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 amendments and remarks, filed on 01/09/2026, are acknowledged. Applicant’s arguments have been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application. Rejections and/or objections not reiterated from the previous office actions are hereby withdrawn.
Status of Claims
Claims 1-3, 9, 11, 13-15, 17, 19, 30, 32, 34-39 are presently under examination.
Claims 4-8, 10, 12, 16, 18, 20-29, 31, 33 are cancelled.
Priority
This application is a 371 of PCT/US19/50102, filed 09/06/2019, which claims benefit of priority to provisional application US 62/728,035, filed 09/06/2018.
Information Disclosure Statement
The information disclosure statement (IDS) document(s) submitted 10/15/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.
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, 9, 11, 13-15, 17, 19, 30, 32, 34-39 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Guidance Step 1:
Regarding claim(s) 1, 39, the claimed invention is directed to a method for performing a process and therefore falls within one of the four statutory categories of invention. MPEP 2106.03.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the claimed steps that are part of the abstract idea are as follows:
Claim 1
b) determining from the sequence information, a taxa group activity component by determining…an abundance of each respective microbial taxon in a plurality of different microbial taxa present in the sample by aligning sequence reads from the sequence information to a library of taxonomic signatures corresponding to the plurality of different microbial taxa…; and c) determining from the sequence information a biochemical pathway activity component by determining…a quantitative measure of gene activity…; (claim 1)
c) using the taxa group activity component and the biochemical pathway activity component to identify a dysbiosis in the gut microbiome, wherein the dysbiosis comprises an amount of a microbial taxon in the plurality of different microbial taxa or a biochemical activity in the sample that is outside a reference range…; (claim 1)
d) determining that the taxa group activity component…is outside a reference range…; (claim 1)
Claim 39
b) determining from the sequence information, a taxa group activity component by determining, using a computer, an abundance of each respective microbial taxon in a plurality of different microbial taxa present in the sample by mapping sequence reads from the sequence information to a library of taxonomic signatures corresponding to the plurality of different microbial taxa to obtain a read coverage of sequence reads mapping to taxonomic signatures corresponding to the respective microbial taxon; (claim 39)
c) determining from the sequence information a biochemical pathway activity component by determining, using the computer, a quantitative measure of gene activity for each respective gene in a plurality of genes encoded by RNA present in the sample by mapping sequence reads from the sequence information to an open reading frame corresponding to the plurality of genes to obtain a read coverage of sequence reads mapping to open reading frames corresponding to the respective gene; (claim 39)
d) determining that the taxa group activity component and the biochemical pathway activity component for the subject is outside a reference range for the taxa group activity component and the biochemical pathway activity component, wherein the reference range is determined from a reference population of healthy control subjects; (claim 39)
Mental Processes
Under the broadest reasonable interpretation, the above steps are not limited to any particular acts or operations and generally require observing or analyzing data and making a decision based on said analysis. The Office's eligibility guidance does not set limit on the number of calculations that can or cannot be performed mentally. MPEP § 2106.04(a)(2)III. In addition, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include only data analysis methods [0027, 0028, 0078]. The courts are also clear that an invention directed to the “collection, manipulation, and display of data” is an abstract process. See Intellectual Ventures, 850 F.3d at 1340; see generally id. at 1340-41. Accordingly, when read in light of the specification, the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III.
