DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after 16 March 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Amendments to the Specification, Affidavit under 37 C.F.R 1.808, Amendments to the Claims and Arguments/Remarks filed 23 July 2026, in response to the Office Correspondence dated 24 February 2026, are acknowledged.
The listing of Claims filed 23 July 2026, have been examined. Claims 1, 3, 4,6-9,11-14 and 17-20 are pending. Claims 1, 3, 4, 7, 8, 11, and 14 are amended, claims 2, 5, 10, 15 and 16 are canceled, and new claims 17-20 have been added.
Response to Amendment
The applicant’s response to the objection concerning species-level identification is persuasive. The previous objection explained that the disclosed 16S rRNA sequence did not reliably distinguish Bacillus siamensis from closely related members of the Bacillus subtilis species complex and advised the applicant to characterize the organism as belonging to the Bacillus subtilis species complex unless additional species-resolving evidence was supplied. The applicant has now adopted that terminology while continuing to identify the biological material by the same deposit number, CECT 30677. The published disclosure identifies PH-023 as the strain isolated from sediment at the mouth of the Vélez river and deposited as CECT 30677.
Because the deposit number continues to identify the same biological material, the change from the prior species designation to the broader taxonomic placement within the Bacillus subtilis species complex does not change the identity of the organism being claimed. Accordingly, the prior specification objection concerning unreliable species-level identification is withdrawn.
The applicant also states that a Statement Under 37 C.F.R. § 1.808 has now been filed addressing unrestricted availability of the deposited material. Under 37 C.F.R. § 1.808, the deposit must be available to persons entitled to access during pendency and restrictions on public availability must, subject to the permitted exception, be irrevocably removed upon grant. Upon verification that the submitted statement is properly executed and satisfies those requirements, the prior deposit-availability requirement is considered overcome.
The applicant’s amendment materially changes the scope relevant to the previous § 112(a) rejection. The prior rejection was principally based on claim 1’s coverage of a potentially very large genus of variants defined by at least 99.5% identity to the 16S rRNA sequence, while the disclosure exemplified only CECT 30677. The previous rejection expressly relied upon the lack of correlation between the 16S identity threshold and the claimed biological phenotypes and upon the experimentation necessary to identify functional members of that genus. That genus limitation has now been deleted. Current claim 1 is limited to, “A strain belonging to the Bacillus subtilis species complex deposited in the Spanish Type Culture Collection under the Budapest Treaty with deposit number CECT 30677.” Accordingly, the factual predicate for the former broad-genus written-description and enablement rejection no longer exists. The previous § 112(a) rejection based upon the 99.5%-identity variant genus is withdrawn. The former § 112(a) issue directed to old claim 4 is likewise no longer applicable to present claim 4 because current claim 4 simply requires a composition comprising the deposited strain.
The applicant’s assertion that the newly added metabolite subject matter has original support is substantially correct. Here, the originally published claims expressly recited a composition containing metabolites resulting from protein-hydrolysate fermentation, including glycil-phenylalanine, indol-acetyl-phenylalanine, indole-3-acetamide, the gibberellin metabolite, methyl jasmonate, pantothenic acid, the cyclic hexapeptide, and siderophores. The original claims also expressly recited the method and kit aspects.
The specification additionally provides substantial technical support, wherein Example 2 expressly cultures PH-023/CECT 30677 using a protein hydrolysate as nitrogen source and provides the fermentation conditions and medium composition. Example 4 identifies glycil-phenylalanine, indol-acetyl-phenylalanine, 16,17-dihydro-16α,17-dihydroxy gibberellin A4, methyl jasmonate, and other claimed fermentation metabolites. The general disclosure expressly identifies protein hydrolysate as a nitrogen source and recites essentially the same metabolite list now appearing in claims 17 and 19.
Upon reconsideration, several of the previously stated rejections are no longer applicable because the applicant has materially narrowed claim 1 by deleting the previously recited genus of variants having at least 99.5% 16S rRNA sequence identity and has limited claim 1 to the particular biological material deposited as CECT 30677.
The applicant’s traversal of the Liu anticipation rejection is persuasive. The former § 102 rejection was expressly based upon Liu’s 16S rRNA sequence having 99.54% identity to SEQ ID NO: 1 and therefore satisfying the former “at least 99.5%” variant limitation. That limitation no longer exists. Current claim 1 requires the particular deposited biological material CECT 30677. Liu has not been shown to disclose CECT 30677 itself. The applicant correctly observes that a different Bacillus strain cannot anticipate the presently claimed deposited strain merely because its 16S sequence is highly similar. Accordingly, the rejection of claims 1 and 3 under 35 U.S.C. § 102(a)(1) over Liu is withdrawn.
The previous Gorai and Altimira rejection reasoned that isolation and characterization of additional Bacillus siamensis strains having known plant-growth-promoting characteristics would have constituted routine strain optimization. That rationale is no longer sufficient for current claim 1. Current claim 1 does not generically encompass additional Bacillus siamensis strains, strains having a particular 16S identity, or strains selected for particular plant-growth-promoting properties. It requires CECT 30677 itself.
Neither Gorai nor Altimira identifies CECT 30677, identifies the environmental sample from which CECT 30677 was isolated, or otherwise directs a skilled artisan toward that particular deposited organism. The presently cited record therefore does not establish that CECT 30677 was one of a finite, identified set of predictable alternatives. Accordingly, the existing § 103 rejection of current claim 1 over Gorai in view of Altimira is withdrawn.
Because Peng and Melgar were previously relied upon only for additional limitations of the composition, formulation, method, and kit claims and do not supply CECT 30677, adding those references does not cure the missing limitation. The previous § 103 rejections of claims 4, 6-9, and 11-14 based on those combinations are therefore likewise withdrawn as presently formulated.
Thus, the prior 35 U.S.C. § 102 and § 103 rejections are withdrawn and superseded by new rejections over the prior art, as detailed below. The amendments and new claims also give rise to new objections, and new rejections under 35 U.S.C. § 101 and § 112, as set forth below.
New Rejections
The following new rejections are made from the previous Office Correspondence dated 24 February 2026, as the applicant's amendments necessitate the new grounds of rejection presented below based on the amended/newly cited limitations.
Claim Objections
Claim 20 is objected to because of the following informalities:
Claim 20 recites, “cyclo-(Gly-Leu-Val-IIe-Ala-Phe)”, where claims 17 and 19 and SEQ ID NO: 2 use “Ile” for isoleucine. The claim is objected to and correction of “IIe” to “Ile” is required. Because SEQ ID NO: 2 otherwise identifies the intended sequence, this particular defect is treated as an informality rather than a separate substantive rejection.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. § 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
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 Applicant regards as his invention.
Claims 6, 7, 13, 17, 19, and 20 are 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, regards as the invention.
Claim 6 recites, “wherein the composition further comprises a carrier, in particular, the carrier is the protein hydrolysate used in the fermentation process as nitrogen source.” Two defects are present. First, “in particular” leaves unclear whether use of the specified protein hydrolysate is an affirmative limitation or merely a preferred example of the broadly recited carrier. MPEP § 2173.05(d) specifically cautions against claim language that juxtaposes a broad limitation and a narrower preferred example without establishing whether the latter limits claim scope. Second, “the fermentation process” lacks a clear antecedent basis. Current claim 4 merely recites a composition comprising the claim 1 strain; unlike former claim 4, it no longer introduces any fermentation process.
To overcome this rejection, claim 6 should be amended, for example, to positively recite either a carrier generally or a specifically identified protein hydrolysate and to affirmatively define its relationship to fermentation of CECT 30677.
