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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 9/15/2025 has been entered.
Status of claims
Claims 1-17 as amended and new claims 21 and 22 as filed on 9/15/2025 are under examination in the instant office action.
Claim Rejections - 35 USC § 112
Indefinite
Claims 1-17 as amended and new claims 21 and 22 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 1 and 6 as amended are indefinite with regard to “the individual” who is treated and monitored in the steps e), f) and g) because the prior steps refer to “the individual prior to acquiring the disease” (steps, b, c and d). The patient as intended for treating a disease is not identified. An individual who might be in need of preventing a disease is not clearly distinguished from a plurality of donors who might as well be in need of preventing a disease.
Claims 1 and 6 as amended are also rendered indefinite by reciting “third party with disease” (step d, last line) as a candidate for therapeutic fecal transplants as intended for “preventing and treating a disease”. No specific definitions are provided in the as-filed specification about a disease of a third party that would be beneficial to an individual in need of preventing and treating this disease.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-17 as amended and new claims 21 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over US 10,561,690 (Borody), Choi et al (“Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives”. Clin Endosc 2016, 49, pages 257-265) and US 11,534,465 (Nieuwdorp et al).
The cited document US 10,561,690 (Borody) teaches a method of preventing and treating a disease in an individual, wherein the method comprises steps of acquiring fecal samples from the individual patients and donors, extracting and sequencing DNA from fecal bacteria to establish diversities of operational taxonomic units (OTUs) associated with donors and associated with patients, administering FMT probiotics (fecal microbiota transplant probiotics) to the patients and monitoring the patients (entire document including example 6). The FMT probiotics are derived from healthy donors and comprise Bifidobacterium, Clostridium, Ruminococcus (col. 21, lines 12-20), Fusobacterium prausnitzii which is previous name of Faecalibacterium prausnitzii (col. 21, line 28). The method comprises administration of antibiotics including vancomycin (col.19, lines 62-67) and rifaximin (col. 20, line 4).
In particular, the cited method of US 10,561,690 (Borody) comprising the steps of:
a) acquiring a fecal sample from the individual patient (example 6; col. 41, lines 60-65);
b, c) processing the fecal sample to extract DNA and to sequence DNA from fecal bacteria of the individual patient (example 6, col. 41, lines 60-65);
d) comparing DNA of bacteria from fecal samples from individual patients and donors to establish diversities of operational taxonomic units (OTUs) associated with donors and associated with patients (example 6; col.42, lines 25-27 and lines 50-54);
c) administering antibiotic to the individual patient (col.19, lines 62-67);
f) administering FMT probiotics that are derived from healthy donors and comprise Bifidobacterium, Clostridium, Ruminococcus (col. 21, lines 12-20), Fusobacterium prausnitzii which is previous name of Faecalibacterium prausnitzii (col. 21, line 28); and
g) monitoring the individual patient post-FMT administration (col. 42, lines 51-67).
Thus, the cited US 10,561,690 (Borody) teaches substantially the same method of “preventing and treating a disease in individual in need thereof” as claimed by administering FMT probiotics derived from a selected healthy donor as encompassed by claims 1 and 6.
However, in the method of the cited US 10,561,690 (Borody) the donor of a probiotic fecal transplant is selected as having a healthy diversity of microbiome and a normal predetermined level of bacteria that are reduced in the patients with the health condition.
The cited US 10,561,690 (Borody) is silent about donors being mother or siblings and about the use of autologous fecal sample (when donor is the same individual as a patient before developing a serious condition of disease).
However, the prior art recognizes same/similar concept about selecting donors of fecal transplant from members of patient’s family or using autologous fecal transplant.
For example: the reference by Choi teaches that donors of fecal transplant should be selected from members of patient’s family; that maternal-line first degree relatives have advantage of sharing the greatest number of microbial species in their intestinal microbiota with the recipients; thus, the adaptive immune elects in the mucosal immune system might be more tolerant of the microbiota from the close relatives (paragraph bridging columns 1 and 2 on page 261). The reference by Choi states that patients with recurrent CDI (Clostridium difficile infection) reported that fecal transplant from a relative donor showed higher resolution rate (93%) compared with unrelated donor (84%); for example: see page 261, col. 2, lines 6-9). The reference by Choi also teaches that probiotic fecal transplant is used to treat a variety of disorders including gastrointestinal disorders and non-gastrointestinal disorders including autism, eczema, Parkinson’s disease (page 260, col. 2, last paragraph and table 1).
