DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Request for Continued Examination
2. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 01/23/26 has been entered.
Information Disclosure Statement
3. The information disclosure statement (IDS) submitted on 02/03/26 was filed and entered. The submission is in compliance with the provisions of 37 CFR 1.97 and has been considered by the Examiner.
Claim Status
4. The amendment, filed 01/23/25, has been entered. Claims 1, 4, 7, 10, 13-14, 16, 37-38, 41 and 50 are pending and under examination. Claims 2-3, 5-6, 8-9, 11-12, 15, 17-36, 39-40, and 42-49 are cancelled. Claim 50 is newly added. Claims 1, 4, 7, 10, and 37 are amended.
Withdrawal of Objections/Rejections
5. The following are withdrawn from the Office Action, filed 10/23/25:
The objection(s) to claim 37 found on page 3 at paragraphs 4 and 5, are each withdrawn in light of Applicant’s amendments thereto.
The rejection of claims 1, 4, 7, 10, 13-14, 16, 37-38, and 44 under 35 U.S.C. 112(b) as being indefinite found on page 4 at paragraph 7, is withdrawn in light of Applicant’s amendments thereto.
New Claim Warning
6. Applicant is advised that should claim 1 be found allowable, claim 37 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing (e.g. same positively recited steps), despite a slight difference in wording (e.g. see preambles), it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim; See MPEP § 706.03(k).
New Rejection: Claim Rejections - 35 USC § 101
7. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
8. Claims 1, 4, 7, 10, 13-14, 16, 37-38, 41 and 50 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e. law of nature) without significantly more.
As amended, claims recite “A method for preparing a composition comprising a plant-associated microorganism having enhanced colonization efficiency, comprising: (a) screening a population of plant-associated microorganisms to determine the presence of a nucleic acid encoding SEQ ID NO: 14 so as to identify a microorganism having enhanced colonization efficiency; and (b) preparing a composition comprising a plant-associated microorganism having enhanced colonization efficiently, wherein said plant-associated microorganism is present at a concentration of at least about 1 x 106 colony-forming units per milliliter” (see claim 1 and similarly for “yield-enhancing” in claim 37) which amounts to surveying naturally occurring microorganisms and looking for a naturally occurring genetic element (i.e. a particular genotype) linked to a naturally occurring functional characteristic (i.e. the corresponding phenotype). Therefore, Step 1 of the Subject Matter Eligibility analysis is yes because the claims are drawn to a statutory category (i.e. methods). However, the claims are directed to a law of nature, i.e., the natural correlation between a genotype and phenotype in a naturally occurring microorganism and accordingly, Step 2A, prong 1, is also yes.
The judicial exception is not integrated into a practical application because the only other positively recited step is preparing a composition … having at least 106 CFU/ml which amounts to merely concentrating the naturally occurring microorganisms comprising the naturally occurring genotypes and phenotypes (i.e. the natural correlation of the presence of SEQ ID NO: 14 and having enhanced colonization efficiency (see claim 1) and/or yield enhancement (see claim 37). It is noted that concentration of a judicial exception, even to non-natural levels, does not markedly change the judicial exception per se from what occurs in nature, just like collecting naturally occurring wildflowers (i.e. a judicial exception) and putting them in a vase, does not convert the otherwise unpatentable judicial exception (e.g. wildflowers) into eligible subject matter. Further, it is noted that there are no other required elements in the composition. Thus, the judicial exception (i.e. the natural correlation) is not integrated into a practical application. Nevertheless, it is also noted that merely adding the words “apply it” (or an equivalent) with the judicial exception, or mere instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea does not integrate a judicial exception into a practical application; see MPEP 2106.05(f). Therefore Step 2A, prong 2, is no.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because there are no other elements in claims 1 and 37 (i.e. there is nothing else in the composition) or in claims 4 or 38, that merely specify the naturally occurring microorganism. With regards to aggregating 10 or more strains, in claim 13, it is noted that the courts have determined that mixtures of otherwise naturally occurring bacteria, even those that did not naturally occur together, were found to be ineligible; see Funk Brothers Seed Co. v. Kalo Inoculant Co. 333 U.S 127 (1948)). With regards to claims 14 and 16, the limitations amount to another functional property (i.e. desiccation tolerant or tolerant to an agricultural chemical) but not to an additional element (i.e. no other element is required). With regards to the additional element(s) of a plant or plant part as found in instant claims 50, 7, 10, and 41 it is noted that plants and their parts are additional judicial exceptions (i.e. also products of nature). Thus, taken alone, the additional elements do not amount to significantly more than the above identified judicial exceptions (i.e. law of nature: natural correlation) and looking at the limitations as an ordered combination adds nothing that is not already present when looking at the elements taken individually. Therefore, Step 2B is no.
