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 .
Applicant’s Response
Applicant’s response, filed 08/25/2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Claims Status
Claim 4 is canceled.
Claim 20 is new.
Claims 1-3 and 5-20 are pending.
Claims 14-17 are withdrawn.
Claims 1-3, 5-13, and 18-20 are examined.
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 1-3, 5-13, and 18-20 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more. Any newly recited portion is necessitated by claim amendments.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims recite a method.
With respect to step (2A)(1): The claims are directed to abstract ideas of mental processes and mathematical concepts, and laws of nature.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claim 1:
wherein specific sequences of the specific microbiota-derived nucleic acids are identified from a training database containing data from reference subject comprising healthy subjects and subjects suffering from a particular disease, the data selected from: (i) metagenomic sequencing data of microbiota from the reference subjects, and (ii) data measured in vitro pertaining to producing rates of short chain fatty acids (SCFAs) and other fermentation metabolites from different dietary fibers in the reference subjects, wherein the metagenomic sequencing data and the production rates of the SCFAs and the other fermentation metabolites of the reference subjects are paired with each other
determining and quantifying relative abundance of the specific microbiota-derived nucleic acids in the biological sample
wherein the response of the test subject to the different dietary fibers is defined as the production rate of SCFAs and other fermentation metabolites in response to challenge with the different dietary fibers
wherein the SCFAs and the other fermentation metabolites are selected from propionate, butyrate, acetate, lactate, formate, succinate, iso-butyrate, valerate, and isovalerate
Mathematical concepts recited in claim 1:
applying a machine learning algorithm trained on the training database to predict the response of the test subject to the different dietary fibers -from the relative abundance of the specific microbiota-derived nucleic acids in the biological samples
Dependent claims 2-5, and 10-13 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 1, and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 2: “wherein the training database comprises data classified according to a predetermined set of classification groups, wherein analysis of fermentation or metabolic capabilities of the reference subject’s microbiota comprise classifying the reference subjects according to a specific type or phenotype”
Claim 3: “wherein the machine learning algorithm further comprises a set of algorithms for linking the data associated with the reference subjects’ microbiome to a medical condition, physical condition, or responsiveness to a therapy”
Claim 5: “wherein treating the test subject with the dietary fiber supplement, the dietary ingredient, or the therapeutic agent is based on identifying the dietary fibers that result in highest and lowest production of metabolites of interest by the test subject’s microbiota”
Claim 10: “wherein the machine-learning algorithm comprises a supervised learning procedure”
Claim 11: “wherein the machine learning algorithm comprises at least one procedure selected from the group consisting of clustering, support vector machine, linear modeling, k-nearest neighbor analysis, decision tree learning, ensemble learning procedure, neural networks, probabilistic model, graphical model, Bayesian network, and association rule learning”
Claim 12: “wherein the different dietary fibers are (1) complex polysaccharides or (2) a dietary ingredient selected from the group consisting of inulin, fructo-oligosaccharide, resistant starch, lignin, tannin, cellulose, hemicellulose, psyllium, polydextrose, chitin, chitosan, pectin, arabinan, and konnyaku/konjac (glucomannan)”
Claim 13: “wherein the other enzymes responsible for degradation of the different dietary fibers are selected from the group consisting of bacterial, archaeal, and fungal enzymes originated from the test subject’s gut microbiota, the reference subjects’ gut microbiota, or a combination thereof.”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and mathematic concepts because the claims recite no more than analyzing sequence data and using a machine learning algorithm to make a prediction based on this analyzed data. Although some of the dependent claims recite limitations of preparing a dietary fiber, because this is an in silico method and there are no steps of application a dietary fiber treatment to a patient, this is interpreted as a mental process of formulating a dietary fiber for the subject based on the results of the machine learning algorithm. Furthermore, the claims are directed to utilizing the law of nature of the association between gut microbiota and the fermentation of fiber to make a prediction.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Claim 1 recites the following additional elements that are not abstract ideas:
in silico method
isolating and extracting specific microbiota-derived nucleic acids from a biological sample from the test subject
