12

Ideal Future Structure of the Patent
Microorganism Deposit System

When filing a patent application for an invention relating to a microorganism, the applicant is obligated bylaw to deposit the relevant microorganism at an institution designated by the JPO Commissioner, in principle,
in order for the specification to meet the disclosure requirement as well as for third parties to have access tosamples of the microorganism. With the recent development of the biotechnological industry, however, the patent
microorganism deposit system has been criticized as having not completely responded to the changes in thecircumstances of the times, and improvements are required both in terms of the system and its operation.
In this research and study, we conducted the interview survey with domestic companies that used themicroorganism deposit system and the questionnaire survey targeting international depositary authorities.
Accordingly, based on the analysis of users needs for the deposit system as well as the differences of the Japanesedeposit system with the systems in Europe and the United States, this report considers an ideal future structureof the patent microorganism deposit system in Japan.

Ⅰ Microorganism-related
Inventions
1

Trends in Microorganism-related Inventionsin Japan(1) Bio-industry trends
Trends in the domestic industry include thesuccessive entry of IT companies into bio-fields,
primarily with the development of bio-informatics
and DNA chip enterprises. Major pharmaceuticalcompanies in Japan are increasing in spending on
genome-related research, in addition to expanding
pharmaceutical product development abroad,focused on clinical trials. There has also been arapid increase in the amount of investment inbio-related fields, including venture capital
specifically for bio-fields and investment funds thatspecialize in the bio-field business.
In comparison, the trend in foreign business isfor pharmaceutical makers in Europe and theUnited States to buy large companies in order toenhance their genome research and development.
As a result, there is a growing gap in company scale
relative to the Japanese companies. There is also a
growing number of alliances between US venturebusinesses in the bio-informatics field and Japanesepharmaceutical manufacturers.
(2) Trends in the industries relating tofermentation/application microorganisms
and bio-process
The fermented drink industry is strongly
conservative, but the development of equipment,
measurement and control processes has been
gradually
progressing.
Japan’sapplication
microorganism industry is included in the top groupin the world. This is indicated by the number ofpatents obtained. 23% of the total patentapplications in this field in the United States are
filed by Japanese applicants. Representatives of the

IIP Bulletin 2003

application microorganism industry include theamino-acid fermentation industry, the antibiotics
production industry, and the enzyme industry.
With regard to the amino-acid fermentationindustry, there is an increasing trend in the amountof amino acid produced globally, but as domesticmakers have shifted to overseas production for the
purpose of cost reduction, the amount of aminoacids produced in Japan has been decreasing.
In the antibiotics production industry, it has
become possible to produce antibiotics cheaply
through the use of gene recombination technology.
There are likely to be increases in the future in theuse of gene recombination technology.
Many enzymes are produced by Japan’s
enzyme industry. In recent years, the productivity
for target enzymes has improved through the use ofgene recombination technology. There are also
research results being reported on improvements
in enzyme characteristics.
In the field of bio-process industries, theconventional production processes for a variety of
products are being replaced by biological processes
that utilize microorganisms and enzyme catalysts.
2

Inventions Relating to Microorganisms

Inventions relating to microorganisms can bebroadlyclassified
into“inventionsofmicroorganisms themselves” and “inventions ofapplications of microorganisms.” The examples
below of inventions relating to microorganisms
includesome
inventions
relating
to“microorganisms” that are not typically included in
the ordinary interpretation of the word
“microorganism” but can be deposited in theInternational Patent Organism Depositary.
(1) Examples of inventions of microorganisms
themselves(a) Bread yeast (Patent Publication No. 52-7477):● 90 ●

A yeast created through a combination of yeasts
with different properties, suitable for leavening
dough with a sweet flavor.
(b) New fat-soluble microorganism (Patent No.
3,077,975): A new microorganism that is lipolytic inplant or animal fats and oils. (S.saprophyticus OD-1
(FERM P17201)) It can be used for processing
waste water that contains plant or animal lipids.
(2) Examples of inventions of microorganisms
applications(a) Method for survival improvement for
Lactobacillus bifidus (Patent No. 3,261,571): A
method of survival improvement of Lactobacillus
bifidus in culture media or cultures with lactitol
added, in order to improve the survivability of the
Lactobacillus bifidus in food and drink.
(b) Formaldehyde decomposition method (Patent
No. 3,007,860): A method of formaldehyde
decomposition using bacteria of the Fusarium
genus that can decompose formaldehyde.
(3) Examples of inventions related to“microorganisms” that are not includedin the ordinary interpretation of“microorganism” but can be accepted at
the patent organism center.
(a) A trophocyte with neo-resistance (Patent No.
3,067,914): A TT2 undifferentiated embryonic cell
derivative. Undifferentiated embryonic cells thatare FERM P-13200 cells with neo-resistance(expressing neomycin phosphotransferase enzymes
and being resistant to neomycin). These cells canbe used as good trophocytes on the introduction ofgenetic material.
3

