DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
2. The information disclosure statements (IDS) submitted on 03/03/23 and 08/28/23 were filed and entered. The submissions are in compliance with the provisions of 37 CFR 1.97 and have been considered by the Examiner.
Election/Restrictions
3. Applicant’s elections of Group I, and a volatile compound having a mint odor; SEQ ID 2 corresponding to SEQ ID NO: 8; SEQ ID NO: 1 corresponding to SEQ ID NO: 3; SEQ ID NO: 49 corresponding to SEQ ID NO: 50; Pseudomonas; and SEQ ID NO: 12, in the reply filed on 12/22/25, is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claim Status
4. The amendment, filed 12/22/25, has been entered. Claims 1-4, 6-7, 11, 13-14, 16-17, 19, 21, 23-26, 34, 36 and 38 are pending. Claims 5, 8-10, 12, 15, 18, 20, 22, 27-33, 35 and 37 are cancelled. Claims 13 and 14 are amended. Claims 6-7, 23 (i.e. see species elections), 34, 36, and 38 have been withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention or species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/22/25. Claims 1-4, 11, 13-14, 16-17, 19, 21, and 24-26 are under examination.
Claim Objections
5. Claims 2 and 3 are each objected to because of the following informalities: misspelled word. Both claims misspell: isochorismate as isochorisomate. Appropriate correction is required.
6. Claims 2, 13, 14 and 21 are each objected to because of the following informalities: improper formatting. MPEP 608.01(m) states that “Each claim begins with a capital letter and ends with a period”. However instant claims 2, 13, and 21 also use periods to separate the method steps (e.g. “a.” line 3); therefore the periods should be removed and only the period at the completion of the claim should remain. The office suggests the use of parenthesis (e.g. “(a)”). Further claim 14 contains a period in line 1 “… claim 1, .(a) wherein…”. Furthermore, claim 21 contains several typos (e.g. see “1s” in lieu of what should be the verb “is” and “(e), (0,” in the list of alternatives in line 14). Appropriate correction for all claims is required.
7. Claims 4 and 11 are each objected to because of the following informalities: improper use of an acronym/abbreviation. Acronyms and abbreviations must be spelled out and/or defined upon first use, in order to be understood without requiring reference to the specification (i.e. see MPEP 2173.05(s); claims are to be complete in themselves); therefore, PCHBA, BSMT1, ATF1, AFT2, BAT2 and/or THI3 must each be explained/defined for at least their first recitation. Appropriate correction is required.
8. Claims 17 and 19 are each objected to because of the following informalities: improper recitation of species names. Latin names of microorganisms are properly recited with the genus name (i.e. first part of binomial identifier) capitalized and species name (i.e. second part of binomial identifier) in lower case, with both in italics, and having the genus name spelled out upon first usage, in order to be understood without requiring reference to the specification (i.e. see MPEP 2173.05(s); claims are to be complete in themselves). Thus, for example, “Pseudomonas” is properly written as “Pseudomonas” upon its first usage. Appropriate correction for all genera is required.
Claim Rejections - 35 USC § 101
9. 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.
10. Claims 1-4, 11, 13-14, 16-17, 19, 21, and 24-26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to nature-based product (e.g. naturally occurring bacteria) without significantly more.
The claims recite An engineered bacterium or population thereof, wherein the engineered bacterium comprises: one or more polynucleotides that each encode one or more enzymes capable of catalyzing one or more reactions to produce a volatile compound, one or more polypeptides produced therefrom, or both and wherein the engineered bacterium is of a strain that is a commensal bacterium strain found in the oral cavity of a mammal (see claim 1); Therefore, the product claims are directed to a statutory category and Step 1 of the subject matter eligibility analysis is yes.
