eLMSG_v5.0_purified_strain

*mandatory fields

Name Controlled vocabullary Description Value format
* Scientific NameScientific name e.g. Zeaxanthinibacter enoshimensis [genus name + species name, a blank between genus name and species name]
* Strain NameStrain name e.g. JHH-2T; KCCM 92030T; JCM 19228T
* TypeCVType strain or not e.g. type strain choose positive, while nontype strain choose negativenegative | 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_IDeLMSG ID eg. MSG001324
Parent_LMSG_IDeLMSG ID eg. MSG001324
Family NameFamily name e.g. Thermaceae
Sequence16S rRNA gene sequence
StrandednessThe quality or state of being stranded eg. single, double
TopologyShapes and spaces of 16SrRNA eg. Linear
Create dateSequencing 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 16SrRNA16S rRNA gene accession number of GenBank e.g. AJ784892
MIDUnique ID in eLMSG e.g. M010301010101001
eLMSG RankRank of the organism in taxonomic tree of eLMSG e.g. Species
EtymologyName 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 TypeThe source where the sample of bacteria was isolated from e.g. water from a mesothermic spring
Procedure OriginThe method how the organism was isolated and enriched e.g. dilution-plating method
Enrichment Culture NameThe name of the enrichment culture e.g. basal culture medium
Enrichment Culture DurationThe 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 TemperatureThe 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 DateThe date that the sampel was collected [YYYY/MM/DD, or YYYY/MM] e.g. 2002/09
Host diseaseThe disease name caused by this train e.g. Hypersensitivity pneumonitis
Host Body-SiteThe host body-site sample was isolated from e.g. blood
EnvironmentThe 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 NameThe geographical origin of the sample as defined by the country or sea name followed by specific region name e.g. Hammam Biadha
LongitudeA 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°
LatitudeA 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°
CountryCountry name where the sample for the microorganism was first collected e.g. Tunisia
ReferencesPublications 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/.
SubmitterThe submitting consortium or first position if a list of organizations e.g. Chinese National Human Genome Center at Shanghai
CoverageThe coverage of the assembly e.g. 30
Assembly statusCVThe current status for the assembly are shown e.g. complete genomecomplete genome | contig | scaffold | chromosome
Assembly classMostly haploid assembly, means the collection of chromosome assemblies, unlocalized and unplaced sequences that represent an organism's genome e.g. haploid
* Rawdata file nameRawdata 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 securityCVThe rawdata for genome e.g. publicpublic | private
Metadata securityCVThe metadata for genome e.g. publicpublic | private
idGenome ID in eLMSG eg. LMSG_G000000183.1
code
filename
Scientific NameScientific name of the organism e.g. Amycolatopsis eurytherma [genus name + species name, a blank between genus name and species name]
Submitter dateThe time when the assembly was submitted [YYYY/MM/DD] e.g. 2012/10/12
Update dateThe time when the assembly was updated [YYYY/MM/DD] e.g. 2012/10/12
Strain NameName of the strain was sequenced e.g. JHH-2T; KCCM 92030T; JCM 19228T
Cross-referencesCross-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 shapeCVThe microorganism cell shape e.g. rodfilament | 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
MotilityCVThe ability of the microorganism to move independently, using metabolic energy e.g. motility choose true+ | - | unknown
FlagellumCVIf the cell has flagellum eg. +, -+ | -
Flagellum arrangementFlagellum arrangement of the microorganism e.g. peritrichous flagella
Ability_spore_formCVAbility of spore formation+ | - | unknown
Type_spore_formType of spore formation e.g. endospore
Description_spore_formDetail description of the spore formation e.g. ellipsoidal spores centrally and paracentrally in unswollen sporangia
Ability_multicelluarCVAbility of forming multicellular complexes (aggregations)true | false | unknown
Medium nameName of the culture medium e.g. yeast extract-malt extract agar
Multicell nameName of the multicell e.g. substrate mycelium
Multicell sizeSize of the multicell size+blank+unit e.g. 200.0-800.0 µm
Multicell colorColor of the multicell e.g. cream-light yellow
Description_multicellularDetail 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 nameName of the pigment e.g. carotenoid
Pigment colorColor of the pigment e.g. yellow
Colony lengthLength 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 colorColor of the colony e.g. white
Colony shapeCVShape of the colony e.g. roundround
Medium nameName of the culture medium e.g. heart infusion agar
Hemolysis abilityCVAbility of hemolysis, which is the lysis of red blood cells and the release of the cytoplasm into surrounding fluidpositive | negative | unknown
Hemolysis typeType of hemolysis e.g. alpha
Incubation periodIncubation 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 typeThe nutrition type of the microorgainsm e.g. autotroph
Substrate_positiveCarbon and nitrogen sources e.g. L-fucose, D-xylose, L-xylose Common carbon and nitrogen sources see sheet carbon and nitrogen sources
