Prosecution Insights
Last updated: April 19, 2026
Application No. 18/518,183

METHODS AND MATERIALS FOR USING BIOMARKERS WHICH PREDICT SUSCEPTIBILITY TO CLOSTRIDIUM DIFFICILE INFECTION

Non-Final OA §102§103§112§DP
Filed
Nov 22, 2023
Examiner
PAPCIAK, SHARON M
Art Unit
1651
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
Mayo Foundation for Medical Education and Research
OA Round
1 (Non-Final)
50%
Grant Probability
Moderate
1-2
OA Rounds
3y 4m
To Grant
72%
With Interview

Examiner Intelligence

Grants 50% of resolved cases
50%
Career Allow Rate
259 granted / 522 resolved
-10.4% vs TC avg
Strong +22% interview lift
Without
With
+22.3%
Interview Lift
resolved cases with interview
Typical timeline
3y 4m
Avg Prosecution
48 currently pending
Career history
570
Total Applications
across all art units

Statute-Specific Performance

§101
7.2%
-32.8% vs TC avg
§103
39.0%
-1.0% vs TC avg
§102
13.4%
-26.6% vs TC avg
§112
29.3%
-10.7% vs TC avg
Black line = Tech Center average estimate • Based on career data from 522 resolved cases

Office Action

§102 §103 §112 §DP
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 . DETAILED ACTION Action Is Non-Final, First Action Status of Claims Claims 1-20 are pending. Claims 1-20 are rejected. Claim 1 is objected to. Priority Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. §119(e) or under 35 U.S.C. §120, §121, or §365(c) is acknowledged. This application is a CON of 17/093,154, filed 11/09/2020, which is a CON of 15/762,203, 03/22/2018, which is a 371 of PCT/US2016/53073, 09/22/2016, which claims benefit of 62/222,034, 09/22/2015, and names the inventor or at least one joint inventor named in the prior application. (The specifications filed with applications 18/518,183 and 17/093,154 appear to be the same; i.e., instant application 18/518,183 does not appear to include any subject matter which would constitute new matter (MPEP 201.07).) In addition, the patent (No. 11,865,146) issued from parent application 17/093,154 was issued/published either on the same day or after the filing date of the instant application. Accordingly, this application constitutes a continuation. Applicant has claimed the benefit of the filing date of the prior application, and designates the instant application as a "CON" of 17/093,154. Applicant has complied with all of the conditions for receiving the benefit of an earlier filing date under 35 U.S.C. §120 or §365(c). However, it is noted that the instantly-claimed subject matter is not fully supported under 35 USC §112 by provisional application 62/222,034 (MPEP 2152.01 (C)). That is, the provisional application does not recite the term ‘amino acid’ and so does not describe a mammal as having an increased level of at least one free amino acid; and, therefore, does not cite specific amino acids. Therefore, claims 9, 10, 19 and 20 have the effective filing date of 22 September 2016 which is the filing date of the 371 document as US2016/53073. Claims 1-8 and 11-18 have the effective filing date of 22 September 2015. Information Disclosure Statement The information disclosure statement(s) (IDS) submitted on 07 January 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the Examiner. It is noted that the information disclosure statement (IDS) and/or the references cited therein (in whole or in part) had been submitted in parent Application Nos. 17/093,154 and 15/762,203. Drawings The drawings were received on 22 November 2023. These drawings are objected to. It is noted that Figures 14, 15, 16, 17, 18 and 19 show tables that are continued on more than one page as a ‘continued (cont.))’ figure. However, the Drawing Standards in MPEP 608.02 (V) recite: 37 CFR 1.84 (u) Numbering of views. (1) The different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation "FIG." Where only a single view is used in an application to illustrate the claimed invention, it must not be numbered and the abbreviation "FIG." must not appear. (2) Numbers and letters identifying the views must be simple and clear and must not be used in association with brackets, circles, or inverted commas. The view numbers must be larger than the numbers used for reference characters. That is, a figure that is only identified by a single number cannot span more than one page with the same single number identifier (appended with the abbreviation ‘cont.’). As recited above, a figure identified by a single number which spans more than one page must have a separate additional qualifier (i.e., a capital letter) appended to the number for each additional page; e.g., Fig. 