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 .
The claims dated 8/11/2026 are under consideration.
The amendments and arguments presented in the papers filed 8/11/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 5/11/2026 listed below have been reconsidered as indicated.
a) The amendments addressing nucleotide sequence disclosure requirements are acknowledged.
b) The amendments to the specification addressing trade name or mark usage and hyperlinks are acknowledged.
c) The rejection of claim 12 under 35 U.S.C. 101 because the claimed invention is directed to judicial exceptions without significantly more is withdrawn in view of the Remarks regarding the “treating” of step (f) (p. 10-12 of 17).
d) The rejections of claim(s) 1-12 under 35 U.S.C. 102(a)(1) as being anticipated by Plata (Communications Biology. 2022. 5:293, 14 pages) are withdrawn in view of the updated priority claim and the 7/16/2026 filing receipt.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
Modified grounds of rejection are detailed below and this action is made FINAL.
Priority
This application is a 371 national stage entry of PCT/US2022/044403 (filed 9/22/2022), which claims benefit of US 63/247,243 (filed 9/22/2021).
Priority is recognized.
Information Disclosure Statement
The listing of references in the specification or the citation of references throughout the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or cited on a submitted IDS, they have not been considered.
Drawings
High resolution copies of the drawings may be accessed via PAIR/Patent Center Retrieval using the Supplemental Content tab.
Claim Objections
Following objections have been maintained and the Remarks do not address the issue being raised.
Claim 2-11 are objected to because of the following informalities: the dependent claims lack a comma after the preamble.
Appropriate correction is required.
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 1-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exceptions without significantly more.
The following rejections have been modified to clarify the Examiner’s position.
The claims are drawn to methods, one of the four statutory categories.
The claim(s) recite(s):
“comparing the core intestinal microbiome of the test organism(s) and of the control organism” (claim 1);
“determining antimicrobial resistance (AMR) gene abundance of the test organism(s)” (claim 1);
“determining which test organism has the most healthy microbiome” (claim 1);
“determining which AGP provides the most healthy microbiome” (claim 1);
“selecting the AGP which provides the most healthy microbiome” claim 1);
“comparing the core intestinal microbiomes of the test organisms and of the control organism” (claim 12);
“determining antimicrobial resistance (AMR) gene abundance of the test organisms” (claim 12);
“determining which test organism has the most healthy microbiome” (claim 12); and
“determining which AGP provides the most healthy microbiome” (claim 12).
Each of the above steps are judicial exceptions as they are abstract ideas that can be performed in a purely mental manner.
The judicial exceptions are not integrated into a practical application because the claims do not involve:
improvements to the functioning of a computer or to any other technology or technical field;
applying or using the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition;
applying the judicial exception with, or by use of, a particular machine; or
effecting a transformation or reduction of a particular article to a different state or thing.
The claimed limitations add insignificant extra-solution activity to the judicial exceptions as they relate to data gathering.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims encompass the use known sequencing platforms as described on page 22 of the instant specification.
Examiner’s Response to the traversal of the 101 rejections
The Remarks summarizes the rejections of the claims under section 101 (p. 7).
The Examiner’s position is detailed in the above rejections.
The Remarks argue claims 1-11 are not directed merely to an abstract mental process but rather they are directed to a practical method of selecting a treatment regimen for animals, not merely to analyzing information. The Remarks argue the Examiner has improperly oversimplified Claim 1 by reducing it to "collecting data and comparing it.", while Claim 1 requires a specific sequence of physical laboratory and animal husbandry steps culminating in the selection of a particular antimicrobial growth promoter for use in domesticated animals. See p. 7.
The arguments have been fully considered but are not persuasive. The Examiner’s has systematically gone through the analysis of the claims: identifying the claims as being drawn to methods; identifying any judicial exceptions set forth in the claims; and analyzing whether the additional steps and elements integrate the judicial exceptions and are more than routine and conventional steps.
The Remarks argue several claim limitations necessarily require physical actions that cannot practically be performed in the human mind (p. 7).