Ability_positiveCVAbility of metabolite utilizationpositive
Substrate_negativeCarbon and nitrogen sources e.g. L-fucose, D-xylose, L-xylose Common carbon and nitrogen sources see sheet carbon and nitrogen sources
Ability_negativeCVAbility of metabolite utilizationnegative
Substrate_variableCarbon and nitrogen sources e.g. L-fucose, D-xylose, L-xylose Common carbon and nitrogen sources see sheet carbon and nitrogen sources
Ability_variableCVAbility of metabolite utilizationvariable
Metabolite productionName of the metabolite production e.g. dihydroxyacetone
ProductionCVAbility of of the metabolite productiontrue | false | unknown
ExcretedProducts of metabolism are eliminated from the microorganism e.g. CO2, H2O
Test type_temparatureCVOptimum temperatureoptimum
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_phCVOptimum pHoptimum
pHOptimum pH values e.g. 6.5
range_phThe range of pH for growth e.g. 6.5-7.5
SaltKind of salt related to halophilic information usually NaCl
Test type_saltCVOptimum salinityoptimum
Salt concentrationOptimum salt concentration concentration+blank+unit e.g. 6.5 %(w/v), 5 %
range_saltThe range of the salt concentration for growth e.g. 0.0-6.0% [numerical value+unit]
Gram stainingCVA method of staining used to distinguish and classify bacterial species into two large groups (gram-positive and gram-negative)positive | negative | variable | unknown
Compound nameName 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 percentPercentage of compound e.g. 0.35% [numerical value+unit]
ConcentrationConcentration of the compound
Concentration unitUnit of concentration e.g. mM
Oxygen requirementThe microorganism respiration requires the use of oxygen or not e.g. aerobic
Metabolite antibiotica_sensitiveName 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 sensitiveThe susceptibility of microorganism to antibiotics
Metabolite antibiotica_resistantName 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 resistantThe susceptibility of microorganism to antibiotics
Metabolite antibiotica_intermediateName 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 intermediateThe susceptibility of microorganism to antibiotics
Biosafety levelBiosafety 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 commentDetail description of biosafety level e.g. Risk group (German classification)
Pathogenicity subjectCVAbility of causing pathological conditions within subject e.g. plantplant | animal | human
GC content [mol%]Guanine-Cytosine content in mol% e.g. 58.1
GC methodThe method used to quantify GC content e.g. HPLC
GC content [mol%]Guanine-Cytosine content in mol% e.g. 58.1
GC methodThe method used to quantify GC content e.g. HPLC
GC content [mol%]Guanine-Cytosine content in mol% e.g. 58.1
GC methodThe method used to quantify GC content e.g. HPLC
Indole productionCVA biochemical test performed on bacterial species to determine the ability of the organism to convert tryptophan into indole + (positive), - (negative), -/+ (variable)+ | - | -/+ | unknown
Voges-Proskauer testCVA test used to detect acetoin in a bacterial broth culture + (positive), - (negative), -/+ (variable)+ | - | -/+ | unknown
Citrate UtilizationCVA 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 reactionCVA test used to identify bacteria producing stable acids by mechanisms of mixed acid fermentation of glucose + (positive), - (negative), -/+ (variable)+ | - | -/+ | unknown
Nitrate reductionCVA test used to detect the ability of an organism to reduce nitrate to nitrite using the enzyme nitrate reductase+ | - | unknown
H2S productionCVA 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 peptonizationCVA test used to detect organisms produce proteolytic enzymes to digest milk casein into peptones and amino acids+ | - | unknown
Milk coagulationCVA test used to detect organisms produce enzymes to make aggregation of milk casein particles form a gel+ | - | unknown
Gelatin hydrolysisCVA test used to detect the ability of an organism to produce gelatinase (proteolytic enzyme) that liquefy gelatin+ | - | unknown
Fatty acids profileThe 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 lipidsPolar 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 quinonesThe 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 sugarThe sugars of the microorganism, which are analyzed after whole-cell hydrolysis e.g. arabinose, madurose
Cell-wall sugarThe cell-wall sugar composition of the microorganism e.g. arabinose, madurose
Cell-wall animo acidThe amino acid composition in the cell wall of the microoriganism e.g. meso-diaminopimelic acid, alanine, glutamic acid
Murein short indexTo save space, a special system has been developed to characterize the different murein types e.g. A11.31
Murein typesCharacterization of the different murein types, including amino acid sequence and amino sugar composition e.g. A4alpha L-Lys-L-Glu
Enzyme_positiveThe 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_positiveCVEnzyme tested activity + (positive), - (negative), -/+ (variable)positive
Enzyme_negativeThe 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_negativeCVEnzyme tested activity + (positive), - (negative), -/+ (variable)negative
Enzyme_variableThe 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_variableCVEnzyme tested activity + (positive), - (negative), -/+ (variable)variable