Therefore, based upon consideration of all of the relevant factors with respect to the claims as a whole, as currently written, the claims are rejected as ineligible subject matter under 35 U.S.C. 101.
Maintained Rejection: Claim Rejections - 35 USC § 112
8. 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.
9. Claims 1, 4, 7, 10, 13-14, 16, 37-38, 41 and 50 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, at the time the application was filed, had possession of the claimed invention.
This is a new matter rejection.
As amended on 09/11/25, claims 1 and 37 encompass methods for preparing a composition comprising screening a population of plant-associated microorganisms to determine the presence of a nucleic acid encoding SEQ ID NO: 14 so as to identify one or more microorganisms with enhanced colonization efficiency and preparing a composition comprising identified microorganisms having a concentration of a least about 1x10^6 colony forming units per milliliter. However, the specification does not describe methods for preparing compositions in general, or methods for preparing compositions comprising screening a population … to determine the presence of a nucleic acid encoding SEQ ID NO: 14 … and preparing a composition having microorganisms having SEQ ID NO: 14 at a concentration of a least about 1x106 colony forming units per milliliter, in particular; and therefore these newly added claim limitations (see claims filed 09/11/25) constitute new matter.
Although the PTO has the initial burden of presenting evidence or reasons why persons skilled in the art would not recognize in the disclosure a description of the invention defined by the claims, when filing an amendment an applicant should show support in the original disclosure for new or amended claims. See MPEP 714.02 and 2163.06 (“Applicant should therefore specifically point out the support for any amendments made to the disclosure.”). Accordingly, it remains the Office’s position that newly added limitations constitute new matter.
Applicant’s Arguments and Response to Arguments
10. All of Applicant’s arguments have been considered but were not deemed persuasive; accordingly, the rejection is maintained for reasons of record. For example:
With regards to the argument that the recited screening step is disclosed in the application as filed in at least paragraph [0053] and Example 1, paragraphs [0069] and [0070]. Determining the presence of SEQ ID NO: 14 is disclosed in at least Example 3, paragraphs [0076] and [0070] with SEQ ID NO: 14 disclosed in Table 2 on p. 29 and 30 and paragraph [0093]. Example 3, paragraph [0078], provides basis for a micro-organism having SEQ ID NO: 14 as being positively correlated with plant colonization and yield. The recited preparing step is disclosed in the application as filed in at least paragraph [0066] - [0067] and Example 1, paragraph [0069]; (see Remarks, page 6); the Office disagrees and notes that a careful evaluation of these paragraphs and examples does not provide adequate support. For example, paragraph 53 and Example 1 (which is paragraphs 69-70) do not discuss any methods for preparing a composition comprising first screening and second making a composition based on that screening. Example 1 is a Dose Response Evaluation for seven strains, none of which are described as having a nucleic acid encoding SEQ ID NO: 14, and wherein results demonstrated that inoculation of 105 CFU/ml could be used to identify Methylobacterium stains with an ability to colonize soybean shoots. The Office notes that methods for identifying strains with functional properties, in general, is not equivalent to methods of making compositions based on screening for a nucleic acid encoding for SEQ ID NO: 14, in particular. Further, with regards to Example 3, which includes paragraph 76 but not 70, and Table 2, this example is an Association Analysis wherein multiple genomes of Methylobacterium were compared; however, Table 2 is merely a list of 27 consensus sequences of amino acids (i.e. not nucleic acids) with variable levels of association and no paragraph within Example 3 describes any methods of making compositions based on a screening of a generic population of plant-associated microorganisms, for a particular nucleic acid encoding SEQ ID NO: 14, and then making a composition based on that screening, as the claims (following amendments on 09/11/25) now require. With regards paragraph [0066] - [0067], the phrase “…is provided in a composition” is not sufficient support for “A method of preparing a composition…” because “is provided” does not describe “preparation” per se (e.g. producing a formulation requires information regarding carriers, dilutants, excipients, surfactants, wetting agents, stabilizers, dissolved oxygen, pH, temperature, salinity, osmotic pressure, etc.) which is not found in the instant specification because the specification, as written, appears to be focused on methods for identifying one or more genetic elements (e.g. see Summary, staring on page 3) and not on the use of that information to prepare compositions. Thus, these arguments are not persuasive because they do not point to support in the specification as filed for the newly added limitations and/or the identified paragraphs and examples are not commensurate in scope with the claims, as written.