14A, Fig. 14B, Fig. 14C etc. An amendment to the specification describing the amended figure labels must be submitted with the replacement drawings. Corrected drawing sheets in compliance with 37 CFR 1.121(d) (and/or appropriate amendment to the specification) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance. Claim Objections Claim 1 is objected to because of the following informalities: Claim 1 recites: “…, wherein said composition restores a heathy gut microbiota in said mammal”, which should read: “…, wherein said composition restores a healthy gut microbiota in said mammal.” Appropriate correction is required. Claim Rejections - 35 U.S.C. § 112 35 U.S.C. § 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. The following is a quotation of 35 U.S.C. §112 (pre-AIA ), second paragraph: The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention. Claim 18 is rejected under 35 U.S.C. §112(b) or 35 U.S.C. §112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. Claim 18 is indefinite, because it recites insufficient, improper or unclear antecedent basis for the limitations in the claim(s). Claim 18 recites: “The method of claim 19, wherein the at least one clinical risk factor…” However, claim 19 does not recite the phrase ‘at least one clinical risk factor’. For the purpose of compact prosecution, the claim will be interpreted to read: “The method of claim 17, wherein the at least one clinical risk factor…” Claim 17 recites: “The method of claim 11, further comprising,…, identifying the mammal as having at least one clinical risk factor of C. difficile infection.” Claim Interpretations Claims 1 and 11 recite: “…: administering a composition comprising at least three bacteria selected from the group consisting of Roseburia, Faecalibacterium, Akkermansia, Blautia, and Bacteroides…” Claims 2 and 12 recite: “The method of claim 1/claim 12, wherein the at least three bacteria comprise Roseburia faecis, Faecalibacterium prausnitzii, and Akkermansia muciniphila.” It is noted that the claims do not stipulate whether or not the at least three bacteria are selected from three different genera (as recited in claims 2 and 12). Therefore, for the purpose of examination, claims 1 and 11 will be interpreted to mean, according to their broadest reasonable interpretations, that the at least three bacteria may be selected from one of the cited genera (e.g., a Roseburia faecis species, a Roseburia intestinalis species and a Roseburia hominis species) or that each of the at least three bacteria may be selected from different genera (e.g., one Roseburia sp., one Blautia sp., and one Bacteroides sp.). Claim Rejections - 35 U.S.C. § 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 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. (a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention. Claims 1-8 and 11-18 are rejected under 35 U.S.C. §102(a)(1)/(a)(2) as being anticipated by Cook et al. (International Patent Application Publication No. WO 2014/121301 A1). Cook et al. addresses the limitations of claims 1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17 and 18. Regarding claims 1 and 11, pertaining to a method for treating Clostridium difficile infection in a mammal [Claim 1]; a method for preventing Clostridium difficile infection in a mammal [Claim 11], Cook et al. shows effective compositions for and methods of preventing or reducing pathogenic bacterial growth (pg. 3, para. [009]). Inhibition of pathogens includes those pathogens such as, minimally, C. difficile (Clostridium difficile) (pg. 16, cont. para. [062]). Subjects become more susceptible to pathogenic infections when the normal intestinal microbiota has been disturbed (pg. 2, cont. para. [005]). Further regarding claims 1 and 11, pertaining to administering a composition comprising at least three bacteria selected from the group consisting of Roseburia, Faecalibacterium, Akkermansia, Blautia, and Bacteroides to a mammal; wherein said composition restores a healthy gut microbiota in said mammal [Claim 1]; wherein said composition restores colonization resistance to C. difficile in said mammal [Claim 11], and regarding claims 2 and 12, Cook et al. shows that the described invention demonstrates effective methods of preventing or reducing pathogenic bacterial growth, proliferation, and/or colonization, whereby bacterial compositions that contain one or more types of non-pathogenic bacteria are introduced into the gastrointestinal tract and effectively compete with pathogenic bacteria for monomeric or polymeric carbohydrate