JCM On-line Catalogue of Strains

 Scientific name 1
 Genus:
 Species:
    Example 1: Genus = Micromonospora
Example 2: Species = aurantiaca
Example 3: Genus = %monospo, Species = %ensis
(Prefix match search at each box. Inside match or suffix match search can be performed by using "%" as a wild-card character like Example 3. Case-insensitive)

 Scientific name 2
 Scientific name:
    Example 1: Scientific name = Micromonospora chalcea
Example 2: Scientific name = Lactobacillus paracasei subsp. paracasei
(Prefix match search. Inside match or suffix match search can be performed by using "%" as a wild-card character. Case-insensitive)

 JCM accession number
   JCM:
    Example: JCM = 12345 (Exact match search)

 Accession number of other culture collection
 Acronym:
 Number:
    Example 1: Acronym = DSM, Number = 43067
Example 2: Acronym = VKM, Number = Ac-636
(Exact match search at both boxes. Case-sensitive)

 Keyword
   Keyword:
    Example: Keyword = genome sequence
(Inside match search. Case-insensitive)

 Culture medium
 JCM Medium No.:
 Name of Medium:
    Example 1: JCM Medium No. = 58
Example 2: Name of Medium = malt extract
(Exact match search for "JCM Medium No." and inside match search for "Name of Medium". Case-insensitive)

FAQ

Ordering The JCM on-line catalogue Deposition
Ordering
Ordering microbial genomic DNA

《Ordering》

1.The JCM on-line catalogue
Q.1 Can you tell me how to use the on-line catalogue?
A.1 Users are able to search the on-line catalogue for JCM strains using the scientific name, JCM accession number, accession number of other culture collections, and other strain data (keyword). JCM strains can also be using the ormer scientific names. If the user encounters an accession number of some culture collection in a journal article, etc., it is possible to search whether or not the strain in question is contained in the JCM collection.
Q.2 How do I find the JCM accession number of strains that were transferred from the IAM culture collection?
A.2 If you would like to search using the IAM number, please use the “Accession number of other culture collection” search. In addition to the isolates strains originally held by the JCM, the current collection contains 1,824 strains (80 actinomycetes, 957 non-actinomycete bacteria, 6 archaea, 102 yeasts, and 679 filamentous fungi. A list is available at <http://jcm.brc.riken.jp/en/iam_info2_e> from the IAM collection.
Q.3 Why does type strain representation for molds and yeasts differ between JCM and other collections?
A.3 The rules for naming fungi (mushrooms, molds, yeasts, etc.) follow the International Code of Nomenclature for algae, fungi, and plants (ICN). The term “type strain” in reference to bacteria is not included in the ICN protocol. For plants and fungi, as a general rule, the “type” attached to a given scientific name cannot be a living organism but, rather, must be a dehydrated specimen or an illustration of the type (although exceptions have been made in recent years for freeze-dried specimens that are metabolically inactive). However, in consideration of the practical utility of a living strain derived from the type s train, the term “ex-type strain” is used to officially designate such strains so that they can be used for purposes of comparison, etc. Accordingly, not only do fungus strains in culture not represent type strains from a nomenclature standpoint, the term “type strain,” in the first place, is not recognized in the official nomenclature rules. That said, the term “type strain” is often used in place of “ex-type strain,” particularly in the case of yeasts, for the benefit of users who deal with microbes including bacteria. Furthermore, considering that many mushrooms and molds are difficult to culture and the fact that the naming of such organisms traces its history back to the time of Linnaeus (1735), ex-type strains do not exist in the vast majority of cases.
Q.4 There’s a strain with a JCM accession number cited in a paper that does not appear in the JCM catalogue. Is it possible to obtain this strain?
A.4 In the case of some newly proposed taxa, preparations are being made to make strains available to users. Alternatively, the strains may be undergoing re-examination if, for example, the strain in question does not exhibit the characteristics described in the publication. In either case, if the user contacts us (inquiry.jcmriken.jp), we will provide information regarding expected availability, etc.
2. Ordering
Q.5 There are both Japanese and English versions of the “Material Transfer Agreement (for distribution).” Can I use either one?
A.5 Because the “Material Transfer Agreement (for distribution)” must be stamped with a ko-in (official seal), users in Japan are required to use the Japanese version of the agreement.
Q.6 How should I fill in the blank after “RECIPIENT” in the preamble section of the Material Transfer Agreement?
A.6 In the RECIPIENT blank of the preamble, please enter the recipient organization name and the name of the principal investigator for Recipient Scientist. In the case of a university, please use the format: ○○○ University, Department of □□□, Principal investigator name or ○○○ University Graduate School, Department of □□□, Principal investigator name. In the case of a company, please use the format: Company name, Principal investigator name.
Q.7 I signed a Material Transfer Agreement with a previous order. If I am submitting an order request for the same strain, is it necessary to submit a Material Transfer Agreement a second time?
A.7 A previously signed Material Transfer Agreement is valid as long as the person in charge, principal investigator, research purpose, and strain are the same. In such cases, enter the number of the previously signed MTA in ORDER FORM (Form M-10).
Q.8 I would like to use strains ordered from RIKEN BRC-JCM for multiple research purposes. How should I fill in Item 2 of the Material Transfer Agreement regarding research purpose?
A.8 Separate Material Transfer Agreements are required for each research purpose. We apologize for the inconvenience but ask that you submit a separate MTA for each research purpose. Please provide a concrete description of the purpose (similar to a journal article title). If a strain is subsequently used for a purpose other than the original purpose, we require that you sign a new Material Transfer Agreement. Please inform RIKEN-BRC beforehand of any intent to change research purpose. In addition, if the results of research utilizing a strain distributed under Material Transfer Agreement (for distribution) Category I (not-for-profit academic research purposes by a not-for-profit institution) are used for commercial purposes (including patent acquisition), we ask that you submit a new Material Transfer Agreement (for distribution) Category II form.
3. Ordering microbial genomic DNA
Q.9 Is it possible to order microbial genomic DNA that is not listed in the on-line catalogue?
A.9 At present, we are considering expanding the range of microbial genomic DNA resources offered. If you are interested in acquiring non-listed resources, please contact (inquiry.jcmriken.jp).

