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 .
Priority
This application is a 371 of PCT/US21/71018 filed 07/27/2021 which claims benefit of provisional application 63/069,931 filed 08/25/2020 and claims benefit of provisional application 63/057,492 filed 07/28/2020. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 11/20/25 complies with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of the Claims
Claims 1, 2, 4-9, 11 and 13-20 are pending. Claims 5 and 9 are amended. Claims 1, 2, 4, 11, 13-20 were withdrawn. Claims 3, 10, 12 and 21 were cancelled.
Claims 5-9 (claims set filed 11/20/2025) are examined on the merits herein.
Withdrawal of Rejections
The response and amendment filed on 11/20/2025 are acknowledged. All of the amendment and arguments have been thoroughly reviewed and considered.
For the purposes of clarity of the record, the reasons for the Examiner's withdrawal and/or maintaining if applicable, of the substantive or essential claim rejections are detailed directly below and/or in the Examiner's response to arguments section.
The previous claims 5-9 and 21 rejection under 35 U.S.C. 112(b) has been withdrawn necessitated by amendment of claims 5 and 9 and cancellation of claim 21.
Maintained/Modified Rejections
The following rejections are maintained and/or modified taking into consideration amendment to claim filed on 11/20/2025.
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.
Claims 5-9 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.
It is apparent that strains recited in claim 5 are required to practice the claimed invention. As such the biological material must be readily available or obtainable by a repeatable method set forth in the specification, or otherwise readily available to the public. If it is not so obtainable or available, the requirements of 35 USC 112, first paragraph, may be satisfied by a deposit of the strains.
The process disclosed in the specification does not appear to be repeatable, it is not clear that the invention will work with commonly available material and it is not apparent if the biological materials considered necessary to make and use the invention is both known and readily available to the public. The specification describes identification of 1008 unique strains for 207 bacterial species (paragraph 00029). The specification provides Table 7 in which multiple strains for the same species are listed with accession numbers SAMN1553xxxx. At the same only single strains with accession numbers SAMN1553xxxx for each species were selected for claim 5 that can indicate beneficial properties of selected strains. The prior art of Fischbach (US 20220023354 A1) teaches defined compositions of gut bacterial species capable of achieving substantial engraftment for treatment of dysbiosis or pathological condition (Abstract). The description of compositions comprises bacterial species with the strain numbers (claims 36-39). Although several bacterial species are the same as claimed species, the strain numbers are different from those in instant claim 5. Thus, a person skilled in the art could not make or use the invention defined without access to the specific biological material. Therefore, a deposit at a recognized depositary may be made for to overcome this rejection.
It is noted that on 10/23/2025 Applicants have deposited the composition of claim 5 at ATCC Patent Depository compliant with the terms of the Budapest Treaty designated MTC01 and filed under Patent Deposit Number PTA-127947 (Receipt in the Case of Original Deposit filed). The viability statement is provided. The depositary information and viability statement filed 10/23/2025 are acknowledged, however, there is no indication as to public availability.
If the deposit is made under the terms of the Budapest Treaty, then a statement, affidavit or declaration by Applicants, or by an attorney of record over his or her signature and registration number, or by someone in a position to corroborate the facts of the deposit, that the instant invention will be irrevocably and without restriction released to the public upon the issuance of a patent, would satisfy the deposit requirement made herein.
If the deposit is a non-Budapest Treaty deposit, then in order to certify that the deposit meets the requirements set forth in 37 CFR 1.801-1.809 and MPEP 2402-2411.05, a statement, affidavit or declaration Applicant, by an attorney of record over his or her signature and registration number, or by someone in a position to corroborate the facts of the deposit would satisfy the requirements herein by stating and providing that:
(a) During the pendency of the application, access to the invention will be afforded to the Commissioner upon request;
(b) All restrictions upon availability to the public will be irrevocably removed upon granting of the patent;
(c) The deposit will be maintained in a public depositary for a period of 30 years, or 5 years after the last request or for the enforceable life of the patent, whichever is longer; and
(d) Provide evidence of the test of the viability of the biological material at the time of deposit (see 37 CFR 1.807).