wherein the specific microbiota-derived nucleic acids comprise (1) gene sequences specific to glycoside and/or polysaccharide hydrolases capable of hydrolyzing or cleaving complex polysaccharides of the different dietary fibers, or (2) gene sequences specific to enzymes from bacterial acetate, propionate, and butyrate production pathways and/or other enzymes responsible for degradation of the different dietary fibers
treating the test subject, according to a predicted response output by the machine learning algorithm, with a dietary fiber supplement, a dietary ingredient, or a therapeutic agent corresponding to a predicted response output by the machine learning algorithm
The steps of isolating and extracting specific microbiota-derived nucleic acids is directed to a data gathering step as it gathers the data on which the judicial exceptions are performed. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). The element of an in silico method is interpreted as the method for simulating being performed on a general computer. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. ... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)). Furthermore, the step of treating the subject according to a predicted response output by the machine learning algorithm with a therapy corresponding the predicted response output does not integrate the judicial exceptions into a practical application, because the treatment has a nominal relationship to the exception. The claims do not outline the relationship between the predicted response output and the treatments, and thus these are mere instructions to apply the exceptions as opposed to a particular treatment (see MPEP 2106.04(d)(2)).
Dependent claims 8, 9, 19, and 20 are directed to further steps of data gathering or limiting the data gathered. Dependent claims 6, 7, and 18 are directed to generic steps of administering a treatment.
None of these dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
Lastly, the claims have been evaluated with respect to step (2B): Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. Under said analysis, Applicant is reminded that the judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d).I, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represent well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claim 1: The additional elements of in silico, isolating and extracting specific microbiota-derived nucleic acids from a biological sample from the test subject, the specific microbiota-derived nucleic acids comprising (1) gene sequences specific to glycoside and/or polysaccharide hydrolases capable of hydrolyzing or cleaving complex polysaccharides of the different dietary fibers, or (2) gene sequences specific to enzymes from bacterial acetate, propionate, and butyrate production pathways and/or other enzymes responsible for degradation of the different dietary fibers, and treating the test subject with a dietary fiber supplement, a dietary ingredient, or a therapeutic agent do not rise to the level of significantly more than the judicial exception. With respect to an in silico method, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). As exemplified in the MPEP at 2106.05(d).II with reference to Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157) and Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017), detecting DNA or enzymes in a sample is a well-understood, routine, and conventional activity. Furthermore, with respect to treating the subject, the prior art Marlett et al. (“Position of the American Dietetic Association: Health Implications of Dietary Fiber”, Journal of the American Dietetic Association, published July 2002) discloses that a high-fiber diet is standard therapy for diverticular disease of the colon (page 997, column 1, paragraph 3). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 6: The additional element of the therapeutic agent comprises one or more pre-biotics, one or more probiotics, one or more antibiotics, or any other drug for therapeutic treatment of a metabolic, immunological, or inflammatory disease or disorder does not rise to the level of significantly more than the judicial exception. The prior art Marlett et al. discloses that a high-fiber diet is standard therapy for diverticular disease of the colon (page 997, column 1, paragraph 3). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 7: The additional element of treating a predisposition to a metabolic, immunological, or inflammatory disease or disorder selected from the group consisting of obesity, a metabolic syndrome or disease, diabetes mellitus, an insulin-deficiency related disorder, an insulin-resistance related disorder, an intestinal gluconeogenesis disorder, an inflammation disorder, inflammatory bowel disease, a systemic or local inflammation related to neurodegeneration, rheumatoid arthritis, a depression or anxiety disorder, food intolerance, constipation, colitis, enteritis, and an allergy and cancer immunotherapy application does not rise to the level of significantly more than the judicial exception. The prior art Marlett et al. discloses that a high-fiber diet is standard therapy for diverticular disease of the colon (page 997, column 1, paragraph 3). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 8: The additional element of the biological sample is selected from the group consisting of a rectal swab, a fecal sample, a biopsy, and a mucosal layer sample does not rise to the level of significantly more than the judicial exception. The prior art to Ingala et al. (“Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution”, Microbiol. April 2018, cited in prior Office Action) discloses that gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal (Abstract). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 9: The additional element of DNA sequencing of specific marker genes, shotgun metagenomics DNA sequencing, PCR, or capillary electrophoresis do not rise to the level of significantly more than the judicial exception. As stated in Applicant’s Response filed 03/12/2026, on page 8, Applicant states that all of these techniques are well-known to those skilled in the art. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 18: The additional element of a product prepared for the test subject, comprising the dietary fiber that results in highest production of metabolites of interest does not rise to the level of significantly more than the judicial exception. The prior art Marlett et al. discloses that a high-fiber diet is standard therapy for diverticular disease of the colon (page 997, column 1, paragraph 3). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 19: The additional element of qPCR does not rise to the level of significantly more than the judicial exception. As stated in Applicant’s Response filed 03/12/2026, on page 8, Applicant states qPCR is one of numerous well-known DNA analysis techniques. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 20: The additional element of nucleic acids stable at room temperature does not rise to the level of significantly more than the judicial exception. The prior art to Lou et al. (“A review of room temperature storage of biospecimen tissue and nucleic acids ) discloses that current room temperature technologies can store purified nucleic acids for years (Abstract; “Highlights”). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
In combination, the collection or generation of the data, acted upon by the judicial exception, fail to rise to the level of significantly more. The data gathering steps provide the data for the judicial exception. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
Response to Arguments
Applicant states that “Amended claim 1 recites a treatment step which is a specific physical act of treating a test subject with a dietary fiber supplement, dietary ingredient, or therapeutic agent correspond to the predicted response output by the machine learning algorithm, which is categorically not abstract. The January 2019 Revised USPTO Guidance identifies three categories of abstract ideas: (A) mathematical concepts, (B) certain methods of organizing human activity, and (C) mental processes. The treatment step recited by amended claim 1, treating a human patient with a dietary fiber supplement, dietary ingredient, or therapeutic agent corresponding to the predicted response output by the machine learning algorithm, does not fall within any of these categories. It is not a mathematical concept, not a method of organizing human activity, and not performable in the human mind. Therefore, amended claim 1, including the treatment step described above, cannot be characterized as an abstract idea. The recited treatment step falls squarely within the category of patent-eligible subject matter under 35 U.S.C. § 101. Courts and the UPSTO have consistently recognized that claims directed to treatment of patients are patent eligible, even when incorporating computation or algorithmic steps. […] In Vanda, the Federal Circuit distinguished the claims from those in Mayo Collaborative Services v. Prometheus Laboratories, 566 U.S. 66 (2012), because the claims required the step of actually treating the patient with a specific drug based on the result of a diagnostic test. Here, claim 1 similarly requires treating the test subject with a specific type of agent […] according to the machine learning algorithm’s predicted response. This treatment step is a well-recognized category of patent-eligible subject matter under the USPTO’s own training materials and examination guideline, which has been consistently recognized as patent eligible.”
It is respectfully submitted that this is not persuasive. The step of treating the test subject is an additional element, and not an abstract idea, however, it does not integrate the judicial exception into a practical application. The limitation of treating the subject “according to a predicted response output by the machine learning algorithm, with a dietary fiber supplement, a dietary ingredient, or a therapeutic agent correspond to the predicted response output by the machine learning algorithm” applies treatment instructions in a generic way to the judicial exceptions. The claims in Vanda recite a method of treating a patient having schizophrenia with iloperidone in patients having a particular genotype associated with poor drug metabolism. The instant claims do not recite such a particular treatment. The claims do not outline more than a nominal relationship between the predicted response output and the treatment and thus these are mere instructions to apply the exceptions as opposed to a treatment administered in response to getting specific predicted response outputs (see MPEP 2106.04(d)(2)). Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emilie A Smith whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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/E.A.S./Examiner, Art Unit 1686
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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