However, this judicial exception (i.e. naturally occurring bacteria) is not integrated into a practical application because none of the polynucleotides in the bacteria are required to be exogenous or heterologous (or otherwise modified) to the bacterium per se and thus the claims, as written, encompass naturally occurring versions of the genes and thus read on naturally occurring bacteria (e.g. see [0079] that states “engineered” generally refer[s] to a non-naturally occurring nucleic acid, emphasis added; which does not restrict the inclusion of the naturally occurring ones – see “generally”). Thus, the claimed bacteria are not markedly different from that which occurs in nature, even when “engineered”, because (1) the “markedly different" inquiry focuses on the structural characteristics of the product itself and not the method by which the natural product was made; and (2) the primary structure of the claimed polynucleotides (i.e. its sequence of nucleotides within the nucleic acid) within the bacteria is the same as the sequence of nucleotides (i.e. the structure) within its natural counterpart since the nucleotides are not required to be modified, exogenous, or heterologous to the bacterium; and as evidenced by the art, for example, Roslund et al. 2020 (On-line profiling of violative compounds produced in vitro by pathogenic oral bacteria; J. Breath Res 14: 016010; p 1-15) teaches Pseudomonas isolated from the oral cavity naturally produce several volatile organic compounds (i.e. necessary require the corresponding genes encoding the enzymes to produce VOCs; e.g. see abstract and Table 1) and Serino et al. 1995 (Structural genes for salicylate biosynthesis from chorismate in Pseudomonas aeruginosa; Mol Gen Genet 249: 217-228) which teaches a 100% sequence identity match to instant claim 1 obtained from Pseudomonas sp.; see alignment below. Therefore, although the product claims are directed to a statutory category, they are also directed to a judicial exception (i.e. nature-based products; Step 2A prong 1 is yes) that is not integrated into a practical application (i.e. Step 2A, prong 2 is no).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because there are no additional elements in claims 1-4, 11, 13-14, 16-17, 19, 21, and 23 that are not themselves also naturally occurring structures (i.e. polynucleotides, expression vectors, and/or regulatory elements). For claims 24-26, the additional element of a liquid, semi-solid, or solid carrier encompasses water (i.e. a liquid); and everything else in claim 24 is optional (see “optionally” in line 2).
Thus, these additional elements are not sufficient to amount to significantly more than the judicial exception because there is no indication that any of these additional elements (i.e. water) changes any structural or functional features of the judicial exception per se (i.e. naturally occurring bacteria having naturally occurring versions of the same genes encoding the same enzymes for the production of the same naturally occurring volatile organic compounds). Therefore, all the components in the composition function as they would individually, and a mere mixture or aggregation of products, natural or not, does not structurally and/or functionally change the nature-based product from what exists in the environment and that in order to be eligible, every embodiment within the broadest reasonable interpretation of the claim must be eligible.
Thus, taken alone, the additional elements do not amount to significantly more than the above identified judicial exceptions (i.e. naturally occurring bacteria). Looking at the limitations as an ordered combination (including any “intended use” limitations in dependent claims 25 and 26) adds nothing that is not already present when looking at the elements taken individually because the additional element(s) are recited at a high level of generality and are well-understood, routine, conventional activities engaged in by the scientific community; as evidenced by the art (see references above). Consequently, the additional element(s) are not sufficient to make the judicial exception eligible for patent protection (Step 2B is no).
Therefore, based upon consideration of all of the relevant factors with respect to the claim as a whole, the claims are held to claim a law of nature and natural products, and are consequently rejected as ineligible subject matter under 35 U.S.C. 101.
Claim Rejections - 35 USC § 112
11. 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.
12. Claims 1-4, 11, 13-14, 16-17, 19, 21 and 24-26 are rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1 is indefinite because it is unclear if the engineered bacterium is required to produce a volatile compound or not, based on the limitation “…one or more polynucleotides that each encode one or more enzymes capable of catalyzing one or more reactions to produce a volatile compound, one or more polypeptides produced therefrom, or both …” which is in the format of “… to produce…” A, B or both which implies A (first choice) or B (second choice) is sufficient to meet the limitation (i.e. a volatile compound is not required to be produced as long as the bacterium produces polypeptides) since the third option requires both. In the interest of compact prosecution, the claim will be interpreted to encompass A and/or B (i.e. A alone, B alone, or both A and B). Nevertheless, clarification is required to remove scope ambiguity and ascertain the metes and bounds of the claim.
Similarly, claim 4 is indefinite because it is unclear if the mint odor is required or not, based on the third option of “…or (c) both (a) and (b)”; see line 4). In the interest of compact prosecution, this claim will also be interpreted to encompass A and/or B (i.e. A alone, B alone, or both A and B). Nevertheless, clarification is required to remove scope ambiguity and ascertain the metes and bounds of the claim.
