DETAILED ACTION
Applicant’s response, filed 23 Jan. 2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
The restriction requirement in the Office action mailed 03 June 2025 has been withdrawn for the reasons discussed in the Office action mailed 05 Nov. 2025.
Status of Claims
Claims 10, 12-15, and 17-18 are cancelled.
Claims 1-9, 11, and 16 are pending.
Claims 1-9, 11, and 16 are rejected.
Claims 1-2, 6, and 16 are objected to.
Priority
Applicant’s claim for the benefit of a prior-filed application, PCT/IN2020/050346 filed 11 April 2020, under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority to IN201921014894 filed 12 April 2019 under 35 U.S.C. 119 (a)-(d). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Accordingly, the effective filing date of the claimed invention is 12 April 2019.
Claim Objections
The objection to claims 1-3, 5, 7, 9, 14, and 16-18 in the Office action mailed 05 Nov. 2025 has been withdrawn in view of claim amendments and cancellations received 23 Jan. 2026.
The following objection is newly recited and necessitated by claim amendment.
Claims 1-2, 6, and 16 are objected to because of the following informalities.
Claim 1 recites “…and information pertaining to the microbe(s) is included…” in line 5 of the first limitation on pg. 3, which should be amended to recite “…and information pertaining to the microbe(s) found in abundance…” to increase clarity and use consistent language.
Claim 1 recites “…wherein microbe(s) found…., wherein the GPE map comprises…” in the first limitation at the top of pg. 3, which is grammatically incorrect and should include an “and”, rather than a comma between the two wherein clauses. Therefore, claim 1 should recite “…wherein microbe(s) found…and wherein the GPE map comprises…”.
Claim 1 recites “…information about active site of each enzyme…” in line 8 of pg. 3, which is grammatically incorrect and should recite “about an active site”.
Claim 1 recites “identifying a list of partial pollutant degraders…, and wherein the identified list comprises multiple partial degraders”, which should be amended to recite “…and wherein the identified list of partial pollutant degraders comprises…” to increase clarity and use consistent language.
Claim 1 recites “designing a second microbial consortia…identified in the collected sample to intermediate product or products…”, which is grammatically incorrect and should recite “…to an intermediate product or products…”.
Claim 2 recites “..creating the…(GPM)..and the plurality of sub-pathways on each genome of the microbial genomes…; creating the genome pathway enzyme (GPE) map…on each genome of the microbial genomes”, which should be amended to recite “the microbial genomes in the DEBG” in each instance to use consistent language and increase clarity.
Claim 6 recites “wherein the second predefined criterion is for each enzyme… in the microbial genome is: a value of 1 is assigned…, and a value of 0 is assigned…”, which is grammatically incorrect and should recite “…is for each enzyme…in the microbial genome and is: assigned a value of 1 assigned a value of 0
Claim 16 recites “…the map of microbes…capable of degrading the pollutant…”, which should be amended to recite “the map of microbes…capable of degrading each pollutant” to use consistent language with claim 1 and increase clarity.
Appropriate correction is required.
Response to Arguments
Applicant’s arguments filed 23 Jan. 2026 regarding the claim objections have been fully considered but they do not pertain to the newly recited objections set forth above.
Claim Interpretation - 35 USC § 112(f)
The interpretation under 35 U.S.C. 112(f) in the Office action mailed 05 Nov. 2025 has been withdrawn in view of the cancellation of claim 17 received 23 Jan. 2026.
Claim interpretation
Claim 1 recites “…degradation of a pollutant either to compounds that are safe for the environment”. In light of Applicant’s specification, compounds that are safe for the environment are interpreted to be compounds other than pollutants.
Claim Rejections - 35 USC § 112(a)
The rejection of claims 17-18 under 35 U.S.C. 112(a) in the Office action mailed 05 Nov. 2025 has been withdrawn in view of the cancellation of these claims received 23 Jan. 2026.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 12-15 and 17-18 under 35 U.S.C. 112(b) in the Office action mailed 05 Nov. 2025 has been withdrawn in view of the cancellation of these claims received 23 Jan. 2026.
