* Scientific Name | | Scientific name
e.g. Zeaxanthinibacter enoshimensis [genus name + species name, a blank between genus name and species name] | |
* Strain Name | | Strain name
e.g. JHH-2T; KCCM 92030T; JCM 19228T | |
* Type | CV | Type strain or not
e.g. type strain choose positive, while nontype strain choose negative | negative | positive |
ANI | |
The value of fastANI identification for the strain with the existing species name, for more detail please check https://github.com/ParBLiSS/FastANI | |
LMSG_ID | | eLMSG ID eg. MSG001324 | |
Parent_LMSG_ID | | eLMSG ID eg. MSG001324 | |
Family Name | | Family name
e.g. Thermaceae | |
Sequence | | 16S rRNA gene sequence | |
Strandedness | | The quality or state of being stranded
eg. single, double | |
Topology | | Shapes and spaces of 16SrRNA
eg. Linear | |
Create date | | Sequencing date of 16S rRNA gene sequence
eg. 31-DEC-2003 | |
Primary accession | |
Primary accession of 16S rRNA gene sequence | |
Length | |
Lenghth of 16S rRNA gene sequence | |
Organism | |
Organism name of 16S rRNA gene sequence
| |
Genbank 16SrRNA | | 16S rRNA gene accession number of GenBank
e.g. AJ784892 | |
MID | | Unique ID in eLMSG
e.g. M010301010101001 | |
eLMSG Rank | | Rank of the organism in taxonomic tree of eLMSG
e.g. Species | |
Etymology | | Name origins of the organism
e.g. en.o.shi.men'sis. N.L. masc. adj. enoshimensis pertaining to Enoshima Island in Japan, where the type strain was isolated | |
Sample Type | | The source where the sample of bacteria was isolated from
e.g. water from a mesothermic spring | |
Procedure Origin | | The method how the organism was isolated and enriched
e.g. dilution-plating method | |
Enrichment Culture Name | | The name of the enrichment culture
e.g. basal culture medium | |
Enrichment Culture Duration | | The time of the enrichment culture cost.[min (minute); h (hour); d (day); w (week); m (month); y (year)]
e.g. 3 d [numerical value+a blank+unit] | |
Enrichment Culture Temperature | | The temperature of the enrichment culture, only support degree celsius (C).
e.g. 37.0 ℃ [numerical value+a blank+unit]
If you are using fahrenheit temperature scale (F), please calculate to degree celsius by using the following formula: C = 5×(F- 32)/9, e.g. 41℉=5.0 ℃
| |
Collection Date | | The date that the sampel was collected [YYYY/MM/DD, or YYYY/MM]
e.g. 2002/09 | |
Host disease | | The disease name caused by this train
e.g. Hypersensitivity pneumonitis | |
Host Body-Site | | The host body-site sample was isolated from
e.g. blood | |
Environment | | The environmental information when the sample was collected
e.g. root:Environmental:Aquatic:Thermal springs:Hot (42-90C):Sediment
Environmental information see sheet Biome | |
Geographic Location Name | | The geographical origin of the sample as defined by the country or sea name followed by specific region name
e.g. Hammam Biadha | |
Longitude | | A geographic coordinate specifies the east–west position of a point on the Earth's surface where the sample for the microorganism was first collected, ranging from 0° at the Prime Meridian to +180° eastward and −180° westward
e.g. 98.43743 °E or 120.13333-120.63333° E [decimalism, five digits after decimal point], [numerical value+unit+E/W]
longitude conversion http://www.ab126.com/Geography/2703.html;
https://blog.csdn.net/weixin_35959554/article/details/86006915
e.g. 104°4´18〞=104+4/60+18/3600=104.07167° | |
Latitude | | A geographic coordinate specifies the north–south position of a point on the Earth's surface where the sample for the microorganism was first collected, ranging from 0° at the Equator to 90° (North or South) at the poles
e.g. 24.95014° N or 37.08333-37.55000° N [decimalism, five digits after decimal point], [numerical value+unit+N/S]
latitude conversion http://www.ab126.com/Geography/2703.html;
https://blog.csdn.net/weixin_35959554/article/details/86006915
e.g. 104°4´18〞=104+4/60+18/3600=104.07167° | |
Country | | Country name where the sample for the microorganism was first collected
e.g. Tunisia | |
References | | Publications related to this organism. The format of the reference should be the same as the format of NCBI pubmed. General format template for a reference to a journal article: Author Surname, Author Initial. Article Title. Journal Title. Date of Publication; Volume(Issue) Pagination. If you need more detail, please refer to https://www.ncbi.nlm.nih.gov/books/NBK7282/. | |
Submitter | | The submitting consortium or first position if a list of organizations
e.g. Chinese National Human Genome Center at Shanghai | |
Coverage | | The coverage of the assembly
e.g. 30 | |
Assembly status | CV | The current status for the assembly are shown
e.g. complete genome | complete genome | contig | scaffold | chromosome |
Assembly class | | Mostly haploid assembly, means the collection of chromosome assemblies, unlocalized and unplaced sequences that represent an organism's genome
e.g. haploid | |
* Rawdata file name | | Rawdata file name
e.g.Zeaxanthinibacter enoshimensis_JHH-2T.fasta [scientific name+"_"+strain name+"."+fasta | |
Review period | |
In the condition that the author would like to keep the rawdata private, the author have to provide the days that paper will be reviewed by the reviewer.