Claim 7 similarly recites a bioactive component and then states, “in particular, the bioactive component is selected from” a specified list. It is unclear whether the pesticide/fungicide/herbicide/plant-growth-modifier/phytohormone group limits the claimed bioactive component or merely identifies preferred embodiments. Claim 7 therefore fails to clearly delimit its scope (see Nautilus v. Biosig, 572 U.S. 898 (2014)).
Claim 13 recites that the plant “is a horticultural crop, particularly” selected from vegetable, woody, and field crops and “more particularly” defines the woody crops. It is unclear which of these nested preferences constitute mandatory claim limitations. The specification may properly identify preferred embodiments, but the claim should positively define the intended scope.
The earlier Office Correspondence specifically identified uncertainty concerning “the inactivated form of gibberellin A4.” The applicant canceled old claim 5 but has now reintroduced substantially the same terminology in new claims 17 and 19.
The intrinsic disclosure is internally inconsistent on this point. The general metabolite listing separately identifies “the inactivated form of Gibberellin A4” and 16,17-dihydro-16α,17-dihydroxy gibberellin A4, suggesting potentially distinct alternatives. Example 4, however, associates the “inactivated form of Gibberellin A4” with 16,17-dihydro-16α,17-dihydroxy gibberellin A4. Thus, claim 17 and claim 19 leave uncertain whether “the inactivated form” is limited to that specifically identified compound or encompasses additional inactive derivatives of GA4.
Claim 18 identifies the specific compound and therefore substantially cures this ambiguity for the narrower claim 18 scope. For clarity, however, the applicant should replace the generic expression in claim 17 with the chemically identified compound if that compound is what is intended.
Claim 20 contains multiple independent definiteness defects. First, claim 20 recites, “The method according to claim 14 …”, but claim 14 is directed to a kit, not a method. Second, claim 14 alternatively permits a kit comprising the strain itself or a composition comprising the strain. Consequently, claim 20’s subsequent reference to “the composition” lacks a clear antecedent when the first claim-14 alternative is selected.
Third, the expression, “the composition further comprises a composition comprising the strain …” creates an ambiguous composition-within-a-composition construction and does not clearly establish what components constitute the claimed article or what step constitutes the alleged method. Fourth, although denominated a “method,” claim 20 adds no discernible active method step. MPEP § 2173 explains that a claim purporting to be a process but failing to set forth operative steps raises a § 112(b) issue. Accordingly, one of ordinary skill in the art could not determine whether claim 20 is intended to claim a method of plant treatment, a kit, or a composition.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. § 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. § 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. § 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 20 is rejected under 35 U.S.C. § 112(d) or pre-AIA 35 U.S.C. § 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
A proper dependent claim must incorporate every limitation of the claim from which it depends and then add a further limitation. Different statutory classes do not automatically make a dependency improper, but the resulting claim must still contain all limitations of its base claim in a coherent combination (see MPEP § 608.01(n); Pfizer, Inc. v. Ranbaxy Labs., Ltd., 457 F.3d 1284 (Fed. Cir. 2006)).
Claim 14 is a kit claim. Claim 20 instead characterizes itself as “the method according to claim 14” and thereafter recites only composition language. It recites neither a method of making the kit nor a method using the kit while retaining the kit limitations. The claim therefore fails to further limit claim 14 in the manner required by § 112(d). If a method is intended, claim 20 should ordinarily depend from claim 11 and positively recite the composition that is applied. If a kit is intended, claim 20 should be rewritten, for example, as “The kit according to claim 14 …” and should further limit the contents of that kit.
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 therefore, subject to the conditions and requirements of this title.
Claims 1, 3, 4, and 14 are rejected under 35 U.S.C. § 101 because, under their broadest reasonable interpretation, they are directed to a naturally occurring product or a claim that merely recites that product without additional limitations sufficient to integrate the product-of-nature exception into a practical application.
Naturally occurring nature-based products fall within the product-of-nature exception (see MPEP § 2106.04(b)). A living organism is not ineligible merely because it is alive, but a naturally occurring organism must possess markedly different characteristics attributable to human intervention to avoid the exception. The Office’s guidance specifically uses a bacterium as an example of a nature-based product subject to this analysis.
The specification states that PH-023/CECT 30677 was isolated from sediment from the mouth of the Vélez river. Claim 1 does not recite genetic modification, mutagenesis, recombinant material, altered structure, or any other characteristic imparted by human intervention. The deposit designation identifies the organism but does not alter it.
The appropriate naturally occurring counterpart is therefore CECT 30677 as it existed in the environmental sample. No markedly different structural, genetic, phenotypic, or functional characteristic is recited in the claim. Accordingly, claim 1 recites a product of nature. Because claim 1 contains no additional element beyond identification of the naturally occurring strain, the judicial exception is not integrated into a practical application and there is no additional limitation capable of supplying significantly more.
Claim 3 merely limits CECT 30677 to “a sporulated form.” The specification itself characterizes the organism as a sporulating Bacillus. The claim does not require an engineered spore or a spore having any structural or functional characteristic different from the naturally occurring sporulated organism. Accordingly, the additional limitation does not establish a markedly different characteristic.
Claim 4 recites only “a composition comprising the strain according to claim 1.” It does not positively require any particular second component, altered physical state, changed bacterial characteristic, or functional interaction that distinguishes the claimed nature-based product from its naturally occurring counterpart. Nature-based bacterial compositions must be analyzed for markedly different characteristics and relies upon Funk Bros. v. Kalo, 333 U.S. 127 (1948) in discussing bacterial inoculants. Under its broadest reasonable interpretation, claim 4 therefore encompasses the same naturally occurring CECT 30677 without any claimed markedly different characteristic or meaningful additional limitation.
Claim 14 recites a “kit” comprising either the claim 1 strain or a composition comprising that strain. It does not affirmatively recite a particular container, device, reagent, instructions, or other non-nature-based component that could be evaluated as an additional element. Merely denominating the claimed article a “kit” does not itself alter the biological material or impose a meaningful practical application of the natural phenomenon. Accordingly, claim 14 is subject to the same product-of-nature defect.
Dependent claims 6-9, 11-13, and 17-20 are not included in this rejection because they include additional processes or non-nature-based elements.
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-AlA) 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.
Claims 1, 4, 7-9, 11-14, and 17 are rejected under 35 U.S.C. § 103 as being unpatentable over Gorai et al. (Bacillus siamensis CNE6- a multifaceted plant growth promoting endophyte of Cicer arietinum L. having broad spectrum antifungal activities and host colonizing potential. Microbiol Res. 2021 Nov; 252:126859. Epub 2021 Sep 11; hereinafter “Gorai”), in view of Altimira et al. (Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis. Microorganisms. 2022 Mar 22;10(4):670; hereinafter “Altimira”), and in further view of Peng et al. (CN113151059A; published 23 July 2021, hereinafter “Peng”), and Melgar et al. (WO2022120503A1; published 16 June 2022, hereinafter “Melgar”).
Gorai teaches isolation and characterization of the naturally occurring strain Bacillus siamensis CNE6 as a plant-growth-promoting microorganism. Gorai reports phosphate solubilization, indole-acetic-acid production, nitrogen fixation, hydroxamate-type siderophore production, ACC-deaminase activity, and broad-spectrum antifungal activity (Abstract; § 3.2.1-3.2.5; § 3.3.1-3.3.2; § 3.4; Tables 1 and 2; Figs. 2, 5, and 8).
Altimira independently teaches another naturally occurring Bacillus siamensis plant-growth-promoting isolate, RGM 2529, identified using taxonomic/genomic methods. RGM 2529 inhibits phytopathogenic fungi through contact, diffusible, and volatile compounds (§ 3.4), solubilizes phosphate and produces IAA (§ 3.5), and improves growth parameters of treated tomato seedlings (§ 3.6). Altimira further identifies genetic determinants associated with antimicrobial peptides, bacteriocins, IAA, cytokinins, acetoin, 2,3-butanediol, polyamines, siderophores, phosphate solubilization, and stress tolerance (§ 3.2, 3.4-3.6, and Discussion).
