理研バイオリソースセンター微生物材料開発室 ·...

理研バイオリソースセンター微生物材料開発室 Japan Collection of Microorganisms, RIKEN BioResource Research Center

Collection, Preservation, Quality Control, Distribution of diverse species of Bacteria, Archaea, Fungi useful for environmental and health sciences to

contribute to scientific community

Staff Members

Head Dr. Ohkuma

Curators 7

Gene Analysis 1

Resource Advancement 3

Agency-staff and Part-timers 17

Postdoctoral Fellows 4

Visiting Scientists 2

Students 2

1981 Establishment in Wako campus

2004 Integrated with RIKEN BRC as Microbe Division

2007 Appointed as a core member of National Bioresource Project

2012 Relocation to Tsukuba campus

Microbial Resources in JCM

1) Strains relevant to researches of human health and environmental

conservation

2) Type strains and related strains of bacteria, archaea, filamentous fungi and

yeasts (confine to BSL 1 and 2 microorganisms)

3) Model microorganisms for academic researches (e.g., genome-sequenced

microorganisms)

Indigenous bacteria in human

intestines, skins and oral cavities

Bacteria that cause metal corrosion Oleaginous yeasts utilizing starch

Symbiotic microbes

associated with plants

and insects/termites

Strain Holding

Bacteria

(18,989)

Archaea

(817)

Total: 27,544 strains

(As of November, 2018)

Filamentous Fungi

(4,031)

Yeasts

(3,681)

Others: micro-algae

(26)

Proteobacteria 40%

Actinobacteria 29%

Firmicutes 23%

Bacteroides 7%

Others (15 phyla) 1%

7,585

404

460

893 5

type strains or derived from

type materials


conservation




microorganisms)


Genome sequence (accession No.)

Genomic DNA

As of October, 2018, genomic

DNA samples of more than 760

strains are available from the

RIKEN DNA BANK.

As of November, 2018, genomic

sequences of more than 2,100

strains are accessible.


conservation




microorganisms)


NBRP (National BioResource Program) Genome Information Upgrading

Program. Under the program, JCM has determined genome sequences of

various microbial strains useful for researchers, in collaboration with the other

genome-sequencing centers/institutes.

Genome Sequencing of JCM strains

FY 2014 Eukaryotic strains, 217 strains, Data publication in 2016

(http://www.jcm.riken.jp/cgi-bin/nbrp/nbrp_list.cgi)

FY 2012 Prokaryotic strains 312 strains, Data publication in 2014

(http://jcm.brc.riken.jp/en/nbrplist_e)

Genome Sequencing of JCM strains

Culture collection

partners

ATCC, BCCM/LMG,

BCRC, CAIM, CBS,

CCUG, CECT, CICC. CIP,

CGMCC, ICMP, JCM,

KCTC, KMM, MUM, NCTC,

NBRC, NCAIM, PCU,

TBRC, TISTR, UCD, VKM

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WFCC Newsletter No.52 (Dec. 2012) Mar 13, 2013

WDCM has been approved by CODATA as its Task Group on Advancing Informatics for Microbiology… Mar 13, 2013

EBRCN International Regulations for Packaging and Shipping of Microorganisms Dec 18, 2012

more

FORDA Culture Collection NEWSLETTER Dec 05, 2012

Algaculture for Biotechnology Course Aug 13, 2012

International course "Computational genomics" Feb 04, 2012

WFCC Bylaws WFCC Task Forces and Activities Microbiological sites

WFCC Statutes The Endangered Collection Task Group (ECTG) WFCC Committees

WFCC Newsletter No.51 (Apr. 2012) Apr 12, 2012

Protect celebrates 30 years of microorganism preservation Jan 17, 2012

The 13th International Conference on Culture Collections(ICCC-13)

WFCC Global Catalogue of Microorganisms

Copyright © 2011 World Federation for Culture Collections All rights reserved.

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The 7th WDCM WorkshopOctober 12-13, 2017, Beijing

Organized by:

➢ Institute of Microbiology, CAS

➢ World Federation for Culture Collections (WFCC)

➢ European Commission

Supported by:

➢ Department of General Administration, CAS

➢ Bureau of Science & Technology for Development, CAS

➢ Bureau of International Co-operation, CAS

➢ National Science and Tech Infrastructure Center, MOST

15 collections from 12 countries➢

ATCC, DSMZ, CBS, JCM, KCTC,

BCCM , TBRC, CGMCC etc.

WDCM GCM 2.0

Contract of the research collaboration (JCM-WDCM Joint Genome Sequencing Project)

Selection of microbial strains to be genome-sequenced

FY2018 51 strains

FY2019- 50-100 strains/year

Preparation of DNA samples

Conclusion of MTA (category II)* for 2018 resource delivery *relevant to for-profit organization(s)



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Timeline of the JCM-WDCM Joint Genome-Sequencing Project

Delivery of the dried DNA samples to BGI@HongKong 15 strains (1st batch): delivered in September 2018

31 strains (2nd batch): will be delivered by January 2019?

December 2017

June 2018

September 2018

May 2018

JCM No. Species name

1. JCM 14781 Amphritea balenae

2. JCM 17466 Anaerostipes butyraticus

3. JCM 31056 Butyricicoccus faecihominis

4. JCM 18676 Butyricimonas faecihominis

5. JCM 18677 Butyricimonas paravirosa

6. JCM 14719 Calditerricola satsumensis

7. JCM 12580 Lentibacillus kapialis

8. JCM 18682 Parabacteroides faecis

9. JCM 23203 Pelagicoccus mobilis

10. JCM 30531 Porphyromonas pasteri

11. JCM 31740 Sulfodiicoccus acidiphilus

12. JCM 13583 Thermogymnomonas acidicola

13. JCM 19902 Thermus composti

14. JCM 30071 Virgibacillus kapii

15. JCM 11219 Vulcanisaeta souniana

including archaea, anaerobic bacteria, thermophilic bacteria, halophilic bacteria

List of First Batch Strains for the Genome-Sequencing

Illumina HiSEQ Platform Scaffold: 31 to 168

N50: 31K to 932K

Output of the Genome-Sequencing

Review the output

Registration in the DDBJ/ENA/GenBank

Further analyses (including

re-sequencing, completion of

the whole genome)

Publication process of the genome sequences

Publication

Public Databases

WDCM GCM website

JCM Online Catalogue



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Acknowledgements

All of the partners involved in

the GCM 2.0 projects

理研バイオリソースセンター微生物材料開発室 ·...

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