nutrients, and/or amino acid nutrients, and/or vitamin nutrients (pg. 16, para. [064]). The bacterial composition comprises at least one and preferably more than one of the following bacteria, including, Bacteroides ovatus, Faecalibacterium prausnitzii, and one strain of Roseburia such as Roseburia faecis (pg. 23, para. [081]). Ten different bacterial compositions were made by the ethanol treated spore preparation methods from 6 different donors (as described). The spore preparations were used to treat 10 patients, each suffering from recurrent C. difficile infection. The OTU (operational taxonomic units) composition of the successful spore preparations was determined. The resulting list of OTUs, clade assignments, and frequency of detection in the spore preparations are shown in Table GB (pg. 100, para. [0298]-[0299]). Table GB includes Akkermansia muciniphila (clade_583, 60%) (pg. 106, cont. Table GB, “Akkermansia_muciniphila”). Regarding claims 3 and 13, in one aspect, the described invention provides a composition comprising bacteria, the bacteria consisting of purified spore forming bacteria, formulated for oral administration to a mammalian subject (pg. 3, para. [009a]). The term ‘subject’ refers to any animal subject including humans (pg. 9, para. [038]). Regarding claims 4 and 14, pertaining to a pill, tablet, capsule, Cook et al. shows that compositions are formulated for oral administration as a solid, semi-solid, gel, or liquid form, such as in the form of a pill, tablet, capsule, or lozenge (pg. 35, para. [0125]). Regarding claims 5 and 15, one experimental means of re-establishing control in animals has been to transplant the normal fecal flora of a healthy animal via an enteral route. In humans, fecal microbiota transplantation (FMT) has shown similar beneficial results (pg. 15, cont. para. [065]). Regarding claims 6 and 16, the bacterial composition can be administered enterically, in other words, by a route of access to the gastrointestinal tract. This includes oral administration, rectal administration (including enema, suppository, or colonoscopy) or by an oral or nasal tube (pg. 40, para. [0141]). Regarding claims 7 and 17, and regarding claims 8 and 18, pertaining to antibiotic use, Cook et al. shows that the gastrointestinal disease, disorder or condition to be treated is diarrhea caused by C. difficile including recurrent C. difficile infection (pg. 41, para. [0148]). The enteric bacterium Clostridium difficile (C. difficile) is an opportunistic pathogen whose infection frequently follows antibiotic treatment (pg. 16, para. [065]). In order to determine that the bacterial composition populates the gastrointestinal tract of a subject, an animal model, such as a mouse model, can be used. The mice can receive an antibiotic treatment to mimic the condition of dysbiosis (pg. 46, para. [0163-0164]). Claim Rejections - 35 U.S.C. § 103 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 of this title, 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. 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. Claims 1-20 are rejected under 35 U.S.C. §103 as being unpatentable over Cook et al. Cook et al. (International Patent Application Publication No. WO 2014/121301 A1) in view of Savidge et al. (WO2014) (International Patent Application Publication No. WO 2014/110493 A1), and Savidge et al. (US2014) (U.S. Patent Application Publication No. 2014/0296134 A1). Claims 1-8 and 11-18 are addressed by Cook et al. in the 35 U.S.C. §102(a)(1)/(a)(2) rejection above. Cook et al. does not show: 1) prior to said administration, identifying the mammal as having an increased level of at least one free amino acid [Claims 9 and 19]; and 2) the at least one free amino acid is selected from the group consisting of proline, alanine, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine [Claims 10 and 20]. Regarding claims 9, 10, 19 and 20, Cook et al. further teaches that, in order to maintain steady-state concentrations in the gastrointestinal tract of a mammalian subject, C. difficile is dependent upon the availability of a small number of nutrients, including, amino acids (pg. 17, para. [066]). In some embodiments, the prevention or treatment of infection will be achieved when the introduced bacterial composition depletes one or more of the nutrients utilized by C. difficile to a concentration that inhibits further growth of C. difficile or alternatively, reduces the rate of growth such that the introduced bacteria and/or other resident bacteria outcompete C. difficile (pg. 17, para. [067] thru