Peng provides still further evidence that persons of ordinary skill routinely isolated, identified, and functionally screened additional Bacillus siamensis agricultural strains. Specifically, Peng introduces Example 1, Isolation and identification of Bacillus siamensis LS275 (¶[0019]), teaches obtaining soil from rhizosphere and non-rhizosphere regions of oil-peony plants (¶[0020]-[0021]), teaches isolation of Bacillus organisms from the soil, including heat treatment at about 85°C followed by dilution and microbial isolation (¶[0022]-[0023]), introduces determination of the plant-growth-promoting functions of LS275 (¶[0043]), identifies IAA, siderophore production, and ACC-deaminase as laboratory-measurable plant-growth-promoting characteristics (¶[0044]), and provides an assay for siderophore production (¶[0045]-[0046]).
Thus, before the instant effective filing date, at least three independently isolated Bacillus siamensis strains (i.e., CNE6, RGM 2529, and LS275) had been selected from environmental or plant-associated sources and characterized for substantially the same plant-growth-promoting and biocontrol characteristics that the instant specification attributes to CECT 30677. Peng is particularly probative because it demonstrates the routine workflow for going from environmental soil sample, heat selection of Bacillus, isolation, taxonomic identification, and screening for IAA, siderophore, and other plant-growth-promoting phenotypes.
The combined references do not expressly identify the particular deposit CECT 30677. The difference between instant claim 1 and the prior art is therefore the selection and deposit identification of another naturally occurring member of the known Bacillus siamensis/Bacillus subtilis complex possessing the agriculturally desirable properties for which such isolates were already being routinely sought.
However, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, confronted with Gorai’s and Altimira’s teachings that Bacillus siamensis strains provide useful and commercially relevant plant-growth-promoting and biocontrol phenotypes, to employ the environmental-isolation and phenotype-screening techniques exemplified by Peng to obtain and characterize additional naturally occurring Bacillus siamensis isolates having those same useful properties. The motivation is supplied by Gorai, Altimira, and Peng, which each sought additional naturally occurring Bacillus isolates having improved or useful agricultural properties.
KSR v. Teleflex, 550 U.S. 417-421 (2007) explains that when the prior art provides a design need or market pressure and there are identified approaches within the technical grasp of the skilled artisan, use of known techniques according to their established functions can support obviousness. In re Kubin, 561 F.3d 1351, 1359-60, 90 USPQ2d 1417, 1423-24 (Fed. Cir. 2009), likewise recognizes that use of standard biotechnology techniques can support an obviousness conclusion where the art provides a known target and the skilled artisan would reasonably expect the routine methods to succeed. An expectation of absolute certainty that every environmental isolate would exhibit every desirable phenotype is not relied upon. Obviousness requires a reasonable expectation of success, not absolute predictability (see In re O’Farrell, 853 F.2d 894, 903-904, 7 USPQ2d 1673, 1681 (Fed. Cir. 1988)).
Nevertheless, it is acknowledged that none of Gorai, Altimira, or Peng expressly identifies CECT 30677 itself. Therefore, the foregoing rationale depends upon the conclusion that obtaining the specifically claimed natural isolate constituted the result of the routine strain-isolation and screening program taught by the art rather than selection from an effectively unlimited universe lacking direction toward the claimed strain.
Regarding instant claim 4, Gorai, Altimira, and Peng establish the use of Bacillus siamensis organisms and their culture products in agricultural applications but do not disclose the particular claim 1 strain.
Melgar expressly teaches agricultural formulations comprising Bacillus siamensis RGM 2529 together with agriculturally acceptable excipients, describing formulations containing the Bacillus siamensis strain in extended-release tablets, wettable powders, effervescent tablets, resuspensions, and bacterial emulsions (¶[0030]-[0031]); see also ¶[0099], describing microbial concentrates used in preparing bacterial formulations). Melgar’s Bacillus siamensis formulation teachings are consistent with the broader disclosure that such formulations contain bacterial cultures and agricultural excipients and may contain RGM 2529 at approximately 3×10^6-4×10^9 CFU/g (claim 2).
Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to formulate an additional agriculturally useful Bacillus siamensis isolate selected according to Gorai, Altimira, and Peng in the conventional agricultural compositions taught by Melgar because Melgar expressly teaches that Bacillus siamensis is delivered to crops in formulated form. This is the predictable use of a known formulation technique for its established purpose (see KSR v. Teleflex, 550 U.S. at 417 (2007).
Regarding instant claim 7, Melgar teaches agricultural compositions containing conventional formulation excipients, including polysorbates/Tweens and other agricultural formulation materials (¶[0030] and ¶[0081]-[0086], particularly ¶[0086], which describes bacterial formulations including Tween 20 and Silwet, i.e., surfactant-type formulation components). Melgar further teaches that its Bacillus siamensis-containing formulations may be administered together with fertilizers (¶[0030] and claim 22). Therefore, the prior art expressly teaches at least the claimed alternative of a composition comprising the Bacillus strain and a surfactant.
Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to include a known agricultural surfactant in the instant claim 4 composition to improve dispersion, wetting, and agricultural delivery, using the surfactant according to its conventional formulation function (see KSR v. Teleflex, 550 U.S. 417 (2007); In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980), wherein combination of compositions known to be useful for the same purpose may be prima facie obvious where the combination predictably serves the same purpose); MPEP § 2144).
Regarding instant claim 8, Melgar teaches Bacillus siamensis bacterial formulations having viable-cell concentrations within the claimed 10^5-10^12 CFU/mL range. In particular, Melgar describes bacterial concentrations of approximately 10^9 CFU/mL for seed treatment and approximately 10^8 CFU/mL for application at the plant stem (¶[0031]), formulation concentrations of approximately 3.4×10^6 to 4×10^8 CFU/g (¶[0083]), and microbial concentrates of approximately 10^9 CFU/mL used in formulations (¶[0099]). Likewise, Melgar identifies preferred RGM 2529 concentrations extending from approximately 3×10^6 to 4×10^9 CFU/g and application concentrations of 10^8-10^9 CFU/mL (claims 2 and 3)
These concentrations fall squarely within the instantly claimed 10^5-10^12 CFU/mL range. An overlapping or encompassed numerical range is sufficient to establish a prima facie case of obviousness absent evidence of criticality or unexpected results associated with the claimed range (see In re Peterson, 315 F.3d 1325, 1329-30, 65 USPQ2d 1379, 1382-83 (Fed. Cir. 2003)).
Melgar teaches multiple formulation types encompassed by instant claim 9. Melgar teaches Bacillus siamensis RGM 2529 formulations in the form of prolonged-release tablets, wettable powders, effervescent tablets, resuspensions, bacterial emulsions, and mixtures thereof (¶[0030]). Melgar particularly describes a wettable-powder formulation (¶[0081]), an effervescent solid formulation (¶[0082]), and liquid/emulsion-type bacterial preparations (¶[0084]-[0086]).
Thus, Melgar therefore teaches at least the claimed alternatives “wettable powder,” “liquid formulation,” “solid formulation,” “suspension concentrate,” and/or “emulsifiable concentrate” or their conventional equivalents. Selecting among these known conventional formulation forms for an agriculturally useful Bacillus strain would have represented a predictable formulation choice (see KSR v. Teleflex, 550 U.S. 417-421 (2007)).
