + | energy source |
43509 | 32323 | glucuronamide | + | energy source |
43509 | 15971 | L-histidine | + | energy source |
43509 | 24996 | lactate | + | energy source |
43509 | 25115 | malate | + | energy source |
43509 | 5291 | gelatin | + | hydrolysis |
43509 | 53424 | tween 20 | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43509 | catalase | + | 1.11.1.6 |
43509 | cytochrome oxidase | + | 1.9.3.1 |
43509 | arginine dihydrolase | - | 3.5.3.6 |
43509 | urease | - | 3.5.1.5 |
43509 | gelatinase | - | |
43509 | alkaline phosphatase | +/- | 3.1.3.1 |
43509 | esterase (C 4) | + | |
43509 | esterase Lipase (C 8) | + | |
43509 | lipase (C 14) | +/- | |
43509 | leucine arylamidase | + | 3.4.11.1 |
43509 | valine arylamidase | +/- | |
43509 | acid phosphatase | + | 3.1.3.2 |
43509 | cystine arylamidase | - | 3.4.11.3 |
43509 | trypsin | - | 3.4.21.4 |
43509 | alpha-chymotrypsin | - | 3.4.21.1 |
43509 | naphthol-AS-BI-phosphohydrolase | - | |
43509 | alpha-galactosidase | - | 3.2.1.22 |
43509 | beta-galactosidase | - | 3.2.1.23 |
43509 | beta-glucuronidase | - | 3.2.1.31 |
43509 | alpha-glucosidase | - | 3.2.1.20 |
43509 | beta-glucosidase | - | 3.2.1.21 |
43509 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43509 | alpha-mannosidase | - | 3.2.1.24 |
43509 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43509 11-methyl-C18:1ω7c 1.3 43509 C12:1 3OH 3.7 43509 C16:0 1.8 43509 C18:0 2.2 43509 C18:1ω7c 90.3 - type of FA analysis: whole cell analysis
- incubation medium: MA plates
- agar/liquid: agar
- incubation temperature: 25
- incubation time: 3
- incubation_oxygen: aerobic
- software version: Sherlock 6.0
- library/peak naming table: TSBA6
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
- @ref: 43509
- sample type: inner content of a sea squirt
- geographic location: Tsingtao Port, Jiaozhou Bay
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Host | #Invertebrates (Other) | #Tunicata |
taxonmaps
- @ref: 69479
- File name: preview.99_65988.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3523;97_4322;98_46572;99_65988&stattab=map
- Last taxonomy: Amylibacter cionae subclade
- 16S sequence: KX790330
- Sequence Identity:
- Total samples: 373
- soil counts: 8
- aquatic counts: 279
- animal counts: 86
Sequence information
16S sequences
- @ref: 43509
- description: 16S rRNA gene sequence
- accession: KX790330
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Amylibacter cionae CGMCC 1.15880 | GCA_014643735 | contig | ncbi | 2035344 |
66792 | Amylibacter cionae strain CGMCC 1.15880 | 2035344.4 | wgs | patric | 2035344 |
GC content
- @ref: 43509
- GC-content: 53.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.624 | yes |
gram-positive | no | 97.085 | yes |
anaerobic | no | 99.076 | yes |
aerobic | yes | 95.321 | yes |
halophile | yes | 85.35 | no |
spore-forming | no | 97.373 | no |
glucose-util | no | 55.614 | yes |
flagellated | no | 98.375 | no |
thermophile | no | 97.732 | yes |
glucose-ferment | no | 89.866 | yes |
External links
@ref: 43509
culture collection no.: KCTC 52581, CGMCC 1.15880
literature
- topic: Phylogeny
- Pubmed-ID: 28866998
- title: Amylibacter cionae sp. nov., isolated from the sea squirt Ciona savignyi.
- authors: Wang D, Wei Y, Cui Q, Li W
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002140
- year: 2017
- mesh: Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, Urochordata/*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 | ||
43509 | Dandan Wang, Yuxi Wei, Qiu Cui, Wenli Li | Amylibacter cionae sp. nov., isolated from the sea squirt Ciona savignyi | 10.1099/ijsem.0.002140 | IJSEM 67: 3462-3466 2017 | 28866998 |
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 |
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 |