For example: US 11,534,465 (Nieuwdorp et al) administrating autologous fecal transplant for individuals with autoimmune diseases including diabetes mellitus, celiac disease, rheumatoid arthritis, asthma (col. 2, lines 27-45) prior to acquiring the disease (col. 2, lines 50-57), wherein probiotics of the fecal samples include Bifidobacterium (col.17, lines 12-14), Clostridium, Subdologranulum, Ruminococcus (col. 12, lines 54-63). US 11,534,465 (Nieuwdorp et al) teaches that autologous fecal transplant stimulates immune system (col. 2, lines 5-14).
Therefore, it would have been obvious to one having ordinary skill in the art at the time the claimed invention was filed to provide fecal probiotic transplant derived from patient’s relative donor who has similar variety of intestinal microbial species as the patient or even identical autologous fecal sample when practicing the method of US 10,561,690 (Borody) with a reasonable expectation of success in preventing and treating disease of patients because due to similarity of microbiomes the patients’ immune system would be more tolerant to the fecal transplant from the relative donor as taught by Choi or even more with autologous sample. One of skill in the art would be motivated to select fecal transplant donor as based on similarity of microbiome because fecal transplant from a relative donor with similar microbiome showed higher resolution rate compared with unrelated donor as taught by Choi. One of skill in the art would be motivated to select autologous fecal transplant donor as based on closest similarity because autologous fecal transplant stimulate immune system as taught by US 11,534,465 (Nieuwdorp et al).
Thus, the claimed invention as a whole was clearly prima facie obvious, especially in the absence of evidence to the contrary.
The claimed subject matter fails to patentably distinguish over the state art as represented be the cited references. Therefore, the claims are properly rejected under 35 USC § 103.
Further, as applied to claims 2 and 7: the Bifidobacterium in FMT probiotics in the method of US 10,561,690 (Borody) is a bacteria which is regarded as being from the actinobacteria phylum.
As applied to claims 3 and 9: The method of US 10,561,690 (Borody) comprises administration of antibiotics including vancomycin (col.19, lines 62-67) and rifaximin (col. 20, line 4).
As applied to claims 10-11: it is noted that it is considered to be obvious to one having ordinary skill in the art at the time the claimed invention was filed to optimize protocol and duration of antibiotic treatments depending on a specific disease and on a severity of condition of a diseased individual. The claim-recited phrase “250 mg of liquid vancomycin” neither indicate vancomycin concentration in a liquid nor any specific dose.
As applied to claims 4, 5, 12-17: the cited document US 10,561,690 (Borody) discloses administering probiotic composition orally, anally or rectally, via suppository, by enema, as food or drink (0105-106, 0137), as fecal transplant (0332) as liquid saline suppository (0106).
As applied to claims 21 and 22: in the disclosure by US 10,561,690 (Borody) diseases to be treated by probiotic from donor fecal sample include ulcerative colitis (col. 2, lines 48-50) and related diseases such as Crohn’s disease and irritable bowel syndrome (col. 1, lines 58-62).
Thus, the claimed subject matter fails to patentably distinguish over the state art as represented be the cited references. Therefore, the claims are properly rejected under 35 USC § 103.
Claims 1-17, 21 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over US 10,561,690 (Borody), Choi et al (“Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives”. Clin Endosc 2016, 49, pages 257-265) and US 11,534,465 (Nieuwdorp et al) as applied to claims 1-17 , 21 and 22 above, and further in view of and US 9,855,302 (Gajewski et al).
The cited US 10,561,690 (Borody), Choi et al and US 11,534,465 (Nieuwdorp et al) as above.
The method of the cited US 10,561,690 (Borody) comprises step of pretreating individuals with antibiotics as explained above. But it is silent about pretreating individuals with antiparasitic agent.
However, US 9,855,302 (Gajewski et al) teaches co-administration of probiotics for modulation of commensal microflora and reestablishment of beneficial commensal microflora in diseased individuals together with antimicrobials (col. 23, lines 48-55) as intended to inhibit level of detrimental microbes (col. 22, lines 37-45), wherein antimicrobials include antibiotics vancomycin and doxycycline (col. 22, lines 54 and 65) and antiparasitic agents such as ivermectin (col. 23, line 28-33) and metronidazole (col. 12, line 53-62). US 9,855,302 (Gajewski et al) teaches administration of probiotics including Bifidobacterium, Clostridium, Ruminococcus (col. 2, lines 10-29).
