DETAILED ACTION
Notice of 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 .
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 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.
Election/Restrictions
Applicant’s election of Group I in the reply filed on 05/19/2026 is acknowledged. Because applicant did not distinctly state the group election with or without traverse nor specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). In this instant application, claims 7-8 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected claims there being no allowable generic or linking claim. Claims 1-6 are being examined on the merits.
Status of the Claims
Claims 1-8 are pending.
Claims 7-8 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, as set forth in the reply filed on 05/19/2026.
Claim 6 is objected to.
Claims 1-6 are examined.
Claims 1-6 are rejected.
Priority
This application US 18/443,879 (02/16/2024) claims benefit of US Application 63/446,304 (02/16/2023) as reflected in the filing receipt mailed on 05/14/2024. The claims to the benefit of priority are acknowledged and the effective filing date of claims 1-6 is 02/16/2023.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 05/08/2024 was considered.
Drawings
In the instant drawings filed 05/02/2024, Fig. 1 and 3 are executed in color. Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification. The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2). There is no recorded decision about color drawings.
Claim objections
Claim 6 is objected to because of the following informality: the recited "administering to the subject one or more compositions" should read "administering to the subject with one or more compositions" for proper grammar. Appropriate correction is required.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 1-6 are rejected under 35 U.S.C. 112(a) as failing to comply with the enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claim 1 recites “(1) determining in a fecal sample taken from the subject the amount of each of bacterial species Roseburia faecis (Species01), Faecalibacterium prausnitzii (Species02), Clostridium_fessum (Species03), Dysosmobacter_welbionis (Species04), Lachnospira pectinoschiza (Species05), Clostridium_sp AM22_11AC (Species06), Anaerotruncus_colihominis (Species07), and Clostridiales Family XI bacteriumBX16 (Species08)”. However, at least for Clostridiumsp AM22_11AC and ClostridialesFamily XI bacteriumBX16, the limitation for "determining the amounts" of these species is not enabled because the instant specification provides no specific details about how to detect said new species (i.e. what are the reagents that finally enabled them to be able to detect those new bacteria in the fecal sample). Thus, a PHOSITA would not be enabled to determine the amounts of said bacteria with just the disclosed names.
In re Wands (8 USPQ2d 1400 (CAFC 1988)) considered the issue of enablement in molecular biology. The following eight factors were to be taken into account: (a) the quantity of experimentation necessary; (b) the amount of direction or guidance presented; (c) the presence or absence of working examples; (d) the nature of the invention; (e) the state of the prior art; (f) the relative skill of those in the art; (g) the predictability of the art; and (h) the breadth of the claims. In considering these factors for the instant claims:
a) In order to practice the claimed invention, one of skill in the art must be able to determine the amount of Clostridiumsp AM22_11AC and ClostridialesFamily XI bacteriumBX16 in a fecal sample. For the reasons below, one would not be able to practice the claimed limitation and the amount of experimentation necessary would be unviable.
b) and c) The instant specification at [0034-0035] indicates that "metagenomic analysis on Clostridiumsp AM22_11AC and ClostridialesFamily XI bacteriumBX16 was able discriminate RBD from healthy controls"; however the instant specification provides no specific details about how to detect said new species (i.e. what are the reagents that finally enabled them to be able to detect those new bacteria in the fecal sample).
d) The nature of the invention is drawn to determining the amount of Clostridiumsp AM22_11AC and ClostridialesFamily XI bacteriumBX16 in a fecal sample (claim 1).
e) and g) The prior art discusses only the morphology or taxonomy regarding Clostridiumsp AM22_11AC and ClostridialesFamily XI bacteriumBX16:
Liu ("Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank." Microbiome 9.1:119 (2021) – Table 1 discloses the morphology of ClostridialesFamily XI bacteriumBX16 – namely Lentihominibacter faecis.
Schoch "NCBI Taxonomy: a comprehensive update on curation, resources and tools." Database baaa062 (2020) discloses the reference for the NCBI database that reveals Clostridiumsp AM22_11AC Taxonomy ID: 2293024.
Based on these teachings, it is clear that the claim recites the limitation for "determining the amounts" Clostridiumsp AM22_11AC and ClostridialesFamily XI bacteriumBX16 but the disclosure does not enable the practice of the claimed invention because the instant specification provides no specific details about how to detect said new species (i.e. what are the reagents that finally enabled them to be able to detect those new bacteria in the fecal sample). Thus, a PHOSITA would not be enabled to determine the amounts of said bacteria with just the disclosed names.
f)The relative skill of those in assay testing is high.
h) The claims encompass determining the amount of Clostridiumsp AM22_11AC and ClostridialesFamily XI bacteriumBX16 in a fecal sample.
Claim Rejections - 35 USC § 112(b)
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.
Claims 1-6 are rejected under 35 U.S.C. 112(b)as being indefinite for failing to particularly point out and distinctly claim the subject matter the invention. Dependent claims are rejected similarly, unless otherwise noted below. The following issues cause the respective claims to be rejected under 112(b) as indefinite:
The following recitations require but lack antecedent basis, rendering their claims indefinite because there is no previous recitations of the followings terms as written:
claim 1, "the amount" (step (1))
claim 3, "the relative abundance"
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 1-6 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 §I). Abstract ideas include mathematical concepts and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)).
