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 .
Claims Status
Claims 1-9, 11-14 and 16 are pending and under current examination in this application.
Amendments to the Specification, Amendments to the Claims, Remarks/Arguments and the XML sequence listing, filed 31 July 2024, are acknowledged. Claims 3-9, 11-14, and 16 are amended and supported by the originally-filed disclosure. Claims 10 and 15 are canceled and no new claims have been added.
Information Disclosure Statement
The Information Disclosure Statement (IDS), filed 01 January 2025, is acknowledged and has been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiencies and the required response to this Office Action are as follows:
While the biological material has been deposited by the applicant, there is no indication in the specification as to public availability. A statement, affidavit or declaration by Applicants, or by an attorney of record over his or her signature and registration number, or by someone in a position to corroborate the facts of the deposit, that the instant invention will be irrevocably and without restriction released to the public upon the issuance of a patent, is required to fulfill the deposit requirement. A letter from the depository stating that a deposit has been made and the condition of deposit is not an adequate substitute for a statement made by said person. (see MPEP 2410.01 and 37 C.F.R 1.808(b)). Thus, the "Sequence Listing" has not been entered into the application because the required statement of support is missing. See 37 CFR 1.825(a)(3) or 1.825(b)(4). The applicant is required to provide a proper statement of support.
Specification Objection
The disclosure is objected to because of the following informalities:
The present invention specifies the 16S rRNA sequence of said strain, deposited as Spanish Type Culture Collection deposit number CECT 30677, comprising the sequence SEQ ID NO: 1 as a strain of Bacillus siamensis. However, the specification Examples, Example 1. Characterization of Bacillus siamensis PH-023 (Strain of the Invention), 1.1. Isolation and Identification, paragraph 2, details a 16S rRNA gene sequencing approach that is not adequate for reliably distinguishing Bacillus velezensis from Bacillus siamensis. The EZTaxon uses the 16S rRNA gene as its primary identifier, which works well for distinguishing genera and most species, but fails for closely related species within the Bacillus subtilis complex, in which the applicant’s 1542 bp sequence showed a 99.5% identity to both species in the database, making definitive identification impossible (see evidentiary reference: Fan et al., Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an "Operational Group B. amyloliquefaciens" within the B. subtilis Species Complex. Front Microbiol. 2017 Jan 20;8:22).
Further, the primers used, 16F27, a standard universal primer positions 8-27 in E. coli, and 16R1488 a standard reverse primer gives a nearly full-length 16S, which is excellent for genus-level ID but useless for this species complex. The cloning into pGEM-T adds unnecessary complexity unless multiple 16S variants are expected in the sample. For pure cultures, direct PCR purification and sequencing is sufficient.
EZTaxon's algorithm may arbitrarily assign it to one species based on the highest percentage, but this assignment is not reliable at the species level for this complex. A BLAST search of the 16S sequence provides multiple matches to Bacillus velezensis, Bacillus amyloliquefaciens, and Bacillus subtilis, all with identities ~99.4-99.7%. The 1354 bp internal region still contains all the conserved and semi-conserved regions that show >99.5% identity between these species. Identity differences of 99.6% versus 99.5%, represents a difference of 1-2 nucleotides out of 1354, which is well within the sequencing error range (e.g., ~0.1% error rate for Sanger sequencing is 1-2 errors per 1354 bp) and intraspecies variation can be as high as 5-6 nucleotides. Thus, a 0.1-0.2% difference in reported identity is statistically and biologically meaningless for species discrimination in this complex.
At minimum, for a reliable species identification, the gyrB gene (DNA gyrase subunit B should be sequenced (e.g., gyrB primers: gyrB-F: 5'-CAGTCAGGAAATGCGTACGTCCTT-3' and gyrB-R: 5'-CAAGGTAATGCTCCAGGCATTGCT-3' with a product size of ~1.2 kb and more discriminatory power with a ~3-5% divergence between Bacillus velezensis and Bacillus siamensis in gyrB) and a mannitol phenotype screen conducted (Bacillus velezensis is mannitol (-) and Bacillus siamensis is mannitol (+)).
In summary, the 16S data is not adequate for specific differentiation between Bacillus velezensis and Bacillus siamensis and species identification based solely on this 16S sequence should not be reported as reliable identification. 16S rRNA gene sequencing placed the strain within the Bacillus subtilis species complex. Due to the high 16S similarity among members of this complex, species-level identification was however not further resolved to identify and assign the strain more specifically.