Technology Trends in Microorganism-related
Inventions

The number of publications of patentapplications filed for the IPC C12R (indexing
scheme relating to microorganisms) of the IPC
category C12 (biochemistry; beer; spirits; wine;
vinegar; microbiology, etc.) was investigated foreach fiscal year. The results from 1993 to 2001
show that there was a peak in 1994 with over 1,700
cases, dropping to a little over 1,000 cases in 2001,
indicating that there is a decreasing trend in thenumber of publications of patent applications forinventions relating to microorganisms. In particular,
inventions relating to Escherichia, including E. coli,
and inventions relating to cell lines have decreased
significantly since 1998. For most other types oforganisms over the long term, there is a decreasing
trend or a steady level, but in this 2 or 3 year period
there is clearly an increase in the inventions
relating to bacteria bacillus.

Ⅱ OutlineofthePatentMicroorganism Deposit System
1

Protection of Biological Inventions andObjectives of the Patent Microorganism
Deposit System

Along with the development of biotechnology,
there has been a growing demand for legal
protection of the fruits of research, namely
biological inventions, and domestic patent laws
have globally expanded the scope of biologicalinventions to be protected on a case-by-case basis.
In Japan and the United States, patents have been
granted to microorganisms, plants and animals. On
the other hand, under the European Patent
Convention, microorganisms are included in thescope of protection whereas plant or animal
varieties and essentially biological processes for the
production of plants and animals are excluded fromthe scope of protection.
When filing a patent application, the applicant
is required to state the invention in thespecification in a manner sufficiently clear andcomplete for the invention to be worked by aperson having ordinary skill in the art to which theinvention pertains. However, in the case of abiological invention, those skilled in the art may not
be able to work the invention unless the relevant
biological materials (including microorganisms) areeasily available to them, no matter how detailed theinvention is described in the specification. The
patent microorganism deposit system is intended tofurnish deposited biological materials to third
parties so that they will be able to work thepatented invention.
2

Outline of the Patent Microorganism
Deposit/Furnishing System in Japan(1) Deposit procedures
A person who seeks to file a patent application
for an invention relating to a microorganism isrequired to deposit the relevant microorganism to
an institution designated by the JPO Commissioner
or an international depositary authority (IDA) anddisclose the deposit number in the application
document, unless the microorganism is easily
available to those skilled in the art. Morespecifically, such a person shall send by post ordeliver in person the relevant microorganism to adepositary institution (in Japan, the “International
Patent Organism Depositary (IPOD)”) with thenecessary documents. The IPOD annually receives
about 500 domestic deposits and about 400
international deposits (including those transferredfrom domestic deposits).
(2) Furnishing procedures
A request for furnishing of samples of thedeposited microorganism may be made when the● 91 ●IIP Bulletin 2003

establishment of the patent right is registered. A
request may also be made under Article 27ter.(1)(ii)and (iii) of the Regulations under the Japanese
Patent Law even before the patent right isregistered. A request may be made by (i) the Japan
Patent Office, (ii) depositor, (iii) a person who has
obtained the approval of the depositor or (iv) a
person who is legally authorized. These persons
may obtain samples of the microorganism bysubmitting the certificate of conditions and arequest for furnishing to the depositary institution.
During the period from 1997 to 2000, the IPOD
furnished samples in response to about 110-150
requests each year.
3

Outline of the International Deposit/
Furnishing System under the Budapest
TreatyThe international deposit system under the
Budapest Treaty is designed to ensure that adeposit of a microorganism to an international
depositary authority in a contracting state will berecognized as an effective deposit in the patent
procedures in all contracting states. Currently, 56
countries have become contracting states of the
Budapest Treaty and 34 depositary institutions in
21 countries have acquired the status ofinternational depositary authority. In Japan, theInternational Patent Organism Depositary (IPOD)
is the only institution that has acquired the status ofinternational depositary authority. The Budapest
Treaty and the Regulations under the treaty provide
for duties and obligations imposed on international
depositary authorities, but do not indicate specificexamples. Responses to individual cases would
vary among international depositary authorities as
to how they would cope with cases based on theirown interpretations of the treaty and theregulations. Under such circumstances, in order toharmonize the rules and procedures of individualinternational depositary authorities, the “Budapest
Treaty: Code of Practice for IDA” was developed in
1998. However, the Code of Practice is not legallybinding for individual international depositary
authorities.
Little difference exists between thedeposit/furnishing procedures under the Budapest
Treaty and the domestic procedures in Japan. This
reportaddresses
thesurveyonthedeposit/furnishing procedures applied by individualinternational depositary authorities.
4