pg. 18, cont. para. [067]). Exemplary nutrients include carbohydrates, amino acids, vitamins, minerals, and cofactors such as germinants. Table XXX5 contains representative nitrogen sources (pg. 18, para. [069]). Table XXX5 contains the amino acids proline, alanine, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine (pg. 222 thru pg. 224, Table XXX5). Savidge et al. (WO2014) and Savidge et al. (US2014) provide information from which one of ordinary skill in the art of treating or preventing a C. difficile infection, as shown by Cook et al., would have been motivated to have determined the level of at least one free amino acid, by way of addressing the limitations of claims 9, 10, 19 and 20. Savidge et al. (WO2014) shows systems, methods, and/or compositions related to recurrent pathogenic infection, including recurrent bacterial infection. In specific embodiments, the described invention concerns systems, methods, and/or compositions related to primary and recurrent Clostridium difficile infection (pg. 1, para. [0004] [nexus to Cook et al.- treat or prevent C. difficile infection]). In certain embodiments, there is a method of treating an individual, comprising the step of administering a treatment to the individual when there are alterations in gut microflora and the alterations are determined by nucleic acid analysis of a sample from the individual. The administered microflora comprises bacteria selected from a group which includes Bacteroides fragilis, Faecalibacterium prausnitzii, Bacteroides ovatus and Bacteroides dorei (pg. 8, para. [0039] [nexus to Cook et al.- bacterial treatment compositions comprising B. ovatus and F. prausnitzii]). Regarding claims 9, 10, 19 and 20, Savidge et al. (WO2014) further teaches that one or more metabolites from a sample are analyzed to ascertain whether or not there is C. difficile infection or whether or not there is a susceptibility to recurrence of C. difficile infection. In specific embodiments, particular metabolites that may be measured include one or more biomarkers selected from 5-aminovalerate, N acetylglutamate, thymine, agmatine, putrescine, gamma-aminobutyrate (GABA), ammonia, X-16563, X-16071, X-15461, or X-15175, for example. The metabolites may be produced by one or more pathogenic bacteria in the individual and/or be a host response to one or more pathogenic bacteria in the individual (pg. 6, para. [0023]). That is, Savidge et al. (WO2014) teaches that measuring biomarker levels in an individual can be used to determine the individual’s status with regard to C. difficile infection and its presence or risk of occurring. Savidge et al. (US2014) shows the identification of biochemical profiles in clinical specimens that classify CDI (Clostridium difficile infection). The biochemical profiles in clinical stool specimens identify susceptibility to disease recurrence. In certain embodiments a metabolic profile can identify a subject with CDI or who has or is at risk for recurrent CDI (pg. 1, para. [0006] [nexus to Savidge et al. (WO2014)- measure metabolic and bacterial biomarkers to determine CDI status]). In one aspect one or more of 5-aminovalerate, thymine, gamma-aminobutyrate (GABA), ammonia, and N-acetylglutamate are measured in combination with one or more of agmatine, serine, N-acetylmuramate, X-16563, X-16071, X-15461 andX-15175 (pg. 1, para. [0017] thru pg. 2, cont. para. [0017] [nexus to Savidge et al. (WO2014)- specific metabolic markers include 5-aminovalerate]). Regarding 9, 10, 19 and 20, non-infected subjects can be distinguished from subjects having a non-recurrent CDI by assessing the levels of one or more of 5-aminovalerate, N-acetylglutamate, thymine, X-15461, and/or X-15175. In certain aspects, the levels of these measured biomarkers are elevated (pg. 2, para. [0028] thru [0029]). Increases or decreases in metabolites related to bacterial activity and inflammation are evident in CDI patients (pg. 2, para. [0033]). Certain embodiments describe a metabolome defined by compounds including metabolites having a p value of less than 0.5, which include glycine, histidine, leucine, methionine, phenylalanine, tryptophan, tyrosine, valine, N-acetylproline, alanylproline, hydroxyproline, and propylhydroxyproline (pg. 5, para. [0089] thru pg. 6, cont. para. [0089]). 