35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, requires the specification to be written in “full, clear, concise, and exact terms.” The applicant is advised to not use the 16S data for species identification in this case and instead, refer to the species currently attributed as Bacillus siamensis in the application as within the Bacillus subtilis species complex, as the appropriate strain resolution placement via the 16S rRNA gene sequence (1354 bp), unless more adequate, reliable, and scientifically defensible distinguishing evidence is provided to differentiate between specific strains within the complex. Appropriate correction is required.
Claim Rejections - 35 USC § 112(a)
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. § 112:
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 of carrying out his invention.
Claims 1-9, 11-14 and 16 rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, 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, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The specification fails to provide an adequate written description and fails to enable the full scope of the claimed invention. Regarding the written description, claim 1 encompass a genus of microbial variants defined by a 99.5% sequence identity in the 16S rRNA gene. The specification, while providing a detailed description of a single deposited strain (CECT 30677), provides no descriptive link between this sequence identity metric and the complex functional phenotypes required by the claims (e.g., plant disease protection, growth promotion). One of ordinary skill would not recognize from the disclosure that the inventor possessed all such variants. The 16S rRNA gene is not unequivocally predictive of these multifactorial traits.
The standard established by Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336 (Fed. Cir. 2010), requires the specification to show the inventor actually possessed the full scope of the claimed invention at the time of filing. Claim 1 claims a genus (i.e., "a variant thereof having at least 99.5% sequence identity...") however in the specification’s disclosure, the applicant possesses and describes in detail only one single species, deposited strain CECT 30677. It asserts that all 99.5% identical variants will be functionally equivalent (¶[0023]), but does not provide evidence to support this assertion. The specification provides no correlation or principle linking the claimed characteristic of 99.5% 16S rRNA identity to the functional characteristics of plant growth promotion and biocontrol. Wherein, in the field of microbiology, 16S rRNA is a taxonomic marker, not a predictor of complex, multi-gene phenotypes. The inventor's possession of one strain does not demonstrate possession of this vast, functionally-defined genus. Dependent claims 2-9, 11-14 and 16 are included in this rejection because none of the claims entirely cure the defect in claim 1 noted above.
In addition, claim 4 is rejected under § 112(a) for lack of written description because the metabolite profiles “resulting from fermentation of a protein hydrolysate” are highly variable depending on fermentation conditions, protein hydrolysate source, and strain, yet “metabolites resulting from fermentation of a protein hydrolysate” are not adequately described as fermentations vary widely with strain and media, and the specification lacks guidance on how to identify or achieve the full claimed profile of metabolites across the full scope. Dependent claims 5-9 are included in this rejection because none of the claims entirely cure the defect in claim 4 noted above.
Claim 2 is rejected under 35 U.S.C. § 112(a) or 35 U.S.C. § 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim 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.
While enabled for a strain of Bacillus siamensis deposited in the Spanish Type Culture Collection with deposit number CECT 30677 comprising the sequence SEQ ID NO: 1, the scope of the claim 2 is not enabled for variants having at least 99.5% sequence identity with the 16S rRNA sequence of a strain of Bacillus siamensis deposited in the Spanish Type Culture Collection with deposit number CECT 30677. To be enabling, the specification of the patent application must teach those skilled in the art how to make and use the full scope of the claimed invention without undue experimentation. In re Wright, 999 F.2d 1557, 1561 (Fed. Cir. 1993), explaining what is meant by “undue experimentation,” the Federal Circuit has stated, “The test is not merely quantitative, since a considerable amount of experimentation is permissible, if it is merely routine, or if the specification in question provides a reasonable amount of guidance with respect to the direction in which experimentation should proceed to enable the determination of how to practice a desired embodiment of the claimed invention.” (PPG v. Guardian, 75 F.3d 1558, 1564 (Fed. Cir. 1996)).
The factors that may be considered in determining whether a disclosure would require undue experimentation are set forth by In re Wands, 8 USPQ2d 1400 (CAFC 1988) at 1404 wherein, citing Ex parte Forman, 230 USPQ 546 (BdApls 1986) at 547 the court recited eight factors: 1) the quantity of experimentation necessary, 2) the amount of direction or guidance provided, 3) the presence or absence of working examples, 4) the nature of the invention, 5) the state of the prior art, 6) the relative skill of those in the art, 7) the predictability of the art, and 8) the breadth of the claims.
