Международная инфраструктура для коллекций культур Василенко А.Н., Озерская С.М

Международная инфраструктура для коллекций

культурВасиленко А.Н., Озерская С.М

Всероссийская коллекция микроорганизмов ИБФМ РАН

E-mail: vanvkm@gmail.com

Ступарь Олег Сергеевич

к.б.н.E-mail: stupar@ibpm.pushchino.ru

ВКМ ИБФМ РАНМосковская обл. 142290

Пущино, Проспект Науки 5

Типовое описание поля RDS1. Field's name

2. Short description of the content (one sentence)

3. Specification of the content

3.1. Detailed description of the content, difference from the other fields that may look similar

3.2. List of subfields and their descriptions

3.3. Specification of the coding for the field and subfields

3.4. The list of possible values (if short) or a reference to file with long list, or reference to thesaurus, or reference to ontology

3.5. Reference to a manual, which describes this field content

3.6. Reference to external standard used for this field

3.7. Samples of correct coding for this field.

The examination shows four factors that cuts the scope of the fields in possible request system and make the values inconsistent: (1) collections have some difference in selection of the fields, (2) Also some differences in understanding of the same fields are apparent, (3) different content while the understanding presumably is the same, (4) different typing for the same content is used.

Factors (1) and (2) are specified by the standard, factors (3) and (4) aren't regulated, they are more difficult to classify, but we can give some examples.

Difference in typing (factor 4). Example: errors in a name

E E E 1 E E E

B K M2 E E R3 E R E4 E R R5 R E E6 R E R7 R R E

R R R 8 R R R

Factor 3: Differences in content.Example:

One strain of Aspergillus brasiliensis Varga et al. 2007 in four catalogues:

Cultures:ATCC 9642CBS 246.65DSM 63263VKM F-1119

Results of comparison

Organism type

Name (Infrasubspecific

names)

Other names (Misapplied

names)

Previous names

ATCC Subcollection: Fungi

Aspergillus brasiliensis Varga et al.

CBS F

Aspergillus brasiliensis Varga, Frisvad & Samson

Aspergillus brasiliensis; Aspergillus niger

DSMZ FAspergillus brasiliensis Varga, Kocsube et al.

VKM F

Aspergillus brasiliensis Varga et al. 2007

Aspergillus niger van Tieghem 1867

Results of comparison

Accession number

Other collection numbers

ATCC 9642Australian Mycol. Panel series 26, CBS 246.65, DSM 63263, IFO 6342, IMI 91855, NRRL 3536, NRRL A-5243, QM 386

CBS 246.65

ATCC 9642;ATHUM 2856;CECT 2700;DSM 63263;IFO 6342;IHEM 3797;IMI 149007;IMI 091855;IMI 091855ii;IMI 091855iii;LCP 74.2280;MUCL 19001;NBRC 105650;NRRL 3536;NRRL A-5243;OECD 14;QM 386;VKM F1119

DSMZ 63263ATCC 9642, CBS 246.65, IFO 6342, IMI 091855, NBRC 6342, NRRL 3536

VKM F-1119

ATCC 9642; CBS 246.65; CCRC 31512; DSM 63263; FERM S-2; IFO 6342; IMI 91855; NRRL A-5243; NRRL A-3536; QM 386

Results of comparison

History of deposit Deposited as Strain

DesignationDepositors

ATCC

Aspergillus niger van Tieghem, anamorph

SN 26 WH Weston

CBS QM, Jul 1965

DSMZ<- IMG, 4518 <- W. Kerner. [QM

386]

Aspergillus niger

VKM<-- INMI, VKM F-

1119 <- ATCC, ATCC 9642

Aspergillus niger

Results of comparison

Isolated from Isolated byGeographic

origin

Additional geographic

data

ATCCwireless radio

equipmentNew South Wales,

Australia

CBSradio

equipment R.E. Klausmeier, Indiana, Crane

Australia, New South Wales;

Sydney

Latitude, longitude coordinates where collected: 33.8833333; 151.2166667

DSMZ Radio setVKM radio set Australia, Sydney

Results of comparisonConditions for

growth - Temperature

Conditions for growth - Medium Storage methods

ATCC

24.0°C

ATCC medium: 336 Potato dextrose agar (PDA): Diced potatoes 300.0 g; Glucose 20.0 g;Agar 5.0 g; Distilled water 1.0 L

CBSDSMZ

30°C

129. POTATO DEXTROSE AGAR Infusion from potatoes (see below) 1000.0 ml Glucose 20.0 g; Agar 15.0 g; Potato infusion: Boil 200 g scrubbed and sliced potatoes in 1000 ml water for 1 hour. Pass through fine sieve. Avoid new potatoes.

VKM

25 C

Medium 12 (Medium CZAPEK MEDIUM (CZ): NaNO3 3.0 g; K2HPO4 1.0 g; KCl 0.5 g; MgSO4 x 7H2O 0.5 g; FeSO4 x 7H2O 0.01 g; Sucrose 30.0 g; Agar 20.0 g; Distilled water 1000.0 ml; pH 6.0; Sterilize at 121 C for 30 min)

F-1, S-5, D-4

Results of comparison

Applications

ATCC

bacterial resistance testing adhesives [21459]; degrades plastics [52928] fungus resistance testing [21552] [92556] [92557] [92558]; fungus resistance testing adhesives [21456]; fungus resistance testing airborne equipment [21535]; fungus resistance testing automotive components; fungus resistance testing cork; fungus resistance testing electrical insulation [21543]; fungus resistance testing leather ; fungus resistance testing polymers [21471]; fungus resistance testing varnish; fungus resistance testing wax [21551]; produces isopullulanase pullulan 4-glucanohydrolase [700]; produces lactoylglutathione glyoxalase I [1390]; testing antimicrobial agent [92595]; testing wood preservatives [55647]

