Strain identifier
BacDive ID: 158612
Type strain:
Species: Sphingobacterium terrae
Strain Designation: Brt-F
Strain history: J. Kim; Kyonggi Univ., South Korea; Brt-F.
NCBI tax ID(s): 2070451 (species)
General
@ref: 65334
BacDive-ID: 158612
keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Sphingobacterium terrae Brt-F is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from oil-contaminated soil.
NCBI tax id
- NCBI tax id: 2070451
- Matching level: species
strain history
- @ref: 67770
- history: J. Kim; Kyonggi Univ., South Korea; Brt-F.
doi: 10.13145/bacdive158612.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Sphingobacterium
- species: Sphingobacterium terrae
- full scientific name: Sphingobacterium terrae Chaudhary and Kim 2018
@ref: 65334
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Sphingobacterium
species: Sphingobacterium terrae
strain designation: Brt-F
type strain: yes
Morphology
cell morphology
- @ref: 65334
- gram stain: negative
- cell length: 0.8-1 µm
- cell width: 0.5-0.6 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 65334
- colony size: 1-1.5 mm
- colony color: cream
- colony shape: circular
- medium used: tryptic soy agar
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
65334 | tryptic soy agar | yes |
65334 | Reasoner's 2A agar (R2A) | yes |
65334 | Nutrient agar (NA) | yes |
65334 | LB (Luria-Bertani) MEDIUM | yes |
65334 | veal infusion agar | yes |
65334 | Marine agar (MA) | yes |
65334 | sorbitol MacConkey agar | no |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65334 | positive | growth | 15-45 | |
65334 | positive | optimum | 25-35 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
65334 | positive | growth | 6.5-10.5 | alkaliphile |
65334 | positive | optimum | 7-8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 65334
- oxygen tolerance: aerobe
spore formation
- @ref: 65334
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
65334 | NaCl | positive | growth | 0-4.5 % |
65334 | NaCl | positive | optimum | 0 % |
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65334 | 16193 | 3-hydroxybenzoate | - | assimilation |
65334 | 37054 | 3-hydroxybutyrate | - | assimilation |
65334 | 17879 | 4-hydroxybenzoate | - | assimilation |
65334 | 17128 | adipate | - | assimilation |
65334 | 27689 | decanoate | - | assimilation |
65334 | 85146 | carboxymethylcellulose | + | hydrolysis |
65334 | casein | - | hydrolysis | |
65334 | 17029 | chitin | - | hydrolysis |
65334 | 17634 | D-glucose | + | assimilation |
65334 | 16899 | D-mannitol | - | assimilation |
65334 | 16024 | D-mannose | + | assimilation |
65334 | 16988 | D-ribose | + | assimilation |
65334 | 17924 | D-sorbitol | - | assimilation |
65334 | 16991 | dna | - | hydrolysis |
65334 | 4853 | esculin | + | hydrolysis |
65334 | 5291 | gelatin | - | fermentation |
65334 | 5291 | gelatin | - | hydrolysis |
65334 | 17234 | glucose | - | fermentation |
65334 | 28087 | glycogen | + | assimilation |
65334 | 17268 | myo-inositol | - | assimilation |
65334 | 17240 | itaconate | - | assimilation |
65334 | 16977 | L-alanine | - | assimilation |
65334 | 30849 | L-arabinose | + | assimilation |
65334 | 16467 | L-arginine | - | fermentation |
65334 | 18287 | L-fucose | - | assimilation |
65334 | 15971 | L-histidine | - | assimilation |
65334 | 17203 | L-proline | - | assimilation |
65334 | 62345 | L-rhamnose | + | assimilation |
65334 | 17115 | L-serine | - | assimilation |
65334 | 16828 | L-tryptophan | - | assimilation |
65334 | 24996 | lactate | - | assimilation |
65334 | 25115 | malate | - | assimilation |
65334 | 17306 | maltose | + | assimilation |
65334 | 28053 | melibiose | + | assimilation |
65334 | 506227 | N-acetylglucosamine | + | assimilation |
65334 | 17632 | nitrate | - | reduction |
65334 | 18401 | phenylacetate | - | assimilation |
65334 | potassium 2-dehydro-D-gluconate | - | assimilation | |
65334 | potassium 5-dehydro-D-gluconate | - | assimilation | |