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The instant claims are directed to a method (claims 1-6) which falls within one of the categories of statutory subject matter. [Step 1: claims 1-6: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Background
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Analysis of instant claims
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas) and mental processes (in particular procedures for observing, analyzing and organizing information) as well as a law of nature or a natural phenomenon are as follows.
Mathematical concepts (in particular mathematical relationships and formulas) include:
• "(2) calculating a probability by the amount of each bacterial species from step (1) and the subject's age (years) and sex:
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(independent claim 1).
The claims identified above read on math. The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation and determined each element performed by mathematical operation. The step directed to “executing a mathematical operation to calculate a probability” requires mathematical techniques as the only supported embodiments because it describes a mathematical technique (MPEP 2106.04(a)(2) pertains). Further support for the mathematical techniques used in the claims is provided in the specification at [0025], which discloses a probability score calculation. Thus, the recited terms correspond to verbal equivalents of mathematical concepts because they constitute actions executed by a group of mathematical steps in a form of a mathematical algorithm; thus mathematical concepts (MPEP 2106.04(a)(2)). A mathematical concept need not be expressed in mathematical symbols, because "words used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). MPEP 2106.04(a)(2) pertains.
Mental processes, defined as concepts or steps practically performed in the human mind such as steps of observations, evaluations, judgments, analysis, opinions or organizing information include:
• "(1) determining in a fecal sample taken from the subject the amount of each of bacterial species Roseburia faecis (Species01), Faecalibacterium prausnitzii (Species02), Clostridium_fessum (Species03), Dysosmobacter_welbionis (Species04), Lachnospira pectinoschiza (Species05), Clostridium_sp AM22_11AC (Species06), Anaerotruncus_colihominis (Species07), and Clostridiales Family XI bacteriumBX16 (Species08)" (independent claim 1);
• "(3) determining presence of prodromal Parkinson's Disease or an elevated risk for prodromal Parkinson's Disease in the subject when the probability from step (2) is at least 50%, or determining absence of prodromal Parkinson's Disease or no elevated risk for prodromal Parkinson's Disease in the subject when the probability from step (2) is less than 50%" (independent claim 1).
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind (i.e. concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) or because the method only requires a user to manually determine action based on an added number. Under the BRI, the recited limitations are mental processes because a human mind is sufficiently capable determine a data value that has been already acquired – for example, reading off a data value from acquired data and determine the presence of a bacteria.
Dependent claim 3 recites further details about the determining step. Furthermore, the instant claims recite a natural correlation by correlating the an amount of a bacteria naturally found in the body with its disease probability. (see MPEP 2106.04(b).I).
[Step 2A Prong One: claims 1-6: Yes ]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2).
Instant claims 5-6 recite additional elements that are not abstract ideas:
• "metagenomic sequencing" (claim 3);
• "treating prodromal Parkinson's Disease upon determining presence of prodromal Parkinson's Disease or an elevated risk for prodromal Parkinson's Disease in the subject" (claim 5) and
• "administering to the subject one or more compositions comprising an effective amount of a dopamine agonist, dopamine metabolism blocker, levodopa metabolism blocker, or adenosine blocker" (claim 6).
Dependent claim 4 recites further details about the subject from which the sample derives.
Considerations under Step 2A, Prong Two
The recited "metagenomic sequencing" (claim 3) reads on data gathering activities; not amounting to a practical application. The type of data doesn’t change that it is mere data gathering or conventional computer receiving means.
Claims directed to "treating" (claim 5) reads on a generic "apply it" step because the claim recites an idea of a solution or outcome without any indication of how the judicial exception impacts or influences this step. Claim 6 recites a particular treatment, but it is not sufficient to integrate the judicial exception into a practical application because there is an embodiment where the subject is not determined to have Parkinson’s or an elevated risk. Therefore, there is an embodiment where no treatment is being administered.
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)).
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
[Step 2A Prong Two: claims 1-6: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination 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).
As discussed above regarding the treatment limitations cannot integrate a judicial exception.
With respect to the instant claims, the prior art review to Lorente-Picón ("New avenues for Parkinson’s disease therapeutics: disease-modifying strategies based on the gut microbiota." Biomolecules 11.3:433 (2021) - newly cited) discloses that the taxonomic composition of gut microbiota can be found via metagenomics. Said portions of the prior art are, for example, pg. 2 para. 4. Further, the prior art review to Lorente-Picón ("New avenues for Parkinson’s disease therapeutics: disease-modifying strategies based on the gut microbiota." Biomolecules 11.3:433 (2021) - newly cited) discloses that using dopamine replacement therapy to improve motor symptoms in the early stage of Parkinson’s disease and treat the altered gut–brain axis is routine, well-understood and conventional in the art. Said portions of the prior art are, for example, pg. 2 para. 2 and pg. 12 para. 3.
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h).
The instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
[Step 2B: claims 1-6: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, the claims in this instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept not clearly anything significantly more.
No prior art has been applied to the following claims
No prior art has been applied to the claims because of the 35 USC 112(a) enablement rejection.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCINI A FONSECA LOPEZ whose telephone number is (571)270-0899. The examiner can normally be reached Monday - Friday 8AM - 5PM ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/F.F.L./Examiner, Art Unit 1685
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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