Regarding instant claim 11, Melgar expressly teaches a method of promoting plant growth and/or increasing crop yield by applying an effective amount of a formulation comprising Bacillus siamensis RGM 2529, describing a method for promoting growth, increasing yield, and/or protecting crops through administration of an effective amount of the disclosed formulation (¶[0035]), teaching seed and stem-base administration (¶[0036]), and reporting increased tomato productivity in treatment using the bacterial formulation together with fertilization (¶[0037]). Altimira independently demonstrates that treatment with Bacillus siamensis RGM 2529 produces improved tomato-seedling growth parameters (§ 3.6 and Figs. 4a, 4c, and 5).
Thus, once an additional agriculturally useful Bacillus siamensis isolate was obtained, applying it or its formulation for the very plant-growth-promoting purpose for which the prior art selected Bacillus siamensis strains would have been the use of a known agent for its expected function (see KSR v. Teleflex, 550 U.S. 417-421 (2007)).
Regarding instant claim 12, Melgar teaches application to the instant claimed plant regions. Melgar describes administration to seed and at the base of the plant stem (¶[0031]), spraying or direct immersion of seed and application to the base of the stem (¶[0036]), and inoculation/soaking of tomato seeds followed by planting in growing substrate containing peat, perlite, and compost (¶[0101]-[0102]; the Verga reference cited below further confirms that beneficial microbial inoculants were conventionally applied to seeds, growth media, or leaves, and teaches applying microbial-inoculant/protein-hydrolysate compositions to a plant or plant growing medium). Accordingly, the particular application locations recited by instant claim 12 represent expressly taught agricultural delivery sites rather than a patentable distinction.
Regarding instant claim 13, Melgar identifies suitable agricultural crops with formulation utility including tomato, pepper, grape, apple, lettuce, and numerous other food and horticultural crops (¶[0033]). Thus, the instant claimed horticultural crop and at least the specifically recited vineyard/grape embodiment were expressly contemplated in the prior art. Selection of a known target crop from the expressly disclosed crop list for application of the same growth-promoting Bacillus formulation would have been obvious (see KSR v. Teleflex, 550 U.S. 421 (2007)).
Regarding instant claim 17, requiring the composition to contain one or more of the listed compounds/metabolites, one expressly permitted alternative being siderophores, Gorai expressly establishes that Bacillus siamensis CNE6 produces hydroxamate-type siderophores (Abstract; § 3.2.5, and § 3.3.1-3.3.2). Melgar provides an even more specific teaching for Bacillus siamensis RGM 2529. Melgar identifies the DhbACEBF gene cluster involved in synthesis of bacillibactin, expressly identified as a siderophore (¶[0129]; see also Figure 24 and Table 17, which identify bacillibactin (siderophore) among the secondary metabolites attributable to RGM 2529). Melgar additionally identify other secondary-metabolite and extracellular-product systems (¶[0130]-[0135]).
Accordingly, prior to the instant effective filing date it was known that agriculturally useful Bacillus siamensis strains produce the expressly claimed class of siderophores. Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to retain the known siderophore-containing fermentation products in a formulation of a plant-growth-promoting Bacillus siamensis strain because the siderophores were already known products of such strains and were associated with their plant-growth-promoting/biocontrol activity. This is a predictable use of a known microbial product according to its established function (see KSR v. Teleflex, 550 U.S. 417-421 (2007)).
Regarding the additional kit limitation of instant claim 14, it would have been obvious at the time of the instant invention to organize a composition comprising the strain according to instant claim 1 into a kit because providing multi-component formulations as separate parts in a single kit is a well-known and conventional practice in the art. This is routinely done for reasons of chemical stability (to prevent interaction between components during storage), convenience in transport and handling, and to provide flexibility to the end-user to mix the components at the time of use (see MPEP § 2144.02, indicating that the rationale to support a rejection under 35 USC 103 may rely on logic and sound scientific principle and , MPEP § 2144 indicating that the rationale supporting a rejection may be reasoned from common knowledge in the art). Separating known components, which are intended to be used together, into a kit is therefore a matter of routine packaging choice. The applicant has not stated why organizing a composition containing the strain of instant claim 1 into a kit would not have been recognized as common knowledge to those of ordinary skill in the art at the time of the invention (see MPEP § 2144.03(c)).
Claims 1 and 3 are rejected under 35 U.S.C. § 103 as being unpatentable over Gorai et al. (Bacillus siamensis CNE6- a multifaceted plant growth promoting endophyte of Cicer arietinum L. having broad spectrum antifungal activities and host colonizing potential. Microbiol Res. 2021 Nov; 252:126859. Epub 2021 Sep 11; hereinafter “Gorai”), in view of Altimira et al. (Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis. Microorganisms. 2022 Mar 22;10(4):670; hereinafter “Altimira”), and in further view of Peng et al. (CN113151059A; published 23 July 2021, hereinafter “Peng”), Melgar et al. (WO2022120503A1; published 16 June 2022, hereinafter “Melgar”), and Schirring et al. (WO2018140542A1; published 02 August 2018, hereinafter “Schirring”).
Gorai, in view of Altimira, and in further view of Peng and Melgar teach the limitations of instant claim 1, as described above, from which instant claim 3 depends, however do not explicitly teach the specific limitations of instant claim 3.
The combination of Gorai, Altimira, and Peng is relied upon as discussed above. Schirring explicitly teaches the additional sporulation limitation. Specifically, Schirring teaches that various Bacillus species form endospores and explains the structure and enhanced environmental resistance of such spores (¶[0003]), states that Bacillus-based agricultural products are generally formulated as mixtures or suspensions of endospores to improve stability and shelf life (¶[0005]) and further teaches plant-growth-promoting Bacillus organisms in agricultural products (claims 1-3).
Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to provide the selected agriculturally useful Bacillus strain in sporulated form because the art expressly teaches that sporulation is an inherent biological capability of Bacillus and that the spore form was conventionally selected for agricultural products precisely because it improves stability and shelf life. That modification merely applies a known preservation/formulation technique to the same class of agricultural microorganism for its expressly taught benefit (see KSR v. Teleflex, 550 U.S. 417-421 (2007)). The skilled artisan would have had a reasonable expectation of success because Schirring does not merely suggest that spores might be useful, it states that it was known in the art to formulate Bacillus-based agricultural products as endospore mixtures or suspensions.
Further evidence supporting the rejection of instant claim 14, as detailed above, is provided by the direct teaching of Schirring including commercial kits of parts containing plant-growth-promoting Bacillus organisms. Specifically, claim 30 of Schirring recites, a kit of parts comprising a plant-growth-promoting Bacillus or Paenibacillus isolate, and an inorganic phosphate component. Schirring claim 36 specifies plant-growth-promoting Bacillus subtilis, Bacillus amyloliquefaciens, and/or Bacillus pumilus as kit microorganisms. Therefore, the prior art establishes kit packaging for plant-growth-promoting Bacillus agricultural products.
Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to package an agriculturally useful Bacillus strain or formulation in the known kit form because Schirring expressly teaches that delivery arrangement for the same type of plant-growth-promoting bacterial product. No new mechanism or unexpected interaction results from merely providing known agricultural bacterial components as a kit.
Claims 1, 4, and 6 are rejected under 35 U.S.C. § 103 as being unpatentable over Gorai et al. (Bacillus siamensis CNE6- a multifaceted plant growth promoting endophyte of Cicer arietinum L. having broad spectrum antifungal activities and host colonizing potential. Microbiol Res. 2021 Nov;252:126859. Epub 2021 Sep 11; hereinafter “Gorai”) in view of Altimira et al. (Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis. Microorganisms. 2022 Mar 22;10(4):670; hereinafter “Altimira”) and in further view of Peng et al. (CN113151059A; published 23 July 2021, hereinafter “Peng”), Melgar et al. (WO2022120503A1; published 16 June 2022, hereinafter “Melgar”), Zhai et al. (CN103215210A; published 08 May 2013, hereinafter “Zhai”), and Verga et al. (WO2021079276A1; published 29 April 2021, hereinafter “Verga”)
Gorai, in view of Altimira, and in further view of Peng and Melgar teach the limitations of instant claims 1 and 4, as described above, from which instant claim 6 depends, however do not explicitly teach the specific the additional protein-hydrolysate/carrier limitation of instant claim 6.