5-Aminovalerate. Selenoproteins can be found in the genome of Clostridium species. Various selenoproteins are found within the D-proline reductase operon. The D-proline reductase operon is responsible for the reductive ring cleavage of D-proline into 5-aminovalerate. Thus, the presence of a bacterium comprising a D-proline reductase operon will result in an increase in 5-aminovalerate (pg. 4, para. [0071]). Non-infected subjects can be distinguished from subjects at risk of recurrent CDI or of having non-recurrent CDI by having elevated levels of one more biomarkers which include 5-aminovalerate (pg. 2, para. [0027] thru [0028]). That is, Savidge et al. (US2014) shows that 5-aminovalerate is elevated in subjects with gut dysbiosis caused by C. difficile infection. Because Savidge et al. (US2014) teaches that 5-aminovalerate results from the cleavage of D-proline, a subject having gut dysbiosis associated with C. difficile infection would also have an increased level of proline (resulting in an increased level of 5-aminovalerate). Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to have modified the method of treating or preventing Clostridium difficile infection, as shown by Cook et al., by: 1) including a step of identifying a mammal having an increased level of at least one free amino acid, prior to treatment, wherein the at least one free amino acid is selected from the group consisting of proline, alanine, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine [Claims 9, 10, 19 and 20], with a reasonable expectation of success, because Savidge et al. (WO2014) teaches that the measurement of one or more metabolites from a subject sample are analyzed to ascertain whether or not there is C. difficile infection or whether or not there is a susceptibility to recurrence of C. difficile infection (CDI), and that particular metabolites are one or more biomarkers that include 5-aminovalerate, which is the biomarker, shown by Savidge et al. (US2014) (MPEP 2143 (I)(G)). With regard to the amino acid proline, Savidge et al. (US2014) teaches that 5-aminovalerate is the breakdown product of the cleavage of the aromatic ring of proline, and that it is elevated in subjects who are at risk of recurrent CDI or of having non-recurrent CDI. Therefore, one of ordinary skill in the art would have understood that because elevated levels of 5-aminovalerate are indicative of CDI in a subject, then the source of 5-aminovalerate (i.e., proline) must also be elevated in the subject (MPEP 2144 (I)). In addition, Cook et al. teaches that bacterial compositions which are administered to subjects for treating a C. difficile infection would be more able to compete for bacterial nutrients, such as amino acids, which are a nutrient source for C. difficile bacteria (i.e., assisting in their growth). Therefore, one of ordinary skill in the art of C. difficile infection detection would have understood that an increased or elevated level of any one amino acid would have indicated a low population of probiotic bacteria in the gut (i.e., not sufficient to deplete the amino acid content in the gut), indicating the potential presence of C. difficile bacteria (MPEP 2143 (I)(G) and MPEP 2144 (I)). One of ordinary skill in the art would have been motivated to have made that modification, because Savidge et al. (US2014) teaches that current FDA-approved diagnostic assays for CDI are limited by their cost, technical complexity, long assay duration and/or sensitivity. No diagnostic assays currently exist that predict disease relapse in CDI, and these are urgently warranted. In certain aspects, methods are directed to measurement of a stool metabolome of CDI patients to identify and predict patterns of disease progression and relapse. Methods are directed to measurement of a stool metabolome of CDI patients to identify and predict patterns of disease progression and relapse. (pg. 2, para. [0035]). Assessment of the described biomarkers can provide an analysis with a misclassification rate of 24% between non-infected and CDI infected patients. Analysis of recurrent versus non-recurrent CDI can be determined with a misclassification rate of 39%. Disease relapse within 6 weeks can be determined in 61 % of patients at the time of original diagnosis (pg. 3, para. [0037]). That is, Savidge et al. (US2014) teaches that the method of measuring biomarkers in order to detect CDI only requires a patient stool sample and the methods are, statistically, highly effective in identifying CDI, including patients experiencing relapse CDI. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention. Double Patenting The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the "right to exclude" granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969). A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP 2159. See MPEP 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b). The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP 706.07(e) and 714.13. The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/ patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/ patents/apply/applying-online/eterminal-disclaimer. Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-10 and 12-18 of Patent No. 11,865,146 B2. The claimed subject matter of instant Application No. 18/518,183 is: Claim 1. A method for treating Clostridium difficile infection in a mammal. The method comprises administering a composition comprising at least three bacteria selected from the group consisting of Roseburia, Faecalibacterium, Akkermansia, Blautia, and Bacteroides to a mammal. Said composition restores a healthy gut microbiota in said mammal. Claim 9. prior to said administration, identifying the mammal as having an increased level of at least one free amino acid. Claim 10. the at least one free amino acid is selected from the group consisting of proline, alanine, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine. Claim 11. A method for preventing Clostridium difficile infection in a mammal. The method comprises administering a composition comprising at least three bacteria selected from the group consisting of Roseburia, Faecalibacterium, Akkermansia, Blautia, and Bacteroides to a mammal. Said composition restores colonization resistance to C. difficile in said mammal. Claim 19. prior to said administration, identifying the mammal as having an increased level of at least one free amino acid. Claim 20. the at least one free amino acid is selected from the group consisting of proline, alanine, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine. The claimed subject matter of Patent No. 11,865,146 B2 is: Claim 1. A method for treating Clostridium difficile infection in a mammal. The method comprises administering a composition comprising at least three bacteria selected from the group consisting of Roseburia, Faecalibacterium, Akkermansia, Blautia, and Bacteroides to a mammal. The mammal is identified as having an increased level of at least one free amino acid, wherein the at least one free amino acid is selected from the group consisting of proline, alanine, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine. Said composition restores a healthy gut microbiota in said mammal. Claim 10. A method for preventing Clostridium difficile infection in a mammal. The method comprises administering a composition comprising at least three bacteria selected from the group consisting of Roseburia, Faecalibacterium, Akkermansia, Blautia, and Bacteroides to a mammal. The mammal is identified as having an increased level of at least one free amino acid, wherein the at least one free amino acid is selected from the group consisting of proline, alanine, glycine, histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, tyrosine, and valine. Said composition restores colonization resistance to C. difficile in said mammal. Although the claims are not identical, they are not patentably distinct from each other because, as demonstrated above in the claim sets from each application, the methods for treating and preventing Clostridium difficile infection in a mammal, described Patent No. 11,865,146 anticipate the methods for treating and preventing Clostridium difficile infection in a mammal, described in instant Application No. 18/518,183. Conclusion No claims are allowed. This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action. Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHARON M PAPCIAK whose telephone number is (571)272-6235. The examiner can normally be reached M-F 8:30am-5:00pm. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Adam Weidner can be reached on 571-272-3045. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /SMP/ Examiner, Art Unit 1651 /Adam Weidner/ SPE, Art Unit 1651
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Prosecution Timeline

Nov 22, 2023
Application Filed
Oct 06, 2025
Non-Final Rejection — §102, §103, §112 (current)

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Study what changed to get past this examiner. Based on 5 most recent grants.

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Prosecution Projections

1-2
Expected OA Rounds
50%
Grant Probability
72%
With Interview (+22.3%)
3y 4m
Median Time to Grant
Low
PTA Risk
Based on 522 resolved cases by this examiner. Grant probability derived from career allow rate.

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