Strain identifier
BacDive ID: 158784
Type strain:
Species: Adhaeribacter swui
Strain Designation: 17mud1-7
Strain history: <- Myung Kyum Kim, Seoul Womens Univ., Korea
NCBI tax ID(s): 2086471 (species)
General
@ref: 65538
BacDive-ID: 158784
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Adhaeribacter swui 17mud1-7 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from wet mud.
NCBI tax id
- NCBI tax id: 2086471
- Matching level: species
strain history
- @ref: 67771
- history: <- Myung Kyum Kim, Seoul Womens Univ., Korea
doi: 10.13145/bacdive158784.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Hymenobacteraceae
- genus: Adhaeribacter
- species: Adhaeribacter swui
- full scientific name: Adhaeribacter swui Kim et al. 2018
@ref: 65538
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Adhaeribacter
species: Adhaeribacter swui
strain designation: 17mud1-7
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
65538 | negative | 2.0-2.5 µm | 0.5-1.0 µm | rod-shaped | no | |
67771 | rod-shaped | no | ||||
67771 | negative | |||||
69480 | negative | 99.999 |
colony morphology
- @ref: 65538
- colony color: pink
- colony shape: circular
- medium used: R2A
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
65538 | Trypticase Soy Agar (TSA) | yes |
65538 | Reasoner's 2A agar (R2A) | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65538 | positive | growth | 18-37 | |
65538 | positive | optimum | 28 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
65538 | positive | growth | 6.0-8.0 |
65538 | positive | optimum | 7.0 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
65538 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69480 | no | 99.855 |
69481 | no | 100 |
halophily
- @ref: 65538
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %(w/v)
observation
@ref | observation |
---|---|
65538 | UV-C radiation resistance |
67771 | quinones: MK-7 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65538 | 17128 | adipate | - | assimilation |
65538 | 27689 | decanoate | - | assimilation |
65538 | 17634 | D-glucose | + | assimilation |
65538 | 16899 | D-mannitol | - | assimilation |
65538 | 16024 | D-mannose | + | assimilation |
65538 | 4853 | esculin | + | hydrolysis |
65538 | 17234 | glucose | - | fermentation |
65538 | 30849 | L-arabinose | + | assimilation |
65538 | 25115 | malate | - | assimilation |
65538 | 17306 | maltose | + | assimilation |
65538 | 506227 | N-acetylglucosamine | + | assimilation |
65538 | 17632 | nitrate | - | reduction |
65538 | 18401 | phenylacetate | - | assimilation |
65538 | 32032 | potassium gluconate | - | assimilation |
metabolite production
- @ref: 65538
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
65538 | cytochrome oxidase | + | 1.9.3.1 |
65538 | catalase | + | 1.11.1.6 |
65538 | arginine dihydrolase | + | 3.5.3.6 |
65538 | urease | + | 3.5.1.5 |
65538 | beta-galactosidase | + | 3.2.1.23 |
65538 | alkaline phosphatase | + | 3.1.3.1 |
65538 | esterase (C 4) | + | |
65538 | esterase Lipase (C 8) | + | |
65538 | leucine arylamidase | + | 3.4.11.1 |
65538 | valine arylamidase | + | |
65538 | cystine arylamidase | + | 3.4.11.3 |
65538 | alpha-chymotrypsin | + | 3.4.21.1 |
65538 | acid phosphatase | + | 3.1.3.2 |
65538 | naphthol-AS-BI-phosphohydrolase | + | |
65538 | 6-phospho-beta-galactosidase | + | 3.2.1.85 |
65538 | alpha-galactosidase | + | 3.2.1.22 |
65538 | beta-glucuronidase | + | 3.2.1.31 |
65538 | alpha-glucosidase | + | 3.2.1.20 |
65538 | beta-glucosidase | + | 3.2.1.21 |
65538 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
65538 | alpha-mannosidase | + | 3.2.1.24 |
65538 | lipase (C 14) | - | |
65538 | trypsin | - | 3.4.21.4 |
65538 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage 65538 C14:1ω5c 3.2 65538 C15:0 iso 19.6 65538 C15:0 anteiso 1.9 65538 C16:1ω5c 8.7 65538 C16:0 1.1 65538 C15:0 iso 3OH 4.5 65538 C17:1ω7c 1.4 65538 C17:1ω6c 1.9 65538 C17:0 iso 3OH 7.9 65538 iso-C19:1 I 1.3 65538 C19:0 iso 1.3 65538 C15:1 iso h / C13:0 3OH 4.2 65538 C16:1ω7c / C16:1ω6c 8.7 65538 iso-C17:1 U / anteiso-C17:1 B 21.3 - type of FA analysis: whole cell analysis
- incubation medium: R2A
- incubation temperature: 25
- incubation time: 3
- library/peak naming table: TSBA6
- system: MIS MIDI
- method/protocol: Sasser, 1990
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|
65538 | wet mud | Boryeong, Chungnam Province | Republic of Korea | KOR | Asia | 36.3368 | 126.615 | R2A | 4-5 days | 25 |
67771 | From wet mud | Boryeong, Chungnam province | Republic of Korea | KOR | Asia | 36.3368 | 126.615 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
Sequence information
16S sequences
- @ref: 65538
- description: 16S rRNA gene sequence
- accession: KY924849
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Adhaeribacter swui KCTC 52873 | GCA_014217805 | complete | ncbi | 2086471 |
66792 | Adhaeribacter swui strain KCTC 52873 | 2086471.3 | complete | patric | 2086471 |
GC content
@ref | GC-content | method |
---|---|---|
65538 | 45.9 | real time PCR (RTD-PCR) |
67771 | 45.9 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 94.279 | no |
gram-positive | no | 97.839 | yes |
anaerobic | no | 99.406 | no |
aerobic | yes | 90.582 | yes |
halophile | no | 93.865 | no |
spore-forming | no | 95.352 | no |
glucose-util | yes | 88.484 | yes |
thermophile | no | 99.184 | yes |
motile | no | 92.635 | no |
glucose-ferment | no | 87.814 | yes |
External links
@ref: 65538
culture collection no.: KCTC 52873, NBRC 112824
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 29458531 | Adhaeribacter swui sp. nov., isolated from wet mud. | Kim DU, Kim KW, Kang MS, Kim JY, Jang JH, Kim MK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002631 | 2018 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 32877325 | Adhaeribacter rhizoryzae sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant. | Chhetri G, Kim J, Kim I, Lee B, Jang W, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004422 | 2020 | Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 33064067 | Adhaeribacter arboris sp. nov., and Adhaeribacter pallidiroseus sp. nov., novel bacteria isolated from birch tree (Betula platyphylla). | Kang H, Kim H, Cha I, Joh K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004516 | 2020 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics, Base Composition, Betula/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/analysis, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Species Specificity | 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 | ||
65538 | Dong-Uk Kim, Kwan Woo Kim, Myung-Suk Kang, Ju-Young Kim, Jun Hwee Jang and Myung Kyum Kim | Adhaeribacter swui sp. nov., isolated from wet mud | 10.1099/ijsem.0.002631 | IJSEM 68: 1096-1100 2018 | 29458531 |
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 | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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 |