Therefore, it would have been obvious to one having ordinary skill in the art at the time the claimed invention was filed to modify method of Borody by substitution of one antiparasitic agent ivermectin taught/suggested by US 9,855,302 (Gajewski et al) for the other antiparasitic agent metronidazole in the method of Borody with a reasonable expectation of success in treating a disease with a probiotic composition because prior art teaches treating diseases associated with modulation of commensal microflora by co-administration of probiotics with various antimicrobials including antibiotics and antiparasitics and because ivermectin and metronidazole are taught/suggested by the prior art as equivalent antiparasitic agents for inhibiting undesirable detrimental microbes.
Thus, the claimed invention as a whole was clearly prima facie obvious, especially in the absence of evidence to the contrary.
The claimed subject matter fails to patentably distinguish over the state art as represented be the cited references. Therefore, the claims are properly rejected under 35 USC § 103.
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.
Claims 1-17 as amended remain/are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon and an abstract idea without significantly more.
The claims recite a method of preventing and treating a generic unspecified disease in a generic individual with a generic unspecified need by administering to the generic individual a composition comprising Bifidobacterium or Faecalibacterium; or a composition comprising Bifidobacterium, Clostridium, Faecalibacterium prausnitzii, Ruminococcus either alone or in combination with a generic antimicrobial.
All claim-recited bacteria are naturally occurring, and they would be found in food products that are obvious substrates for heterotrophic bacteria as the claim-recited bacteria. The claimed bacteria are present in milk and in yogurt products, for example: see Demirci et al (Food Science and Technology, 2022, 154, 112860, pages 1-9). The antimicrobial is generic; or, at least vancomycin is a naturally occurring glycopeptide antibiotic produced by soil bacteria Amycolatopsis. The subject under treatment is a generic individual. Thus, an edible composition with bacteria and other natural ingredients is administered for ingestion of unlimited population. Therefore, the method as claimed is a mere act of eating and or of basic nutrition which is a natural phenomenon.
The “comparing” steps d) and “monitoring” steps g) of the claims 1 and 6 are mental steps; and, thus, drawn to abstract ideas.
The additional steps of acquiring samples, processing and sequencing DNA are common, routine and conventional practices.
Therefore, this judicial exception is not integrated into a practical application because claimed elements in combination do not add a meaningful limitation or extra-solution to the claimed method, and the claimed method as a whole is nothing more than an attempt to generally link the claimed invention to a particular technological environment.
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because when considered separately and in combination, they do not add significantly more (also known as an “inventive concept”) to the exception.
Response to Arguments
Applicant's arguments filed on 9/15/2025 with regard to the claims as amended on 9/15/2025 have been fully considered but they are not persuasive.
With regard to claim rejection under 35 USC § 103 Applicants argue that Borody’s concept for selecting fecal transplant donor as based on a larger diversity of bacterial microbiome including the use of a multi-donor sample and that Choi only suggests a probability that donor selected from close relatives would provide for best beneficial outcomes.
This line of arguments is not found convincing with respect to the instant claims because instant claims do not point out who is a patient under administration of a probiotic derived from a selected donor, thus, rendering screening steps non relevant to a method of treating a disease. Besides, Borody describes steps of screening and comparing microbiomes DNAs of patients after probiotic treatment and remission, thereby, prior to acquiring a comeback disease or another disease.
With regard to claim rejection under 35 U.S.C. 101 Applicants argue that the claimed step of “comparing the DNA” is not a mental step and it could not be performed in mind due to nanoscopic nature of DNA for visualization. This argument is not found convincing since DNA libraries are compared by software and/or algorithms which qualify as an abstract idea. Further, instant claims are indefinite with regard the individual under administration of a probiotic. The individual under administration of a probiotic is not a patient diagnosed with some certain disease and is not different form a general representative of a healthy population.
No claims are allowed.
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Vera Afremova
October 14, 2025
/VERA AFREMOVA/ Primary Examiner, Art Unit 1653