CBS

Enzymes: amylase; isopullulanase; lipase Decomposition: plastics Testing: assay of wood preservative chemicals; testing fungus resistance of plastics

DSMZAssay of wood preservative chemicals (3693), assay of fungus resistance test (3732)

VKM

Results of comparison

Comments Genotype

ATCCThis strain was recently re-named as Aspergillus brasiliensis according to the reference Varga et al. 2007. [92930]

CBS

A novel species, Aspergillus brasiliensis sp. nov., is described within Aspergillus section Nigri. This species can be distinguished from other black aspergilli based on intergenic transcribed region, beta-tubulin and calmodulin gene sequences, by amplified fragment length polymorphism analysis and by extrolite profiles. A. brasiliensis isolates produced naphtho-gamma-pyrones, tensidol A and B and pyrophen in common with Aspergillus niger and Aspergillus tubingensis, but also several unique compounds, justifying their treatment as representing a separate species. None of the isolates were found to produce ochratoxin A, kotanins, funalenone or pyranonigrins. The novel species was most closely related to A. niger, and was isolated from soil from Brazil, Australia, USA and The Netherlands, and from grape berries from Portugal. The type strain of Aspergillus brasiliensis sp. nov. is CBS 101740(T) (=IMI 381727(T)=IBT 21946(T)).

DNA sequence ITS rDNA: >gb|DQ900597|CBS 246.65|Aspergillus brasiliensis strain CBS 246.65 internal transcribedspacer 1, partial sequence; 5.8S ribosomal RNA gene, completesequence; and internal transcribed spacer 2, partial sequence.| (length of sequence: 465)DNA sequence Beta tubuline: >gb|DQ900607|CBS 246.65|Aspergillus brasiliensis strain CBS 246.65 beta-tubulin gene,partial cds.| (length of sequence: 355)

DSMZVKM

Results of comparisonPrice Permits/Forms Keyword(s) Restrictions

ATCC $155.00

In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location.

Biosafety Level: 1

CBS155

EURO

GENBANK/MB510581 Aspergillus/*classification/genetics/isolation & purification/metabolism DNA, Fungal/genetics DNA, Ribosomal Spacer/genetics Molecular Sequence Data Phylogeny Polymorphism, Restriction Fragment Length

DSMZ 65 EURO

Risk group: 1 (classification according to German TRBA)

VKM Risk group: 4

Типовое описание поля RDS1. Field's name

2. Short description of the content (one sentence)

3. Specification of the content

3.1. Detailed description of the content, difference from the other fields that may look similar

3.2. List of subfields and their descriptions

3.3. Specification of the coding for the field and subfields

3.4. The list of possible values (if short) or a reference to file with long list, or reference to thesaurus, or reference to ontology

3.5. Reference to a manual, which describes this field content

3.6. Reference to external standard used for this field

3.7. Samples of correct coding for this field.

Their URLs:WFCC Nmbr

Acronim Country URL (dated 18.09.2010)

803 RCDM Armenia http://wdcm.nig.ac.jp/catalogue/rcdm/rcdm.html13 ACM Australia www.babs.unsw.edu.au/files/babs_cultures_catalogue.pdf

532 CCLM/CSIRO Australia http://www.csiro.au/places/Australian-National-Algae-Culture-Collection--ci_pageNo-1.html

839 ACBR Austria http://www.acbr-database.at/BioloMICS.aspx909 BIM Belarus http://www.mbio.bas-net.by/296 BCCM/LMG Belgium http://bccm.belspo.be/about/lmg.php308 BCCM/MUCL Belgium http://bccm.belspo.be/about/mucl.php642 BCCM/IHEM Belgium http://bccm.belspo.be/about/ihem.php643 BCCM/LMBP Belgium http://bccm.belspo.be/about/lmbp.php110 IBSFB Brazil http://www.splink.org.br/index364 BR Brazil http://splink.cria.org.br/manager/detail?resource=BR&setlang=pt575 INCQS Brazil http://www.splink.org.br/index604 URM Brazil http://www.splink.org.br/index712 CG Brazil http://www.splink.org.br/index731 CLIOC Brazil http://www.splink.org.br/index823 CBMAI Brazil http://webdrm.cpqba.unicamp.br/cbmai/867 CCGB Brazil http://splink.cria.org.br/manager/detail?resource=CCGB&setlang=pt947 IOC Brazil http://www.splink.org.br/index

BGB, SinBiota, HUERS, CFAF

Brazil http://www.splink.org.br/index

135 NBIMCC Bulgaria http://www.nbimcc.org/cabricat/Main.php

6 HER Canada http://www.phage.ulaval.ca/index.php?pageDemandee=search

73 UAMH Canada http://www.devonian2.ualberta.ca/uamh/on-line_catalog.htm338 SGSC Canada http://people.ucalgary.ca/~kesander/catalogue.html605 CPCC Canada http://www.phycol.ca/search/node/582 CICC China http://www.china-cicc.org/English/english.html65 CCM Czech http://sci.muni.cz/ccm/index.html