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim includes any additional steps/elements that integrate the recited judicial exception into a practical application of the exception. In this case, the additional steps/elements that are not part of the abstract idea are as follows:
Claim 1
a) generating a metatranscriptomic dataset for the about a human subject by: i) determining data from a gut microbiome from the subject by: (1) obtaining nucleic acids from a sample comprising gut microbiome from the subject, wherein the nucleic acids obtained comprise RNA;(2) removing from the nucleic acids DNA and non-informative RNAs comprising microbial rRNA and subject rRNA, whereby the RNA is essentially free of non-informative RNAs; (3) reverse transcribing the RNA into cDNA; and (4) obtaining metatranscriptomic sequence information representative of the nucleic acids; (claim 1)
e) transmitting, to an electronic device accessible by the subject, (i) a report comprising the abundance of each respective microbial taxon…and (ii) a recommendation for one or more dietary items to the subject, thereby altering a diet of the subject, responsive to determining that the taxa group activity and the biochemical pathway activity for the subject is outside the reference ranges wherein the recommendation comprises microbes of one or more microbial taxa…(claim 1)
Claim 39
a) generating a metatranscriptomic dataset for the subject by: i) obtaining nucleic acids from the sample, wherein the nucleic acids obtained comprise RNA; ii) removing, from the nucleic acids, (1) DNA and (2) non-informative RNAs comprising microbial rRNA and subject rRNA, thereby causing the RNA in the nucleic acids to be essentially free of non-informative RNAs; iii) reverse transcribing the RNA in the nucleic acids into cDNA; and iv) obtaining metatranscriptomic sequence information representative of the nucleic acids; (claim 39)
d) administering one or more dietary items to the subject, thereby altering a diet of the subject, wherein the one or more dietary items comprise: responsive to a deficiency of the microbial taxon in the gut of the subject, microbes of the microbial taxon, and responsive to an overabundance of the microbial taxon in the gut of the subject, one or more probiotic microbes other than the microbial taxon. (claim 39)
With regards to the generating steps (step a), these steps are generically recited and directed to gathering data for use by the abstract idea. As such, these steps/elements amount to insignificant extra-solution activity. See MPEP 2106.05(g). With regards to the claimed “libraries”, it is noted with particularity that the claimed invention does not even comprise a computer/processor. That being said, the libraries are additional elements that are recited at a high level of generality and are broadly interpreted as databases. However, this type of limitation merely confines the use of the abstract idea to a particular technological environment (presumably a computer) and/or amounts to mere instructions to apply the abstract idea on a generic computer and thus fails to add an inventive concept to the claims. See MPEP 2106.05(h).
With regards to the transmitting (claim 1), this step results in transmitting a report and a recommendation. However, this amounts to insignificant post-solution activity (i.e. outputting information) or merely including instructions to implement an abstract idea on a computer, as discussed in MPEP § 2106.05(f) and MPEP § 2106.05(g). In addition, although the additional elements do limit the use of the abstract idea, they merely confine the use of the abstract idea to a particular technological environment (i.e. computer) and thus fails to add an inventive concept to the claims, as discussed in MPEP § 2106.05(h).
With regards to the administering (claim 39), the administering generically recited dietary items to a subject do not impose any boundaries on type or amount of said items (other than ‘probiotics’ which are also a generic category). Accordingly, the claims do not amount to applying or using a judicial exception to effect a particular treatment for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2). In other words, this step does not necessarily amount to administering a particular treatment. See also the Vanda Memo (June 2018), which also clearly identifies a particular drug and dosage to a particular patient population. As such, this step is not indicative of integration into a practical application.
C. Guidance Step 2B:
Under the 2019 PEG, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. In this case, the claims do not include additional steps and/or elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons:
As discussed above, the non-abstract steps/elements amount to nothing more than insignificant extra-solution activity. Applicant’s own specification teaches that methods for isolating and sequencing samples, e.g. NGS, were routine and conventional in the art [see, e.g. 0002, 0043-46, 0050-52]. A review of the specification also provides a laundry list of nutrients, supplements, and vitamins that can be administered to a subject, all of which are well known in the art and applicant does not make any claims to the propriety of these compounds or medically effective amounts of these compounds (alone or in combination) [0082-0084]. Moreover, Peano et al. (Microbial Informatics and Experimentation, 2013, 3:1, pp.1-11) teaches methods for generating metatranscriptome data that include removing non-target RNA sequences and reverse transcribing RNA to obtain cDNA (see at least “Methods”, page 9, col. 2). Alternatively, Stewart et al. (The ISME Journal (2010) 4, 896–907) also teaches methods for generating metatranscriptome data that include subtracting non-target RNA sequences and reverse transcribing RNA to obtain cDNA (see entire). Lastly, MacFarland et al. (BMJ Open, 2014, 4:e005047, pp.1-18) teaches methods for administering probiotics to correct dysbiosis in subjects [See entire]. Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract elements/steps. See MPEP 2106.05(d)(Part II). In other words, there is nothing unconventional about how data is being obtained. Therefore, these steps remain insignificant extra-solution activity even upon reconsideration, and do not amount to significantly more. Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible.