Claim 21 is indefinite because it is unclear what the combinations of polynucleotides includes or excludes based on the limitation having “…(d), (e), (0, or…” (see option “f.” and line 14) because it is unclear what “(0” includes. Thus, clarification is required to remove scope ambiguity and ascertain the metes and bounds of the claim.
Claim 25 is indefinite because it is unclear what “…wherein the formulation is W a foodstuff…” which appears to be a typo (see random W) but could be an incomplete phrase. Claim 25 is also unclear based on the lack of a conjunction between options (b) and (c). Consequently, it is unclear if all three limitations must be met (i.e. a, b, and c) or if only one is sufficient (i.e. a, b, or c). In the interest of compact prosecution, the claim will be interpreted to encompass A, B and/or C. Nevertheless, clarification is required to remove scope ambiguity and ascertain the metes and bounds of the claim.
Other dependent claims do not clarify the issues identified above; therefore, clarification is required to remove scope ambiguity and thereby ascertain the metes and bounds of these claims.
Claim Rejections - 35 USC § 112
13. 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.
14. Claims 1-4, 11, 13-14, 17, 19, 21, and 24-26 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor had possession of the claimed invention. This is a written description rejection.
Instant claims are drawn to an engineered bacterium or population thereof, wherein the engineered bacterium comprise one or more polynucleotides that each encode one or more enzymes capable of catalyzing one or more reactions to produce a volatile compound, one or more polypeptides produced therefrom, or both and wherein the engineered bacterium is of a strain that is a commensal bacterium strain found in the oral cavity of a mammal (see claim 1); and further (see dependent claims) to wherein (a) the BSTM1 gene or mRNA has a polynucleotide sequence that is about 90-100 percent identical to any one of SEQ ID NO: 2, 8, 11, or 13; (b) the PCHBA gene or mRNA has a polynucleotide sequence that is about 90-100 percent identical to SEQ ID NO: 1 or 10; (c) the AFT gene or mRNA has a polynucleotide sequence that is about 90-100 percent identical to SEQ ID NO: 49 or 51; (d) the BAT2 gene or mRNA has a polynucleotide sequence that is about 90-100 percent identical to SEQ ID NO: 53; and/or (e) the THI3 gene or mRNA has a polynucleotide sequence that is about 90-100 percent identical to SEQ ID NO: 55; and/or (a) wherein one or more of the one or more polynucleotides has a sequence that is about 40-100 % identical to any one of SEQ ID NO: 1, 2, 8, 10-11, 13, 49, 51, 53, or 55 or any region therein of at least 20 nucleotides; and/or (b) wherein one or more of the one or more polynucleotides encodes a polypeptide having a sequence that is about 40 to 100 % identical to any one of SEQ ID NO: 3-7, 9, 50, 52, 54, or 56.
Consequently, it is the Office’s position that (1) the claim(s) constitute(s) a "broad generic claim” based on the lack of guidance regarding generically claimed (a) bacteria; (b) one or more polynucleotides; (c) one or more enzymes capable of catalyzing (d) one or more reactions; (e) volatile compounds; (f) polypeptides produced therefrom; and (g) “variants” (i.e. which 10 to 60% of nucleotides in the polynucleotide may be substituted within a claimed sequence while maintained the functional ability to encode the corresponding enzyme still capable of catalyzing a reaction to produce the volatile compound and/or polypeptide therefrom); and (2) the claimed genus has substantial variation because of the numerous options and combinations permitted.
Overall, with regards to the generically claimed, mixed-and-matched, combinations of bacteria, polynucleotides, enzymes, reactions, volatile compounds, and polypeptides, it is the Office’s position that none of these, alone or in combination, have been described with sufficient particularity, such that one skilled in the art would recognize that Applicant had possession of the entire claimed genus, at the time of filing, because of (A) a lack of a correlation, known or disclosed, between the claimed functional requirements (i.e. produce a volatile compound) and the structures that meet those requirements (i.e. which bacteria in combination with which polynucleotides and/or sequence variants thereof, for which enzymes, for which reactions, for which compounds or the polypeptides therefrom?); and (B) a lack of a representative number and variety of species to constitute possession of the full scope of the genus.