The arguments have been fully considered but are not persuasive. The Examiner’s position is not that the entire claim may be carried out in the human man, but rather the particular steps identified in the above rejection are abstract ideas capable of being performed in the human mind or with the aid of pen and paper. The additional steps and elements, which include laboratory or “wet” steps, fail to integrate the judicial exception as noted in the rejection above and further encompass routine and conventional laboratory processes as acknowledged by the instant specification.
The Remarks argue Claim 1 integrates that analysis into a practical application claim 1 is directed to improving antimicrobial treatment selection in domesticated animals by experimentally evaluating candidate AGPs and selecting the AGP that produces the healthiest intestinal microbiome while evaluating antimicrobial resistance gene abundance. See p. 8.
The arguments have been fully considered but are not persuasive. The is no evidence of how the judicial exceptions improve upon or inform how the additional elements and steps are implemented in the method. All the additional elements and steps are utilized prior to carrying out the judicial exceptions. As such, the additional elements and steps are data gathering steps recognized by the MPEP.
The Remarks argue the claimed selection is the practical objective of the method and directly affects subsequent treatment of domesticated animals and the claim applies laboratory-generated genomic information to achieve a concrete veterinary management objective. The Remarks argue the 2019 PTO Eligibility Guidance explains that a claim integrates an alleged judicial exception into a practical application when it applies the exception to effect a particular treatment or other real-world use and here, and the claimed method improves livestock management by identifying the AGP producing the healthiest intestinal microbiome while minimizing antimicrobial resistance gene abundance. See p. 8.
The arguments have been fully considered but are not persuasive. The arguments fail to identify any additional elements or steps in the claim itself that integrate the judicial exceptions. The claim is silent regarding administering the selected AGP to livestock and assessing antimicrobial resistance gene abundance. It is simply the “comparing” of step (c) as broadly claimed that is done with the purpose of assessing antimicrobial resistance gene abundance but does not provide any active method steps of actually doing so. The arguments provide no evidence of the alleged improvement. Furthermore, the “determining which test organism has the most healthy microbiome” is not based on any of the DNA collected or the analysis of it. Lastly, there is no tangible active method step and integrates the judicial exception that could arguably lead to the alleged improvement.
The Remarks argue the administration of AGPs, DNA collection, sequencing, microbiome characterization and antimicrobial resistance gene determination are not ancillary data-gathering steps as they are indispensable components of the claimed experimental protocol. See p. 8-9. The Remarks argue the steps define the technological process by which the claimed result is achieved and the sequencing limitations are analogous to laboratory testing steps that courts have recognized as integral to diagnostic or treatment methods rather than insignificant pre- or post- solution activity. See p. 9.
The arguments have been fully considered but are not persuasive. The additional elements and steps are recited at a high level of generality. For example, no particular sequencing method is required nor is a particular target DNA sequenced, e.g., antimicrobial resistance genes, rRNA sequences, etc. The nature of steps (a) to (d) are analogous to preforming clinical tests on individuals to obtain data for input in an equation and determining the level of a biomarker in blood, which have been found to insignificant extra-solution activity. MPEP 2106.05.g. Here while steps (a) to (d) may not be a “clinical test”, they are similar in that they gather data, e.g., sequence information, which is then used as input in the aspects of step (d), steps (e) and (f). Similarly, determining what the microbiome of an organism looks like is similar to measuring a “biomarker” as each measure the amount or level of an element in a sample from a subject.
The Remarks argue the claim is narrowly confined to a specific protocol and does not preempt all methods of selecting AGPs, nor does it monopolize the idea of evaluating animal microbiomes. See p. 9.
The arguments have been fully considered but are not persuasive. The Examiner’s position is consistent with the guidance provided in the MPEP and preemption is but one factor of consideration. In view of the total consideration of all factors detailed in the MPEP, the claims remain rejected.
The Remarks argue the claims elements amount to significantly more. See p. 9-10. The Remarks argue the specific laboratory methodology employing modern genomic sequencing technology improves AGP selection and claim 1 therefore represents substantially more than merely observing data or making a mental determination. See p. 10.