These factors are always applied against the background understanding that scope of enablement varies inversely with the degree of unpredictability involved (In re Fisher, 57 CCPA 1099, 1108, 427 F.2d 833, 839, 166 USPQ 18, 24 (1970)). Keeping that in mind, the Wands factors are relevant to the instant fact situation for the following reasons:
1) Experimentation quantity needed:
Prohibitive. To identify which of the multitude of 99.5% identical strains actually "retain or improve" the specified activities of claim 2, a skilled artisan would have to isolate or create each candidate variant and test it in the full battery of assays from the examples (e.g., tomato growth trials, antifungal plate assays). This is undue experimentation because the nature of the art is considered unpredictable and the immense quantity of possible variants, wherein a 0.5% genetic difference in a typical bacterial genome (millions of base pairs) can result in thousands of distinct strains. Testing a "multitude" of these individually is a monumental task, wherein small genetic variations (even <0.5%) can lead to significant functional changes. There is often no predictable way to know which mutations will enhance or destroy properties like antifungal activity or plant growth promotion without physical testing, given the patent specification does not provide clear direction or working examples on which specific genetic markers correlate with the desired traits, the researcher is left with a blind trial-and-error process and screening for complex biological activities, such as broad antibacterial activity or plant disease protection, requires extensive, time-consuming bioassays rather than simple, routine laboratory tests.
2) Guidance/direction provided:
The specification provides no guidance (e.g., a specific genetic marker, a reliable screening assay) to identify functional variants without performing the full, lengthy testing protocol on each candidate.
3) Existence working examples:
While strong for the deposited strain, the examples only highlight the gap for the claimed genus. They show what must be proven for each variant, not how to find them without exhaustive screening.
4) Invention nature:
Functional characteristics of plant growth promotion and biocontrol requires specific biological interactions (e.g., pathogen inhibition, growth response modulation, etc.). Specification does not sufficiently describe how the invention achieves plant growth promotion and biocontrol across all claimed scenarios.
5) Prior art state:
The field of general biocontrol and plant growth promotion is complex, and prior art does not suggest a generalized solution. Without detailed guidance, undue experimentation would be required to achieve the claimed effect.
6) Relative skill those in the art:
The enablement rejection is further supported by an assessment of the ordinary skill level in the relevant art, which underscores why undue experimentation would be required to practice the claimed invention.
A person of ordinary skill in the art in the field of microbiology or agricultural sciences would typically possess a Ph.D. or M.D. in the relevant or a closely related discipline with at least 2 years of experience in agricultural formulations or master’s degree with at least 5 years of relevant applied research experience, and familiarity with standard experimental models for evaluating biocontrol and plant growth promotion. Given the skill level, specification deficiencies are critical because of the unpredictability of biological systems, wherein even highly skilled researchers cannot extrapolate with absolutely certainty functionality from sequence homology without significant experimental data (e.g., empirical determination). While a person of ordinary skill in the art could design experiments to test the claim’s breadth, it demands open-ended trial-and-error.
Broad functional claims require "full scope" enablement—general principles alone are insufficient for unpredictable arts (Amgen Inc. v. Sanofi, 598 U.S. 594 (2023)), wherein even skilled artisans cannot compensate for missing critical details (e.g., dosing, mechanism; In re Wands (1988)). The specification’s gaps would require undue experimentation (e.g., iterative testing) to ensure achievement the claimed biocontrol and plant growth promoting properties.
7) Art predictability level:
Biological systems are highly unpredictable (e.g., Amgen Inc. v. Sanofi, 598 U.S. 594 (2023)). Microbial genetics and phenotype are not predictable from a single conserved gene like 16S rRNA. There is no known principle that 99.5% 16S identity guarantees four distinct, complex agricultural functions. The specification provides no data to support that the claimed method is guaranteed to reliably achieve the complex agricultural functions.
Given the lack of certainty in the predictability in the art between 16S rRNA sequence and the claimed agricultural functionalities, and the absence of any disclosed principle or method for identifying which variants meeting the sequence threshold will also meet the functional threshold, a person of ordinary skill would be required to engage in undue experimentation. They would need to isolate or create each potential variant and empirically test it across the full range of assays disclosed (e.g., Examples 1 & 3) to determine if it falls within the claim scope. The specification provides no guidance to avoid this extensive, iterative screening process.