Claims 6-9, dependent on claim 5, do not resolve the issue mentioned above and are rejected.
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
The Receipt in the Case of Original Deposit and the Viability Statement filed 11/20/2025 are acknowledged. However, the public availability statement is not provided and therefore the 35 U.S.C. 112(b) rejection is maintained and modified to acknowledge the depository information.
Since the deposit is made under the terms of the Budapest Treaty, then a statement, affidavit or declaration by Applicants, or by an attorney of record over his or her signature and registration number, or by someone in a position to corroborate the facts of the deposit, that the instant invention will be irrevocably and without restriction released to the public upon the issuance of a patent, would satisfy the deposit requirement made herein.
Claim Rejections - 35 USC § 101
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 5-9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to natural products without significantly more. The claim 5 recites bacterial strains which are naturally occurring bacterial species isolated from human donors. Caballero (US 20200405775 A1) teaches compositions of bacterial strains including claimed species which were isolated from the microbiome of healthy individuals (paragraph 0117). The specification describes identification of 1008 unique strains for 207 bacterial species from 9 healthy donor and 13 recipients (paragraph 00029). The specification discloses that the strains were sequenced and identified as unique strains with <96% genome similarity (paragraph 0029). However, the strains were not modified and hence their characteristics are not markedly different from those of naturally occurring strains.
This judicial exception is not integrated into a practical application because in addition to bacterial species claim 5 recite identifying numbers that are insignificant extra solution.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the identification numbers are recited at a high level of generality and it is routine and conventional to provide identification numbers to selected strains.
Based on the above, claim 5 is rejected as ineligible.
Dependent claims 6 and 7 are directed to conditions of culturing of the claimed strains. Claims 8 and 9 are directed to facultative aerobic strains to be able to grow in the presence of the claimed strains and strains being susceptible to antibiotics. These features are recited at high level of generality and are not sufficient to amount to significantly more than the judicial exceptions because they do not impart a structural limitation and do not alter the judicial exception or make it markedly different. Besides, the conditions for strains culturing and growth and susceptibility to antibiotics are recited at a high level of generality and is routine and conventional as evidenced by Caballero and Allen-Vercoe (WO 2013037068 A1). Caballero teaches culturing bacterial strains isolated from donors in anaerobic conditions and in media devoid of animal components (paragraphs 0117, 0254) and discloses that some compositions can include bacterial strains which are facultative anaerobes (paragraph 0216). Allen-Vercoe teaches detection of the susceptibility of bacterial strains isolated from the donor to antibiotics and determines that they are not antibiotic resistant (p. 37, 2nd paragraph). Therefore, claims 6-9 are rejected as ineligible.
Based on the above claims 5-9 are rejected as directed to ineligible subject matter.
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
Applicant argues (addressing p. 8-9 of the Remarks) that claims do not recite individual strains, or even all of the strains isolated from a single individual, but recite a specific mixture of strains isolated from 22 individuals, cultured and tested for their effectiveness in treating individuals with a C. difficile infection. Applicant discusses examples 1, 3 and 6 from “101 examples 1 to 36” to support eligibility of claim 5.