Zhai teaches Bacillus siamensis L13 (CGMCC 7285) and the agricultural use of its fermentation liquor. More particularly, optimization and production of the Bacillus siamensis L13 fermentation culture (¶[0040]-[0043]), an optimized fermentation medium comprising peptone at 1.0-3.0 g/L, together with yeast powder, glucose, soybean cake powder, minerals, and other nutrients (¶[0042]) and the resulting fermentation product (¶[0043]), wherein claim 10 again recites the peptone-containing fermentation-medium formulation. Thus, Zhai teaches fermenting a Bacillus siamensis strain in the presence of peptone is an art-recognized protein hydrolysate/organic nitrogen nutrient. Zhai further teaches using the resulting bacterial fermentation liquor directly in a microbial agricultural fertilizer, rather than requiring complete removal of the fermentation-medium components (claims 6-9).
Verga independently teaches agricultural compositions comprising a microbial inoculant together with a protein-containing hydrolysate, identifying Bacillus subtilis, Bacillus velezensis, and Bacillus amyloliquefaciens among preferred organisms (p. 14, ll. 2-22). Verga teaches preparation of hydrolysates through enzymes acting on the protein component and peptide bonds, including peptidases, proteases, and proteinases (claim 4), and specifically describes compositions containing the resulting hydrolysate (claim 1) and beneficial Bacillus inoculants (p. 14, ll. 2-22). Verga also teaches that these hydrolysate/microbial compositions are useful for promoting plant growth ( p. 14, ll. 9-11) and that the hydrolysate can be used in liquid agricultural formulations (p. 15, ll. 22-30, and p. 16, ll. 25-28).
Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to use a protein hydrolysate as the organic nitrogen nutrient when fermenting an agriculturally useful Bacillus strain, as expressly exemplified for Bacillus siamensis by Zhai, and to retain/use that hydrolysate-containing fermentation material in the final agricultural formulation, as suggested by Zhai’s direct agricultural use of fermentation liquor and Verga’s microbial-inoculant/hydrolysate compositions. The modification reduces unnecessary separation and replacement of a formulation-compatible nutrient already present in the fermentation broth and allows the same hydrolysate to perform its known nutrient/formulation-medium function (see KSR v. Teleflex Inc., 550 U.S. 398 (2007), where simplifying a process by combining or reducing steps is seen as a reasonable modification if the prior art discloses the components and the resulting product is the same). The combined teachings would have suggested use to one of ordinary skill in the art, even though the references employ different Bacillus strains (see In re Keller, 642 F.2d at 425, 208 USPQ at 881).
Claims 1, 4, 17, and 18 are rejected under 35 U.S.C. § 103 as being unpatentable over Gorai et al. (Bacillus siamensis CNE6- a multifaceted plant growth promoting endophyte of Cicer arietinum L. having broad spectrum antifungal activities and host colonizing potential. Microbiol Res. 2021 Nov;252:126859. Epub 2021 Sep 11; hereinafter “Gorai”) in view of Altimira et al. (Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis. Microorganisms. 2022 Mar 22;10(4):670; hereinafter “Altimira”) and in further view of Peng et al. (CN113151059A; published 23 July 2021, hereinafter “Peng”), Melgar et al. (WO2022120503A1; published 16 June 2022, hereinafter “Melgar”), Ceccarelli et al. (Foliar Application of Different Vegetal-Derived Protein Hydrolysates Distinctively Modulates Tomato Root Development and Metabolism. Plants (Basel). 2021 Feb 8;10(2):326; hereinafter “Ceccarelli”), Ishida et al. (Synthesis and structure–activity relationship of 16,17-modified gibberellin derivatives, Phytochemistry Letters, Volume 49, 2022, Pages 162-166; hereinafter "Ishida"), Di Muzino et al. (US20210276927A1; published 09 September 2021, hereinafter “Di Muzino”), and Mañero et al. (WO2000043497A1; published 27 July 2000, hereinafter “Mañero”).
Gorai, in view of Altimira, and in further view of Peng and Melgar teach the limitations of instant claims 1, 4 and 17, as described above, from which instant claim 18 depends, however do not explicitly teach the specific limitations of instant claim 18.
Ceccarelli investigates the metabolic effects of plant protein hydrolysates (Abstract) and Table 1 (p. 7), expressly identifies 16α,17-epoxy gibberellin A4 among the gibberellin-related metabolites detected in the metabolomic analysis of treated tomato plants.
Ishida independently establishes that 16,17-dihydro-16α,17-dihydroxy GA4 was a known chemical entity, identifies it in the GA4-deactivation pathway, and describes synthesis and biological evaluation of 16,17-modified gibberellin derivatives (Abstract). Ishida reports that 16,17-dihydro-16α,17-dihydroxy GA4 had previously been identified as the aglycone of its glucoside from rice (p. 162, Introduction, ¶1) and addresses 16,17 modification as a route of GA deactivation (Abstract). Thus, the exact compound recited in instant claim 18, and its relationship to inactivation/deactivation of GA4, were known before the instant effective filing date.
Thus, one of ordinary skill in the art, prior to the instant effective filing date, developing a plant-biostimulant composition involving microbial metabolites, protein hydrolysates, and plant-hormone-associated compounds would have recognized the exact 16,17-dihydro-16α,17-dihydroxy GA4 metabolite as a known GA4-deactivation product and as a metabolite associated with protein-hydrolysate-treated plant systems. However, neither Ceccarelli nor Ishida expressly teaches adding this compound to a Bacillus siamensis composition or establishes that a Bacillus siamensis fermentation necessarily produces it. Accordingly, while these references establish that the chemical species and its GA4-deactivation identity were known.
Di Muzino teaches agricultural/plant-biostimulant compositions containing Bacillus (Abstract, claim 1) and teaches that the bacterial strain can be combined with protein hydrolisates [hydrolysates] and with hormones or hormone-like compounds, including gibberellins, gibberellin-like compounds (¶[0131]). Further Mañero teaches that Bacillus pumilus B3 (CECT 5105) and Bacillus licheniformis B12 (CECT 5106) of the subtilis group, of the genus Bacillus, which produce phytohormones that regulate plant growth in the group of the gibberellins, in the presence of GA4 (Abstract). Thus, a person of ordinary skill in the art, prior to the instant effective filing date, had evidence that multiple Bacillus species produce gibberellin and that closely related agricultural Bacillus organisms of the subtilis group can produce GA4 specifically. Therefore, prior to the applicant's filing date, the exact compound was not an obscure hypothetical structure selected retrospectively from millions of possibilities. It was a known, naturally occurring GA4 metabolite expressly investigated as part of GA4 deactivation chemistry, and its reduced plant-elongation activity had been experimentally established.
Mañero specifically teaches that plant-growth-promoting Bacillus strains of the Bacillus subtilis group produce multiple gibberellins including GA4 in liquid bacterial culture. Hence, production and use of gibberellin phytohormones constituted a known plant-growth-promoting mechanism of Bacillus organisms. Di Muzino further expressly teaches agricultural plant-biostimulant compositions comprising a Bacillus strain together with additional molecules, including protein hydrolysates, and specifically states that gibberellins and gibberellin-like compounds may advantageously be used in combination with the Bacillus strain, providing an explicit reason for a person of ordinary skill to include a gibberellin or gibberellin-like compound in a plant-growth-promoting Bacillus composition rather than merely demonstrating that such compounds independently existed. Ishida teaches the specifically claimed 16,17-dihydro-16α,17-dihydroxy GA4, explaining that it had been identified naturally as an aglycone of its glucoside in rice and demonstrating that 16,17-dihydroxylation of GA derivatives significantly decreases their growth-promoting activity, consistent with stepwise deactivation of bioactive GA4.