130 CNCTC Czech http://www.szu.cz/cnctc/a/uvod.php486 CAUP Czech http://botany.natur.cuni.cz/algo/caup-list.html558 CCBAS Czech http://www.biomed.cas.cz/ccbas/fungi.htm905 CCALA Czech http://www.butbn.cas.cz/ccala/index.php?page=se&st=as935 SCCAP Denmark http://www.sccap.dk/search/926 CELMS Estonia http://www.miccol.ut.ee/385219139 VTT Finland http://culturecollection.vtt.fi/779 HAMBI Finland http://www.mm.helsinki.fi/mmkem/hambi/639 CFBP France http://www-intranet.angers.inra.fr/cfbp/recherche_e.php759 CRBIP/CIP France http://www.crbip.pasteur.fr/onglet.jsp?tab=bact788 CIRM-Levures France http://genome.jouy.inra.fr/cirm/bdd/796 ALGOBANK France http://www.unicaen.fr/ufr/ibfa/algobank/EN/catalogue/catalogue1.php

829 RCC France http://www.sb-roscoff.fr/Phyto/RCC/index.php?option=com_dbquery&Itemid=34

879 LeishCryoBank

France http://www.parasitologie.univ-montp1.fr/catalogue_list.asp

917 CIRM-BP France http://www.tours.inra.fr/cirm_bp_eng/commander_une_souche/le_catalogue

918 CIRM-BIA France http://jwsdp.jouy.inra.fr/Consult/exeRequete.jsp?cirm=gisilbia192 SAG Germany http://sagdb.uni-goettingen.de/274 DSMZ Germany http://www.dsmz.de/microorganisms/main.php?menu_id=2807 CCAC Germany http://www.ccac.uni-koeln.de/recherche.shtml919 FSU Germany http://www.frc.uni-jena.de/stammsammlung.php940 CCCryo Germany http://cccryo.fraunhofer.de/web/strains/485 NCAIM Hungary http://web.uni-corvinus.hu:8089/NCAIM/frameset.jsp

3 NCIM India http://www.ncl-india.org/ncim/catelogue.jsp?mid=29773 MTCC India http://mtcc.imtech.res.in/catalogue.php945 CRA-PAV Italy http://www.collezionedimicrorganismi.com/index.cfm?cis=1#strt195 HUT Japan http://home.hiroshima-u.ac.jp/hut/567 JCM Japan http://www.jcm.riken.jp/JCM/catalogue.shtml591 NIES Japan http://mcc.nies.go.jp/637 MAFF Japan http://www.gene.affrc.go.jp/databases-micro_search_en.php825 NBRC/IFO Japan http://www.nbrc.nite.go.jp/e/index.html597 KCTC Korea http://www.brc.re.kr/English/ekctc.aspx806 KACC Korea http://www.genebank.go.kr/903 CFGR Korea http://genebank.riceblast.snu.ac.kr/500 CDBB Mexico http://micro500.cs.cinvestav.mx/817 LIH-UAM Mexico http://www.histoplas-mex.unam.mx/index_i.html883 CCMM Morocco http://www.ccmm.ma/catalogue.htm133 CBS Netherlands http://www.cbs.knaw.nl/databases/797 NCCB Netherlands http://www.cbs.knaw.nl/databases/

589 ICMP New Zealand

http://nzfungi.landcareresearch.co.nz/icmp/search_cultures.asp

212 IAFB Poland http://kkp.ibprs.pl/914 CCBA Poland http://pasat.ocean.univ.gda.pl/~ccba/ipl.php?id=ba-cya816 MUM Portugal http://www.micoteca.deb.uminho.pt/906 ACOI Portugal http://acoi.ci.uc.pt/342 VKM Russia http://www.vkm.ru596 IPPAS Russia http://www.ippras.ru/cfc/768 IEGM Russia http://www.iegm.ru/iegmcol/strains/index.html836 CCIBSO Russia http://www.rbcar.ro/catalogues.htm412 CECT Spain http://www.cect.org/english/32 CCUG Sweden http://www.ccug.se/

603 UPSC Sweden http://www-hotel.uu.se/evolmuseum/fytotek/651 FCUG Sweden http://www2.dpes.gu.se/FCUGsrch.html475 VTT/CCTM Switzerland http://culturecollection.vtt.fi/ccdb/html?p=s59 BCRC/CCRC Taiwan http://www.ccrc.firdi.org.tw/

383 TISTR Thailand http://www.biotec.or.th/tncc/tistr_dete.html705 BBPP/DOA Thailand http://www.biotec.or.th/tncc/dbstore/DOAC_search.asp707 DMST Thailand http://www.biotec.or.th/tncc/783 BCC Thailand http://www.biotec.or.th/bcc/InternetSearch.asp828 RSKK Turkey http://www.rshm.gov.tr/en/index.php?

option=com_content&task=view&id=34&Itemid=61126 NCPPB UK http://www.ncppb.com/ncppbsearch.cfm128 FLY UK http://www.mba.ac.uk/culturecollection.php134 NCWRF UK http://www.bio-aware.com/cabi/Defaultinfo.aspx?Page=Home137 ECACC UK http://www.hpacultures.org.uk/collections/ecacc.jsp154 NCTC UK http://www.hpacultures.org.uk/collections/nctc.jsp

169 NCYC UK http://www.ncyc.co.uk/184 NCPF UK http://www.hpacultures.org.uk/collections/ncpf.jsp214 IMI UK http://www.bio-aware.com/cabi/Defaultinfo.aspx?Page=Home522 CCAP UK http://www.ccap.ac.uk/ccap_search.php653 NCIMB UK http://www.ncimb.com/search.php?parent=culture814 NCPF UK http://www.hpacultures.org.uk/collections/ncpv.jsp