These arguments are not persuasive because: although claim 5 recites the mixture of selected strains, this mixture is not shown to be markedly different than the individual strains which are naturally occurring and not modified strains. Example 3, Applicant is referring to, recites a mixture of naturally occurring substances joined together with natural polymeric materials and hence having the composition structurally different from the natural components. In instant case, individual strains are mixed in the composition without any recited additional elements and have the same structure as being present in the intestinal tract. Example 1, Applicant is referring to, recites a combination of naturally occurring substances (potassium nitrate, charcoal and sulfur) that can be used as a gunpower and hence has markedly different characteristics from its components. Example 6 recites a combination of bacterial species of R. californiana and R. phaseoli that has different biological function that individual species, i.e. can infect a new group of plants which is markedly different from the individual species. In instant case, the mixture of selected strains is not markedly different from the individual strains. The specification describes a correlation between engraftment of selected bacterial species and positive clinical outcome in C. difficile infection (CDI) patients (Example 10, paragraphs 00070-00073). The strains with the high engraftment efficiency and supposedly effective against CDI were selected for the instant composition (paragraph 00077) and hence strains were selected based on their similar properties. Besides, the individual strain selected for the composition were shown to have similar properties of being strict anaerobes and not inhibiting growth of control organisms (paragraph 00078). Therefore, individual strains have the same properties as their mixture and the strains were not modified. Thus, the instant mixture of strains does not have any structural or functional characteristics that are different from the naturally occurring bacteria and is not markedly different from the individual strains occurring in nature and therefore the 35 U.S.C. 101 rejection is maintained.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 5-8 are rejected under 35 U.S.C. 103 as being unpatentable over Caballero (US 20200405775 A1) as evidenced by Moreira de Gouveia (Moreira de Gouveia et al. Biology, 2024, 13, 142, 1-14).
Regarding claim 5, Caballero teaches compositions and methods for suppressing multidrug resistant organisms in a subject (paragraph 0004). Caballero discloses that bacterial strains were isolated from healthy individuals and that compositions originating from different individuals can be combined (paragraph 0117). Caballero describes multiple compositions of bacterial strains. The composition in paragraph 0181 comprises strains of the following claimed species: Bacteroides uniformis, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Bacteroides caccae, Bacteroides cellulosilyticus, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Coprococcus comes, Dorea longicatena, Eubacterium rectale, Parabacteroides merdae and Odoribacter sp. That composition includes all species recited in claim 5 except Parabacteroides distasonis and Odoribacter splanchnicus although Odoribacter sp. are included. However, Odoribacter splanchnicus is mentioned in the list of species identified in donors in Table 9 and 11 (paragraph 0287) and Parabacteroides distasonis are included in multiple compositions, e.g. in compositions recited in paragraphs 0159, 0163 and 0165. Caballero mentions that the disclosed microbial compositions can suppress colonization of multi-drug resistant organisms and treat diseases associated with bacterial colonization or immune response induced by bacteria and can suppress pathogenic organisms such as Clostridium difficile (paragraphs 0046, 0110). Note that although the mixture of isolated bacterial strains is recited with the transitional phrase “consisting”, a composition is recited with transitional phrase “comprising” and hence composition can include additional bacteria besides claimed. Caballero does not teach bacterial strains with the instant identification numbers.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the combination of compositions of bacterial strains from Caballero teaching. One would have been motivated to do that since Caballero teaches compositions which can be used for treatment of diseases associated with bacterial colonization of multi-drug resistant organisms and that compositions originating from different donors can be combined. A skilled artisan would have reasonably expected success in preparation of microbial compositions following the description of the prior art.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that instant bacterial strains included in the composition are the same or an obvious variants of strains of Caballero teaching. One would have been motivated to suggest that with reasonably expected success since strains are natural strains isolated from human individuals, belong to the same species, were not modified and hence are expected to have the same properties and are taught to suppress pathogenic organism such as Clostridium difficile and colonization of multi-drug resistant organisms. Therefore absent evidence to the contrary, if the strains are not the same, the use of an obvious variants of the corresponding strains with the same properties and for the same purpose is obvious.
Thus, Caballero teaching renders claim 5 obvious.
Regarding claim 6, Caballero teaches that bacterial strains of the compositions are grown in anaerobic conditions in the media free of animal products: “Culture media such as BL media and EG media, or similar versions of these media devoid of animal components, can be used to support the growth of the bacterial species (paragraph 0254). Thus, Caballero teaching renders claim 6 obvious.