8) Claim breadth:
The breadth of claim 1 is extremely broad and encompasses an unknown, potentially massive number of bacterial variants across all Bacillus siamensis and beyond. In addition, claim 4, claiming compositions comprising “the compounds and/or metabolites resulting from the fermentation of a protein hydrolysate by the strain, wherein the protein hydrolysate is used as nitrogen source” are also broader than the actual working examples and the specification lacks enabling disclosure across the scope of all possible protein hydrolysates, conditions of fermentation (pH, temperature, media components, inoculum, fermentation time, etc.), all claimed metabolites, and the production or isolation of such metabolites in functional form. The specification offers limited examples of metabolites identified under specific conditions, and does not provide sufficient guidance such that a person of ordinary skill in the art would be able to make and use the full breadth of claimed metabolite compositions without undue experimentation. Furthermore, while not the basis for a formal rejection at this stage, the examiner notes that the extremely broad ranges and lists in the specification (e.g., the list of hundreds of plants in ¶[0076]-[0083], the list of potential additives and other microorganisms in ¶[0048]-[0063]) may raise issues of enablement and written description under 35 U.S.C. 112(a) for claims that are broadly directed to these categories. The applicant should be prepared to demonstrate that the specification reasonably enables the full scope of these claimed embodiments or to consider limiting the claims to exemplified embodiments.
Accordingly, the claim 1 does not comply with the enablement requirement of 35 U.S.C. § 112, first paragraph, since to practice the claimed invention a person of ordinary skill in the art would have to engage in undue experimentation, with no assurance of success. Consequently, the specification also fails to describe or enable the full scope of compositions derived from the fermentation of such variants. While the specification enables the production of the specific compounds of claim 5 from the deposited strain CECT 30677, it does not do so for the universe of claim 1 variants. One of ordinary skill could not make or use the claimed compositions across their full scope without undue experimentation to first identify which microbial strains qualify as claim 1 variants. Dependent claims 2-9, 11-14 and 16 are included in this rejection because none of the claims entirely cure the defect in claim 1 noted above.
To overcome this rejection, the applicant may limit claims to significantly narrow the claims to enabled embodiments tied to a measurable effect with working examples in relevant models (e.g., claim only the deposited strain CECT 30677 or if some variant scope is to be retained, it must be explicitly and narrowly limited by a specific functional test disclosed in the examples). The core issue is that the specification is excellent for a single strain and its specific uses, but the claims attempt to claim a broad biological principle that the specification does not support. The law requires the claims to match what the inventor has actually invented and disclosed. A response must address each Wands factor or narrow the claim to supported embodiments.
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 3-9 and 16 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.
In claim 5 it is unclear, as to which compound precisely is meant with "the inactivated form of gibberellin A”. The specification, filed 31 July 2024, lists the inactivated form of gibberellin A on page 9, line 3, separately from 16,17-dihydro-16a,17-dihydroxy gibberellin A, indicating the inactivated form of gibberellin A4 and 16,17-dihydro-16a,17-dihydroxy gibberellin A4 are distinct compounds, as does claim 5, however the specification at page 41, lines 4-6, indicates the inactivated form of gibberellin A4 is 16,17-dihydro-16a,17-dihydroxy gibberellin A4. It is not clear, whether this refers to 16a,17-dihydro-16a,17-dihydroxy gibberellin A4 or a different compound as inactivation of gibberelllins may occur at least via three different pathways.
In addition, claim 8 is indefinite. Claim 8 depends on claim 4 and defines the concentration of the microbial strain. However, according to claim 4, the microbial strain is not necessarily present. Appropriate correction is required.
In addition to these rejections, claims 3-9 are rejected under 35 U.S.C. § 112(b) for lack of antecedent basis:
Claims 3-6, and 8 refer to "the strain," but claim 1 recites "a strain... or a variant thereof". Claim 1 introduces two possibilities: "A strain of Bacillus siamensis... or a variant thereof...", however the use of "the strain" in the subsequent claims implies a single, previously identified strain. Thus, rendering the reference to "the strain" ambiguous and lacking clear antecedent basis. Dependent claims 7 and 9 are included in this rejection because none of the claims entirely cure the defect in claim 4 noted above.
