Soon Gyu Hong1, Min Chul Lee1, Cheng-Dae Choe2 and Hong Kum Lee1

KOPRI BioDBA part of Korea Polar Data Center

1 Korea Polar Research Institute2 Newgex Co. (Boram Pharm. Bioinfo team)

Databases to manage Bio-resources

Samples from Polar areaSoil, sediment, water, glacier, lichens, plants, animals

Samples from Polar areaSoil, sediment, water, glacier, lichens, plants, animals

Microbial and tissue culture

Microbial and tissue culture

Identification by phylogenetic analysis

Identification by phylogenetic analysis

Polyphasic classification

Polyphasic classification

Metagenomic DNA isolation

Metagenomic DNA isolation

Metagenomelibrary

Metagenomelibrary

Genomelibrary

Genomelibrary

Selection of clones

Selection of clones

CharacterizationCharacterization

Sample DBSample DB

Strain DBStrain DB

Sequence DBSequence DB

Genomic DNA DB

Genomic DNA DB

Genome Library DB

Genome Library DB

Metagenome Library DB

Metagenome Library DB

Clone DBClone DB

Enzyme DBEnzyme DB

Polymer DBPolymer DB

Metabolite DBMetabolite DB

Samples from Polar Areas

Locality water sediment soil glacier plant animal

Fungi(lichens) biofilm total

Sejong Station 21 1 260 7 289

Dasan Station 15 4 4 6 41 7 140 21 238

Barents/Cara 156 235 22 50 10 31 504

Okhotsk/Bering 129 426 555

Austria 8 7 15

Baikal 44 44

etc 10 82 92

total 331 665 34 14 135 17 513 28 1,737

Ny-Ålesund2006.7.14-2006.7.31

Cultural strains

Bacteria: 4,500 strains

Molds: 30 strains

Moss: 8 strains

Microbial cultures

Preservation

Liquid nigrogen (-180C)

deep freezer (-80C)