D. Dependent Claims
Dependent claims 2-3, 9, 11, 13-15, 17, 19, 30, 32, 34-38 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. In particular, 2, 3, 14, 32, 34, further limit the specificity of the abstract idea set forth above and therefore are also directed to an abstract idea (Step 2A, prong 1 analysis). Regarding claim(s) 35, this claim requires determining a naturally occurring relationship between microbiome data obtained from a subject and a disease state. See MPEP 2106.04(b). Regarding claim(s) 9, 11, 13, 15, 17, 19, 30, 36-38, these claims further limit the nature of the data being used by the abstract idea or how the data is being obtained. As such, these claims are not drawn to eligible subject matter as they are directed to insignificant extra-solution activity for reasons discussed above (Step 2A, prong 2, and Step 2B analysis). For additional guidance, applicant is directed generally to the 2019 Revised Patent Subject Matter Eligibility Guidance published in the Federal Register (84 FR 50) on January 7, 2019.
Response to Arguments
Applicant’s arguments, filed 01/09/2026, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the “generating” steps include multiple physical limitations that cannot be performed by the human mind. In response, this argument is not persuasive as the “generating” steps were not interpreted as part of the abstract idea and therefore were analyzed under “Step 2A, prong 2” and “Step 2B” analysis. Applicant appears to have a fundamental misunderstanding of the two-prong inquiry necessary for patentability. See the flowchart in MPEP § 2106, subsection III.
Applicant argues that the amended “determining” steps also cannot be performed by the human mind because they require a computer to process the sequence information. In response, as set forth above, the determining steps are recited at a high level of generality and do not impose any limitations on how this step is performed (but for using a computer). As such, these steps encompass observations, analyzing sequence data, and/or making a decision based on said analysis. Therefore, the above step clearly falls within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III. Therefore, when read in light of the specification, the examiner maintains that the claimed steps clearly encompass an abstract idea in the form of a mental process [Step 2A, Prong 1: YES].
Applicant additionally argues that the “transmitting” step cannot be performed in the human mind. In response, this argument is not persuasive because this step was not interpreted as part of the abstract idea and therefore were analyzed under “Step 2A, prong 2” and “Step 2B” analysis.
Applicant argues that the claims provide an improvement to the functioning of a computer or to a technology or technical field. In response, the MPEP is clear that the word "improvements" in the context of this consideration is limited to improvements to the functioning of a computer or any other technology/technical field, whether in Step 2A Prong Two or in Step 2B. MPEP 2106.04(d)(1). In this case, applicant has not provided any objective evidence to support the case that the claims result in an improvement to the functioning of a computer and no such evidence is provided in the specification. The claims fail to identify any elements that provides for a new transmission technology. To the extent that applicant is arguing that the “determining” steps (i.e. the abstract idea) is providing the improvement, Applicant is reminded that the claimed invention’s use of the ineligible concept to which it is directed (i.e. the abstract idea) cannot supply the inventive concept that renders the invention ‘significantly more’ than that ineligible concept.” BSG Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1290 (Fed. Cir. 2018). Moreover, the courts have recently instructed that “[t]he different use of a mathematical calculation, even one that yields different or better results, does not render patent eligible subject matter.” Board Of Trustees Of Leland Stanford Junior University, 991 F.3d 1245, 1251 (Fed. Cir. 2021).
In response to applicant’s aggregate arguments regarding additional improvements (e.g. reducing the amount of abundant non-target DNA and existing methods for subject evaluation, monitoring, and reporting), these arguments are not persuasive. As set forth above, the transmitting of a report and a recommendation amounts to insignificant post-solution activity (i.e. outputting information) or merely including instructions to implement an abstract idea on a computer, as discussed in MPEP § 2106.05(f) and MPEP § 2106.05(g), and merely confine the use of the abstract idea to a particular technological environment (i.e. computer) and thus fails to add an inventive concept to the claims, as discussed in MPEP § 2106.05(h). The claims do not provide any improvement with regards to how the data is being transmitting or to what is being administered to a subject. The claims do not constitute a technological improvement to computer capabilities or an improvement to existing technology, but instead relate to an improvement to an apparent business practice. To the extent that microbiome analysis is a business practice, the optimization of a business process through modification to perform it more efficiently (i.e., faster or cheaper) is a common economic act which is ordinarily performed in the course of conducting a business. See MPEP 2106.04(a)(2)(II) citing Bilski, wherein the concept of optimizing a business practice recited in applicant’s claims "is a fundamental economic practice long prevalent in our system of commerce." Alice, 573 U.S. at 216 (citations and internal quotation marks omitted). Additionally, the claimed invention also does not result in an “unconventional technological solution to a technical problem” and applicant has not provided any evidence that there is anything unconventional with regards to the non-abstract “generating” steps. Indeed, the claim relies upon routine and conventional data collection steps in combination with the abstract idea steps. That is not the kind of “technological” improvement that suffices for patent eligibility. See also Amdocs Ltd. v. Openet Telecom, Inc., 841 F.3d 1288, 1300, 1302 (Fed. Cir. 2016) (the claim “entail[ed] an unconventional technological solution (enhancing data in a distributed fashion) to a technological problem (massive record flows [that] previously required massive databases)” that “improve[d] the performance of the system itself.”).