The arguments have been fully considered but are not persuasive for the reasons outlined in the above rejection and the Examiner’s response above. An improvement to the judicial exception, e.g., selecting an AGP, is not adequate to integrate the judicial exception, as it is not an element or step that is in addition to the judicial exception.
Claim Rejections - 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-7 and 12 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Costa (PLOS ONE. 2017. 12(2):e0171642; cited on the 7/18/2024 IDS).
The following rejections have been maintained.
Regarding claims 1, 2, 3, 4, 5, 6 and 12, Costa teaches “providing a plurality of test organisms and a control organism” through the arrival of 624 chicks at a farm that will be fed a control or AGP diet (p. 2 of 13, Study design).
Costa teaches “administering a regular regimen of a different AGP to test organism” by feeding the chicks zinc bacitracin, enramycin, halquinol, virginiamycin or avilamycin for about 35 days, e.g. 42 days (p. 2 of 13, Study design).
Costa teaches “collecting DNA” and “sequencing the DNA” from cecal contents (p. 2 of 13, Study design; p. 3 of 13, DNA extraction and sequencing). The sequencing is done to obtain a taxonomic profile based on the V4 region of the gene 16S rRNA (p. 3 of 13, DNA extraction and sequencing). The claim states that the “sequencing” step results in “defining a core intestinal microbiome of the test organism(s) and of the control organism”. There is no explicit recitation of any additional elements required in order to achieve the result; and the language does not further limit how the acts of “collecting DNA” and “sequencing the DNA” are actually carried out.
Costa teaches “comparing” the sequencing results (Tables 1 and 2), which the claim states determines “antimicrobial resistance gene abundance of the test organisms” and determines which test organism has the “most healthy microbiome” based on weight gain and viability (Table 4). There is no explicit recitation of any additional elements required in order to achieve the result; and the language does not further limit how the act of “comparing” is actually carried out.
Costa teaches “selecting” avilamycin as the only drug associated with higher weight gain and feed conversion (p. 9 of 13). It is noted the claim does not define how the “selection” is carried out or the criteria on which “most healthy microbiome” is determined.
Regarding claim 7, Costa teaches feeding the chicks from days 1 to 21 (p. 2 of 13, Study design), which includes “administering a regular regimen of a different AGP to each test organism for about 14 days”. It is noted the claim does not limit the “administering” for up to 14 days or no more than 14 days.
Examiner’s response to the traversal of the 102 rejection over Costa
The Remarks summarize the rejection over Costa (p. 12).
The Examiner’s position is detailed in the above rejection.
The Remarks provides a summary of the considerations for making a section 102 rejection (p. 12).
The claims have been rejected over Costa in view of the broadest reasonable interpretation of the claims as described in the above rejections.
The Remarks argue Independent Claims 1 and 12 expressly require:
"...thereby determining antimicrobial resistance (AMR) gene abundance of the test organism(s)...". The Remarks further argue Costa does not perform metagenomic sequencing or any other analysis directed to antimicrobial resistance gene because Costa sequences only the 16S rRNA V4 region, which is a taxonomic marker used to identify bacterial taxa. See p. 13.
The arguments have been fully considered but are not persuasive. Claims 1 and 12 recite:
comparing the core intestinal microbiome of the test organism(s) and of the control organism, thereby determining antimicrobial resistance (AMR) gene abundance of the test organism(s); and
comparing the core intestinal microbiomes of the test organisms and of the control organism, thereby determining antimicrobial resistance (AMR) gene abundance of the test organisms (emphasis added by the examiner),
respectively. The “thereby” clause of each step states a result of the action of “comparing the core intestinal microbiomes”. In view of MPEP 2111.04, such a clause in a method claim is not given weight when it simply expresses the intended result of a process step positively recited, as it does here. It is further noted that the claim itself does not specify that AMR sequence data is collected as part of the step of “sequencing”. The “sequencing” step is broadly applied to the DNA of the intestinal content of at least one test organism and of the control organism. The claim does require performing metagenomic sequencing or any other analysis directed to antimicrobial resistance gene as argued. The arguments rely upon features (i.e., maetagenomic sequencing or any other analysis directed to antimicrobial resistance gene) that are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Thus, the teachings of Costa are encompassed by the broadest reasonable interpretation of the claims.