Regarding claim 7, Caballero teaches that the bacterial strains in the compositions are obligate anaerobes (paragraph 0216). Thus, Caballero teaching renders claim 7 obvious.
Regarding claim 8, Caballero teaches that some compositions can include bacterial strains which are facultative anaerobes (paragraph 0216) indicating that anaerobic strains of the compositions can grow in the presence of facultative aerobes or anaerobes. Additionally, Caballero discloses that the compositions can include one or more pathogen-antagonizing strains among which Escherichia coli is included (paragraph 0175). Escherichia coli is known to be facultative anaerobe as evidenced by Moreira de Gouveria (p. 3, 1st paragraph). Moreira de Gouveria teaches that: “As facultative anaerobes, most Enterobacteriaceae, and in particular E. coli, deplete oxygen diffusing from the mucosal surface and therefore participate to the establishment of a perfect environment for strict anaerobes which constitute almost all members of the gut microbiota.” Thus, Caballero teaching as evidenced by Moreira de Gouveria teaching renders claim 8 obvious.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Caballero (US 20200405775 A1) in view of Allen-Vercoe (WO 2013037068 A1 on record in IDS).
The teaching of Caballero has been set forth above.
Caballero does not teach susceptibility of bacterial strains in the composition to antibiotics.
Regarding claim 9, Allen-Vercoe teaches synthetic stool preparations comprising bacteria isolated from a fecal sample of healthy individual to use for treatment of disorders of the gastrointestinal tract (Abstract). Allen-Vercoe discloses bacterial strains isolated from the donor which include strains of Caballero teaching and claimed strains except Bacteroides caccae (Tables 1, 2 and 7). Allen-Vercoe describes that the bacterial strains in the synthetic stool preparation are not resistant to different antibiotics: “In a particular embodiment, the bacterial strains in the synthetic stool preparation are not resistant to pipericillin, ceftriaxone, metronidazole, amoxicillin/clavulanic acid, imipenem, moxifloxacin, vancomycin and/or ceftazidime.” (p. 37, 2nd paragraph). Allen-Vercoe provides results of testing of bacterial strains for antibiotic resistance in Example 2 (p. 48) and Tables 3, 4 and 8.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow guidance of Allen-Vercoe and determine antibiotic resistance of the bacterial strains in Caballero compositions. One would have been motivated to do so since Allen-Vercoe teaches that bacterial strains isolated from human stool sample are not antibiotic resistant and provide instructions for antibiotic susceptibility testing which is an important safety feature for human studies. A skilled artisan would have reasonably expected success in that because Caballero and Allen-Vercoe teach the same bacterial species for treatment of gastrointestinal disorders. Thus, Caballero and Allen- Vercoe teachings render claim 9 obvious.
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
Applicant argues (addressing p. 9-10 of the Remarks) that Caballero does not teach the instant strains and cannot arrive at the mixture of strains recited in claim 5. These arguments are not persuasive because: although Caballero does not teach the strains with the same identification numbers, those strains can be the same or obvious variants to instant strains since (i) strains are natural strains isolated from human donors; (ii) strains were not modified; (iii) strains belong to the same species; (iv) strains taught by Caballero can suppress a pathologic microorganism, i.e. C. difficile in humans (paragraph 0046, 0049) and instant strains are tested on patients with C. difficile infection and are suggested for treatment of that infection (specification, paragraphs 00070-00073). Therefore, absent evidence to the contrary, if the strains are not the same, they are expected to be an obvious variants of the corresponding strains with the same properties.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LIOUBOV G KOROTCHKINA whose telephone number is (571)270-0911. The examiner can normally be reached Monday-Friday: 8:00-5:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila G Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/L.G.K./ Examiner, Art Unit 1653
/SHARMILA G LANDAU/ Supervisory Patent Examiner, Art Unit 1653