Accordingly, a person of ordinary skill in the art seeking to formulate the known plant-growth-promoting Bacillus composition with a gibberellin/gibberellin-like component, as expressly suggested by Di Muzino, would have had reason to select a known function-limited derivative of the physiologically relevant GA4 scaffold, such as the specific 16,17-dihydro-16α,17-dihydroxy GA4 taught by Ishida, in order to provide or modulate gibberellin-associated plant-growth regulation while reducing the excessive elongation associated with highly active GA species. Such selection would amount to employing a known GA4-derived molecule according to its experimentally established activity profile for the same general agricultural plant-growth-regulation purpose taught by the prior art.
The proposed combination does not depend upon hindsight identification of the presently claimed compound from an undifferentiated universe of metabolites. Before the effective filing date, the art had independently identified gibberellin production as a plant-growth-promoting mechanism of Bacillus, including B. siamensis; demonstrated bacterial production of GA4 by subtilis-group Bacillus; expressly recommended combining Bacillus biostimulants with gibberellins and gibberellin-like compounds; identified the precise claimed GA4 metabolite as a naturally occurring GA4-deactivation product; and demonstrated that its 16,17-dihydroxylation reduces GA bioactivity. This constitutes the predictable use of prior-art elements according to their established functions under KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 417-421 (2007). The collective teachings would have suggested such to the ordinarily skilled artisan (see In re Keller, 642 F.2d 413, 425, 208 USPQ 871, 881 (CCPA 1981)).
Claims 1 and 19 are rejected under 35 U.S.C. § 103 as being unpatentable over Gorai et al. (Bacillus siamensis CNE6- a multifaceted plant growth promoting endophyte of Cicer arietinum L. having broad spectrum antifungal activities and host colonizing potential. Microbiol Res. 2021 Nov;252:126859. Epub 2021 Sep 11; hereinafter “Gorai”) in view of Altimira et al. (Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis. Microorganisms. 2022 Mar 22;10(4):670; hereinafter “Altimira”) and in further view of Peng et al. (CN113151059A; published 23 July 2021, hereinafter “Peng”), Melgar et al. (WO2022120503A1; published 16 June 2022, hereinafter “Melgar”), and Zhai et al. (CN103215210A; published 24 July 24, 2013, hereinafter “Zhai”).
Gorai, in view of Altimira, and in further view of Peng and Melgar teach the limitations of instant claim 1, as described above, from which instant claim 19 depends, however do not explicitly teach the specific limitations of instant claim 19.
Gorai teaches a plant-growth-promoting strain identified as Bacillus siamensis CNE6. Gorai specifically reports plant-growth-promoting properties including phosphate solubilization, indole-acetic-acid production, nitrogen fixation, and production of hydroxamate-type siderophores (Abstract; § 3.2.5, Siderophore production). Gorai therefore expressly teaches that a Bacillus siamensis strain produces a member of the broad “siderophores” alternative presently recited in instant claim 19.
Gorai further evaluates the extracellular products of CNE6, and reports antagonistic activity attributable to the Bacillus strain (§ 3.3.1, Antagonistic activity of CNE6), wherein § 3.3.2, “Inhibition of radial growth of phytopathogens,” reports that a 50% cell-free supernatant obtained from CNE6 culture produced approximately 60-80% inhibition of radial growth of the tested pathogenic fungi (see also Abstract). Thus, Gorai does not merely predict that Bacillus siamensis possesses metabolic biosynthetic machinery, it experimentally establishes production of siderophores and biological activity residing in the cell-free culture fraction containing extracellular metabolites.
Gorai does not, however, identify CECT 30677 and does not expressly state that the CNE6 fermentation medium employs a protein hydrolysate as a nitrogen source.
Melgar independently teaches agricultural fermentation and metabolite production by another Bacillus siamensis strain, RGM 2529. Specifically, Melgar, teaches that, for preparation of the bacterial cultures of Bacillus safensis RGM 2450 and Bacillus siamensis RGM 2529, the organisms were subjected to fed-batch fermentation in stirred-tank bioreactors up to 5 L (¶[0098]). Melgar further teaches harvesting the resulting microbial concentrates and using those concentrates to prepare agricultural bacterial formulations (¶[0099]). Thus, Melgar establishes fermentation, recovery, and agricultural formulation of a Bacillus siamensis culture product.
More particularly, Melgar teaches that Bacillus siamensis RGM 2529 would secrete antimicrobial compounds and expressly states that genome analysis demonstrated the presence of the DhbACEBF gene cluster involved in synthesis of bacillibactin, which Melgar expressly identifies as “a siderophore” having antifungal activity (¶[0129]; Figure 24, which identifies the DhbACEBF cluster as involved in synthesis and assembly of the bacillibactin siderophore; Table 17, which expressly lists Bacillibactin (siderophore) among compounds attributed to Bacillus siamensis RGM 2529).
Melgar further identifies other secondary-metabolite biosynthetic systems of RGM 2529, including fengycin, bacillomycin D, surfactin, and bacillaene (¶[0130]-[0134]), and describes additional extracellular enzymes (¶[0135]). These teachings reinforce that fermentation of Bacillus siamensis was understood to produce a chemically diverse extracellular metabolite product rather than merely bacterial biomass. Accordingly, Gorai and Melgar together teach that agriculturally useful Bacillus siamensis strains are cultured/fermented and that such strains produce extracellular secondary metabolites including the expressly claimed genus siderophores. However, Gorai and Melgar do not expressly disclose the particular claimed choice of a protein hydrolysate as the nitrogen source. Zhai supplies that limitation.
Zhai teaches Bacillus siamensis L13 (CGMCC No. 7285) and uses fermentation broth of that strain in agricultural compositions and growth-promoting applications (¶[0040]-[0043]), directed to optimization of the Bacillus siamensis fermentation culture. In particular, Zhai inoculates the prepared Bacillus siamensis L13 seed culture into fermentation medium and optimizes fermentation conditions (¶[0041]), then provides the optimized fermentation-medium formulation, including peptone at 1.03.0 g/L, together with yeast powder, glucose, soybean cake powder, mineral components, and other nutrients (¶[0042]). The resulting fermentation product and viable-cell concentration (¶[0044]). The same peptone-containing fermentation formulation is recited in Zhai claim 10.
Peptone was conventionally recognized in the microbiological fermentation art as a protein hydrolysate used as an organic nitrogen source. Thus, a person of ordinary skill would have understood Zhai’s use of peptone in the Bacillus siamensis fermentation medium as teaching precisely the claimed use of a protein hydrolysate as a nitrogen source. Zhai therefore supplies an express prior-art teaching of fermenting a Bacillus siamensis strain using a fermentation medium containing a protein-hydrolysate nitrogen nutrient.
Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to produce a Bacillus siamensis-derived agricultural metabolite composition using the fermentation teachings of Melgar and/or Zhai while obtaining the known extracellular metabolites, including siderophores, taught by Gorai and Melgar.
Gorai provides experimental evidence that a Bacillus siamensis strain produces hydroxamate-type siderophores and that extracellular material present in a cell-free culture supernatant possesses substantial biological activity (Abstract; § 3.2.5, § 3.3.1-3.3.2). Melgar teaches fed-batch fermentation of Bacillus siamensis RGM 2529 (¶[0098]), while ¶[0129], Figure 24, and Table 17 specifically associate that strain with biosynthesis of the siderophore bacillibactin. Zhai supplies the conventional choice of a peptone/protein-hydrolysate nutrient in fermentation of yet another Bacillus siamensis strain (¶[0040]-[0043], particularly ¶[0042]).