The Remarks ague the examiner asserts that sequencing inherently defines the claimed core intestinal microbiome because the instant claims recite no further steps. The Remarks argue the instant claims requires: "...thereby defining core intestinal microbiome..." The term "core intestinal microbiome" has a recognized meaning in microbiome science and it refers to the microbial taxa consistently shared among individuals within a population under specified criteria. The Remarks argue Costa merely reports relative abundance of bacterial taxa present in samples and does not: 1) identifies taxa shared among members of each treatment group; 2) determines taxa consistently present across animals; 3) defines a core microbiome according to any threshold; 4) identifies a conserved microbial community. The Remarks argue simply generating sequencing reads does not inherently define a core microbiome. See p. 13.
The arguments have been fully considered but are not persuasive. The examiner’s position is that Costa teaches sequencing the DNA of the intestinal content of at least one test organism and of the control organism and obtaining a taxonomic profile. The claim states in a “thereby” clause that the result of the sequencing of the DNA and obtaining a taxonomic profile is “defining core intestinal microbiome of the test organism(s) and of the control organism”. In view of MPEP 2111.04, the clause does not limit the scope of the claim. The claim does not require active method steps of 1) identifying taxa shared among members of each treatment group; 2) determining taxa consistently present across animals; 3) defining a core microbiome according to any threshold; and 4) identifying a conserved microbial community. The claim does not require a plurality of test organisms are administered each different AGP and rather broadly encompasses administering different AGPs to single organisms, e.g. one individual organism is given AGP 1, one individual organism is given AGP 2, etc. Thus, even if the claim implicitly required the before mentioned four steps, the claim does not require a sufficient number of test organisms to carry out such analytical steps. Similar to the previous arguments, these arguments rely upon features that are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
It is further noted that no evidence is provided that establishes “core intestinal microbiome” has a recognized meaning.
The claim also states the sequencing is done to obtain “optionally a functional profile, thereby defining core intestinal microbiome of the test organism and the control organism”. Thus, the obtaining of the optional functional profile arguably leads to defining core intestinal microbiome of the test organism and the control organism, and is not a result of the broad step of “sequencing the DNA”.
It is noted that Fig. 3 of Costa demonstrates the abundance of different species within the different AGP treated groups and the ratios of different types of bacteria between different AGP treated groups and “core” microbes associated with each AGP treated group.
Lastly, the “core instestinal microbiome” is of a “test organism(s)” and a “control organism”, and not for a population of multiple test organisms and a population of control organisms.
The Remarks argue the examiner equates improved weight gain and feed conversion with determining "the most healthy microbiome." and this is an improper interpretation of the instant claims. The Remarks argue the instant claims require determining: "...which test organism has the most healthy microbiome...", which is made by comparing the microbiome profiles generated by sequencing together with AMR gene abundance. The Remarks argue Costa never evaluates microbiome health and Costa merely reports production metrics such as: 1) weight gain; 2) feed conversion; and 3) mortality. The Remarks argue improved production performance is not equivalent to determining that one microbiome is healthier than another. See p. 14.
The arguments have been fully considered but are not persuasive. The claim does not require making an determination based on generating microbiome profiles sequencing and comparing the microbiome profiles together with AMR gene abundance. The argument relies upon elements not recited in the claim. The claim broadly encompasses “determining which test organism has the most healthy microbiome” based on any criteria as the claim does not specify how such a determination is made.
