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 Application
The Amendment and Response filed March 18, 2026 is acknowledged.
Claims 1-17, 19-20 and 22 were pending. Claims 1-5, 17, 19-20 and 22 are being examined on the merits. Claims 6-16 remain withdrawn.
Response to Arguments
Applicant’s arguments filed March 18, 2026 have been fully considered.
The following rejections are WITHDRAWN in view of Applicant’s arguments and amendments to claims:
Rejection of claim 20 under 35 USC § 112(b), indefiniteness
Prior art rejections
Response to arguments regarding prior art rejections
Applicant argues that the prior art rejections should be withdrawn because the cited art does not teach or suggest various limitations in instant claim 1 (Remarks, p. 11). Specifically, Applicant argues that Brandon and Holman do not teach or suggest that “the abundance of a specific biomarker correlates to the risk or presence of BRD in a cow, or that cows can be selected or treated for BRD based on the level of the biomarker” (Remarks, p. 11).
The Examiner agrees in part and disagrees in part. The Examiner notes that the only biomarker being examined is Lactobacillus plantarum, the elected species. The Examiner agrees that the prior art does not teach or suggest that cows that can be treated for BRD based on the level of the Lactobacillus plantarum biomarker. The Examiner does not agree that claim 1 or any of the dependent claims encompass or are directed to embodiments that assess the risk of developing BRD. Rather, claim 1 is limited to “treating the cow for [BRD]”. Thus, whether the cited art teaches or suggests an embodiment relating to assessing the risk is not relevant to the instant claims.
The prior art rejections are withdrawn as to the elected species of biomarker.
The following rejections are MODIFIED in view of the instant claim amendments:
Rejections of claims under 35 USC § 101
Response to arguments regarding 35 USC § 101 rejections
Applicants argue that the 35 USC § 101 rejections should be withdrawn because the amendment to claim 1 reciting “treating the cow for [BRD] if it is determined to be treated based on the analysis” integrates the judicial exception into a practical application, thus making claim 1 eligible at Step 2A, prong 2 of the analysis (Remarks, pp. 9-10). Applicant additionally argues that the “treatment step, when considered in combination with the other elements of claim 1, amounts to significantly more than the judicial exception” because “[t]he present methods provide the ability to screen cows and determine whether they are at risk for BRD or have BRD based on the level of a biomarker, thus allowing earlier treatment” (Remarks, p. 10).
The Examiner disagrees. As to the first argument, the Examiner notes that the recitation of administering a treatment alone is not sufficient. Rather, the treatment must additionally be “particular”, meaning that is must be “specifically identified so that it does not encompass all applications of the judicial exception”. Further, a claim that recites instructions to “apply” the exception in a generic way (i.e., “treat[] the cow”) is also insufficient to integrate the judicial exception. See MPEP 2106.04(d)(2)(a).
As to the second argument, the Examiner reiterates that claim 1 does not encompass embodiments related to determining if a cow is at risk for BRD. Further, the Step 2B analysis relates only to additional elements in the claims (if any), other than the judicial exception. See MPEP 2106.05 (“an ‘inventive concept’ is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception”). As noted below, the judicial exception elements of claim 1 are (1) the correlation between the relationship between the presence of the biomarker in the sample and the presence of bovine respiratory disease is a natural law, and (2) the step of correlating the abundance of the biomarker to the need to treat the cow is an abstract idea, as is (3) deciding to treat the cow. The only limitations in claim 1 that are not directed to the judicial exceptions are “collecting a nasal swab”, “measuring the level of [a] … biomarker” and “treating the cow for [BRD]”. As noted below, those elements of claim 1 are routine and conventional, as evidenced by Brandon. Further, regarding the “treat[] the cow” limitation, MPEP 2106.05(I)(A) states “[a]dding the words “apply it” (or an equivalent) with the judicial exception” is not enough to qualify as “significantly more”.
These arguments are not persuasive. The rejections are modified in view of the instant claim amendments.
Claim Interpretation
Claim 1 recites the limitation “[Clostridium] clostridioforme” in l. 6. The square brackets around the genus are being construed as indicating that the name awaits appropriate action by the research community to be transferred to another genus or the organism is otherwise taxonomically ambiguous1. Additional bacteria in the claims are recited in the same format (i.e., “[Genus] species”), and the brackets are being construed accordingly in each instance.
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 1-5, 17, 19-20 and 22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Eligibility is considered in light of MPEP 2106 III, which incorporates the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG) published on January 17, 2019 (84 Fed. Reg. 50) and is clarified in the October 2019 Update.
As can be seen in the MPEP 2106 III Figure, eligibility analysis requires one to address the following questions: (i) Step 1 – Is the claim directed to one of the four statutory categories (i.e., process, machine, manufacture or composition of matter); (ii) Step 2A – Is the claim directed to a judicial exception (i.e., a natural phenomenon, law of nature or abstract idea); and (iii) Step 2B – does the claim recite additional elements that amount to significantly more than the judicial exception. In addition, as can be seen in the MPEP 2106.04 II Figure, Step 2A is a two-prong inquiry, with Prong One asking whether the claims recite a judicial exception (i.e., an abstract idea, natural phenomenon or law of nature) and Prong Two asking whether the claims recite additional elements that integrate the judicial exception into a practical application.
In this case, as to Step 1, claims 1-5, 17, 19-20 and 22 are directed to one of the four statutory categories since they are drawn to a process.