Therefore, all of Applicant’s arguments have been considered but were not deemed persuasive; accordingly, the rejection is maintained for reasons of record.
Maintained Rejection: Claim Rejections - 35 USC § 112
11. 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.
12. Claims 1, 4, 7, 10, 13-14, 16, 37-38, 41, and 50 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, at the time the application was filed, had possession of the claimed invention.
This is a written description rejection.
Instant claims are drawn to A method for preparing a composition comprising a plant-associated microorganism having enhanced colonization efficiency, comprising: (a) screening a population of plant-associated microorganisms to determine the presence of a nucleic acid encoding SEQ ID NO: 14 so as to identify a microorganism having enhanced colonization efficiency (see claim 1) and/or yield-enhancing (see claim 37); and (b) preparing a composition comprising a plant-associated microorganism having enhanced colonization efficiently, wherein said plant-associated microorganism is present at a concentration of at least about 1 x 106 colony-forming units per milliliter”.
Consequently, it is the Office' s position that (1) the independent claim(s) each constitute(s) a "broad generic claim” based on generically claimed compositions to be prepared; and/or generically claimed plant-associated microorganisms (e.g. all viruses, bacteria, protists, parasites, fungi, helminths, larval insects, etc.); and/or generically claimed plants and/or plant parts; and/or the nucleic acids back-translated from the generically claimed but not fully described SEQ ID NO: 14 (i.e. back-translated from a partial structure); and (2) the claimed genus has substantial variation because of the numerous options and combinations of options permitted.
First, based on the amendments (see claims filed 01/23/26; i.e., see step (b) “a plant-associated microorganism”), the microorganism found in the screening of step (a) is not actually required to be in the composition prepared in step (b) otherwise step (b) would read “said plant-associated microorganism”. Further, the claims, as written, encompass all methods of making all compositions comprising all other methods of identifying all plant-associated microorganisms having a nucleic acid that encodes a incompletely described SEQ ID NO: 14 and having enhanced colonization efficiency and/or yield enhancement and/or tolerance to desiccation and/or agricultural chemicals, on all parts, of all plants, under all conditions, and using all known techniques. However, the specification does not adequately describe methods for preparing a composition comprising (a) screening a population of plant-associated microorganisms to determine the presence of a nucleic acid encoding SEQ ID NO: 14 so as to identify a microorganism with enhanced colonization efficiency (or yield enhancement) and (b) preparing a composition comprising a microorganism having a concentration of a least about 1x106 colony forming units per milliliter because the specification does not describe methods for preparing compositions in general, or methods for preparing compositions comprising a microorganism having a nucleic acid encoding SEQ ID NO: 14 at a concentration of a least about 1x106 colony forming units per milliliter, in particular. Therefore, it remains the Office’s position that methods of making compositions in general, and those relying on a nucleic acid back-translated for encoding the incomplete structure of SEQ ID NO: 14 in particular, have not been described with sufficient particularity, such that one skilled in the art would recognize that Applicant had possession of the claimed invention, at the time of filing, because of the lack of a structure function correlation disclosed (i.e. the degeneracy of the genetic code does not provide for a nucleic acid back-translated from an incomplete amino acid sequence) and the lack of a representative number and variety of species (i.e. zero) to constitute possession of the full scope of the claimed genus.
The specification merely states “Compositions useful for treatment of plants or soil in which plants are grown are also provided” (see [0066]). However, the specification does not adequately describe any methods of preparing any compositions and “compositions … are also provided” (see above) is insufficient to provide written description support for all methods of making all compositions comprising all methods of identifying all plant-associated microorganisms having a nucleic acid that encodes for SEQ ID NO: 14 and enhanced colonization efficiency and/or yield enhancement and/or tolerance to desiccation and/or agricultural chemicals, on all parts, of all plants, under all conditions, and using all known techniques because merely stating the compositions “are provided” does not constitute a representative number or variety of species to constitute possession of the genus. For example, the specification does not adequately describe any components (e.g. buffers, excipients, diluents, binders, fillers, surfactants, carriers, etc.) or any physical or chemical properties (e.g. pH, polarity, color, density, viscosity, salinity, osmotic pressure, temperature, etc.) other than the presence of microorganisms having a nucleic acid back translated from an incomplete listing of amino acids within SEQ ID NO: 14. Therefore, even SEQ ID NO: 14 is not adequately described because at least 22 of the residues are Xaa (i.e. permitted to be any amino acid, rather than a specific amino acid) thereby encompassing billions and billions of unique sequences (i.e. since there are 22 places that may include any one of the 20 naturally occurring amino acids, the total number of unique sequences of amino acids is calculated as 20 (options) raised to 22 (places), which equals 4 x 10^28, which is the number 4 followed by 28 zeros); each of which requires back translation into an encoding nucleic acid; but it’s not one to one because of the degeneracy of the genetic code (i.e. a known nucleic acid sequence produces one unique protein sequence, but the reverse is not true as even a fully defined protein sequence could be encoded by multiple, distinct, nucleic acids). Therefore, the number and diversity of unique sequences encompassed by the limitation “…a nucleic acid encoding SEQ ID NO: 14” is almost unfathomable. Further, the specification does not describe compositions further comprising a plant part selected from the group consisting of a stem, leaf, root, tuber, or seed (i.e. see claims 7 and 41) other than the soybean (seeds, shoots and roots) and corn (roots and seedlings) in Examples 2, 4, and 5. The specification does not describe a nexus between these limited results and the breadth and diversity encompassed by all plants and the parts thereof. The specification does not adequately describe any microorganisms other than Methylobacterium and does not provide a nexus between the limited results provided and all other microorganisms.