Costa notes that productivity of organisms has been demonstrated to be linked to intestinal microbiota (p. 11) and the potential of the intestinal microbiota in increasing feed efficiency has been shown (p. 2). Costa also notes a better characterization of how AGPs impact the cecal microbiota of chickens could be the keystone for the development of alternative methods to improve growth efficacy in this species (p. 2). Thus, increased productivity of organisms is linked to more beneficial instestinal microbiotra, i.e., the “most healthy microbiome”, for that productivity element. Based on this demonstrated linkage, Costa infers the most healthy microbiome by identifying those treatments leading to better weight gain, feed conversion or mortality.
The Remarks argue the instant claims require selecting an AGP because it provides "...the most healthy microbiome." and, Costa reaches no such conclusion. The Remarks argue Costa merely reports that avilamycin improved certain production characteristics. The Remarks argue Costa does not state: avilamycin produces the healthiest microbiome; avilamycin minimizes dysbiosis; avilamycin preserves microbiome diversity; or avilamycin reduces antimicrobial resistance gene abundance. The Remarks argue selecting an AGP because of production performance is fundamentally different from selecting it because it produces the healthiest microbiome. See p. 14.
The arguments have been fully considered but are not persuasive. The claim does not specify any criteria for what is or is not the “most healthy microbiome” and the arguments rely on features not required by the claims. Thus, identifying or “selecting” which AGP leads to better weight gain, or feed conversion or mortality, indirectly identifies the AGP that leads to the “most healthy microbiome” as broadly encompassed by the claim.
The Remarks argue the instant claims require that the sequencing and comparison are performed, thereby defining the core intestinal microbiome, thereby determining AMR gene abundance, thereby determining which AGP provides the healthiest microbiome and these are affirnative process limitations describing what the comparison accomplishes. The Remarks argue Costa performs none of these determinations and an anticipation rejection cannot be sustained by substituting different analyses or by assuming that unperformed analyses could have been carried out using Costa's sequencing data. See p. 14.
The arguments have been fully considered but are not persuasive. In view of MPEP 2111.04, the “thereby” clauses of the claims do not limit the scope of the claim as they describe the result of carrying out the positively recited method step. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). In the present application, the specification is not read to require additional steps to the generic step of “sequencing the DNA of intestinal content of at least one test organism and of the control organisms” in order to obtain a taxonomic profile and define a core intestinal microbiome of the test organism(s) and of the control organism. Similarly, the specification is not read to require additional specific steps to the generic step of “comparing the core intestinal microbiome of the test organism(s) and of the control organism” as broadly claimed.
The Remarks argue a feature is inherent only when it is necessarily present in the prior art reference and even if Costa's raw sequencing data might later be reanalyzed to derive additional information, Costa never performs: a core microbiome analysis; antimicrobial resistance gene abundance analysis; or microbiome health determination. These analyses are not inevitable consequences of sequencing the 16S V4 region. Thus, inherency has not been established. See p. 15.
The arguments have been fully considered but are not persuasive. The claims are rejected in view of the broadest reasonably interpretation of the claims. The examiner is not relying upon inherency as it is the Examiner’s position that the elements the Remarks rely on are not required elements of the claims as currently presented.