Claim 4 recites, “the fermentation of a protein hydrolysate by the strain...", wherein the fermentation of a protein hydrolysate is introduced here for the first time. Dependent claims 5-9 are included in this rejection because none of the claims entirely cure the defect in claim 4 noted above.
In addition, claim 5 introduces the term "a hydrolysed protein" it is unclear if the "a hydrolysed protein" has an antecedent relationship to "a protein hydrolysate" in claim 4 or is intended to refer to a separate newly introduced hydrolysed protein, as currently written. This creates confusion.
To overcome these rejections, correcting the antecedent basis problems, especially the ambiguous "the strain" is necessary (e.g., replace "the strain" with "said strain or variant thereof" to encompass both possibilities from claim 1). For internal consistency, claim 4 should be amended (e.g., "...fermentation of a protein hydrolysate by said strain, wherein said protein hydrolysate is used as nitrogen source.") and clai~m 5 should be amended (e.g., "...fermentation of said protein hydrolysate as nitrogen source by said strain...").
Claim 16 is also indefinite for failing to clearly define a tangible, structural article of manufacture. A plant, in its natural state, is a product of nature. While the claim includes the limitation of being "inoculated or coated", this is a transitory, non-structural modification that does not impart a distinct and different characteristic to the plant itself. The claim appears to be an attempt to claim a process of application as a product (see also the following 35 USC § 101 rejection).
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. § 102 and 103 (or as subject to pre-AIA 35 U.S.C. § 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. § 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-3 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by Liu et al. (Bacillus velezensis strain NJ-4 16S ribosomal RNA gene, partial sequence; GenBank Accession No. OP753706.1; nucleotide sequence. GenBank. National Center for Biotechnology Information; published 02 Nov 2022, https://www.ncbi.nlm.nih.gov/nuccore/OP753706.1; accessed 10 February 2026, hereinafter referred to as “Liu”).
The publicly available GenBank entry OP753706.1 by Liu, accessible before the priority date of the instant application, discloses a Bacillus velezensis strain having a 16S rRNA sequence with at least 99.5% identity to SEQ ID NO: 1, anticipating the claimed Bacillus siamensis strain and its variants, wherein the activity of instant claim 2 and sporulation of instant claim 3 are inherent to the strain.
The GenBank entry OP753706.1 discloses a Bacillus velezensis strain whose 16S rRNA sequence shares 99.54% sequence identity with SEQ ID NO: 1 provided in the instant application (National Library of Medicine (US), National Center for Biotechnology Information, BLAST (version 2.17.0), accessed on 10 February from URL (https://blast.ncbi.nlm.nih.gov/Blast.cgi) using the BLASTN program and core_nt database; accessed 10 February 2026). A sequence identity of 99.54% meets or exceeds the “at least 99.5%” identity limitation recited in instant claim 1 for variants of the deposited strain CECT 30677.
The claim defines the invention based on 16S rRNA sequence identity, not on species designation. Whether the prior art strain is labeled Bacillus velezensis or Bacillus siamensis is irrelevant, because the claim covers any variant meeting the 99.5% identity threshold, regardless of taxonomic name. Further, many other Bacillus subtilis species complex species, including Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus velezensis and Bacillus siamensis, share over 99.5% 16S rRNA sequence homology and could be similarly used to anticipate the claims as well. The claim language “or a variant thereof having at least 99.5% of sequence identity” is broad enough to include any bacterial strain, regardless of species designation, that meets the identity threshold (see In re Pearson, 494 F.2d 1399 (C.C.P.A. 1974)).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. § 102 and 103 (or as subject to pre-AIA 35 U.S.C. § 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. § 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. § 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. § 102(b)(2)(C) for any potential 35 U.S.C. § 102(a)(2) prior art against the later invention.
Claims 1-3 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 referred to as “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 referred to as “Altimira”). .
Gorai discloses the strain Bacillus siamensis CNE6 with16S identification, which exhibited plant growth promoting properties, such as phosphate solubilisation, indole acetic acid production, nitrogen fixation, production of hydroxamate type siderophores and antagonistic activity against plant pathogenic fungi. The latter activity is mediated by means of lipopeptide antibiotics such as surfactins, fengycin and iturin (Abstract; ¶ 3.2.1-3.2.5, 3.3.1-3.3.2, 3.4; Tables 1 and 2; Figures 2, 5 and 8).