1 ATCC USA http://www.lgcstandards-atcc.org/ATCCCulturesandProducts/tabid/979/Default.aspx

2 CCMP USA https://ccmp.bigelow.org/search_strains97 NRRL USA http://nrrl.ncaur.usda.gov/cgi-bin/usda/

112 ARSEF USA http://arsef.fpsnl.cornell.edu/mycology/ARSEF_Culture_Collection.html#Catalogs

115 FGSC USA http://www.fgsc.net/scripts/catalog.asp530 LMS USA http://www.carolina.com/573 BGSC USA http://www.bgsc.org/606 UTEX USA http://web.biosci.utexas.edu/utex/Search.aspx827 CGSC USA http://cgsc.biology.yale.edu/849 DSC USA http://www.dictybase.org/StockCenter/StockCenter.html888 UCD-FST USA http://www.phaffcollection.org/933 VTCC Viet Nam http://biotechvnu.edu.vn/vtcc/

Real fields namesGeographic origin, History of deposit, Species, Accession number, Antagonism, Applications, Carbon source assimilation, Carbon source fermentation, Cell wall, Class, Clonal, Collected date, Collector, Collector number, Comments, Conditions for growth - Medium, Conditions for sporulation, Constructed by, Coordinate of Location, Country, Date of identification, Date of isolation, Date of isolation, Decomposes, Deposition date, Description of Location, Description of morphology, Deterioration abilites, Division, DNA-DNA relatedness, EditDate, EntryDate, Enzyme production, Family, Fatty acid profile, Filamentous Growth, Form of supply, G+C (Mol%)\GC, Genotype, Genus, Geographic origin, Growth in broth, Host, Identified by, Images, Infrasubspecific names, Isolate Number, Isolated by, Isolated from, Isolation method, Kingdom, light, Literature, MatingType, MaxMinTemperature, Metabolites, Misapplied names, Mutant, Mycoparasiitism, Name and taxonomy, National name, Numerical taxonomy, O2, Order, Organism type, Other collection numbers, Parents strain, Pathogenicity, pH, Phylum, Pigment, Plasmid, Polar lipid, Quinone, Race, Restrictions, Salt Tolerant, Sensitive to, Serotype, Serovar, Sexual state, Sole Sources of Nitrogen, Status, StorageMethods, Strip test, Synonyms, Temperature, Toxicity, Toxicity type, Toxicity value, Transformation, Veg. compatibility, Yeast physiological data

The data standards compared:

- MINE Bacterial- MINE Fungal- CABRI / OECD MDS+RDS+FDS- Darwin Core- ABCD- Straininfo

MINE The Microbial Information Network Europe

1985 - 1993Sponsored by the CEC, MINE was established to coordinate, harmonize and integrate data on microbial cultures held in collections of 9 EC countries: Belgium, Germany, France, Greece, Italy, Netherlands, Portugal, Spain, U.K.

In 1989 MINE consisted of 32 Culture Collections

Database was planned separately in 9 national nodes. DEC VAX minicomputers (BASIS software) and microcomputers PC AT (ORACLE database).

In 1989 there was on-line access to DSM, CMI, CBS, NCYC, LMG nodes via modem connection. Menu request system, search with AND/OR operators.

Thesaurus files in BASIS aid in maintaining consistency during data entry.

Integrated database was planned in DSM, and Responsible Committee was to make decisions on conflicting strain data.

Group of fields in MINE standardField groups Fungal Bacterial

1 Name + +2 Strain Administration + +

3 Status + +4 Environment and history + +

5 Biological interactions + +6 Sexuality + +7 Properties cytology,

biomolecular data

morphological, cultural and chemota-

xonomical data8 Genetics + -9 Mutants, Plasmids and Phages - +

10 Growth conditions + +11 Chemistry and enzymes + +

12 Practical applications + +

Fields in MINE FungalA. Internal administrationEDI Date of input.EDM Date of last update.SEC Security code.ID Typist's identification.OT Organism type. B = Bacteria, F = Filamentous Fungi, Y = Yeasts.

B. NameSP Species nameSSP Subspecies nameVAR Variety nameF Form nameFSP Epithet of forma specialisRACE Race name, authorsSERO Serotype, serovarMIS Misapplied nameTAX Taxonomy. Contains names of suprageneric taxaMOR Morph: A = anamorph; T = teleomorph.ILL IllustrationsTAXREM Taxonomic remarksLIT Taxonomic and other literature

C. Strain administration

STN Strain numberOCC Numbers in other collectionsEDA Date of accessionEDR Date of receiptCORR Correspondence. Refers to lettersSPINF Special information availableREM General remarks.CHK Internal check of identity at collection.PRE Mode of preservation / storagePREREM Remarks on preservationRESTR Restrictions, care and precautions

D. StatusSTAT Status: T = type strain; NT = neotype; PVRS = pathovar, etc.

E. Environment and history

SUSP Substratum specificitySSTR Original substratumHAB Habitat (original biotope)LOC Origin / location of original material (country, locality).COLL Collector.HERB Herbarium where specimen is depositedISOL Isolated by. Name of isolator, original number of isolate, date.ISOM Source and method of isolationDET Identified byDEP Depositor.HIS History (between isolation and deposit)NAMCH Name changes / previous namesECOLIT Literature on ecologyECOREM Remarks on ecology and environment

F. Biological interactionsSYMB SymbiosisMPAR MycoparasitismPATH PathogenicityALLER AllergenicityTOX Toxicity to other organismsANT Antagonistic activities against other organismsPATHLIT Literature on biological interactionsPATHREM Remarks on pathogenicity