The Remarks argue the examiner further asserts that Costa determines which test organism has the "most healthy microbiome" based on weight gain and viability (Table 4), while, the present specification teaches that a healthy microbiome may include increased Lactobacillus populations, increased capacity to synthesize biomass from diverse carbon and nitrogen sources, fewer metabolite requirements for microbial growth, and may be associated with numerous specific functional characteristics, including increased metabolism of aromatic amino acids, propanediol utilization, molybdenum-containing cofactor synthesis, CO2 fixation through the Wood-Ljungdahl pathway, protein synthesis, biotin synthesis, methionine metabolism, glycolysis, sporulation, isoprenoid synthesis, betaine biosynthesis, pyridoxine biosynthesis, bacterial stress response, bacterial secretion systems, antimicrobial resistance, tryptophan synthesis, urea degradation, heme biosynthesis, bilirubin and biliverdin metabolism, and xylose utilization. The Remarks further argue the specification further teaches that a healthy microbiome may be characterized by defined metabolomic signatures, including increased metabolites from primary and secondary bile acid metabolism, increased metabolites related to hemoglobin and porphyrin metabolism, fructose and galactose metabolism, tocopherol, inositol, riboflavin, nicotinate and nicotinamide metabolism, as well as decreased levels of microbial genes associated with degradation of matrix polysaccharides and bile salt hydrolase (BSH) genes and increased levels of riboflavin synthase genes. The Remarks conclude the claimed "healthy microbiome" is defined by specific microbiological, functional, genomic, and metabolic characteristics of the intestinal microbial community; i.e., not by animal production parameters such as weight gain, feed conversion, or viability and that Costa does not evaluate any of these characteristics. See p. 15. The Remarks argue Costa's observation that avilamycin produced greater weight gain and improved feed conversion cannot reasonably be equated with the claimed determination that an AGP "provides the most healthy microbiome." The Remarks argue improved growth performance and a healthy microbiome are distinct concepts, and Costa contains no teaching that one necessarily implies the other. See p. 16.
The argument have been fully considered but are not persuasive. The instant specification does not provide any limiting definition of a “healthy microbiome” or the “most healthy microbiome”. The claims does not identify any criteria for making such a determination. As noted above, the arguments rely on elements not presently claimed and the instant specification will not be read to require any specific additional steps to the generically claimed steps.
As noted above, Costa acknowledges the relationship between the microbiome and productivity outcomes and the relationship between microbiome impacting AGPs and productivity outcomes. Thus, it is logical and reasonably to equate AGPs and productivity outcomes with “the most healthy microbiome” for that AGP associated outcome.
It is further noted that in dependent claims 8-10, a “healthy microbiome” is defined, not based on the “core intestinal microbiome” but rather on factors that simply looking at the “core intestinal microbiome” would not provide. In other words, claim 1 encompasses analyzing other factors to determine which microbiome is the “most healthy microbiome”.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 8-10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Costa (PLOS ONE. 2017. 12(2):e0171642; cited on the 7/18/2024 IDS) in view of Choi (Poultry Science. 2018. 97:970-979; cited on the 7/18/2024 IDS).
Regarding claims 8-10, Costa teaches “providing a plurality of test organisms and a control organism” through the arrival of 624 chicks at a farm that will be fed a control or AGP diet (p. 2 of 13, Study design).
Costa teaches “administering a regular regimen of a different AGP to test organism” by feeding the chicks zinc bacitracin, enramycin, halquinol, virginiamycin or avilamycin for about 35 days, e.g. 42 days (p. 2 of 13, Study design).
Costa teaches “collecting DNA” and “sequencing the DNA” from cecal contents (p. 2 of 13, Study design; p. 3 of 13, DNA extraction and sequencing). The sequencing is done to obtain a taxonomic profile based on the V4 region of the gene 16S rRNA (p. 3 of 13, DNA extraction and sequencing). The claim states that the “sequencing” step results in “defining a core intestinal microbiome of the test organism(s) and of the control organism”. There is no explicit recitation of any additional elements required in order to achieve the result; and the language does not further limit how the acts of “collecting DNA” and “sequencing the DNA” are actually carried out.
Costa teaches “comparing” the sequencing results (Tables 1 and 2), which the claim states determines “antimicrobial resistance gene abundance of the test organisms” and determines which test organism has the “most healthy microbiome” based on weight gain and viability (Table 4). There is no explicit recitation of any additional elements required in order to achieve the result; and the language does not further limit how the act of “comparing” is actually carried out.
Costa teaches “selecting” avilamycin as the only drug associated with higher weight gain and feed conversion (p. 9 of 13). It is noted the claim does not define how the “selection” is carried out or the criteria on which “most healthy microbiome” is determined.
Costa does not specifically teach the additional elements specific to claims 8-10.
However, Choi teaches evaluating different parameters in the context of AGP administration.
Regarding claim 8, Choi teaches observing an increase in using more diverse carbon sources, e.g., fructose and mannose metabolism, and nitrogen sources, e.g., amino acid metabolism (Figure 5).