65334 | 32032 | potassium gluconate | - | assimilation |
65334 | 17272 | propionate | - | assimilation |
65334 | 17814 | salicin | + | assimilation |
65334 | 32954 | sodium acetate | - | assimilation |
65334 | 53258 | sodium citrate | - | assimilation |
65334 | 62983 | sodium malonate | - | assimilation |
65334 | 28017 | starch | - | hydrolysis |
65334 | 9300 | suberic acid | - | assimilation |
65334 | 17992 | sucrose | + | assimilation |
65334 | 53423 | tween 40 | - | hydrolysis |
65334 | 53426 | tween 80 | - | hydrolysis |
65334 | 18186 | tyrosine | - | hydrolysis |
65334 | 16199 | urea | - | fermentation |
65334 | 31011 | valerate | - | assimilation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
65334 | 15688 | acetoin | no |
65334 | 16136 | hydrogen sulfide | no |
65334 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test |
---|---|---|---|---|
65334 | 17234 | glucose | - | |
65334 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
65334 | catalase | + | 1.11.1.6 |
65334 | cytochrome oxidase | + | 1.9.3.1 |
65334 | alkaline phosphatase | + | 3.1.3.1 |
65334 | leucine arylamidase | + | 3.4.11.1 |
65334 | trypsin | + | 3.4.21.4 |
65334 | acid phosphatase | + | 3.1.3.2 |
65334 | naphthol-AS-BI-phosphohydrolase | + | |
65334 | alpha-glucosidase | + | 3.2.1.20 |
65334 | beta-glucosidase | + | 3.2.1.21 |
65334 | alpha-mannosidase | + | 3.2.1.24 |
65334 | alpha-fucosidase | + | 3.2.1.51 |
65334 | valine arylamidase | + | |
65334 | cystine arylamidase | + | 3.4.11.3 |
65334 | alpha-galactosidase | + | 3.2.1.22 |
65334 | esterase (C 4) | - | |
65334 | esterase Lipase (C 8) | - | |
65334 | lipase (C 14) | - | |
65334 | alpha-chymotrypsin | - | 3.4.21.1 |
65334 | beta-galactosidase | - | 3.2.1.23 |
65334 | beta-glucuronidase | - | 3.2.1.31 |
65334 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
fatty acid profile
fatty acids
@ref fatty acid percentage 65334 C14:0 0.3 65334 C16:0 4.8 65334 C15:0 anteiso 0.6 65334 C15:0 iso 27.8 65334 iso-C15:0 F 0.2 65334 C17:0 iso 0.4 65334 C16:1ω5c 0.8 65334 C14:0 2OH 0.2 65334 C15:0 iso 3OH 3.1 65334 C16:0 2OH 0.3 65334 C16:0 3OH 1 65334 C16:0 iso 3OH 0.2 65334 C17:0 iso 3OH 19.1 65334 C16:1ω7c and/or C16:1ω6c 36.3 65334 C17:1 iso I and/or C17:1 anteiso B 0.4 65334 C18:1ω7c and/or C18:1ω6c 1.3 65334 iso-C17:1ω9c and/or C16:010-methyl 2.1 - type of FA analysis: whole cell analysis
- incubation medium: tryptic soy agar
- incubation temperature: 28
- software version: Sherlock 6.0B
- library/peak naming table: TSBA6
- system: MIS MIDI
- 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 | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|
65334 | oil-contaminated soil | petroleum distribution center of Biratnagar, Morang | Nepal | NPL | Asia | 26.4922 | 87.2767 | tryptic soy broth | 15 days | roomtemperature | modified culture technique with six-well polycarbonate Transwell plates |
67770 | Oil-contaminated soil sample of Biratnagar | Morang | Nepal | NPL | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Contamination | #Oil (Fuel) |
#Environmental | #Terrestrial | #Soil |
Sequence information
16S sequences
- @ref: 65334
- description: 16S rRNA gene sequence
- accession: MF405100
- database: nuccore
GC content
- @ref: 65334
- GC-content: 43.4
- method: high performance liquid chromatography (HPLC)
External links
@ref: 65334
culture collection no.: KEMB 9005-691, KACC 19392, JCM 32159
literature
- topic: Phylogeny
- Pubmed-ID: 29303695
- title: Sphingobacterium terrae sp. nov., isolated from oil-contaminated soil.
- authors: Chaudhary DK, Kim J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002552
- year: 2018
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
- 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 | ||
65334 | Dhiraj Kumar Chaudhary, Jaisoo Kim | Sphingobacterium terrae sp. nov., isolated from oil-contaminated soil | 10.1099/ijsem.0.002552 | IJSEM 68: 609-615 2018 | 29303695 |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ |