DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicants preliminary amendment filed July 5, 2024 has been received and entered. Claims 2-4, 6-9, 15-17, 19-20, 23, 25, 27-28, 30, 32-35, 37, 39-44, 46-120, 122, and 124-154 have been cancelled. Accordingly, claims 1, 5, 10-14, 18, 21-22, 24, 26, 29, 31, 36, 38, 45, 121, and 123 are pending in the instant application.
Claim Objections
1. Claim 11 is objected to because of the following informalities:
Claim 11 refers to node 52630 of the bac120 phylogentic tree from the Genome Taxonomy Database but fails to provide any SEQ ID TAG.
Applicants claim fails to comply with 37 CFR 1.821 through 1.825. Each sequence of four or greater amino acids or 10 nucleotides is required to have an appropriate SEQ ID TAG. As this claim refers to sequences longer than 10 nucleotides and are not identified by a SEQ ID TAG, they cannot be searched. Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
2. Claims 1, 5, 10-14, 18, 21-22, 24, 26, 29, 121 and 123 are not directed to patent eligible subject matter. Based upon an analysis with respect to the claim as a whole, claim(s) 1, 5, 10-14, 18, 21-22, 24, 26, 29, 121 and 123 do not recite something significantly different than a judicial exception. The rationale for this determination is explained below:
Claims 1, 5, 10-14, 18, 21-22, 24, 26, 29, 121 and 123 are directed to naturally occurring bacteria.
The claims drawn to naturally occurring bacteria and are not patent eligible merely because they have been isolated.
Applicants specification sets forth that the Mediterraneibacter faecis strains of the instant invention were isolated from healthy humans. (See Example 1).
Accordingly, the instant claims encompass naturally occurring microorganisms and are thereby deemed to be a judicial exception.
The Supreme Court in Diamond v. Chakrabarty, 447 U.S. 303, 206 USPQ 193 (1980), held a claim to a genetically engineered bacterium eligible, because the claimed bacterium was not a “product of nature” exception. (Emphasis added). As the Court explained, the modified bacterium was patentable because the patent claim was not to a “hitherto unknown natural phenomenon,” but instead had “markedly different characteristics from any found in nature,” due to the additional plasmids and resultant capacity for degrading oil. 447 U.S. at 309-10, 206 USPQ at 197.
Subsequent judicial decisions have made clear that the Supreme Court’s decision in Chakrabarty is “central” to the eligibility inquiry with respect to nature-based products. See, e.g., Association for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. _, 133 S. Ct. 2107, 2116, 106 USPQ2d 1972, 1979 (2013). For example, the Federal Circuit has indicated that “discoveries that possess ‘markedly different characteristics from any found in nature,’ … are eligible for patent protection.” In re Roslin Institute (Edinburgh), 750 F.3d 1333, 1336, 110 USPQ2d 1668, 1671 (Fed. Cir. 2014) (quoting Chakrabarty, 447 U.S. at 310, 206 USPQ2d at 197). In Roslin, the claimed invention was a live-born clone of a pre-existing, non-embryonic, donor mammal selected from cattle, sheep, pigs, and goats. An embodiment of the claimed invention was the famous Dolly the Sheep, which the court stated was “the first mammal ever cloned from an adult somatic cell.” Despite acknowledging that the method used to create the claimed clones “constituted a breakthrough in scientific discovery”, the court relied on Chakrabarty in holding the claims ineligible because “Dolly herself is an exact genetic replica of another sheep and does not possess ‘markedly different characteristics from any [farm animals] found in nature.’” Roslin, 750 F.3d at 1337, 110 USPQ2d at 1671.
Further, the claims recite a pharmaceutical composition comprising a pharmaceutically acceptable carrier, diluent or excipient. However, water, ever present in a bacterial environment can be a pharmaceutically acceptable carrier. Thus naturally occurring Lactobacillus in the presence of naturally occurring water remains a product of nature.
As the Mediterraneibacter faecis strains of the instant invention remains identical to the naturally occurring Mediterraneibacter faecis strains isolated from volunteers, the instantly claimed compositions are deemed to be a naturally occurring judicial exception.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
3. Claims 1, 12-14, 18, 21-22, 24, 26, 29, 31, 36, 38, and 45 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The specification lacks complete deposit information for the deposit of V21/006223, V21/006224, V21/006225 and V21/006226, it is not clear that strains possessing the identical properties of V21/006223, V21/006224, V21/006225 and V21/006226 are known and publicly available or can be reproducibly isolated from nature without undue experimentation.
Exact replication of a strain is an unpredictable event. Although applicant has provided a written description of a method for selecting the claimed strain, this method will not necessarily reproduce cells which are chemically and structurally identical to those claimed. Undue experimentation would be required to screen all of the possible species to obtain the claimed cells.
Because one skilled in the art could not be assured of the ability to practice the invention as claimed in the absence of the availability of the V21/006223, V21/006224, V21/006225 and V21/006226, a suitable deposit for patent purposes, evidence of public availability of the V21/006223, V21/006224, V21/006225 and V21/006226 strains or evidence of the reproducibility without undue experimentation is required.
If the deposit has been made under the provisions of the Budapest Treaty, filing of an affidavit or declaration by applicant or assignees or a statement by an attorney of record who has authority and control over the conditions of deposit over his or her signature and registration number stating that the deposit has been accepted by an International Depository Authority under the provisions of the Budapest Treaty, that all restrictions upon public access to the deposit will be irrevocably removed upon the grant of a patent on this application and that the deposit will be replaced if viable samples cannot be dispensed by the depository is required. This requirement is necessary when deposits are made under the provisions of the Budapest Treaty as the Treaty leaves this specific matter to the discretion of each State. Amendment of the specification to recite the date of deposit and the complete name and full street address of the depository is required. As a possible means for completing the record, applicant may submit a copy of the contract with the depository for deposit and maintenance of each deposit.
If the deposits have not been made under the provisions of the Budapest Treaty, then in order to certify that the deposits comply with the criteria set forth in 37 CFR §1.801-1.809, assurances regarding availability and permanency of deposits are required. Such assurance may be in the form of an affidavit or declaration by applicants or assignees or in the form of a statement by an attorney of record who has the authority and control over the conditions of deposit over his or her signature and registration number averring:
(a) during the pendency of this application, access to the deposits will be afforded to the Commissioner upon request;
(b) all restrictions upon the availability to the public of the deposited biological material will be irrevocably removed upon the granting of a patent on this application;
(c) the deposits will be maintained in a public depository for a period of at least thirty years from the date of deposit or for the enforceable life of the patent of or for a period of five years after the date of the most recent request for the furnishing of a sample of the deposited biological material, whichever is longest; and
(d) the deposits will be replaced if they should become nonviable or non-replicable.
In addition, a deposit of biological material that is capable of self-replication either directly or indirectly must be viable at the time of deposit and during the term of deposit. Viability may be tested by the depository. The test must conclude only that the deposited material is capable of reproduction. A viability statement for each deposit of a biological material not made under the Budapest Treaty must be filed in the application and must contain:
1) The name and address of the depository;
2) The name and address of the depositor;
3) The date of deposit;
4) The identity of the deposit and the accession number given by the depository;
5) The date of the viability test;
6) The procedures used to obtain a sample if the test is not done by the depository; and
7) A statement that the deposit is capable of reproduction.
As a possible means for completing the record, applicant may submit a copy of the contract with the depository for deposit and maintenance of each deposit.
If the deposit was made after the effective filing date of the application for patent in the United States, a verified statement is required from a person in a position to corroborate that the cell line described in the specification as filed is the same as that deposited in the depository. Corroboration may take the form of a showing of a chain of custody from applicant to the depository coupled with corroboration that the deposit is identical to the biological material described in the specification and in the applicant's possession at the time the application was filed.
Applicant's attention is directed to In re Lundack, 773 F.2d. 1216, 227 USPQ 90 (CAFC 1985) and 37 CFR §1.801-1.809 for further information concerning deposit practice.
4. Claims 1, 10-14, 18, 21-22, 24, 26, 29, 31, 36, 38, and 45 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1, 10-14, 18, 21-22, 24, 26, 29, 31, 36, 38, and 45 recite Mediterraneibacter faecis strains V21/006223, V21/006224, V21/006225 or V21/006226 or derivatives thereof and phylogenetic descendants of the MRCA of M. faecis and M. lactaris. (Emphasis added).
The specification and claims do not indicate what distinguishing attributes are shared by the members of the genus. Thus, the scope of the claims includes numerous structural variants, and the genus is highly variant because a significant number of structural differences between genus members is permitted. Since the disclosure fails to describe the common attributes or characteristics that identify members of the genus, and because the genus is highly variant, "derivatives thereof and phylogenetic descendants of the MRCA of M. faecis and M. lactaris” alone is insufficient to describe the genus. One of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus. Thus, applicant was not in possession of the claimed genus.
Adequate written description requires more than a mere statement that it is part of the invention and a reference to a potential method of isolating it. The protein itself is required. See Fiers v. Revel, 25 USPQ 2d 1601 at 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Lts., 18 USPQ2d 1016.
Vas-Cath Inc. V. Mahurkar, 19 USPQ2d 111, clearly states that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." Generally, in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See Enzo Biochem, 323 F.3d 956, 966, 63 USPQ2d 1609, 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004).
5. Claims 21-22, 24, and 45 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 21-22, 24 and 25 recite an improper Markush claim.
A Markush grouping is a closed group of alternatives, i.e., the selection is made from a group "consisting of" (rather than "comprising" or "including") the alternative members. Abbott Labs., 334 F.3d at 1280, 67 USPQ2d at 1196. If a Markush grouping requires a material selected from an open list of alternatives (e.g., selected from the group "comprising" or "consisting essentially of" the recited alternatives), the claim should generally be rejected under 35 U.S.C. 112(b) as indefinite because it is unclear what other alternatives are intended to be encompassed by the claim. See In re Kiely, 2022 USPQ2d 532 at 2* (Fed. Cir. 2022) (each independent claim recites "a selection from the group comprising a person, an animal, an animated character, a creature, an alien, a toy, a structure, a vegetable, and a fruit." … (emphasis added). "Given the breadth of variation among the specified alternatives and the use of the open-ended word ’comprising’ to define the scope of the list, we affirm the Board's conclusion that the pending claims recite improper Markush language and are indefinite under § 112(b)."). If a claim is intended to encompass combinations or mixtures of the alternatives set forth in the Markush grouping, the claim may include qualifying language preceding the recited alternatives (such as "at least one member" selected from the group), or within the list of alternatives (such as "or mixtures thereof"). Id. at 1281. See also MPEP § 2111.03.
7. Claims 1, 12-14, 18, 21-22, 24, 26, 29, 31, 36, 38 and 45 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.
The claim is vague and indefinite in the use of the phrase "derivative thereof." Since it is unclear what amount of chemical modification is permitted as implied by the recitation of "derivative thereof." Since it is unclear how the composition is to be varied as referred to in the claims, there is no way for the person of skill in the art to ascribe a discrete and identifiable definition to said phrase.
8. Regarding claim 38, the phrase "for example" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
9. Claim 10 recites the limitation "the MRCA of M. faecis and M. lactaris." There is insufficient antecedent basis for this limitation in the claim.
10. Claim 29 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 29 recites the bacterial strain is “M lactaris.” However, claim 29 depends on claim 1 which recites the strain is Mediterraneibacter faecis. As M. lactaris is mutually exclusive from M. faecis claim 29 fails to further limit, and improperly removes a limitation found in the base claim.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
11. Claim 123 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 123 recites the composition of claim 121, wherein the therapy was for treatment or prevention. However, the composition of claim 123 remains structurally identical to the composition of claim 121 (e.g., further comprising a pharmaceutically acceptable carrier, diluent, etc.). As the intended use of the composition carries no patentable weight, and the composition remains identical in both claims, claim 123 fails to further limit the composition as recited in claim 121.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
12. Claim(s) 1, 10, 12-14, 18, 21-22, 24, 26, 121 and 123 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Togo et al.
The claims are drawn to a composition comprising a cell or a biologically pure culture of Mediterraneibacter faecis strain deposited under any one of accession numbers V21/006223, V21/006224, V21/006225, or V21/006226, or a derivative thereof.
Togo et al (Antonie van Leeuwenhock Vol. 111, pp 2107-2128, 2018) disclose of isolated strains of Mediterraneibater faecis and Mediterraneibacter lactaris. (See page 2107). Togo et al further disclose the strain to be lactose positive. (See table 1).
It is noted that Togo et al do not refer to the strain as “for use in therapy.” However, the recitation of therapy is merely an intended use of the claimed composition. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention's limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation"); Kropa v. Robie, 187 F.2d at 152, 88 USPQ2d at 480-81 (preamble is not a limitation where claim is directed to a product and the preamble merely recites a property inherent in an old product defined by the remainder of the claim); STX LLC. v. Brine, 211 F.3d 588, 591, 54 USPQ2d 1347, 1350 (Fed. Cir. 2000) (holding that the preamble phrase "which provides improved playing and handling characteristics" in a claim drawn to a head for a lacrosse stick was not a claim limitation). Compare Jansen v. Rexall Sundown, Inc., 342 F.3d 1329, 1333-34, 68 USPQ2d 1154, 1158 (Fed. Cir. 2003) (In a claim directed to a method of treating or preventing pernicious anemia in humans by administering a certain vitamin preparation to "a human in need thereof," the court held that the preamble is not merely a statement of effect that may or may not be desired or appreciated, but rather is a statement of the intentional purpose for which the method must be performed. Thus the claim is properly interpreted to mean that the vitamin preparation must be administered to a human with a recognized need to treat or prevent pernicious anemia.); In re Cruciferous Sprout Litig., 301 F.3d 1343, 1346-48, 64 USPQ2d 1202, 1204-05 (Fed. Cir. 2002) (A claim at issue was directed to a method of preparing a food rich in glucosinolates wherein cruciferous sprouts are harvested prior to the 2-leaf stage. The court held that the preamble phrase "rich in glucosinolates" helps define the claimed invention, as evidenced by the specification and prosecution history, and thus is a limitation of the claim (although the claim was anticipated by prior art that produced sprouts inherently "rich in glucosinolates")).
Accordingly, Togo et al disclose of each and every limitation of the instantly filed claims.
13. Claim(s) 1, 5, 10, 12-14, 18, 21-22, 24, 26, 29, 31, 36, 38, 45, 121 and 123 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Schneider et al.
The claims are drawn to a composition comprising a cell or a biologically pure culture of Mediterraneibacter faecis strain deposited under any one of accession numbers V21/006223, V21/006224, V21/006225, or V21/006226, or a derivative thereof.
Schneider et al (WO 2017/218680) disclose of isolated compositions of Ruminococcus faecis/Mediterraneibater faecis. (See composition F; Table F1). Schneider et al further disclose of administering the strains to mice and conferring protection against C. difficile infection. (See Examples 1 and 4-5). The strains of R. faecis produced acetate, lactate and did not produce butyrate. (See Figures 13-14). Schneider et al further disclose of sequences having greater than 98% identity with the instantly recited SEQ ID NO: 1-24. (See SEQ ID NO: 29, 40, 46, 48, 51, 55-56, 70 and 96).
Products of identical composition cannot have mutually exclusive properties. A composition and its properties are inseparable. Therefore, if the prior art teaches administration of the identical composition, (Mediterraneibacter faecis) the properties applicant discloses and/or claims (enhance mucosal healing, improve gut barrier function) are necessarily present. In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Accordingly, Schneider et al disclose of each and every limitation of the instantly filed claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Mark NAVARRO whose telephone number is (571)272-0861.
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/ALBERT M NAVARRO/Primary Examiner, Art Unit 1645 November 28, 2025