Applicant argues that the claims are patent eligible because they recite a particular transformation (citing the use of physical microbiome samples). In response, while the claimed “generating” step includes a plurality of physical steps wherein a sample undergoes physical transformations, these steps perform the function of obtaining sequence data for use by the abstract idea and amount to insignificant extra-solution activity (as discussed above, Step 2A, prong 2). However, the MPEP is clear that a transformation that contributes only nominally or insignificantly to the execution of the claimed method (e.g., in a data gathering step or in a field-of-use limitation) does not provide significantly more (or integrate a judicial exception into a practical application). See MPEP 2016.05(c). In addition, merely transmitting data is also extra-solution activity or a field-of-use and is not considered an eligible transformation. See MPEP 2016.05(c).
With regards to the administering step, unlike the claims in Vanda, the instant step is not directed to a specific method of treatment, does not identify specific patients, does not recite a specific compound, and does not prescribe particular doses. Accordingly, the claims do not amount to applying or using a judicial exception to effect a particular treatment for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2).
Applicant provides aggregate arguments the claims are patent eligible because they include additional elements (directed to sample processing and curation) that amount to significantly more than the judicial exception. In response, as set forth above (Step 2B analysis), Applicant’s own specification teaches that methods for isolating and sequencing samples, e.g. NGS, were routine and conventional in the art [see, e.g. 0002, 0043-46, 0050-52]. A review of the specification also provides a laundry list of nutrients, supplements, and vitamins that can be administered to a subject, all of which are well known in the art and applicant does not make any claims to the propriety of these compounds or medically effective amounts of these compounds (alone or in combination) [0082-0084]. Moreover, Peano et al. (Microbial Informatics and Experimentation, 2013, 3:1, pp.1-11) teaches methods for generating metatranscriptome data that include removing non-target RNA sequences and reverse transcribing RNA to obtain cDNA (see at least “Methods”, page 9, col. 2). Alternatively, Stewart et al. (The ISME Journal (2010) 4, 896–907) also teaches methods for generating metatranscriptome data that include subtracting non-target RNA sequences and reverse transcribing RNA to obtain cDNA (see entire). In addition, MacFarland et al. (BMJ Open, 2014, 4:e005047, pp.1-18) teaches methods for administering probiotics to correct dysbiosis in subjects [See entire]. In other words, there is nothing unconventional about how data is being obtained. Therefore, the examiner maintains that these steps remain insignificant extra-solution activity even upon reconsideration, and do not amount to significantly more.
Applicant additional argues that the amended claims recite an unconventional combination of steps. In response, absent any evidence to the contrary, this argument is not persuasive for reasons set forth above (Step 2B analysis).
Applicant additionally argues that the transmission of a report to an electronic device provides a method for improving the condition of a subject. In response, this argument is not persuasive for reasons set forth above. Merely transmitting data is insignificant post-solution activity or a field-of-use and is not considered an eligible transformation, as discussed in MPEP 2016.05(c), and merely confine the use of the abstract idea to a particular technological environment (i.e. computer), as discussed in MPEP § 2106.05(h). The claims do not provide any improvement with regards to how the data is being transmitting or to what is being administered to a subject, and thus fail to add an inventive concept to the claims. The claims do not constitute a technological improvement to computer capabilities or an improvement to existing technology. For the above reasons, the rejection is maintained.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619
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