For example, if you input 90, the system will automatically keep this data private for 90 days. | |
* Rawdata security | CV | The rawdata for genome
e.g. public | public | private |
Metadata security | CV | The metadata for genome
e.g. public | public | private |
id | | Genome ID in eLMSG
eg. LMSG_G000000183.1 | |
code | | | |
filename | | | |
Scientific Name | | Scientific name of the organism
e.g. Amycolatopsis eurytherma [genus name + species name, a blank between genus name and species name] | |
Submitter date | | The time when the assembly was submitted [YYYY/MM/DD]
e.g. 2012/10/12 | |
Update date | | The time when the assembly was updated [YYYY/MM/DD]
e.g. 2012/10/12 | |
Strain Name | | Name of the strain was sequenced
e.g. JHH-2T; KCCM 92030T; JCM 19228T | |
Cross-references | | Cross-references to other databases,for example if you want to put cross-references to the NODE database (https://www.biosino.org/node/), you can fill here as following:
[database name+":"+ID in the database],eg NODE:OEP000073
if you have more than one ID, you can fill as following:
[database name+":"+ID in the database]+","+[database name+":"+ID in the database], eg NODE:OEP000073,NODE:OEP000074,NODE:OEP000074 | |
Cell shape | CV | The microorganism cell shape
e.g. rod | filament | rod | coccus | coccobacillus |
Cell length [µm] | | Length of the cell, the unit here is automatically considered asµm, if you are using other unit, please convert to µm.
e.g. 3.6-5.1 | |
Cell width [µm] | | Width of the cell, the unit here is automatically considered asµm, if you are using other unit, please convert to µm.
e.g. 3.6-5.1 | |
Motility | CV | The ability of the microorganism to move independently, using metabolic energy
e.g. motility choose true | + | - | unknown |
Flagellum | CV | If the cell has flagellum
eg. +, - | + | - |
Flagellum arrangement | | Flagellum arrangement of the microorganism
e.g. peritrichous flagella | |
Ability_spore_form | CV | Ability of spore formation | + | - | unknown |
Type_spore_form | | Type of spore formation
e.g. endospore | |
Description_spore_form | | Detail description of the spore formation e.g. ellipsoidal spores centrally and paracentrally in unswollen sporangia | |
Ability_multicelluar | CV | Ability of forming multicellular complexes (aggregations) | true | false | unknown |
Medium name | | Name of the culture medium
e.g. yeast extract-malt extract agar | |
Multicell name | | Name of the multicell
e.g. substrate mycelium | |
Multicell size | | Size of the multicell
size+blank+unit
e.g. 200.0-800.0 µm | |
Multicell color | | Color of the multicell
e.g. cream-light yellow | |
Description_multicellular | | Detail description of the multicell e.g. wrinkly and twisty surface, septate hyphae broke, at a later stage, into fragments of various sizes and rod-shape spore elements | |
Pigment name | | Name of the pigment
e.g. carotenoid | |
Pigment color | | Color of the pigment
e.g. yellow | |
Colony length | | Length of the colony on distinct medium and temperature after a certain time of cultivation
length+blank+mm
e.g. 0.5-1.0 mm | |
Colony color | | Color of the colony
e.g. white | |
Colony shape | CV | Shape of the colony
e.g. round | round |
Medium name | | Name of the culture medium
e.g. heart infusion agar | |
Hemolysis ability | CV | Ability of hemolysis, which is the lysis of red blood cells and the release of the cytoplasm into surrounding fluid | positive | negative | unknown |
Hemolysis type | | Type of hemolysis
e.g. alpha | |
Incubation period | | Incubation period in context with the description of colony morphology.[min (minute); h (hour); d (day); w (week); m (month); y (year)]
e.g. 4 d [numerical value+a blank+unit] | |
Nutrition type | | The nutrition type of the microorgainsm
e.g. autotroph | |
Substrate_positive | | Carbon and nitrogen sources
e.g. L-fucose, D-xylose, L-xylose
Common carbon and nitrogen sources see sheet carbon and nitrogen sources | |
Ability_positive | CV | Ability of metabolite utilization | positive |
Substrate_negative | | Carbon and nitrogen sources
e.g. L-fucose, D-xylose, L-xylose