G. SexualitySEX Sexual behaviourSEXST Sexual state

H. Properties (cytology, biorolecular data)NUCL Number of nucleiFSTR Fine structure dataWCONS Wall constituentsCCONT Cell contentsCOO Coenzyme-Q systemSTAIN Staining reactionsPIGMENT Pigment production and autofluorescence.GRWTH Growth characteristicsTKIT Results of test-kitPROPLIT Literature on morphological, taxonomic, fine structure characteristics

I. GeneticsGENOT GenotypeGC Guanine-cytosine content of DNADNAD Hybridization DNA-DNA with other strainsDNAR Hybridization DNA-r.RNA with other strainsRNAD Hybridization r.RNA-DNA with other strainsMUT MutantsMUTMET Method by which mutation was inducedHYBR HybridsPLS Plasmid out/in the hostKIL Killer properties of yeastGENREM Remarks on genetics, DNA data, mutations, plasmidsGENLIT Literature on genetics and mutants

J. Growth conditionsCONDS Conditions for growth and maintenance on solid mediaCONDL Conditions for growth in liquid mediaCONDSP Conditions for fruiting or sporulationCONDGER Conditions for germinationCSOR Carbon sources that have been tested for growth

NSOR Nitrogen sources that have been tested for growthCNSOR Single compounds tested as sole carbon and nitrogen source for growthNUGR Nutritional requirements and growth factors requiredDEF DeficienciesTOL Tolerances and sensitivitiesTEMPR Temperature relationships for growthsTEGR Cardinal temperatures for growthTESP Temperature optimum range for sporulationHEATR Heat resistancePHR pH requirements for growthPHC pH conditionsETHC Ethanol conditionsSALR Salinity requirements for growthSALC NaCl concentrationSUGC Optimum and maximum sugar concentrationsOSM Osmophily and xerophilyWATC Conditions of water activityLC Light conditions

K. Chemistry and enzymesENZ Enzymes producedDEC Decomposition and deteriorating capacitiesMET Metabolites producedBIOTR BiotransformationsCHREM Remarks on chemical dataCHLIT Literature on the impact of chemical and physical factors

L. Practical applicationsAPPL Industrial and general applicationsTEST Applications in testing (assay).BIOM Production of biomass, edibilityPATENT Patent(s)CTR Control of the microorganism in questionAPLIT Literature on application, patents, etc

Fields in MINE BacterialA. Internal AdministrationOT Organism type. B = bacteria; F = fungi; P = plasmids; Y = yeastsEDI Date of inputEDM Date of latest updateID Typist identificationSEC Security code

B. NameSP Species nameSSP Subspecies namePVAR Pathovar nameVAR Infrasubspecific namesSVAR Serovar OTHNAM Other namesSTAT Status: T = type strain; NT = neotype; PVRS = pathovar TAX Taxonomy. Names of suprageneric taxaTAXREM Taxonomic remarksTAXLIT Taxonomic literatureILL IllustrationREM General remarksLIT General references

C. Strain AdministrationSTN Strain number in collectionOCC Other collections numbersEDR Date of receiptEDA Date of accessionCORR CorrespondenceSPINF Special informationCHK Collection checkPRE Preservation type PREREM Remarks on preservationPRELIT Literature on preservationRESTR Precautions and restrictionsSUPPLY Form of supplyADMREM Administrative remarks

D. Environment and HistoryHABI Specific habitat. Indicates restrictions to substratesISOFR Isolated fromLOC Geographic location

COLL Collector of sampleISOL Isolated byISOM Isolation methodDET Identified byDEP DepositorHIS History NAMCH Name changes ENHISLIT Literature on environment and history ENHISREM Remarks on environment and history

E. Properties (morphological, cultural and chemotax-onomical data)FSTR Fine structure dataWCONS Cell wall constituentsCINC Cell inclusionsCHTAX Chemotaxonomical markersGRAM Gram behaviourKOH KOH testAMPEP Aminopeptidase testSTAIN Staining reactionsCELL Shape, arrangement and size of cellMOT MotilityPIGM PigmentsGRWTHL Growth characteristics in liquid media GRWTHS Growth characteristics on solid media

QUADGER Quantitative data on growth RESTST Resting structures. C = cyst, ENS = endospore, EXS = exospore, MS = myxospore, F = fruiting bodyGC Guanine-cytosine content of DNADNAD Hybridization DNA-DNA with other strainsDNAR Hybridization DNA-r.RNA with other strainsRNAD Hybridization r.RNA-DNA with other strains DNASQ DNA sequencesRNASQ RNA sequencesPHYLO Other phylogenetic dataTKIT Result of testkit PROPLIT Literature on propertiesPROPREM Remarks on properties

F. Mutants, Plasmids and PhagesMUT MutantMUTMET Method of mutationMUTREM Remarks on genetics, mutations, DNA dataMUTLIT Literature on genetics and mutants GENOT Genotype, chromosomal marker SEXST Sexual state HYBR Hybrid PLS Plasmids infoPHAGE PhagePLPREM Remarks on plasmids and phages PLPLIT Literature on plasmids and phages

G. Growth ConditionsCONDS Conditions for growth on solid mediaCONDL Conditions for growth on liquid mediaCONDGER Conditions for germinationNUGR Nutritional requirements and growth factorsTOL Tolerances and sensitivitiesDEF DeficienciesMETY Metabolic typeCNUT Carbon nutrition typeCSOR Single carbon sources tested for growthNSOR Single nitrogen sources tested for growth CNSOR Single compounds tested as C and N source for growth OXR Oxygen relationshipsGAS Gas phase. Percentage of gases TEMPR Temperature relationshipsTEGR Cardinal temperatures for growth HEATR Heat resistancePHR pH relationshipsPHC pH conditionsLC Light conditionsSALR Salinity relationshipsSALC Salinity conditionsSUGC Sugar concentrationWATC Conditions of water activity

