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 .
Status of the Claims
Claims 1-14, 16-21, 23-24, 26, and 29-209 have been cancelled. Claims 15 and 22 have been amended. Claim 211 has been added. Therefore, claims 15, 22, 25, 27-28, and 210-211 are pending and currently under examination (claim set filed 05/29/2025).
Withdrawal of Rejections
The response and amendments filed on 05/29/2025 are acknowledged. Any previously applied minor objections and/or minor rejections (i.e., formal matters), not explicitly restated here for brevity, have been withdrawn necessitated by Applicant’s formality corrections and/or amendments. For the purposes of clarity of the record, the reasons for the Examiner’s withdrawal, 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.
Briefly, the previous claim rejections under 35 U.S.C. 112(b) for indefiniteness have been withdrawn necessitated by Applicant’s amendments. The previous claim rejections under 35 U.S.C. 112(a) for lack of written description have been withdrawn necessitated by Applicant’s amendments; however, new grounds of rejection are set forth below. The previous claim rejections under 35 U.S.C. 101 for ineligible subject matter have been withdrawn necessitated by Applicant’s amendments. The previous claim rejections under 35 U.S.C. 103 for obviousness have been withdrawn necessitated by Applicant’s amendments; however, new grounds of rejection have been set forth below.
The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
New Grounds of Rejection Necessitated by Amendments
Claim Rejections - 35 USC § 112(a), Written Description
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 15, 22, 25, 27-28, and 210-211 are rejected under 35 U.S.C. 112(a) 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Independent claim 15 recites “u114”, “genera 5-7N15”, and “BF311”. The instant Specification does not describe what bacteria are encompassed within “u114”. The instant Specification does not describe what bacteria are compassed within “genera 5-7N15”. The instant Specification does not describe what bacteria are encompassed within “BF311”. Due to the lack of written description for u114, genera 5-7N15, and BF311, the instant Specification does not describe these genera in enough specificity such that the Applicant has shown possession of the entire genus for each substance. Moreover, Applicant has not provided a representative number of species for each claimed genus because Applicant has not described which bacterial species encompass the claimed genera, and the Applicant does not provide examples with u114, 5-7N15, and BF311; therefore, the written description has not been satisfied (see, e.g., MPEP 2163(II)(A)(3)(ii)).
With regard to the state of the art, Fernandes (Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamic of Microbial Communities following Dietary Change, 2014 – previously cited) teaches that “BF311” is a genus within the Bacteroidaceae family (see, e.g., Fernandes, abstract). It is unclear from the prior art if there are specific bacterial species encompassed within the BF311 genus. Huang (The day-to-day stability of the ruminal and fecal microbiota in lactating dairy cows; 2020 – previously cited) teaches that 5-7N15 is a highly abundant bacterial genus within the microbiome of lactating dairy cows (see, e.g., Huang, abstract). It is unclear from the prior art if there are specific bacterial species encompassed within genera 5-7N15. Penesyan (Antimicrobial activity observed among cultured marine epiphytic bacteria reflects their potential as a source of new drugs; 2009 – previously cited) teaches u114 is a gram-positive bacteria isolate represented by the phyla Actinobacteria (see, e.g., Penesyan, “Results and Discussion”, pg. 119). Thus, the state of the art does not define which bacteria are encompassed within the genera 5-7N15 and BF311.
Accordingly, claims 15, 22, 25, 27-28, and 102 do not meet the written description requirement. Claims 25, 27-28, and 102 depend on rejected claim 15 and fail to rectify the noted deficiencies.
Examiner’s Response to Arguments
Regarding Applicant’s remarks pertaining to the 35 U.S.C. 112(a), written description rejection (remarks, page 10), Applicant only provides statements and remarks pertaining to phrases that have been cancelled from the claims; however, Applicant does not provide arguments pertaining to the lack of written description for u114, 5-7N15, and BF311. Moreover, as stated in the 35 U.S.C. 112(a) rejection above, u114, 5-7N15, and BF311 lack written description in light of the instant Specification and/or state of the art; therefore, the 35 U.S.C. 112(a) rejection is still set forth.