The references therefore address the same technical endeavor, cultivation of agriculturally useful Bacillus siamensis strains and production/formulation of their biologically active fermentation products, and their teachings would naturally have been considered together by one of ordinary skill in the art seeking to obtain a Bacillus siamensis fermentation product containing extracellular plant-beneficial metabolites.
Obviousness may be established where a claimed combination amounts to the predictable use of prior-art elements according to their established functions (see KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417, 82 USPQ2d 1385, 1396 (2007)). The present modification does not require changing the function of any component. The Bacillus siamensis strain is fermented as taught by Melgar and Zhai, the protein hydrolysate/peptone performs its established fermentation-nutrient function as taught by Zhai, and the microorganism produces its known extracellular metabolites, including siderophores, is taught by Gorai and Melgar.
Moreover, the proper inquiry is not whether the references can be bodily combined verbatim but what their combined teachings would have suggested to a person of ordinary skill (see In re Keller, 642 F.2d 413, 425, 208 USPQ 871, 881 (CCPA 1981)). Thus, it is immaterial that Gorai employs CNE6, Melgar employs RGM 2529, and Zhai employs L13. The references collectively establish the state of the art concerning fermentation and extracellular-metabolite production of Bacillus siamensis strains. Thus, one of ordinary skill would also have had a reasonable expectation of success. Gorai experimentally demonstrates siderophore production by Bacillus siamensis CNE6, Melgar teaches actual fed-batch fermentation of Bacillus siamensis RGM 2529 and identifies its bacillibactin biosynthetic machinery, and Zhai actually ferments Bacillus siamensis L13 in a peptone-containing medium. The three references provide substantially more than a generalized invitation to experiment because each material part of the proposed fermentation (i.e., organism type, fermentation of the organism, protein-hydrolysate nutrient, and production of the claimed siderophore alternative) was already demonstrated or expressly taught in the art.
Instant claim 19 is further drafted in product-by-process form because it claims a “composition” partly by reference to the process by which the compounds/metabolites are generated (namely, “resulting from the fermentation of a protein hydrolysate by the strain.”). Under MPEP § 2113, patentability of a product-by-process claim is determined principally from the product itself. In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985), holds that if the claimed product is the same as, or obvious from, a prior-art product, the product is not rendered patentable merely because the claim recites a different process for producing it. The Federal Circuit has reiterated that a product made by a claimed process may be anticipated by or obvious from a prior-art product even though the prior-art product was manufactured through another process (see Amgen Inc. v. F. Hoffmann-La Roche Ltd., 580 F.3d 1340, 1370 n.14, 92 USPQ2d 1289, 1312 n.14 (Fed. Cir. 2009)).
The process language is not ignored, structure or compositional characteristics necessarily imparted to the product by the recited process have been considered. Here, however, instant claim 19 does not recite a concentration, metabolomic fingerprint, metabolite ratio, purity, molecular distribution, chromatographic profile, or other structural/compositional property distinguishing the fermentation product of CECT 30677 from the broad siderophore-containing Bacillus siamensis fermentation products suggested by the prior art. This point is especially significant because instant claim 19 requires only “one or more” of the listed compounds/metabolites, and “siderophores” is itself one expressly permitted alternative. Thus, the prior art is not required to establish a fermentation product containing glycil-phenylalanine, indol-acetyl-phenylalanine, indole-3-acetamide, the specified gibberellin metabolite, methyl jasmonate, pantothenic acid, the cyclic hexapeptide, and siderophores simultaneously. Under the broadest reasonable interpretation of the claim language, a fermentation-derived composition satisfying the broad siderophore alternative is sufficient.
Here, Gorai establishes actual siderophore production by Bacillus siamensis, Melgar establishes fermentation of Bacillus siamensis RGM 2529 and expressly associates the strain with bacillibactin siderophore biosynthesis, and Zhai establishes fermentation of Bacillus siamensis using a peptone/protein-hydrolysate nutrient. These teachings provide a reasonable evidentiary basis for concluding that the broadly claimed siderophore-containing fermentation composition would have been at least an obvious product of the combined prior art.
The applicant may submit evidence demonstrating that fermentation of CECT 30677 specifically with the claimed protein hydrolysate necessarily produces a structural or compositional characteristic that distinguishes the resulting claimed composition from the prior-art Bacillus siamensis fermentation products. In the absence of such evidence or a claim limitation defining such a distinction, however, the source/process limitation alone does not overcome the prima facie case.
In summary, before the instant effective filing date, Gorai taught Bacillus siamensis production of the expressly claimed siderophore class and extracellular biologically active culture metabolites, Melgar taught fed-batch fermentation of Bacillus siamensis and specifically identified bacillibactin siderophore biosynthesis in RGM 2529, and Zhai taught fermenting Bacillus siamensis in a medium comprising peptone, an art-recognized protein-hydrolysate nitrogen source. A person of ordinary skill in the art would have had reason to combine these teachings to prepare an agricultural Bacillus siamensis fermentation product using a protein-hydrolysate nitrogen source and containing a siderophore, with a reasonable expectation of successfully obtaining that known class of extracellular metabolite. The claimed product is not distinguished by any affirmative structural or compositional limitation attributable uniquely to fermentation by CECT 30677.
Claims 1, 14 and 20 are rejected under 35 U.S.C. § 103 as being unpatentable over Gorai et al. (Bacillus siamensis CNE6- a multifaceted plant growth promoting endophyte of Cicer arietinum L. having broad spectrum antifungal activities and host colonizing potential. Microbiol Res. 2021 Nov;252:126859. Epub 2021 Sep 11; hereinafter “Gorai”) in view of Altimira et al. (Genomic and Experimental Analysis of the Biostimulant and Antagonistic Properties of Phytopathogens of Bacillus safensis and Bacillus siamensis. Microorganisms. 2022 Mar 22;10(4):670; hereinafter “Altimira”) and in further view of Peng et al. (CN113151059A; published 23 July 2021, hereinafter “Peng”), Melgar et al. (WO2022120503A1; published 16 June 2022, hereinafter “Melgar”), and Schirring et al. (WO2018140542A1; published 02 August 2018, hereinafter “Schirring”), and Zhai et al. (CN103215210A; published 24 July 24, 2013, hereinafter “Zhai”).
Gorai, in view of Altimira, and in further view of Peng and Melgar teach the limitations of instant claims 1 and 14, as described above, from which instant claim 20 depends, however do not explicitly teach the specific limitations of instant claim 20.
Because claim 20 presently recites “The method according to claim 14,” although claim 14 is directed to a kit, the claim is interpreted for purposes of prior-art examination as requiring the claim 14 Bacillus kit/composition to include or be used with a composition comprising the strain and fermentation-derived compounds/metabolites produced using a protein hydrolysate as nitrogen source.
Schirring teaches the underlying kit containing a plant-growth-promoting Bacillus organism in claims 30 and 36. Melgar teaches fermentation of Bacillus siamensis RGM 2529 and use of the resulting microbial concentrate in agricultural formulations (¶[0098]-[0099]). Melgar additionally teaches the bacillibactin siderophore biosynthetic system of RGM 2529 (¶[0129], Figure 24, and Table 17).
Zhai teaches actual fermentation of Bacillus siamensis L13 in a medium containing 1.0-3.0 g/L peptone, an art-recognized protein hydrolysate nitrogen nutrient (¶[0040]-[0043], and claim 10). Zhai further uses the resulting Bacillus siamensis fermentation liquor in an agricultural microbial fertilizer (claim 6-8). Gorai independently confirms that Bacillus siamensis produces the claimed alternative siderophores (Abstract and § 3.2.5).