ELDO Electron donorENERS Energy sourceELAC Special electron acceptorsCONDREM Remarks on growth conditions CONDLIT Literature on growth conditions

H. Chemistry and EnzymesENZ Enzymes producedDEC Decomposition, degradation and utilization capacitiesDETER BiodeteriorationMET MetabolitesLEACH Leaching BIOLUM Bioluminescence HAEMOL HaemolysisMISPROP Miscellaneous propertiesCHREM Remarks on chemical data and metabolic properties CHLIT Literature on chemical data and metabolic properties

I. Biological InteractionsSYMB Symbiosis or synthrophyPATH Pathogenicity and virulenceALLER AllergenicityTOX ToxicityANT Antagonistic activityBINTLIT Literature on biological interactions BINTREM Remarks on biological interactions

J. Practical ApplicationsAPPL General and industrial applicationTEST Applications in testing and assaysCTR Procedures for controlPATENT PatentAPLIT Literature on applications, patentsAPREM Remarks on applications and patents

Example of field specification in MINEName Contents Descriptions

SUGC Sugar concentration

Sugar concentration. In STR. Names of sugars and optimum and maximum concentration (in that order) in % (without "%", but with indication w/w, v/v, w/v, where "w" is weight and "v" is volume). The subfields containing the name of a sugar and the values of the concentrations are separated by ";". Subsubfields containing the values are separated by ",". If a subsubfield contains no data, care must be taken that the comma which terminates this empty subfield is entered. If growth has been tested for a particular sugar at a particular concentration without establishing the range, name and concentration are indicated with the growth response ( + ,-,v). Examples: saccharose, 20, v/v; glucose 3-5,20; glycerol 22-25, w/w

CABRI / OECD MDS+RDS+FDS-OECD Best Practice Guidelines for Biological Resource Centres. OECD, 2007, 115 p.- CABRI (http://www.cabri.org/guidelines.html)

CABRI: MDS+RDS+FDS for Bacteria and Archea, Fungi, Yeast, Plasmids, Phages, Animal and Human Cells, DNA probes, Plant Cells, Plant Viruses

OECD: MDS+RDS for Microbial Accessions (Filamentous fungi, Yeasts, Microalgae, Bacteria, Cyanobacteria, Archaea, Plasmids, Protozoa, Phages, Viruses), DNA, tissues and isolated cells, cell line, primary cultured cells, transformed cells

1 Accession number FY M AcB M M2 Other collection numbers FY M AcB M M3 Restrictions FY M AcB M M4 Organism type FY M AcB M M5 Name FY M AcB M M6 Race FY R R7 Status FY M AcB M M

8 Misapplied names/Other names FY R AcB R R9 History of deposit FY M AcB M M

10 Conditions for growth FY M AcB M M11 Form of supply FY M AcB M M12 Isolated from FY R AcB R R13 Geographic origin FY R AcB R M14 Mutant FY R AcB R R15 Sexual state FY R AcB F R16 Literature FY R AcB R R17 Infrasubspecific names AcB M -18 Serovar AcB R R19 Genotype FY F AcB R R20 Pathogenicity FY F AcB F21 Enzyme_production FY F AcB F F22 Metabolite_production FY F AcB F F23 Applications FY R AcB F F24 Remarks FY F AcB F F25 Price_code FY F AcB F F26 Catalogue_entry AcB F F27 Plasmids AcB F F

Darwin Corehttp://rs.tdwg.org/dwc/, 184 fields

The Darwin Core standard was originally conceived to facilitate the discovery, retrieval, and integration of information about modern biological specimens, their spatiotemporal occurrence, and their supporting evidence housed in collections

Keeps expanded list of geographical and geological fields and fields for taxonomy. We did not find the fields: Restrictions, Toxicity, Identification, Deposition and Isolation data, Conditions for growth, Storage Methods, Race, Mutant, Serovar, Kind of relationship, Applications, group of fields Phenotype.

Simple Darwin Core http://rs.tdwg.org/dwc/terms/simple/index.htmDarwin Core Terms: A quick reference guide http://rs.tdwg.org/dwc/terms/

Darwin Core (versions DwC 1.21, DwC 1.3 and DwC 1.4) makes a part of TDWG group of standards.

ABCDAccess to Biological Collections Data Standard

This schema is a common data specification for biological collection units, including living and preserved specimens, along with field observations that did not produce voucher specimens. It is intended to support the exchange and integration of detailed primary collection and observation data.

http://www.tdwg.org/activities/abcd/

1305 fields in version 2.06, including containers, makes a part of TDWG group of standards.

Based on BioCASE software.

Description of fields is given on http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcepts.

The biggest group of items is DataSets/DataSet/Units/Unit/Gathering/ (423 fields) - the elements describing the event and site of collecting a microbial unit - description of the place, geographical data (even bigger than in Darwin Core). ABCD presents a very big list of fields with contact data: for institutions and people, which keep the database or the records, or acquired microorganisms – names, phones, E-mails, etc. – in various formats. Also pictures, property fields (including IPR), bibliography and comments. Ruther short opportunities for most of other types of data in microbial CC. We didn’t find the fields Pathogenicity, Race, Price code, the field Applications is specified but with no definition inside.

Standard is very difficult in use.