With specific regards to claim 1, the claim recites “…one or more polynucleotides that each encode one or more enzymes capable of catalyzing one or more reactions to produce a volatile compound, one or more polypeptides produced therefrom, or both” which encompasses as little as one polynucleotide that encodes as little as one enzyme capable of catalyzing as little as one reaction but produces a volatile compound; and encompasses as little as one polynucleotide that encodes multiple enzymes to catalyze multiple reactions to produce one volatile compound and multiple polypeptides; and encompasses multiple polynucleotides that encode for as little as one enzyme capable of catalyzing as little as one reaction to produce one polypeptide and no volatile compounds. However, in all cases, the polynucleotides meeting both these structural requirements and functional features have not been adequately described (see also State of the Art below regarding the complexity of pathways for producing volatile organic compounds in engineered microorganisms). Similarly, claims 4 and 11 allow for mixing and matching DNA sequences (see “genes” in lists) and RNA sequences (see “mRNA” in lists) with the options of “any combination thereof”; but the specification does not describe structures in which DNA and RNA molecules are combined.
With specific regards to claims comprising the 10-60% polynucleotide sequence variants, and/or any region therein of at least 20 nucleotides, the specification does not provide adequate written description to identify the broad genus of the claims because, inter alia, the specification does not disclose a correlation between the necessary structure of the polynucleotide (e.g. which nucleotides must be maintained and which may be substituted in a variant) and the claimed function to be maintained (e.g. encode for an enzyme capable of catalyzing one or more reactions to produce a volatile compound and/or the polypeptides therefrom). It is noted that while the description of the ability of a claimed sequence of a polynucleotide may generically describe that molecule's function, it does not describe the molecule itself. For example, the specification fails to identify critical subsequences within SEQ ID NO: 1, 2, 3, 8, 49 or 50 (i.e. elected sequences) that must be retained in order to maintain the claimed functional activity. Consequently, the specification fails to describe the common attributes or structural characteristics that identify the members of this genus and because the genus of sequences is highly variable (i.e. each sequence has a unique structure; see MPEP 2434), the characteristics of the ability to encode something else, is insufficient to describe the genus. Thus, the specification does not provide substantive evidence for possession of this large and variable genus, encompassing a massive number of partial structures claimed only by a functional characteristic because, without an art-recognized structure-function correlation, the capability to recognize or understand the structure from the mere recitation of function and minimal structure is highly unlikely. Thus, disclosure of function alone is little more than a wish for possession and it does not satisfy the written description requirement; See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (written description requirement not satisfied by merely providing "a result that one might achieve if one made that invention"); In re Wilder, 736 F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming a rejection for lack of written description because the specification does "little more than outline goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate").
Further, MPEP §2163 states that if a biomolecule is described only by a functional characteristic (as in the instant case), without any disclosed correlation between function and structure of the sequence (as in the instant case), it is not sufficient for written description purposes, even when accompanied by a method of obtaining the claimed sequences. MPEP §2163 does state that for a generic claim the genus can be adequately described if the disclosure presents a sufficient number of representative species that encompass the genus. If the genus has a substantial variance, the disclosure must describe a sufficient variety of species to reflect the variation within that genus. Although the MPEP does not define what constitutes a sufficient number of representative species, the courts have indicated what does not constitute a representative number to adequately describe a broad genus. For example, the courts determined that the disclosure of two chemical compounds within a subgenus did not describe that subgenus (e.g. see In re Gostelli, 872, F.2d at 1012, 10 USPQ2d at 1618). Furthermore, the disclosure of only one or two species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us]. "See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) "[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated."). "A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when ... the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed." In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004).
In the instant case, with regards to engineered bacteria, the specification appears to describe two new isolates of Pseudomonas (i.e. one or two species of bacteria; referred to as DOG53 and DOG91; see Example 2 and Figure 5) that were transformed with the same BSTM1 containing plasmid (i.e. one expression vector comprising the same polynucleotide sequences) to produce methyl salicylate (i.e. one volatile organic compound; see Example 2, Figure 3 and [0231]). The specification does not adequately describe any other genetically engineered bacterial species, polynucleotides, enzymes, reactions, volatile compounds, and/or polypeptides as the highly generic claims encompass. The specification does not adequately describe a nexus between the limited results obtained and the breadth and diversity of the entire genus claimed. With regards to the sequence variants, the specification provides complete structural information for SEQ ID NO: 1, 2, 3, 8, 49, and 50; but the claims, as written, also encompass partial structures (i.e. sequence variants of these sequences and/or sections as small as 20 nucleotides) which are not adequately described. By extension, the specification also does not adequately describe expression vectors comprising these partial structures (see claim 21).