Altimira discloses genomic and 16S rRNA sequence identity analysis as basis for taxonomic definition of the Bacillus siamensis variant strain RGM 2529. The strain inhibited the growth of phytopathogenic fungi by directed contact via diffusible and volatile compounds (¶3.4 and 4; Figure 3). As for plant growth promoting properties, the strain was able to solubilise phosphate and produces indole acetic acid (¶3.5), wherein strain treated tomato seedlings showed improved growth parameters (¶3.6; Figure 4a, 4c, and 5). The genome revealed the presence of gene clusters which encode factors involved in pathogen control (antimicrobial non-ribosomal peptides, ribosomal peptides and bacteriocins), plant growth stimulation (IAA; cytokines, acetoin, 2,3-butanediol, polyamines, siderophores, P solubilisation), and plant tolerance for biotic and abiotic stress (GABA degradation) (¶5).
Sporulation is a fundamental and inherent trait of Bacillus species (e.g., via conserved Spo0A genetic pathways) and is well known in the art.
Gorai and Altimira establish that Bacillus siamensis strains with plant growth promoting properties are known in the art. Isolation, modification, or selection of variants with equal expected properties or improved traits relative to a known strain is considered routine experimental optimization of a microbial strain and does not require inventive skill. It would have been obvious to a person of ordinary skill in the art at the time of invention to isolate and identify additional Bacillus siamensis strains having plant growth promoting and biocontrol properties, and characterize it using standard microbiological and 16S rRNA identity sequencing methods once the species was known from Gorai and Altimira.
The instant claimed limitation, “a variant thereof having at least 99.5% of sequence identity with the 16S rRNA sequence of said strain”, does not represent a patentable distinction, as one of ordinary skill would have a reasonable expectation that such closely related microbiological variants would retain similar bioactivity and biocontrol and growth-promoting functions. While, 16s rRNA sequence identity cannot be expected with absolute certainty to predict properties and functional activity, it would be obvious to a skilled artisan to try to test any new strain of Bacillus siamensis for the properties ascribed to the known strains, with a reasonable expectation of success, although not guaranteed.
Even if the strain CECT 30677 is novel, the invention must not be an obvious variation of what is already known. The instant claimed CECT 30677 strain, as disclosed, is merely another strain in a well-known functional species of Bacillus siamensis strains and isolating a new naturally occurring strain with expected properties is obvious, absent unexpected results (see In re Kubin, 561 F.3d 1351 (Fed. Cir. 2009)). Routine taxonomic characterization would have been readily achieved by BLAST or similar alignment tools once the sequence of the type strain is known. Accordingly, instant claims 1-3 would have been prima facie obvious to one of ordinary skill in the art prior to the instant effective filing date over Gorai in view of Altimira using routine methods of microbial taxonomy.
Claims 1, 4 and 5 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 referred to as “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 referred to as “Altimira”) and in further view of Peng et al. (CN-113151059-A; published 23 July 2021, hereinafter referred to as “Peng”).
Gorai and Altimira teach the limitations of instant claim 1, as described above, from which instant claims 4 and 5 depend, however does not explicitly teach the specific limitations of instant claims 4 and 5.
Gorai teaches, “Prominent growths of the CNE6 [Bacillus siamensis strain] on nitrogen free Burk’s medium suggested its probable N2 fixing property. Positive result for ammonia production also supported nitrogen fixing ability of the isolate.” (¶3.2.3) and the production of hydroxamate type siderophores as discussed above.
Gorai in view of Altimira does not explicitly disclose, “compounds and/or metabolites resulting from the fermentation of a protein hydrolysate by the strain”. However, the patentability of a product does not depend on its method of production, even if a product is created using a new process. If the resulting product is identical to a prior art product, it is unpatentable (i.e., a product defined by how it is made is still the same product; see In re Thorpe, 777 F.2d 695, 227 USPQ 964 (Fed. Cir. 1985) and M.P.E.P. § 2113). Thus, the prior art provides evidence that the compounds and/or metabolites exist per se, wherein the source is irrelevant (i.e., “resulting from fermentation”), and accordingly, the compounds and/or metabolites resulting from the fermentation of a protein hydrolysate by the Bacillus siamensis strain or a ≥99.5% sequence homology variant thereof of are obvious.