Example from this descriptionIdentifier: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/LongitudeDecimalDocumentation: The longitude of the gathering site, expressed in decimal degrees.Content: The longitude of the gathering site, expressed in decimal degrees. Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required. A FAO/IPGRI multi-crop passport descriptor (MCPD), description and examples taken from EURISCO descriptor list dated July 3, 2002. Maps to Darwin Core 2: Longitude.Example Value: 0762510W

Straininfo MCL 2.1 (2011)http://www.straininfo.net/projects/mcl/reference.

MCL presents Strainifo database content in XML format.

103 fieldsFields structure, descriptions, recommended values, references to external data standards: MINE, DCMI Metadata, PRISM, WGS84

Any microbial culture collection that has programmer and sufficiently good catalogue presentation in Internet, can become Straininfo partner and upload its catalogue into Straininfo database. The collection catalogue is to be converted to XLM file according to MCL specification.

Examples presented on pages http://www.straininfo.net/projects/mcl/reference and http://www.straininfo.net/projects/mcl/ are quite sufficient for this job.

ABCD MINE F MINE B Real Darwin Core0 SERO 1 0 Serotype 0

.../Serovar 1 SERO 1 SVAR 1 Serovar 0

.../MycologicalLiveStage 1 SEX 1 0 Sexual state lifeStage 10 NSOR 1 NSOR 1 Sole Sources of Nitrogen 00 STAT 1 STAT 1 Status typeStatus 10 PRE 1 PRE 1 StorageMethods 00 TKIT 1 TKIT 1 Strip test 0

.../Temperature 1 >CONDL 1 0 Temperature 00 <TOX 1 <TOX 1 Toxicity 0

Comparison of the standards.Fragment of the table

Compliance with Real Related to CCABCD 24(252) 26% 19%MINE B 71 76% 55%MINE F 81 87% 72%OECD 50 54% 100%DwC 31 33% 17%Straininfo 20 22% 19%

Comparison of the standards.Final results

Combined list of fieldsLocationEng, Depositor, AuthoritySp, Strain nmbr, Antagonism, Applications, Carbon source assimilation, Carbon source fermentation, Cell wall, Class (-), Clonal, Collected date, Collector, Sample number, General remarcs, StrainComments, GrowthMedium liquid, Conditions for sporulation, Constructed by, decimalLatitude (?), countryCode (-), IdentificateDate, Date of isolation, IsolationDate, Degradation, ReceivedDate, AreaDetail , CellMorphology, Deterioration abilites, Division (-), DNA-DNA relatedness, EditDate, EntryDate, Enzyme production, family (-), Fatty acid profile, Filamentous Growth, Supply, G+C (Mol%)\GC, Genotype, Genus, stateProvince, Growth in broth, associatedTaxa, IdentificateByEng, Images, AuthoritySubSp, IsolateNumber, IsolatedBy, IsolatedFrom, Isolation method, kingdom (-), Light conditions, References, MatingType, Sexual state, MaxMinTemperature, Metabolites, OtherName, Mutant, Mycoparasiitism, originalNameUsage (?), Taxcomments, ColonyMorphology, Oxygen relationships, order (-), Subcollection, OtherCol, Parents strain, Pathogenicity, pH relationships, phylum (-), Pigment, Plasmid, Polar lipid, Quinone, Race, PhytopatogenLevel, Salt Tolerant, Tolerances and sensitivities, Serotype, Serovar, State, Sole Sources of Nitrogen, Type, StorageMethods, Results of test-kit, Synonym, IncubationTempLiquid, Toxicity, Toxicity type, Toxicity value, Transformation, Veg. compatibility, Yeast physiological data

Results of comparison

Compliance with Real Related to CCABCD 24(252) 26% 19%MINE B 71 76% 55%MINE F 81 87% 72%OECD 50 54% 100%DwC 31 33% 17%Straininfo 20 22% 19%Combined 93 100% 100%

Combined standardTaxonomy

CCname, Organism type, Genus, Species, Authors of species, date, Subspecies, Variant, Authors of variant, date, Forma, FormaSpecies, Pathovar, Serotype, Serovar, Race, Synonym, Misapplied name, Name changes, Type strain, Strain nmbr, IdentificationComments, IdentificationReferences, IdentificateDate, IdentificateBy, Taxlit, Taxcomments

History of strain, Sample, EcologyCorrespondence, ReceivedDate, Date of accession, Depositor, History, OtherCol, IsolateNumber, IsolationDate, Isolation method, IsolatedBy, IsolatedFrom, Collector, Sample number, CountryCode, Country, Height, DecimalLatitude, DecimalLongitude, Altitude, MaximumDepthInMeters (?), MinimumDepthInMeters (?), NamedArea, AreaDetail , Geographic location, Island, Habitat, associatedTaxa, Ecollit, Ecol comments

Growth and maintenance conditionsGrowthMedium solid, GrowthMedium liquid, Remarks on growth conditions, Growth in liquid , Growth on solid , Filamentous Growth, Carbon nutrition type, Carbon source assimilation, Carbon source fermentation, Energy source, Sugar concentration, Sole Sources of Nitrogen, Oxygen relationships, Percentage of gases, Ethanol condition, Growth factors, Conditions of water activity, MaxMinTemperature, Temperature relationships, Light conditions, pH conditions, pH relationships, Quantitative data on growth, Growth conditions lit, Temperature for sporulation, Conditions for sporulation, Conditions for germination, StorageMethods, Storage Comments, Data of storage, Storage Lit

