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
The instant application claims benefit to US Provisional Application No. 63554616, filed on 02/16/2024 and is acknowledged. The instant claims herein are examined using the effective filing date of 02/16/2024 for the basis of any prior art rejections.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 02/14/025 was properly filed in compliance with 37 CFR 1.97. Accordingly, the information disclosure statement(s) was considered.
Claim Rejections - 35 USC § 112
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.
Claims 1-8 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.
Claim 1 recites in the preamble “a method for treating an individual who has inflammatory bowel diseases and spondyloarthritis” but the last line of the claim recites “to thereby treat the IBD”. It is unclear, based on the claim language, what the method is intended to treat (both IBDs and spondyloarthritis? Only IBDs? Either disease?). Thus, the claim is indefinite. Please note that claims 2-8 are also indefinite due to dependency on claim 1. For the purposes of compact patent prosecution, the examiner is interpreting the claims to treat both disease states.
It is noted any interpretation of the claims set forth above does not relieve Applicant of the responsibility of responding to this rejection. If the actual interpretation of the claims is different than that posited by the Examiner, additional rejections and art may be readily applied in a subsequent final Office action.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
First rejection
Claims 1-6 are rejected under 35 U.S.C. 103 as being unpatentable over Borody (US20170348360A1) in view of Borody (US 11071759 B2; hereinafter “Borody2”).
Borody teaches a method of treating inflammatory bowel diseases and ankylosing spondylitis (i.e., spondyloarthritis) by administering Faecalibacterium prausnitzii as an important supplier of butyrate to the colonic epithelium (see abstract, claims 14-21, paragraph 0013-14, 0018, 0067, Table 2; Example 3). Borody also teaches the method includes further administration of sulfasalazine (see paragraph 0058, 0095) as sulfasalazine is one of the most commonly used drugs that helps control inflammation in patients with inflammatory diseases (see paragraph 0058).
Borody does not explicitly teach selecting the individual based on a determination from a biological sample obtained from the individual that the gastrointestinal system of the individual comprises a microbiome lacking bacteria that provide functional folate trap.
However, Borody2 teaches treatment of ulcerative colitis (i.e., an inflammatory bowel disease) in a subject in need thereof by administering preparation of non-pathogenic bacteria like Faecalibacterium prausnitzii (see abstract, claims). Borody2 explicitly teaches that prior to administering the bacteria one may determine the subject's baseline gut bacterial diversity and determining the level of one or more bacteria including Ruminococcus (i.e., determining individual comprises a microbiome lacking bacteria that has functional folate trap) including by assessing and analyzing the Shannon's diversity of the subject's fecal sample prior to the treating step (see col 3; see also col 12-13).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the method of treating IBD as taught by Borody by including the pre-treatment microbiota assessment as taught by Borody2 to arrive at the claimed invention. One of ordinary skill would have been motivated to make the modification because Borody explicitly teaches such an assessment can be performed to advantageously determine altered metabolic profiles associated with IBDs (see col 1, lines 25-41).
Regarding claim 2, Borody teaches administration of F. pausnitzii.
Regarding claim 3, Borody and Borody2 teach administration of R. Callidus (see paragraph 0117-18).
Regarding claim 4, Borody teaches administration of C. aerofaciens (see paragraph 0117).
Regarding claim 5, Borody2 teaches analyzing a biological sample prior to administering the sulfasalazine and bacteria (see above).
Regarding claim 6, Borody2 teaches the biological sample is a fecal sample.
Accordingly, the claimed invention was prima facie obvious at the time of filing, especially in the absence of evidence to the contrary.
Second rejection
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable Borody and Borody2 as applied to claims 1-6 above, and further in view of McKenzie et al (US 9011834 B1; filed in Applicant’s IDS 02/14/2025; hereinafter “McKenzie”).
As discussed above, the claimed invention was rendered prima facie obvious by the combined teachings of Borody and Borody2.
Neither reference explicitly teaches determining the gastrointestinal system of the individual comprises a microbiome lacking the bacteria that provide the functional folate trap comprises measuring relative abundance of F. prausnitzii in the microbiome with shotgun metagenomic sequencing of the microbiome or 16S ribosomal RNA based polymerase chain reaction.