Common carbon and nitrogen sources see sheet carbon and nitrogen sources | |
Ability_negative | CV | Ability of metabolite utilization | negative |
Substrate_variable | | Carbon and nitrogen sources
e.g. L-fucose, D-xylose, L-xylose
Common carbon and nitrogen sources see sheet carbon and nitrogen sources | |
Ability_variable | CV | Ability of metabolite utilization | variable |
Metabolite production | | Name of the metabolite production
e.g. dihydroxyacetone | |
Production | CV | Ability of of the metabolite production | true | false | unknown |
Excreted | | Products of metabolism are eliminated from the microorganism
e.g. CO2, H2O | |
Test type_temparature | CV | Optimum temperature | optimum |
Temperature [°C] | | Optimum temperature value, the unit here is automatically considered as degree Celsius [°C]
e.g. 37.0 | |
Temperature range [°C] | | Range of growth temperature, the unit here is automatically considered as degree Celsius [°C]
e.g. 25.0-42.0 | |
Test type_ph | CV | Optimum pH | optimum |
pH | | Optimum pH values
e.g. 6.5 | |
range_ph | | The range of pH for growth
e.g. 6.5-7.5 | |
Salt | | Kind of salt related to halophilic information usually NaCl | |
Test type_salt | CV | Optimum salinity | optimum |
Salt concentration | | Optimum salt concentration
concentration+blank+unit
e.g. 6.5 %(w/v), 5 % | |
range_salt | | The range of the salt concentration for growth
e.g. 0.0-6.0% [numerical value+unit] | |
Gram staining | CV | A method of staining used to distinguish and classify bacterial species into two large groups (gram-positive and gram-negative) | positive | negative | variable | unknown |
Compound name | | Name of compound, which the microorganism withstands or endures
e.g. KCN
If have level percent or concentration, fill in KCN (0.1%), or KCN (40 mM) [numerical value+%], [numerical value+a blank+unit]
If several compounds, using comma and a blank let them seperate
e.g.KCN, NaNO3 | |
Level percent | | Percentage of compound
e.g. 0.35% [numerical value+unit] | |
Concentration | | Concentration of the compound | |
Concentration unit | | Unit of concentration
e.g. mM | |
Oxygen requirement | | The microorganism respiration requires the use of oxygen or not
e.g. aerobic | |
Metabolite antibiotica_sensitive | | Name of antibiotics
e.g. ampicillin
If have concentration, fill in name of antibiotics+(+concentration value+a blank+unit+)
e.g. ampicillin (10 µg)
If several compounds, using comma and a blank let them seperate
e.g.ampicillin, chloramphenicol | |
Antibiotic sensitive | | The susceptibility of microorganism to antibiotics | |
Metabolite antibiotica_resistant | | Name of antibiotics
e.g. ampicillin
If have concentration, fill in name of antibiotics+(+concentration value+a blank+unit+)
e.g. ampicillin (10 µg)
If several compounds, using comma and a blank let them seperate
e.g.ampicillin, chloramphenicol | |
Antibiotic resistant | | The susceptibility of microorganism to antibiotics | |
Metabolite antibiotica_intermediate | | Name of antibiotics
e.g. ampicillin
If have concentration, fill in name of antibiotics+(+concentration value+a blank+unit+)
e.g. ampicillin (10 µg)
If several compounds, using comma and a blank let them seperate
e.g.ampicillin, chloramphenicol | |
Antibiotic intermediate | | The susceptibility of microorganism to antibiotics | |
Biosafety level | | Biosafety level defined for the strain (Biosafety is used to protect from harmful incidents. Many laboratories handling biohazards employ an ongoing risk management assessment and enforcement process for biosafety. )
e.g. 2 | |
Biosafety level comment | | Detail description of biosafety level
e.g. Risk group (German classification) | |
Pathogenicity subject | CV | Ability of causing pathological conditions within subject
e.g. plant | plant | animal | human |
GC content [mol%] | | Guanine-Cytosine content in mol%
e.g. 58.1 | |
GC method | | The method used to quantify GC content
e.g. HPLC | |
GC content [mol%] | | Guanine-Cytosine content in mol%
e.g. 58.1 | |
GC method | | The method used to quantify GC content
e.g. HPLC | |
GC content [mol%] | | Guanine-Cytosine content in mol%