Accordingly, the specification does not provide substantive evidence for possession of this large and variable genus of methods of preparing compositions, encompassing the use of a nucleic acid back-translated from of an incompletely described SEQ ID NO: 14 to identify microorganisms with increased colonization efficiency and/or yield enhancement and/or tolerance to desiccation and/or tolerance to agricultural chemicals because the specification amounts to, at best, merely a wish or plan for obtaining the invention claimed; see, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004); MPEP 2163. Thus, it remains the Office’s position that even one of skill in the art would not conclude that Applicant was in possession of the entire genus claimed.
With regards to the state of the art, methods for making compositions comprising screening for nucleic acids and selecting plant-associated microbes with increased colonization efficiently (and/or enhanced crop yields) was still under development and therefore, necessarily unpredictable, as evidenced by, for example, Cole et al. 2017 (Genome-wide identification of bacterial plant colonization genes; PLoS Biology 15(9): e2002860) teaches that diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood (see abstract) and that many of the identified genes that are correlated with colonization have no, or at best only vague, annotations (see page 7, page 11, and page 12). Cole teaches that some strains showed quantitatively weaker or no significant phenotypes in validation screens, suggesting that their fitness is higher when they are rare members of a diverse population (i.e. unpredictable). Therefore, Cole teaches a structure-function correlation for which genetic elements (e.g. nucleic acids) predictably result in colonization efficiency and/or enhanced yield is not art-recognized for plant-associated microorganisms in general, or for plant-associated bacteria, or pink-pigmented facultative methylotrophic bacteria, or Methylobacterium in particular. In addition, Madhaiyan et al. 2015 (Leaf-residing Methylobacterium species fix nitrogen and promote biomass and see production in Jatropha curcas; Biotechnology for Biofuels; 8:222; of record) teaches microbial density varies with both the part of the plant sampled and with the media employed (i.e. the means by which the micro-organism is identified and/or measured affects the results obtained; e.g. see page 2, bridging section). Madhaivan teaches the results for Jatropha shared a high similarity with those of soybean and potato plants but were significantly different to those of switchgrass and wild rice (e.g. page 4, left column and references cited therein). Therefore, Madhaiyan also teaches a structure-function correlation for which genetic elements predictably result in colonization efficiency and/or enhanced yield is not art-recognized for plant-associated microorganisms in general, or for plant-associated bacteria, or pink-pigmented facultative methylotrophic bacteria, or Methylobacterium in particular. Madhaiyan also supports the level of unpredictability in the ability of laboratory results to reliably predict results obtained in the field and that results for the roots of two plants may or may not extend to other plants and/or other plant parts. By extension, methods for preparing composition based on the identification of genetic elements is also not supported by the art.
Therefore, neither the specification nor the state of the art provides sufficient written description to support the genus encompassed by the claims. Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.).
Therefore, it remains the Office’s position that Applicant has not satisfied the requirements as set forth under 35 U.S.C. 112(a).
Applicant’s Arguments and Response to Arguments
10. Applicant did not specifically argue this rejection (i.e. only the first 112(a) for new matter). Thus, the rejection is maintained for reasons of record.
Conclusion
11. No claims are allowed.
12. Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY MAILLE LYONS whose telephone number is (571)272-2966. The examiner can normally be reached on Monday-Friday 8 am to 5 pm EST. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http: //www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Dan Kolker can be reached on (571)-272-3181. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
13. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MARY MAILLE LYONS/Examiner, Art Unit 1645
February 23, 2026