Strain propertiesFine structure data, CellMorphology, Cell wall, Cell contents, ColonyMorphology, MatingType, Sexual state, Morph, Resting structures, Motility, Images, Gram stain, Staining reactions, Deficiencies, Heat resistance , Salinity relationships, Salt Tolerance, Osmophily and xerophily, Bioluminescence, Coenzyme-Q, Haemolysis, Killer properties, Metabolic type, Pigment, Tolerances and sensitivities, Results of test-kit, Aminopeptidase test, Electron donor, Special electron acceptors, Propertieslit, Remarks on properties, Allergen, Pathogenicity, Risk group, Restrictions, Toxicity, PhytopatogenLevel, Pathcomments, Interactions type, Interactions lit, Parasitism, Symbiosis, Antagonism, Chemical control, Chemlit, Metabolites, MetabolComments, TestSystems, Biofertilizer, Biopesticide, Bioremediation, Transformation, Degradation, Deterioration abilites, Enzyme production, Applications, Applicationslit, Miscellaneous properties, Production of biomass, Patent, Remarks on applications, References, General remarks, StrainComments

Genetic characteristics of strainHybrids, Plasmidslit, Mutant, Plasmid, Gencomments, Remarks on plasmids and phages, Phage, DNA sequences, DNA-DNA relatedness, G+C (Mol%)\GC, Genotype, Hybridization DNA-r.RNA, Hybridization r.RNA-DNA, GenMitlit, Other phylogenetic data, RNA sequences

Processing dataCurator, Security code, Supply, Category, EditDate, EntryDate, Date of last check , Date of last transfer

Genetic data standardsThe International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org) includes:- GenBank - the National Center for Biotechnology Information - NCBI, USA http://www.ncbi.nlm.nih.gov/genbank/ - EMBL-Bank at the European Molecular Biology Laboratory http://www.ebi.ac.uk/embl/- DDBJ - the DNA Data Bank of Japan, Japan http://www.ddbj.nig.ac.jp/Each of these databases is daily updated at the expense of interchanging the new DNA sequences submitted to any one of them.These three organizations have slightly different submit procedures for new genetic data, but according their exchange data procedure we can speak of the unified data base DDBJ/EMBL-Bank/GenBank and, accordingly, one unified data standard.

Genomic Standards Consortium (GSC http://gensc.org/gc_wiki/index.php/Main_Page) in 2008 - 2011 prepared new standards - "minimum information" checklists:- MIGS/MIMS - The reporting of genomes and metagenomes (http://gensc.org/gc_wiki/index.php/MIGS/MIMS)- MIMARKS - The reporting of environmental sequencing including ribosomal genes (http://gensc.org/gc_wiki/index.php/MIMARKS)

In the project "MIGS/MIMS Structured Comment" GSC is also working with INSDC to develop a way to submit these data standards to DDBJ/EMBL-Bank/GenBank

In project BRIO we communicate with MIGS/MIMS component.

MIGS/MIMS specification in XLS file has two worksheets:- MIGS_MIMS checklist with 47 standard fields presenting common data, and- environmental packages with 653 fields presenting features of the 14 types of microbial source: air, host-associated, human-associated, human-gut, human-oral, human-skin, human-vaginal, microbial mat/biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater/sludge, water. 193 fields from this list are unique.

19 fields from MIGS_MIMS checklist have or may have some compliance with usual CC catalogue data, the main problem - there is no microorganism name in this list.193 fields of environmental packages present detailed (mostly chemical) information on the source (habitat), that potentially can be compliant to the properties of microorganisms extracted, but this is the subject of additional study.

WDCM Reference Strain Catalogue

This catalogue was produced to enable broader and easier access to the reference strains listed by the ISO TC 34 SC 9 Joint Working Group 5 and by the Working Party on Culture Media of the International Committee on Food Microbiology and Hygiene (ICFMH-WPCM).

DB for Microorganisms in Extreme Environment

Hot spring

Volcanic

Volcanic salt and alkali lakes

中国科学院微生物研究所

Isolation

• Temperature• Humidity• PH value• Elevation• Vegetation• Date

Application

• Usage• Industry use

Physiological and

biochemical

properties

• Medium• Culture

conditions• Biochemical

reactions• Metabolites

Sequences

• Sequence• Genome • Annotation

• Information sharing to resources sharing• Get benefits according to CBD• Strains even outside of CCs• For both scientific and industry users

Database

DB for Microorganisms in Extreme Environment

• CODATA Task Group on Advancing Informatics for Microbiology (TG-AIM)

Общие требования включают:

•гарантии устойчивого функционирования в течение длительного времени (с указанием источников финансирования);

•наличие квалифицированного персонала;•обязательства по выполнению своих функций (в строгом

соответствии с национальной нормативно-правовой базой): прием и хранение первичного образца, поддержание образцов (консервация, проверка идентичности) и др.;

•обязательства по ведению документооборота;•ведение компьютерной базы данных с описанием депонированного

биологического материала и его происхождения, доступной через Интернет;

•обязательства по использованию стандартных сред и реагентов для поддержания коллекций;

•обеспечение контроля качества биологического материала, проверки его на безопасность (или проверки соответствия декларированному уровню биологической опасности)

ISO 2000, ISO 9001, ISO 14001, ISO 14004, ISO 14010, ISO 14012, ISO 19011

Участник Страна

DSMZ DE

CABI UK

IP FR

SPP-PS BE

KNAW/CBS NL

UGOT SE

UVEG-CECT ES

UGENT BE

INRA-CIRM FR

JacobsUni DE

UMinho-MUM PT

MUT IT

CSIC-IMEDEA ES

VKM RU

IAFB-CCIM PL

USMI IT

Благодарю за внимание

Василенко Александрvanvkm@gmail.com