《Deposition》

Q.10 Is it possible to deposit unidentified strains or new species, etc. whose descriptions have not yet been published and whose scientific name have not yet been determined?
A.10 Yes, it is possible. In such cases, please fill out use a description such as “unidentified bacterium.” in the column of scientific name on the Deposition Data Sheet (Form M-8). Please provide information including the strain designation, isolation data, country of origin, etc. There are places for this information to be entered on the Deposition Data Sheet (Form M-8).
Q.11 I am currently preparing a manuscript on a strain that I am planning to deposit in the RIKEN BRC-JCM. I would like to make citation of the paper a condition for deposition. How should I state this on the Material Transfer Agreement (for deposition).
A.11 Please include a statement to that effect for Item 6 of the Material Transfer Agreement (for deposition) along with information regarding the paper (author name(s), title, etc.). The Material Transfer Agreement will be concluded based on that information. Upon publication of the paper, please send us a reprint or information regarding the paper (author name(s), title, journal name, volume, pages, publication year) as soon as possible. This information will be used to revise the Material Transfer Agreement and will be published on the website as a condition for ordering. Please be aware that the strain in question will be made available upon publication of the paper, but the deposition conditions will not be applied until the paper reprint or information is provided by the depositor.
Q.12 I would like the deposited strain to be released to the public after the paper that I am currently preparing has been published. How should I request this on the Material Transfer Agreement?
A.12 There is no specific location on the Material Transfer Agreement to do so. Please inform us of your request using the Deposition Data Sheet (item 15, for bacteria and archaea; item 18, for yeasts and filamentous fungi). Note that the strain will be made accessible to the public at the discretion of the JCM five years after the deposition date.
Q.13 There are both Japanese and English versions of the “Material Transfer Agreement (for deposition).” Can I use either one?
A.13 Because the document must be stamped with a ko-in (official seal), users in Japan are required to use the Japanese version of the agreement.
Q.14 How should I fill in the blank after “DEPOSITOR” in the preamble sections of the Material Transfer Agreement (for deposition)?
A.14 In the DEPOSITOR blank of the preamble, please enter the depositor organization name and the name of the principal investigator for Depositor Scientist. In the case of a university, please use the format: ○○○ University Department of □□□, Principal investigator name or ○○○ University Graduate School, Department of □□□, Principal investigator name. In the case of a company, please use the format: Company Name, Principal investigator name.
Q.15 When can I expect to receive a Certificate of Deposition or Availability?
A.15 For a new species, etc. to be published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) or to submit a request for publication of a new species name on the IJSEM Validation List requires certification that the strain has been deposited in culture collections in at least two different countries and that the strains are available to the public. Please submit an application if you require such certification. A certificate will be issued after the strain has been examined for viability and purity and confirmed the authenticity by the 16S rRNA gene sequencing. We ask for your understanding and cooperation as some time may be required between receipt of a request for certification and issuance of the certificate in order to perform this examination.
Q.16 When did or will get to the certificate was issued by the public as well as the deposit.
A.16 When you contact the post of new species such as the Validation List of IJSEM or if, will be announced the new species, such as International Journal of Systematic and Evolutionary Microbiology magazine (IJSEM), the type strain of the species such as microorganisms save institutions of two or more countries proof that has been deposited, it’s released to the general public as they have their request, please apply necessary one. Microbial strain has been deposited in JCM, and has issued this certificate after as well as I am allowed to test for such contamination and survival of the ampoule, such as cultured and stored in the JCM. There may be a case to have time after I have an contact of your request for the certificate, but we ask for your understanding and cooperation.