Accordingly, the specification also does not provide adequate written description to identify the broad and variable genus of the claims because, inter alia, it does not describe a sufficient number and/or a sufficient variety of representative species to reflect the variation within the genus. Furthermore, based on the lack of information within the specification, there is evidence that a representative number and a representative variety of the numerous combinations of engineered bacteria, polynucleotides and/or sequence variants thereof, enzymes, reactions, volatile compounds, and polypeptides, have not yet been identified. MPEP 2163 which states an adequate written description of a chemical invention requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed; emphasis added; see, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004). Consequently, it is the Office’s position that one of skill in the art would not accept the disclosure of two new isolates of Pseudomonas, transformed with the same BSTM1 containing plasmid, to produce one volatile organic compound (i.e. methyl salicylate), as either a sufficient number and/or variety of “representative species” for all of the bacteria, polynucleotides, enzymes, reactions, volatile compounds, and polypeptides, encompassed by the broad and variable generic claims. Therefore, it is the Office’s position that one of skill in the art would not conclude that Applicant was in possession of the entire genus claimed.
With regards to the state of the art, engineering bacteria to produce volatile organic compounds was still under development and thus necessarily unpredictable. For example, Bution et al. 2015 (Genetic and metabolic engineering of microorganism for the development of new flavor compounds from terpenic substrates; Critical Reviews in Biotechnology; 35(3): 313-325) teaches several processes for genetically engineering microbes to produce volatile organic compounds (e.g. terpenes) remain not suitable for industrial application due to problems encountered during the process including the absence of product accumulation and product degradation, chemical instability of substrates, toxicity of substrates, low solubility and/or high volatility of substrates, multiple metabolic pathways resulting in formation of a mixture of products, low product yields, undetectable enzyme activity, long incubation times and/or short biocatalyst lifetimes (e.g. page 321, left column, section on Limitations). Bution teaches it is unlikely that one strain capable of producing a particular compound will be able to produce other compounds because of the different toxicities of the intermediates and that challenges remain regarding identification of pathway enzymes in native organism to yield de novo activities desired for a given pathway including problems with functional expression of foreign enzymes in the host cells (e.g. page 321, Section on Perspective).
Similarly, Choo et al. 2019 (Synthesis of Three Bioactive Aromatic Compounds by Introducing Polyketide Synthase Genes into Engineered Escherichia coli; J. Agric. Food Chem 67: 8581-8589) teaches engineered bacteria require multiple genes to produce volatile organic compounds, for example, salicylic acid synthesis in microbes is mediated by at least two enzymes, including isochorismate and isochorismate pyruvate lyase to produce an intermediate product and then at least 2 additional ones for successful biosynthesis (see page 8585, bridging section). Choo demonstrated there is variability in results obtained based on the constructs (i.e. genes) used; see page 8586, results and Figure 3). Choo teaches methylation requires additional steps (e.g. page 8587, left column). Choo teaches that methods for engineering microbes to produce compounds of interest require identifying bottlenecks, adjusting flux of intermediate metabolites, and/or optimizing parameters such as promoter strength, gene combinations, and copy number (e.g. page 8588, right column).
Likewise, Poblete-Castro et al. 2012 (Industrial biotechnology of Pseudomonas putida and related species; Appl Microbiol Biotechnol 93:2279-2290) teaches Pseudomonas strains are valuable to create novel chemicals and materials because of their naturally high tolerance to extreme and toxic conditions together with their flexible genetic modifications and display making them an excellent starting point of further development into a production platform but that will require experimental and computation systems level strategies to disentangle the complexity of Pseudomonas metabolic pathways towards their targeted optimization (see page 2286, right column).