e.g. 58.1 | |
GC method | | The method used to quantify GC content
e.g. HPLC | |
Indole production | CV | A biochemical test performed on bacterial species to determine the ability of the organism to convert tryptophan into indole
+ (positive), - (negative), -/+ (variable) | + | - | -/+ | unknown |
Voges-Proskauer test | CV | A test used to detect acetoin in a bacterial broth culture
+ (positive), - (negative), -/+ (variable) | + | - | -/+ | unknown |
Citrate Utilization | CV | A test used to detect the ability of an organism to use citrate as the sole source of carbon and energy
+ (positive), - (negative), -/+ (variable) | + | - | -/+ | unknown |
Methyl red reaction | CV | A test used to identify bacteria producing stable acids by mechanisms of mixed acid fermentation of glucose
+ (positive), - (negative), -/+ (variable) | + | - | -/+ | unknown |
Nitrate reduction | CV | A test used to detect the ability of an organism to reduce nitrate to nitrite using the enzyme nitrate reductase | + | - | unknown |
H2S production | CV | A test used to determine whether the microbe reduces sulfur-containing compounds to sulfides during the process of metabolism
e.g. Hydrogen sulfide production is negative. | + | - |
Milk peptonization | CV | A test used to detect organisms produce proteolytic enzymes to digest milk casein into peptones and amino acids | + | - | unknown |
Milk coagulation | CV | A test used to detect organisms produce enzymes to make aggregation of milk casein particles form a gel | + | - | unknown |
Gelatin hydrolysis | CV | A test used to detect the ability of an organism to produce gelatinase (proteolytic enzyme) that liquefy gelatin | + | - | unknown |
Fatty acids profile | | The fatty acid compositions of the microorganism e.g. The major fatty acids are iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 0 3-OH, C17 : 1v6c,iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 4(comprising iso-C17 : 1 I and anteiso-C17 : 1 B) when grown at 25 ℃. | |
Polar lipids | | Polar lipids of the microorganism, which have a hydrophilic head and a hydrophobic tail that help themselves-orient to form a double layer in which the polar end points outward and the nonpolar end points inward
e.g. phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid | |
Major quinones | | The major quinones of the microorganism, which are essential electron carriers in the respiration chain of the microrganism
e.g. menaquinone-6, menaquinone-8 | |
Whole-cell sugar | | The sugars of the microorganism, which are analyzed after whole-cell hydrolysis
e.g. arabinose, madurose | |
Cell-wall sugar | | The cell-wall sugar composition of the microorganism
e.g. arabinose, madurose | |
Cell-wall animo acid | | The amino acid composition in the cell wall of the microoriganism
e.g. meso-diaminopimelic acid, alanine, glutamic acid | |
Murein short index | | To save space, a special system has been developed to characterize the different murein types
e.g. A11.31 | |
Murein types | | Characterization of the different murein types, including amino acid sequence and amino sugar composition
e.g. A4alpha L-Lys-L-Glu | |
Enzyme_positive | | The name of enzyme, which are synthesized by microorganism
e.g. catalase
If several enzymes, using comma and a blank let them seperate
e.g.catalase, urease
Common enzymes see sheet enzyme | |
Ability_positive | CV | Enzyme tested activity
+ (positive), - (negative), -/+ (variable) | positive |
Enzyme_negative | | The name of enzyme, which are synthesized by microorganism
e.g. catalase
If several enzymes, using comma and a blank let them seperate
e.g.catalase, urease
Common enzymes see sheet enzyme | |
Ability_negative | CV | Enzyme tested activity
+ (positive), - (negative), -/+ (variable) | negative |
Enzyme_variable | | The name of enzyme, which are synthesized by microorganism
e.g. catalase
If several enzymes, using comma and a blank let them seperate
e.g.catalase, urease
Common enzymes see sheet enzyme | |
Ability_variable | CV | Enzyme tested activity
+ (positive), - (negative), -/+ (variable) | variable |