Acceptable Biological
Depositary Institutions

Materials

at

The IPOD has expanded the scope of
acceptable biological materials. Currently, a total of
11 kinds of organisms can be deposited at the
IPOD: fungi, yeasts, bacteria, actinomytetes,

IIP Bulletin 2003

isolated plasmid, animal cells, embryos, protozoa,
plant cells, seeds and algae. This report presents
the results of the survey targeting international
depositary authorities with respect to the kinds ofacceptable biological materials, the average numberof days required for the viability test, and themodes of depositing biological materials.
5

Domestic
DepositDeposit

andInternational

Japan has both an international deposit system
under the Budapest Treaty as its contracting state
and a conventional domestic deposit system. Thereis difference between the domestic and theinternational deposit systems in terms of fees,
permission for withdrawal, etc.
6

Deposit at Depositary Institutions Other
Than the IPOD

When filing a patent application in acontracting state of the Budapest Treaty, if theapplicant deposits a microorganism at any of theinternational depositary authorities designatedunder the Budapest Treaty, that deposit shall beeffective in all contracting states. However, whenfiling a patent application for an invention relating
to a microorganism in a country (or region) that has
not joined the Budapest Treaty, the applicant should
deposit the relevant microorganism at the patent
microorganism depositary institution designated by
the country under the domestic law of that country.
Recently, the number of Japanese filing patentapplications in Taiwan with respect to inventions
relating to microorganisms has been increasing. As
Taiwan is not a contracting state of the Budapest
Treaty, Japanese applicants have to deposit
microorganisms at a depositary institution
designated in Taiwan. Currently, the Food Industry
Research & Development Institute (FIRDI) is the
only domestic depositary institution designated in
Taiwan. Accordingly, this report addresses theresults of the survey on the outline of the deposit
system and its operation as well as the kinds ofacceptable biological materials at the FIRDI.
7

Self-deposit

In the case where the applicant cannot deposit
the biological material concerning his patentapplication at the patent organism depositary
institution for the reason that the material is notincluded in the scope of acceptable biologicalmaterials at the institution, he must store thematerial by himself and guarantee furnishing ofsamples of the material. This system, which iscalled “self-deposit,” exists only in Japan and it israrely used nowadays due to the fact that it is notrecognized as a legal system by other countries and● 92 ●

that there is no guarantee that the sample to be
furnished to a third party is identical to thedeposited material. In addition, the expanded scopeof acceptable materials at the IPOD renders thissystem unnecessary.
8

Current Status of Culture Collections(1) Culture collections in Japan
Culture collection originally means a strain
storage institution. In this report, institutions thatcollect and store plant cells and animal cells are also
treated as culture collections. In Japan, there are 22
culture collections that are registered at the World
Data Center for Microorganisms (WDCM), andmore than 30 when including those not registeredat the WDCM. This report presents the results ofthe survey targeting these culture collections interms of the competent ministries and agencies
governing them, the kinds of organisms stored andthe number of samples furnished.
In addition to the IPOD, the Institute for
Fermentation, Osaka (IFO), which is one of theJapanese culture collections dealing with biologicalmaterials concerning patent applications, isdesignated as a patent organism depositary
institution by the European Patent Office. Samples
of general microorganisms that had been stored at
the IFO have been transferred to the NITE
Biological Resource Center (NBRC) that wasestablished in April 2002. The Center will enhance
its collection of samples with the aim of storing andproviding about 100,000 types of biologicalresources by 2010.
(2) Culture collections abroad
The IPOD only deals with microorganisms thatare deposited for patent applications and fails tofunction as a general culture collection. On theother hand, most European and U.S. depositary
institutions that serve as international depositary
authorities were first established as culturecollections and then have expanded their activities
to include patent deposit functions: therefore, these
foreign authorities perform both culture collection
functions and patent deposit functions. This reportprovides the number of cultures stored at foreignculture collections.