Thus, the combined prior art teaches packaging plant-growth-promoting Bacillus materials in a kit (Schirring), fermenting Bacillus siamensis and formulating the microbial concentrate (Melgar), fermenting Bacillus siamensis using a protein-hydrolysate nitrogen nutrient (Zhai), and production by Bacillus siamensis of the expressly claimed siderophore alternative (Gorai). Thus, it would have been prima facie obvious to one of ordinary skill in the art, prior to the instant effective filing date, to combine these known agricultural-product teachings to provide a kit containing or used with a Bacillus siamensis fermentation composition generated using a protein-hydrolysate nitrogen nutrient and containing the known siderophore products of the organism.
Each component would continue to perform the function for which the art already employed it: the Bacillus provides plant-growth-promoting activity, the protein hydrolysate supplies fermentation nutrition, the siderophore is a known microbial metabolite, and the kit provides conventional storage/delivery of the agricultural components. Such a combination is within KSR v. Teleflex, 550 U.S. 417-421 (2007) predictable-use rationale. The references are considered for their combined teachings rather than for literal bodily incorporation (see In re Keller, 642 F.2d at 425 (CCPA 1981)).
Response to Arguments
Applicant Arguments/Remarks of the reply, filed 23 July 2026, have been fully considered. The prior rejection of claim 1 under 35 U.S.C. § 102(a)(1) as anticipated by Liu is withdrawn. Claim 1 no longer recites “a variant thereof having at least 99.5% sequence identity.” Liu discloses a 16S rRNA sequence, but does not disclose the deposited strain CECT 30677. Therefore, Liu does not anticipate the current claim 1.
In addition, the previous 35 U.S.C. § 103 rejections based on Gorai/Altimira/Peng/Melgar have been withdrawn. The previous Gorai/Altimira rejection reasoned that isolation and characterization of additional Bacillus siamensis strains having known plant-growth-promoting characteristics would have constituted routine strain optimization. That rationale is no longer sufficient for current claim 1, and dependent claims 3, 4, 6-9, and 11-14 based on those combinations. The previously cited evidence does not establish why CECT 30677 itself would have been selected from a finite, identified set in the first instance.
It is noted that the applicant’s “absolute certainty” statement is not accepted as the governing legal standard. The applicant argues that a skilled artisan “could not have expected with absolute certainty” that a new strain would exhibit the same activities. Obviousness does not require absolute predictability or absolute certainty. The relevant inquiry is whether a person of ordinary skill would have had a reasonable expectation of success, not absolute certainty or guaranteed success (see In re O’Farrell, 853 F.2d at 903-04; KSR v. Teleflex, 550 U.S. at 421 (2007)). The Federal Circuit has repeatedly recognized that absolute predictability is not necessary, particularly where the art provides working examples and routine techniques for reaching the proposed result (see MPEP § 2143).
Here, Gorai, Altimira, Peng, Zhai, and Melgar each provide actual working Bacillus siamensis strains possessing agricultural or fermentation properties, rather than merely a theoretical suggestion that the species might be useful. Peng further supplies an actual environmental-isolation and phenotype-screening protocol. One of ordinary skill in the art therefore would have reasonably expected the established procedures to yield additional agriculturally useful Bacillus isolates and would have reasonably expected conventional fermentation, formulation, spore stabilization, CFU concentration, plant application, and kit techniques to function for those isolates.
The applicant is correct, however, that O’Farrell distinguishes a permissible obvious-to-try rationale from an impermissible search through numerous possibilities where the art gives no indication of which choice is likely to produce the specifically claimed result. That principle has been considered in determining whether the present art sufficiently directs the skilled artisan to CECT 30677 specifically, rather than merely to the broader class of useful Bacillus siamensis strains.
In addition, the applicant repeatedly argues that because claim 1 should be allowable, its dependent claims should be allowable “as a matter of law.” The argument is persuasive only to the extent a particular rejection of a dependent claim relies upon a reference combination that fails to satisfy a limitation incorporated from claim 1. It does not immunize dependent claims from separate statutory grounds arising from their additional limitations. A dependent claim incorporates every limitation of its parent claim and adds a further limitation, but the resulting combination remains independently subject to 35 U.S.C. § 101, § 102, § 103, and § 112 (see MPEP § 608.01(n)). Thus, withdrawal of the existing obviousness rationale against current claim 1 does not require allowance of claims having independent defects or of newly presented claim 19, which is separately unpatentable for the reasons above.
Further, the applicant’s field-trial evidence does not establish unexpected results commensurate with claim 1. The applicant’s evidence of nitrogen fixation, bacilycin production, and field trial results is not commensurate with the scope of claim 1 because claim 1 is not limited to any of those functional properties. Claim 1 is directed only to a deposited strain, without reciting any specific activity (the sporulated form, is obvious because sporulation is an inherent and well-known property of Bacillus species). Evidence of unexpected results must be commensurate with the claim scope (see MPEP § 716.02(d)). It cannot impart patentability to a claim that does not require those properties.
The applicant relies upon Examples 7-9 concerning peach, pepper, and lettuce as evidence of nonobvious properties of CECT 30677. Those experiments do not isolate the effect of the bare strain recited by claim 1. The specification expressly defines Product 1, used for the in vivo/open-field program, as a formulation containing PH-023/CECT 30677, its fermentation broth obtained using protein hydrolysate as nitrogen source, and protein hydrolysate as carrier. Examples 7-9 then test Product 1, including an 18-20% peach-yield increase and the reported pepper and lettuce responses.
Thus, those data do not by themselves establish that the results are attributable to the deposited bacterial strain independent of the fermentation broth and carrier. The specification’s field trials employ a formulated product containing CECT 30677 together with its fermentation broth and protein hydrolysate carrier, rather than isolated claim 1 strain alone. Thus, the evidence does not presently isolate whether the asserted improvement results from the strain itself, the fermentation metabolites, the protein hydrolysate, or their combination.
In conclusion, for the reasons above, claims 1, 3, 4, 6-9, 11-14, and 17-20 are rejected under 35 U.S.C. § 103 according to the respective combinations set forth above. Gorai teaches Bacillus siamensis CNE6, plant-growth-promoting properties, nitrogen fixation, IAA, siderophores, and antifungal/cell-free-supernatant activity. Altimira teaches Bacillus siamensis RGM 2529, antagonism, phosphate solubilization, IAA, genomic biostimulant determinants, and increased tomato growth. Peng teaches environmental isolation of Bacillus siamensis LS275 and routine functional screening for IAA/siderophore/PGP characteristics.
Melgar teaches Bacillus siamensis formulations, CFU concentrations, formulation forms, application to crops/seeds/stems, fermentation, and bacillibactin/siderophore production. Schirring teaches Bacillus endospores for agricultural-product stability and kits containing plant-growth-promoting Bacillus. Zhai teaches Bacillus siamensis fermentation in a peptone-containing medium and agricultural use of the resulting fermentation liquor.
Verga teaches protein hydrolysates produced by peptide-bond/protein hydrolysis, Bacillus microbial-inoculant/hydrolysate compositions, 10^5-10^10 CFU/mL, and application to plants, seed, foliage, and growing media. Ceccarelli teaches identification of 16,17-dihydro-16α,17-dihydroxy GA4 in metabolomic analysis associated with protein-hydrolysate-treated plants. Ishida teaches prior identification and synthesis of 16,17-modified GA derivatives, including 16,17-dihydro-16α,17-dihydroxy GA4 and its relationship to GA4 deactivation.
Conclusion
No claims are allowed.
The applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (87 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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/RL Scotland/
Examiner, Art Unit 1615
/Jeffrey T. Palenik/Primary Examiner, Art Unit 1615
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