The analysis cannot be streamlined, so the claims are considered with respect to Step 2A.
With respect to Prong One of Step 2A, claims 1-5, 17, 19-20 and 22 recite a judicial exception. Specifically, in claim 1, the relationship between the presence of the biomarker in the sample and the presence of bovine respiratory disease is a natural law. In addition, the step of correlating the abundance of the biomarker to the need to treat the cow is an abstract idea, as is deciding to treat the cow, as recited in claims 1 and 5.
With respect to Prong Two of Step 2A, the claims do not recite additional elements that integrate the judicial exception into a practical application for the following reason. In particular, the claims do not recite additional elements that integrate the judicial exception into a practical application because the elements in the claim other than the judicial exceptions (i.e., obtaining a sample, detecting a nucleic acid corresponding to the biomarker) constitute insignificant extra-solution activity as described in the 2019 PEG and MPEP 2106.05(g).
Further, the recitation of particular treatment may integrate the exception into a practical application. However, the recitation of administering a treatment alone is not sufficient. Rather, the limitation must affirmatively recite an action that effects a “particular” treatment for a disease, meaning that is must be “specifically identified so that it does not encompass all applications of the judicial exception”. MPEP 2106.04(d)(2)(a). Here, when the biomarker is analyzed and a determination is made that the cows need treatment (i.e., the judicial exception), the same approach is taken as to all of the cows; that is, they are “treated … for [BRD]”. Thus, the administration step encompasses all applications of the judicial exception, and is insufficient to integrate the exception into a practical application.
Thus, the answer to step 2A is “Yes, the claims are directed to a judicial exception,” and the analysis moves to Step 2B, which asks if the additional elements in the claim amount to significantly more than the judicial exception.
In this case, claims 1-5, 17, 19-20 and 22 do not include additional elements that are sufficient to amount to significantly more than the judicial exception because claims 2-5 do not comprise any elements other than the judicial exceptions, and because, in claims 1, 17, 19-20 and 22, only routine and conventional elements are recited in combination with the judicial exceptions. As evidenced by Brandon2 (US Patent App. Pub. No. 2016/0145696), obtaining a sample, detecting a nucleic acid corresponding to the biomarker, and treating a cow (e.g., paras. 21, 24, 65, 79, 91, 140, 306) were all performed routinely prior to the effective filing date of the claimed invention. Therefore, the additional elements in claims 1, 17, 19-20 and 22 are not non-routine or unconventional.
In view of the foregoing, claims 1-5, 17, 19-20 and 22 are rejected under 35 U.S.C. 101 as being drawn to a judicial exception without significantly more.
Prior Art
The elected species of claim 1 is free of the art. Instant claim 1 is directed to a method of selecting cows for treatment comprising, in part, measuring a level of a nucleic acid biomarker associated with Lactobacillus plantarum (the elected species), analyzing the abundance of the biomarker, and treating the cow for bovine respiratory disease (BRD). Holman3 (The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot, BMC Microbiol., 17:70, 1-12, 2017) teaches that BRD is a bacterial infection of cattle that can be caused by various bacteria such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni and Mycoplasma bovis, and teaches that BRD is treated by antimicrobials against such bacterial pathogens (p. 12, left col., paras. 1-2). Holman also teaches that cattle with certain nasopharyngeal microbiota are at higher risk for developing BRD, and suggests that such cattle should be administered supplements to adjust their microbiota accordingly to prevent BRD infection (p. 2, left col., para. 2; p. 10, right col., para. 2). Brandon4 (US Patent App. Pub. No. 2016/0145696) teaches testing respiratory tract samples from cows for the presence of bacteria, optionally Lactobacillus plantarum, to determine if the cow needs to be administered an antibiotic for an infection caused by that particular bacterium (paras. 21, 24, 65, 79, 91; Table 2). Thus, the prior art teaches that cattle with, perhaps, dysbiosis of their nasopharyngeal microbiome are more susceptible to develop BRD, and teaches that the microbiome dysbiosis itself should be treated to return the cattle to a, perhaps, “normal” risk status for BRD. The prior art also teaches detecting Lactobacillus plantarum biomarkers and administering therapeutics to modify Lactobacillus plantarum levels. However, the prior art does not teach or suggest a link between the presence of Lactobacillus biomarkers and “treating the cow for [BRD]”, e.g., with an antibiotic for the BRD pathogen Mannheimia haemolytica, if it is “determined to be treated based on the analysis [of Lactobacillus plantarum levels]” as recited in instant claim 1. Further, Holman teaches that the goal of adjusting the microbiome is to “reduce antimicrobial use in livestock” with “new strategies [for] management or antimicrobial alternatives” (p. 2, left col., para. 2). Thus, the prior art does not teach or suggest treating BRD in response to an analysis of the abundance of Lactobacillus plantarum biomarkers in the nasopharyngeal microbiome.
Conclusion
Claims 1-5, 17, 19-20 and 22 are being examined, and are rejected. 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 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 CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 See NCBI Taxonomy Browser, [Clostridium] clostridioforme CM201, 2025.
2 Brandon was cited in the Information Disclosure Statement submitted September 25, 2024.
3 Holman was cited in the Information Disclosure Statement submitted September 25, 2024.
4 Brandon was cited in the Information Disclosure Statement submitted September 25, 2024.
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