New Grounds of Rejection Necessitated by Amendments
Claim Rejections - 35 USC § 103, Obviousness
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 15, 22, 25, 27-28, and 210 are rejected under 35 U.S.C. 103 as being unpatentable over Apte (WO 2016/065075; Date of Publication: April 28, 2016 – previously cited) in view of Saulnier (Gastrointestinal Microbiome Signatures of Pediatric Patients with Irritable Bowel Syndrome; 2011 – previously cited) and of McLaren (WO 2018/010013; Date of Publication: January 18, 2018 – previously cited).
Apte’s general disclosure relates to “A method for diagnosing and treating an immune microbial dysfunction in a subject” comprising the generation of a microbiome composition dataset as a diagnostic for irritable bowel syndrome (IBS) (see, e.g., Apte, abstract). Apte discloses that the method comprises: “receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the immune microbial dysfunction based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset, wherein the characterization is diagnostic of at least one of Crohn's disease, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), ulcerative colitis, and celiac disease; based upon the characterization, generating a therapy model configured to correct the immune microbial dysfunction; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model” (see, e.g., Apte, abstract).
Regarding claim 15 pertaining to determining the efficacy of a microbiome treatment for IBS, Apte teaches a method for diagnosing and treating IBS through the use of microbiome-derived diagnostics (see, e.g., Apte, abstract & [0002]).
Regarding claim 15 pertaining to detecting a baseline level of gut microbiome bacteria, Apte teaches “receiving a biological sample from a subject S210; characterizing the subject with a form of an immune microbial dysfunction based upon processing a microbiome dataset derived from the biological sample” (see, e.g., Apte, [0003]). Based on this method, Apte teaches obtaining, processing, and detecting a baseline level of gut microbiome bacteria from subjects.
Regarding claim 15 pertaining to administration of a microbiome modulating treatment, Apte teaches “promoting a therapy to the subject with the immune microbial dysfunction based upon the characterization and the therapy model” (see, e.g., Apte, [0003]). Furthermore, Apte teaches that the methods of characterizing a subject’s gut microbiome allows for one to “generate models that can be used to classify individuals and/or provide therapeutic measures (e.g., therapy recommendations, therapies, therapy regimens, etc.) to individuals based upon microbiome analysis for a population of individuals” (see, e.g., Apte, [0004]). Therefore, based on the baseline levels of gut microbiome bacteria, Apte teaches the promotion/administration of a therapy to the subject.
Regarding claim 15 pertaining to obtaining a second gut microbiome samples, Apte teaches “Variations of the second method 200 can further facilitate monitoring and/or adjusting of therapies provided to an individual, for instance, through reception, processing, and analysis of additional samples from an individual throughout the course of therapy” (see, e.g., Apte, [0004]). Therefore, variations of the method set forth by Apte can allow for second (i.e., “additional”) samples throughout the course of therapy.
Regarding claim 15 pertaining to comparing the treatment levels of the gut microbiome bacteria, Apte teaches “ the therapy model can be derived in relation to identification of a "normal" or baseline microbiome composition and/or functional features” (see, e.g., Apte, [0057]). Additionally, Apte teaches “characterization can be based upon features derived from a statistical analysis (e.g., an analysis of probability distributions) of similarities and/or differences between a first group of subjects exhibiting a target state (e.g., a health condition state) associated with the immune microbial dysfunction, and a second group of subjects not exhibiting the target state (e.g., a "normal" state) associated with the immune microbial dysfunction” (see, e.g., Apte, [0034]). Furthermore, Apte teaches “potential therapy formulations and therapy regimens that can shift microbiomes of subjects who are in a state of dysbiosis toward one of the identified baseline microbiome compositions and/or functional features” (see, e.g., Apte, [0054]).
However, Apte does not teach: detection of Haemophilus within the gut microbiome for IBS patients (claims 15 and 210); or wherein the dosage regimen is about 1-4 weeks (claims 15 and 25); or wherein the microbiome modulating compound is resistant potato starch (claims 22 and 27); or wherein the effective amount is 2 to 40 g per day of resistant potato starch (claim 28) and wherein the IBS-related symptoms are selected from the group consisting of diarrhea, constipation, bloating, abdominal pain, and gas (claim 211).