Ⅲ Problems in the Existing Patent
Microorganism Deposit System
1

Problems of the Patent Microorganism
Deposit System from the User’s
Perspective(1) Interview survey with domestic bio-relatedcompanies
In order to identify the current status andproblems of the existing patent microorganism

deposit system, interviews were held with 10 majordomestic bio-related companies whose deposits of
microorganisms and requests for furnishingaccounted for the majority of deposits and requests
received by the IPOD. The questions andresponses are outlined below.
(i) Questions and responses concerning depositc What problems do they find when using aforeign depositary institution? : Many respondents
stated problems concerning deposits in Taiwan.
There was also a complaint that the fees required
for an international deposit by the IPOD are higher
than those to be paid to foreign depositary
institutions.
d Do they think the scope of acceptablebiological materials at the IPOD is wide enough? :The 10 companies answered that the current scopeis wide enough and there is no necessity to expandit.
e What problems do they have with the IPOD’soperations? : There was an opinion that the relation
between the date of the viability test and the date ofissuance of the receipt of the deposit should beclarified. Another opinion was that information on
the transfer of biological materials from domestic
deposit to international deposit should be disclosed,
criticizing the present situation in which cataloguesof biological materials stored by the IPOD have notbeen made public.
f What do they think about increasing thenumber of domestic depositary institutions? : 7
companies agreed to the increase without
conditions, 2 companies agreed but with conditions,and 1 company answered that it was not necessary
to increase the number of domestic institutions.
(ii) Questions
andresponses
concerning
furnishingc What problems do they find when furnishingsamples to a third party? : Some respondents wereconcerned that the third party who has obtained
furnished samples of biological materials would
assign them to another party or use them forindustrial purpose instead of research purpose.
d What problems do they find when making arequest for furnishing? : There was an opinion that
it was difficult to obtain biological materials in thecase where a notice of change was not submitted
when the materials were transferred from domestic
deposit to international deposit and official
publications on these materials were issued withthe domestic deposit numbers.
(iii) Other questions and responsesc What do they think about depositary
institutions also functioning as culture collections? :The majority found no problem and agreed to thisidea.
(2) Problems concerning deposits from theuser’s perspective based on the interviews
Significant problems from the user’s
perspective include c the relation between the● 93 ●IIP Bulletin 2003

time of the viability test and the time of issuance ofthe receipt of the deposit, d the amount of the fee
required for international deposit, and e deposits in
Taiwan.
(3) Problems concerning furnishing from theuser’s perspective based on the survey
results
Significant problems from the user’s perspective
include c development of rules for furnishing andd disclosure of information on biological materials
that are transferred from domestic deposit tointernational deposit.
2

Problems of the Patent Microorganism
Deposit System from the Perspective of
Depositary Institutions

According to the investigations of various
documents and the questionnaire survey targetinginternational depositary authorities in foreigncountries, the problems that are to be found with
the Japanese patent microorganism deposit system
are as follows: c budgetary stability; d handling of
biological materials for which the prescribed termof storage has expired; e safety measures for
personnel engaging in handling deposited biologicalmaterials; f enhancement of human resources, andg promotion of interaction with other international
depositary authorities.

seems necessary to review the fee payment
method in order to make it more convenient for theusers.
4

According to the results of the interviews,
there is not such a strong need for the review of thetime of issuance of the receipt of the deposit.
However, in light of the Code of Practice under the
Budapest Treaty providing that the receipt of thedeposit shall be issued after the viability test in thecase of a deposit of new material, it seems
necessary to review the current system andconsider the necessity of introducing the systemprovided under the Code of Practice.
5

An ideal future structure of the patent
microorganism deposit system is considered basedon the survey results.
Increasing the Number of Microorganism
Depositary Institutions

This issue should be positively considered inlight of the needs from the industry and advantages
to be brought about by the increase.
2

Expanding the Scope of Acceptable
Biological
Materials
atDepositary
Institutions

In reality, there is no biological material thatcannot be accepted at depositary institutions inJapan. Therefore, there is no necessity to expand
the scope of acceptable biological materials for thepresent.
3

Reviewing the Mode of Paying Fee

Currently, all fees for domestic andinternational deposit are paid with patent stamps. It

IIP Bulletin 2003

Development of Culture Collections for
the Purpose of Developing the IntellectualFoundation for Biological Resources inJapanConsidering that many respondents agreed tomake the IPOD also function as a culture collection
and that depositary institutions in foreign countries
carry out culture collection functions as well as
patent deposit functions, it seems necessary toconsider the possibility of adopting this idea.

Ⅳ Ideal Future Structure of the
Patent Microorganism Deposit
System1

Reviewing the Time of Issuance of theReceipt of the Deposit● 94 ●（Senior Researcher: Mamoru Sakashita）

● 95 ●IIP Bulletin 2003