Freeze-dry

Actinobacteria113

Crenarchaeota1

Gam m aproteobacteria534

Betaproteobacteria10

Alphaproteobacteria59 Firm icutes

688

Bacteroidetes171

1583 STRAINS 99 GENERA

Microbial Cultures

Arthrobacter, 41

Leifsonia, 12Microbacterium , 3

Micrococcus , 16

Nocardioides , 1

Plantibacter, 1

Rhodococcus , 5

Salinibacterium , 17

Sanguibacter, 6

Subtercola, 1

Agrococcus , 1

Brachybacterium , 2

Brevibacterium , 3Cellulom onas , 1

Knoellia, 2

Curtobacterium , 1

ACTINOBACTERIA

Microbial Cultures

16 genera113 strains

Cellulophaga, 26

Flaviramulus, 6

Flavobacterium, 35

Formosa, 2

Gaetbulibacter, 2

Gelidibacter, 2

Gillisia, 2

Leeuwenhoekiella, 4

Maribacter, 22

Olleya, 9

Pedobacter, 2

Persicivirga, 1

Polaribacter, 10

Sediminicola, 2

Sejongia, 6

Sphingobacterium, 5

Tamlana, 2

Tenacibaculum, 1

Ulvibacter, 1

Winogradskyella, 4

Zobellia, 10Algibacter, 1

Aequorivita, 1

Aquimarina, 3

Bizionia, 1

Arenibacter, 2

Algoriphagus, 9

BACTEROIDETES FIRMICUTES

Bacillus , 578

Paenibacillus , 50

Planococcus, 11

Staphylococcus, 2

Pullulanibacillus , 1

Planom icrobium, 3

Sporosarcina, 19

Halolactibacillus , 1

Marinibacillus , 12

Halobacillus , 6

Lis teria, 1

Virgibacillus , 2

Trichococcus, 1

Terribacillus , 1

Arthrobacter, 41

Leifsonia, 12Microbacterium , 3

Micrococcus, 16

Nocardioides , 1

Plantibacter, 1

Rhodococcus, 5

Salinibacterium , 17

Sanguibacter, 6

Subtercola, 1

Agrococcus, 1

Brachybacterium , 2

Brevibacterium , 3Cellulom onas, 1

Knoellia, 2

Curtobacterium , 1

ALPHAPROTEOBACTERIA

Pseudoalterom onas ,234

Pseudom onas , 51

Psychrobacter, 98

Dasania, 1Colwellia, 5

Photobacterium , 2Marinom onas , 1

Halom onas , 6Granulos icoccus , 1

Glaciecola, 8

Alterom onas , 66

Psychrom onas , 10

Rheinheim era, 1

Shewanella, 44

Stenotrophom onas ,6

GAMMAPROTEOBACTERIA

27 genera171 strains

13 genera688 strains

16 genera59 strains

15 genera534 strains

Information for Culture Condition

Temperature : 4 – 37CMedia: R2A, ZB, MR2A, TSA, NA

Enzyme and polymer Production

Protease test on ZoBell or 0.1x NA with skim milkLipase test on ZoBell or 0.1x NA with TBAChitinase test on ZoBell or 0.1X NA with coloidal chitinPolymer test on SZoBell with high glucose content

Tests at 10C and 20 C

Management and sharing of bio-resources from

polar areas

Sharing biodiversity information with national and

international organization

Needs for KOPRI BioDB

Central directory system containing all Antarctic data set descriptions

gathered by NADCs.

Hosted by the Global Change Master Directory (GCMD)

AMD: Antarctic Master Directory

AntarcticMasterDirectory

GlobalChangeMasterDirectory

NationalAntarcticData Centre

KoreaPolarData Centre

Scientist Metadataentry

Scientist Metadatasearch

NationalAntarcticData Centre

Metadata entry

Scientist Scientist

Data entry Data search

ADMSAntarctic Data Management System

Data Management

KOPRI BioDB(Culture Collection)

KOPRI BioDB(Culture Collection)

CuratorsCurators

Public databasesPublic databases

Public usersPublic users

search

Datadownload

Public users Contributors

Public users Contributors

Deposit of resources

Delivery of resources

• Long-term preservation of bio-resources• Identification• Characterization• Data updates

• Metadata upload (AMD)• Original data transfer (EBA, SCAR-Marbin etc)

• Data download (GenBank Taxonomy etc)

DB Structure

Sample DBSample DB

Strain DBStrain DB

Reference DBReference DB

Taxonomy DBTaxonomy DB

Nomenclature DBNomenclature DB

Media DBMedia DB

Environmental dataGeographical data

Media composition

ReferencesTaxonomic hierarchyNomenclature (Authors, year, Korean name)

Schema

Sample Database

Sample Database

Sample Database

Sample Database

Sample Database

Schema for Strain DB

Strain DB

Strain DB

Strain DB

Strain DB

Workflow for delivery

User Search

Curator 1

SelectionShopping

Cart

Order

Curator 2

Curator 3

Sorting by curator (Work order on the DB system and E-mail alert)

save

User

E-mail of order information and strain information

DeliveryUser

ClaimWhen strains have problems(no revival, contamination, misidentification etc) Curator

Receive Claim

Records for Claim

Revival testPurity checkRe-identification

Taxonomy Geography HabitatsCharacterist

icsOthers

Data Search : click next category for search or use boolean search option

Taxonomy

Species

Genus

Family

Order

Class

Phylum

Kingdom

Division

Boolean Search

Bacillussubtilis

Search History

Search Results

AND / OR / NOT

AND / OR / NOT

AND / OR / NOT

AND / OR / NOT

AND / OR / NOT

AND / OR / NOT

AND / OR / NOT

AND / OR / NOT

Bacillus [genus] AND subtilis [species]

Show results

Further Search 1231 results from : Bacillus [genus]

Show results

Further Search 153 results from : Bacillus [genus] AND subtilis [species]

Select Strain Species Locality Habitat Characteristics Availability KOPRI 25231 Bacillus subtilis Antarctic marine protease at 4˚C

strain KOPRI 22321 Bacillus subtilis Barents sea marine lipase at 15, 20 and 25˚C

none KOPRI 23215 Bacillus subtilis Cara sea marine lipase at 20 and 25˚C

strainOrderShopping

cartDownload

Data

Search

Welcome any advices and comments

Soon Gyu Hong (Korea Polar Research Institute)polypore@kopri.re.kr