With regards to the diversity of bacteria found in the oral cavity of a mammal, Portilho et al. 2023 (Microbial Complexity of Oral Cavity of Healthy Dogs Identified by Mass Spectroscopy and Next-Generation Sequencing; Animals 13: 2467) teaches over 200 bacterial isolates, including Pseudomonas species and Escherichia coli were found in the oral microbiome of healthy canines (see Table 1).
Thus, the state of the art supports that even the skilled artisan requires guidance on the critical structures and/or combinations of the engineered bacteria, polynucleotides and/or sequence variants thereof, enzymes, reactions, volatile compounds, and/or polypeptides and therefore does not provide adequate written description support for the missing information in the instant disclosure. Consequently, neither the specification nor the state of the art provides sufficient written description to support the genus encompassed by the claims. Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.). Given the above analysis of the factors as a whole, which the courts have determined are critical in determining whether Applicant is in possession of or the specification supports the claimed invention, it is the Office’s position that Applicant has not satisfied the requirements as set forth under 35 U.S.C. 112(a).
Claim Rejections - 35 USC § 112
15. Claims 1-4, 11, 13-14, 17, 19, and 24-26 are rejected under 35 U.S.C. 112(a) as failing to comply with the enablement requirement. The claim(s) contains 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. This is a biological deposit rejection.
The invention appears to employ novel biological materials, specifically a newly isolated and characterized species of Pseudomonas as evidenced by Example 2, including the statements “…the most promising bacteria … was previously uncharacterized from the genera Pseudomonas” (see page 55, lines 4-5, of [0229]) and “This evidences that this is a new species of Pseudomonas” (see page 55, lines 3-4 of [0230]). Since the biological materials are essential to the claimed invention, they must be obtainable by a repeatable method set forth in the specification or otherwise readily available to the public. If the biological materials are not so obtainable or available, the requirements of 35 U.S.C. § 112 may be satisfied by a deposit of the biological materials.
If the deposit is made under the Budapest Treaty, then an affidavit or declaration by Applicant, or a statement by an attorney of record over his or her signature and registration number, stating that “…the specific biological materials have been deposited under the Budapest Treaty and that the biological materials will be irrevocably and without restriction or condition released to the public upon the issuance of a patent”, would satisfy the deposit requirement made herein. If the deposit has not been made under the Budapest Treaty, then in order to certify that the deposit meets the criteria set forth in 37 C.F.R. §§ 1.801-1.809, Applicant may provide assurance of compliance by an affidavit or declaration, or by a statement by an attorney of record over his or her signature and registration number, showing that:
(a) during the pendency of this application, access to the invention will be afforded to the Commissioner upon request;
(b) all restrictions upon availability to the public will be irrevocably removed upon granting of the patent;
(c) the deposit will be maintained in a public depository for a period of 30 years or 5 years after the last request or for the effective life of the patent, whichever is longer;
(d) a test of the viability of the biological material at the time of deposit will be made (see 37 C.F.R. § 1.807); and
(e) the deposit will be replaced if it should ever become inviable.
Applicant's attention is directed to M.P.E.P. §2400 in general, and specifically to §2411.05, as well as to 37 C.F.R. § 1.809(d), wherein it is set forth that "the specification shall contain the accession number for the deposit, the date of the deposit, the name and address of the depository, and a description of the deposited material sufficient to specifically identify it and to permit examination." The specification should be amended to include this information; however, Applicant is cautioned to avoid the entry of new matter into the specification by adding any other information.
Claim Rejections - 35 USC § 102
16. 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.
17. 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.
18. Claims 1, 16-17, 19, and 24-26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Poblete-Castro 2012 (Industrial biotechnology of Pseudomonas putida and related species; Appl Microbiol Biotechnol 93:2279-2290).
Poblete-Castro teaches compositions comprising genetically engineered Pseudomonas (i.e. a commensal strain found in the oral cavity of a canine) having heterologous expression vectors (e.g. mini-transposons) comprising polynucleotides for pathway manipulation of enzymes for biosynthesis of economically important volatile organic compounds (e.g. see page 2281, section titled “Genetic Engineering”; and Table 3; meeting limitations found in claims 1, 16, 17, and 19). Poblete-Castro teaches that when grown in culture (i.e. necessarily requires a liquid, semi-solid or solid carrier), and unlike other industrial microorganisms, such as E. coli, Pseudomonas is capable of using substrates such as raw glycerol (e.g. see page 2280, left column and Table 1; meeting broadest reasonable interpretation of claim 24 – only required additional element, see “optionally” in line 2).