Regarding claim 9, Choi teaches observing an increase in sporulation (Figure 5).
Regarding claim 10, Choi teaches observing an increase in fructose metabolism porphyrin/hemoglobin metabolism, and inositol metabolism (Figure 5).
It would have been prima facie obvious to the ordinary artisan at the time of invention to have modified the method of Costa by analyzing for a “healthy microbiome” based on the above features of Choi and correlating them to the species present in the microbiome. One would have been motivated to do so because it provides a more holistic picture of the microbiome of the chicken by taking into account additional parameters.
Claim(s) 11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Costa (PLOS ONE. 2017. 12(2):e0171642; cited on the 7/18/2024 IDS) in view of Abiuso (Dissertation. “Influence of different prebiotics and mode of their administration on growth, carcass traits and meat quality in broiler chickens”. 2014/2015 Academic Year).
Regarding claim 11, Costa teaches “providing a plurality of test organisms and a control organism” through the arrival of 624 chicks at a farm that will be fed a control or AGP diet (p. 2 of 13, Study design).
Costa teaches “administering a regular regimen of a different AGP to test organism” by feeding the chicks zinc bacitracin, enramycin, halquinol, virginiamycin or avilamycin for about 35 days, e.g. 42 days (p. 2 of 13, Study design).
Costa teaches “collecting DNA” and “sequencing the DNA” from cecal contents (p. 2 of 13, Study design; p. 3 of 13, DNA extraction and sequencing). The sequencing is done to obtain a taxonomic profile based on the V4 region of the gene 16S rRNA (p. 3 of 13, DNA extraction and sequencing). The claim states that the “sequencing” step results in “defining a core intestinal microbiome of the test organism(s) and of the control organism”. There is no explicit recitation of any additional elements required in order to achieve the result; and the language does not further limit how the acts of “collecting DNA” and “sequencing the DNA” are actually carried out.
Costa teaches “comparing” the sequencing results (Tables 1 and 2), which the claim states determines “antimicrobial resistance gene abundance of the test organisms” and determines which test organism has the “most healthy microbiome” based on weight gain and viability (Table 4). There is no explicit recitation of any additional elements required in order to achieve the result; and the language does not further limit how the act of “comparing” is actually carried out.
Costa teaches “selecting” avilamycin as the only drug associated with higher weight gain and feed conversion (p. 9 of 13). It is noted the claim does not define how the “selection” is carried out or the criteria on which “most healthy microbiome” is determined.
Costa does not teach the additional elements specific to claim 11.
However, Abiuso teaches evaluating different parameters in the context of AGP administration.
Regarding claim 11, Abiuso teaches the following: 1) AGP inhibit endemic subclinical infection, thus reducing the metabolic cost of the innate immune system; 2) AGP reduce the growth-depressing metabolites produced by microbes, such as ammonia and bile degradation products; 3) AGP reduce microbial use of nutrients; and 4) AGP enhance the uptake and use of nutrients, due to the thinning of the intestinal wall in AGP-fed animals (p. 11).
It would have been prima facie obvious to the ordinary artisan at the time of invention to have modified the method of Costa by analyzing for a “healthy microbiome” based on the above features of Abiuso. One would have been motivated to do so because it provides a more holistic picture of the microbiome of the chicken by taking into account additional parameters.
Examiner’s response to the traversal of the 103 rejections
The Remarks argue claims 8-11 are narrower in scope than independent Claim 1 and are not obvious for at least the reasons discussed under the anticipation rejection (p. 16).
The arguments have been fully considered but are not persuasive. Costa is not deficient in view of the broadest reasonable interpretation of the claims. The Remarks further do not address and the teachings of Choi and Abiuso regarding the effects of AGP on the intestinal microbiome that may be used to evaluate and identify a “most healthy microbiome” as the result of AGP administration.
Conclusion
No claims 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.
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/JOSEPH G. DAUNER/ Primary Examiner, Art Unit 1682