However, McKenzie teaches methods of treating dysbiosis including inflammatory bowel disease, ulcerative colitis, and Crohn’s by administering germinatable bacterial spores and a pharmaceutically acceptable excipient to a subject (see abstract, claims, see col 34). McKenzie teaches screening of bacteria in the microbiome using 16S rRNA based PCR to determine OTUs and OTU or Whole Genome Shotgun (WGS) sequence characterization of microbes or a microbial community within the subject and determining whether a bacterial populates a subject's GI tract including F. prausnitzii (see col 51-52 and col 37; see also Table GF).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the method of treating IBD as taught by Borody and Borody2 by including the screening of bacteria using 16S rRNA and shotgun sequencing in a subject to determine whether a bacteria populates the subject’s GI tract as taught by McKenzie to arrive at the claimed invention. One of ordinary skill would have been motivated to make the modification because McKenzie explicitly teaches these methods of characterization allows successful determination of a subject’s GI microbial make-up for treatment of bowel diseases.
Accordingly, the claimed invention was prima facie obvious at the time of filing, especially in the absence of evidence to the contrary.
Third rejection
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Borody and Borody2 as applied to claims 1-6 above, and further in view of Li et al (Intestinal Microbiota and Metabolomics Reveal the Role of Auricularia delicate in Regulating Colitis-Associated Colorectal Cancer. Nutrients. 2023 Dec 4;15(23):5011; hereinafter “Li”).
As discussed above, the claimed invention was rendered prima facie obvious by the combined teachings of Borody and Borody2.
Neither reference explicitly teaches measuring baseline thymine fecal levels or baseline fecal deoxyuridine levels, or a combination thereof.
However, Li teaches that the regulation of inflammation and host metabolism is significantly influenced by the intestinal microbiota. Li teaches the combined analysis of intestinal microbiota and metabolomics revealed a positive correlation between the Oscillospira bacterium and 2′-deoxyuridine, as well as a negative correlation between the genus Parabacteroides and creatinine, 1-palmitoyl lysophosphatidylcholine, and choline. Li further teaches that generally, the detection of 2′-deoxyuridine can serve as an inflammatory biomarker to evaluate inflammatory damage (see pg. 11, paragraph 1).
Therefore, it would have been prima facie obvious to one of ordinary skill to modify the method of treating IBD as taught by Borody and Borody2 by including detection of deoxyuridine as taught by Li to arrive at the claimed invention. One of ordinary skill would have been motivated to make the modification because Li explicity teaches that detection of 2′-deoxyuridine can advantageously serve as an inflammatory biomarker to evaluate inflammatory damage.
Accordingly, the claimed invention was prima facie obvious at the time of filing, especially in the absence of evidence to the contrary.
Examiner’s Note
The examiner notes that instant claim 1 recites “a method for treating an individual who has inflammatory bowel diseases (IBD) and spondyloarthritis, the method comprising: selecting the individual based on a determination from a biological sample obtained from the individual that the gastrointestinal system of the individual comprises a microbiome lacking bacteria that provide functional folate trap; ii) administering to the individual selected as in i) sulfasalazine with bacteria comprising a functional folate trap to thereby treat the IBD.”
The claims were initially considered to raise an issue under 35 USC 101 for reciting an abstract idea/mental step. Step i) of the claim is a very generic selection step based on a determination that the individual lacks bacteria that provides a functional folate trap (i.e., a mental step that can be performed in the human mind), however, step ii) of the method recites specifically treating that individual by administering sulfasalazine and a bacteria comprising a functional folate trap. MPEP 2106.04(d)(2) states that “A claim reciting a judicial exception is not directed to the judicial exception if it also recites additional element(s) demonstrating that the claim as a whole integrates the exception into a practical application. One way to demonstrate such integration is when the additional elements apply or use the recited judicial exception to affect a particular treatment or prophylaxis for a disease or medical condition. The application or use of the judicial exception in this manner meaningfully limits the claim by going beyond generally linking the use of the judicial exception to a particular technological environment, and thus transforms a claim into patent-eligible subject matter. Such claims are eligible at Step 2A, because they are not "directed to" the recited judicial exception.” Thus, the rejection under 35 USC 101 was considered but was not made of record.
Conclusion
NO CLAIMS ALLOWED.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GEORGIANA C REGLAS whose telephone number is (571)270-0995. The examiner can normally be reached M-Th: 8:00am-2:00pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Melenie Gordon can be reached at 571-272-8037. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/G.C.R./Examiner, Art Unit 1651
/THOMAS J. VISONE/Supervisory Patent Examiner, Art Unit 1672