In addition, the use of protein hydrolysate as a nitrogen source in microbial fermentation in agricultural inoculants is common practice and would have been obvious to try for optimizing microbial metabolite profiles. Furthermore, Peng discloses the strain Bacillus siamensis LS275 (CGMCC 19505) that strongly inhibits root rot caused by Fusarium solani (claims 1-4). The strain is applied to the plant as a bacterial suspension, preferably as a diluted fermentation broth by irrigation (claims 5 and 6). A use in promoting plant growth is suggested (claim 7).
Peng demonstrates that the strain produces indole acetic acid, siderophores and can fix nitrogen (Example 2). Thus, indicating it was known in the art at the time of the invention to use a Bacillus siamensis strain fermentation product, containing resulting compounds and/or metabolites as a nitrogen source that produces siderophores. Therefore, the instant claimed compositions using protein hydrolysates from the microbal fermentation of a Bacillus siamensis strain as a nitrogen source would have been prima facie obvious to one of ordinary skill in the art prior to the instant effective filing date as an obvious combination of known elements yielding predictable results.
Claims 1, 4, 6-9, 11-14 and 16 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 referred to as “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 referred to as “Altimira”) and in further view of Peng et al. (CN-113151059-A; published 23 July 2021, hereinafter referred to as “Peng”) and Melgar et al. (WO-2022120503-A1; published 16 June 2022, hereinafter referred to as “Melgar”).
Gorai and Altimira teach the limitations of instant claims 1 and 4, as described above, from which instant claims 6-9, 11-14 and 16 depend, however does not explicitly teach the specific limitations of instant claims 6-9, 11-14 and 16.
Melgar discloses the strain Bacillus siamensis RGM 2529, producing antimicrobial compounds with an antimicrobial effect against phytopathogenic fungi (Tables 4-7). Different formulations comprising carriers and bacterial cells are described, including gelatinized slow-release tablets, wettable powders or effervescent tablets (Example 2; Table 8). Melgar teaches the application of the RGM 2529 strain to tomato seeds and grape berries for biostimulation and bioprotection of plants (Example 3; Tables 9-11) and a method of achieving biostimulation and bioprotection via application of a Bacillus siamensis RGM 2529 strain formulation by spraying or direct immersion of the seed of the target crop (claim 18), seed impregnation (claim 19) or application at the base of the plant stem (claim 20). Table 8 provides example embodiments of RGM 2529 utilizing a range from 3.4x106-3x107 CFU/mL, encompassed within the instant claim 8 range of 105-1012 CFU/mL. Compounds liberated by Bacillus siamensis RGM 2529 include bacteriocins, lipopeptides (e.g., fengycin, bacillomycin D, surfactin), siderophores (e.g., bacillibactin), polyenes (e.g., bacillaene) and aurantinin (Table 17).
It would have been prima facie obvious to one of ordinary skill in the art prior to the instant effective filing date to combine the known biologically active metabolites of Bacillus siamensis with standard carriers, surfactants, and formulations, as taught by Melgar, to prepare compositions suitable for agricultural application. The use of protein hydrolysate as a nitrogen source in microbial fermentation and as a carrier/ingredient in agricultural inoculants is common practice and would have been obvious to try for optimizing microbial metabolite profiles. The claimed methods are obvious choices for using compositions of known elements yielding known predictable effects, and there is no evidence of unexpected results beyond what is taught in the prior art.
In addition, Melgar teaches a method to promote growth and/or increase crop yield and/or protect against diseases and pests via the use of the Bacillus siamensis RGM 2529 strain may be in a formulation administered together with fertilizers (claim 22). Providing multi-component agricultural 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 (e.g., 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. Separating known components, which are intended to be used together, into a kit is a matter of routine commercial and packaging choice, not inventive ingenuity. Since the prior art Melgar teaches that the combination of the Bacillus siamensis RGM 2529 strain and a fertilizer may be applied together, the motivation to combine these same two agents in a single kit for the same foliar application purpose is clear and compelling. There is no inventive step in merely taking a known combination and packaging its components separately to achieve the exact same result that was already known in the art. Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the instant effective filing date to modify the teaching of Melgar to provide a Bacillus siamensis strain and a fertilizer agent in a kit-of-parts format, as this represents a routine and conventional approach to the packaging and use of such agrochemical compositions.
Conclusion
No claims are allowed.
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/RL Scotland/
Examiner, Art Unit 1615
/Robert A Wax/Supervisory Patent Examiner, Art Unit 1615