With regards to “…for administration to the oral cavity of a mammal” in claim 25 and “…wherein the mammal is a non-human-animal” in claim 26; it is noted that neither limitation adds a component to the claimed formulation per se and thus, both have been interpreted as the intended use of the claimed product; see MPEP 2144.07. Nevertheless, Poblete-Castro teaches it would be beneficial to couple genetically engineered Pseudomonas strains to various streams of renewable feedstocks and/or sugar pipelines because of its naturally high tolerance to extreme and toxic conditions together with flexible genetic modifications (e.g. see page 2286, right column).
Therefore, Poblete-Castro anticipates the invention as claimed.
Claim Rejections - 35 USC § 102
19. Claims 1-4, 11, 16-17, 21, and 24-26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Choo et al. 2019 (Synthesis of Three Bioactive Aromatic Compounds by Introducing Polyketide Synthase Genes into Engineered Escherichia coli; J. Agric. Food Chem 67: 8581-8589).
Choo teaches compositions comprising engineered Escherichia coli bacteria (i.e. a commensal strain found in the oral cavity of a canine) comprising entC or pchA (i.e. isochorismate synthase genes) and pchB (isochorismate pyruvate lyase gene; together with pchA constitutes PCHBA gene) genes and NMT (i.e. N-methyltransferase) expressed from one or more plasmids (i.e. expression vectors) comprising regulatory elements (i.e. a promoter) and capable of producing one or more bioactive, volatile, aromatic compounds; e.g. see page 8581, Materials and Methods; Figure 1; Table 1; and page 8585, left column, Results; meeting limitations found in instant claims 1, 2, 3, 4, 11, 16, and 17). Choo teaches the bacteria cultured in media and/or resuspended in M9 and YM9 solutions (i.e. liquid carriers; liquid solution for administration; see page 8584, left column; meeting broadest reasonable interpretation of claim 24 – only required additional element, see “optionally” in line 2; and intended use limitations in claim 25 and 26).
With regards to “…for administration to the oral cavity of a mammal” in claim 25 and “…wherein the mammal is a non-human-animal” in claim 26; it is noted that neither limitation adds a component to the formulation per se and thus, both have been interpreted as the intended use of the claimed product; see MPEP 2144.07.
With regards to an expression vector “…capable of expressing…” similar genes found in claim 21; it is noted that the particular genes recited in claim 21 are not actually required to be expressed, but rather that the expression vectors would be capable of expressing them; and Choo teaches expression vectors, coupled to one or more regulatory elements, that are capable of expressing isochorismate synthase, isochorismate pyruvate lyase, and methyltransferase genes and thus, it is the Office’s position that one of ordinary skill in the art would recognize that Choo meets the broadest reasonable interpretation of claim 21.
Therefore, Choo anticipates the invention as claimed.
Claim Rejections - 35 USC § 102
20. Claim(s) 1-4, 11, 13-14, 16-17, 19, 21 and 24-26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Serino et al. 1995 (Structural genes for salicylate biosynthesis from chorismate in Pseudomonas aeruginosa; Mol Gen Genet 249: 217-228).
Serino teaches compositions comprising nutrient yeast broth (i.e. liquid solutions) and genetically engineered E.coli and/or Pseudomonas bacteria comprising expression vectors comprising pchA and pchB (i.e. PCHBA) genes including a 100% sequence identity match to instant SEQ ID NO: 1, thereby meeting limitations found in instant claims 1, 2, 3, 4, 11, 13, 14, 16, 17, 19, 21 and 24; see page 218, bridging methods section; and page 219, left column; and the following alignment):
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286
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302
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832
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901
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906
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With regards to “…for administration to the oral cavity of a mammal” in claim 25 and “…wherein the mammal is a non-human-animal” in claim 26; it is noted that neither limitation adds a component to the formulation per se and thus, both have been interpreted as the intended use of the claimed product; see MPEP 2144.07.
Therefore, Serino anticipates the invention as claimed.
Conclusion
21. No claims are allowed.
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/MARY MAILLE LYONS/Examiner, Art Unit 1645
January 26, 2026