Saulnier’s general disclosure relates to defining “the intestinal microbiomes of healthy children and pediatric patients with irritable bowel syndrome (IBS)” (see, e.g., Saulnier, abstract). Saulnier discloses that pediatric IBS is associated with significantly greater percentages of Haemophilus influenzae, signifying that the intestinal microbiota is involved in IBS (see, e.g., Saulnier, abstract).
Regarding claims 15 and 210 pertaining to detection of Haemophilus, Saulnier teaches the detection of Haemophilus in microbiomes from healthy and IBS patients (see, e.g., Saulnier, “Results – Comparisons of pediatric gut microbiomes in healthy children and children with IBS”, pg. 5).
Regarding claim 211 pertaining to the IBS-related symptoms, Saulnier teaches that IBS-related symptoms are recurrent abdominal pain and diarrhea (see, e.g., Saulnier, Introduction, pg. 2).
McLaren’s disclosure relates to changes in the gut microbiome due to the consumption of resistant potato starch (see, e.g., McLaren, abstract). Additionally, McLaren discloses supplementation of the elderly with resistant potato starch, which is a dietary prebiotic, to correct dysbiosis of the gut microbiome, wherein dysbiosis of the gut microbiome can lead to IBS (see, e.g., McLaren, pg. 1, lines 15-16; pg. 2, line 30; pg. 3, lines 25-29).
Regarding claims 15 and 25 pertaining to the suitable period of time, McLaren teaches “the suitable period of time may be from one week, two weeks, a few weeks, one month, two months, a few months, 12 weeks or several months” (see, e.g., McLaren, pg. 26, lines 8-10).
Regarding claims 22 and 27 pertaining to the microbiome modulating compound, McLaren teaches resistant potato starch to modulate intestinal function (see, e.g., McLaren, pg. 1, lines 13-16).
Regarding claim 28 pertaining to the effective amount of resistant potato starch, McLaren teaches an effective amount of resistant potato starch is 0.25-40 grams daily (see, e.g., McLaren, pg. 25, lines 18-26; pg. 26, line 30).
It would have been first obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to assess the efficacy of a microbiome modulating treatment, as taught by Apte, wherein one specially measures Haemophilus, as taught by Saulnier. One would have been motivated to measure Haemophilus levels because Saulnier teaches that “IBS microbiomes were characterized by greater percentages of Haemophilus (in class Gammaproteobacteria)” (see, e.g., Saulnier, “Results – Comparisons of pediatric gut microbiomes in healthy children and children with IBS”, pg. 5). Moreover, Apte teaches that the methods of characterizing a subject’s gut microbiome allows for one to “generate models that can be used to classify individuals and/or provide therapeutic measures (e.g., therapy recommendations, therapies, therapy regimens, etc.) to individuals based upon microbiome analysis for a population of individuals” (see, e.g., Apte, [0004]). Therefore, based on the teachings of Apte and Saulnier, it would have been obvious to measure Haemophilus levels within the gut microbiome because the abundance of Haemophilus bacteria is increased in IBS patients.
It would have been secondly obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to assess the efficacy of a microbiome modulating treatment, as taught by Apte, wherein one specially measures IBS-related symptoms, such as diarrhea and abdominal pain, as taught by Saulnier. One would have been motivated to do so because Saulnier teaches that recurrent abdominal pain and diarrhea is associated with IBS (see, e.g., Saulnier, Introduction, pg. 2), and children with IBS and recurrent abdominal pain had increased Haemophilus levels (see, e.g., Saulnier, Discussion, pg. 7). Moreover, Apte teaches “potential therapy formulations and therapy regimens that can shift microbiomes of subjects who are in a state of dysbiosis toward one of the identified baseline microbiome compositions and/or functional features” (see, e.g., Apte, [0054]). Therefore, based on the teachings of Apte and Saulnier, it would have been obvious to measure IBS-related symptoms because this would allow one to determine if a therapy formulation or regimen is shifting the microbiome from a state of dysbiosis to baseline by using Apte’s modeling system. One would have expected success because Apte and Saulnier both teach measuring bacteria within the gut microbiome to determine levels of gut microbiome bacteria within IBS patients.
It would have been thirdly obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to assess the efficacy of a microbiome modulating treatment, as taught by Apte, wherein the microbiome modulating treatment is resistant potato starch, as taught by McLaren. One would have been motivated to do so because McLaren teaches that resistant potato starch is an effective dietary prebiotic supplement that modulates intestinal function and has application in the treatment of gastrointestinal disorders (see, e.g., McLaren, pg. 1, lines 15-19). Moreover, Apte teaches “potential therapy formulations and therapy regimens that can shift microbiomes of subjects who are in a state of dysbiosis toward one of the identified baseline microbiome compositions and/or functional features” (see, e.g., Apte, [0054]). Additionally, Apte teaches that the methods of characterizing a subject’s gut microbiome allows for one to “generate models that can be used to classify individuals and/or provide therapeutic measures (e.g., therapy recommendations, therapies, therapy regimens, etc.) to individuals based upon microbiome analysis for a population of individuals” (see, e.g., Apte, [0004]). Therefore, based on the teachings of Ape and McLaren, it would have been obvious to apply Apte’s modeling system for determining the therapy regimens for individuals upon microbiome analysis, wherein the therapy regimen is resistant potato starch because resistant potato starch is a prebiotic supplement that can treat gastrointestinal disorders. One would have expected success because Apte and McLaren both teach measuring bacteria within the gut microbiome and administration of treatment regimens.
Examiner’s Response to Arguments
Applicant’s amendments and arguments filed on 05/29/2025 have been filly considered but they are not persuasive and deemed insufficient to overcome the prior arts of record.
In response to Applicant’s argument that Apte does not provide any data or evidence for comparison between populations (see remarks, page 12), this argument is not persuasive. The Broadest Reasonable Interpretation (BRI) of independent claim 15 is a method of determining the efficacy of a microbiome modulating treatment by detecting baseline levels of a bacterium, administering a microbiome modulating treatment, and measuring the levels of the same bacterium measured at baseline after treatment in order to determine this the microbiome modulating treatment is effective. Apte teaches the instantly claimed invention because Apte teaches “receiving a biological sample from a subject S210; characterizing the subject with a form of an immune microbial dysfunction based upon processing a microbiome dataset derived from the biological sample” (see, e.g., Apte, [0003]) and “promoting a therapy to the subject with the immune microbial dysfunction based upon the characterization and the therapy model” (see, e.g., Apte, [0003]). Furthermore, Apte teaches that the methods of characterizing a subject’s gut microbiome allows for one to “generate models that can be used to classify individuals and/or provide therapeutic measures (e.g., therapy recommendations, therapies, therapy regimens, etc.) to individuals based upon microbiome analysis for a population of individuals” (see, e.g., Apte, [0004]). Additionally, Apte teaches “Variations of the second method 200 can further facilitate monitoring and/or adjusting of therapies provided to an individual, for instance, through reception, processing, and analysis of additional samples from an individual throughout the course of therapy” (see, e.g., Apte, [0004]). Therefore, based on the BRI of independent claim 15, Apte teaches determining the efficacy of a microbiome modulating treatment by detecting baseline levels of a bacterium, administering a microbiome modulating treatment, and measuring the levels of the same bacterium measured at baseline after treatment in order to determine this the microbiome modulating treatment is effective.
Applicant has traversed the previous 35 U.S.C. 103 rejections in view of Apte, Saulnier, and McLaren, in light of the amendment of claim 15 which introduces new limitations (remarks, pages 12-13). As discussed above, all rejections have been withdrawn and new rejections are presented due to Applicant’s amendment on 05/29/2025. As such, Applicant’s arguments regarding the teachings of Apte, Saulnier, and McLaren are moot.
Conclusion
Claims 15, 22, 25, 27-28, and 210-211 are rejected.
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
Correspondence Information
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/NATALIE IANNUZO/Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653