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.
Claims 1-9, 11, and 16 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor. Any newly recited portion is necessitated by claim amendment.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “wherein the complete degradation pathway refers…” and “wherein the partial degradation pathway in the given microbe…”. Claim 1 previously recites “information pertaining to complete degradation pathways and partial degradation pathways” and “a list of microbes…possessing a complete or partial pollutant degradation pathway”. Therefore, it is unclear if the wherein clause pertaining to “the complete degradation pathway” and “the partial degradation pathway” is further limiting a complete or partial degradation pathway of the information stored in the knowledgebase or the complete or partial degradation pathway of the list of microbes. Clarification is requested. If Applicant intended to refer to the complete or partial degradation pathway in the list of microbes limitation, Applicant should reinsert the word “particular” and refer to “a list of microbes…possessing a particular complete or partial pollutant degradation pathway” and subsequently “wherein the particular complete degradation pathway…”.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “a database of abundant environmental microbes (DEGB), wherein microbe(s) found in abundance in a plurality of environmental samples…”. The terms “abundant” and “in abundance” are relative terms which render the claim indefinite. The terms “abundant” and “in abundance” are not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Therefore, it is unclear what environmental microbes are intended to included or excluded from the database. Clarification is requested.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “wherein the knowledgebase comprises…a database of abundant environmental niches (DEBG), wherein microbes found in abundance in a plurality of environment samples and residing in different environmental niches are curated and information pertaining to the microbe(s) is included in the…(DEGB)”. MPEP 2111.04 I. states, examples of claim language, although not exhaustive, that may raise a question as to the limiting effect of the language in a claim are "wherein" clauses, and further explains a "wherein" clause limited a process claim where the clause gave "meaning and purpose to the manipulative steps"). In In re Giannelli, 739 F.3d 1375, 1378, 109 USPQ2d 1333, 1336 (Fed. Cir. 2014). However, the court noted that a "‘whereby clause in a method claim is not given weight when it simply expresses the intended result of a process step positively recited.’" Id. (quoting Minton v. Nat’l Ass’n of Securities Dealers, Inc., 336 F.3d 1373, 1381, 67 USPQ2d 1614, 1620 (Fed. Cir. 2003)). In the instant case, the limiting effect of the wherein clause “wherein microbes found in abundance….are curated” is unclear because it is not clear if the wherein clause is expressing an intended result or purpose of the DEBG to store/include curated information, or if Applicant intends to further limit the step of creating the knowledgebase to comprise curating microbe(s) found in abundance and including information pertaining to the microbe(s) in the database. Clarification is requested. If Applicant intends to further limit the step of creating the knowledgebase, the claim can be amended to recite “…wherein creating the knowledge base comprises curating….and including…in the database of abundant environment microbes (DEBG)”.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “…a genome pathway master (GPM) map”. The metes and bounds of what maps and/or data structures that would fall within the metes and bound of a GPM map are unclear because a genome pathway master map is not a term of art, and it is not clear what embodiments of a genome pathway map would fall within the metes and bounds of a genome pathway master map. Thus, claims 1 and 17-18 are indefinite. It is noted that claim 2 (and thus claims 6-8) do serve to clarify the metes and bounds of the GPM, and thus is not indefinite for this reason. However, dependent claims 3-5, 9, 11, and 16 are indefinite for the same reasons as claim 1. For purpose of examination, the GPM will be interpreted as explained in claim 2.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “re-administering a new concoction…by adding a set of microbes which…combinatorially degrade the one or more pollutants identified in the collected sample”. The previous step of claim 1 was amended to recite “checking efficacy….of the one or more pollutants identified in the collected sample from the environmental site, wherein the checking efficacy is done by identifying a remaining set of pollutants from the collected sample”, now requiring the checking efficacy is done on the collected sample rather than an additional collected sample of the environmental site (after administration) as previously interpreted under 112(b). As a result, it is now unclear in what way the efficacy of the administered concoction is being checked by identifying remaining pollutants in the collected sample from the environment, given the prior administering step was performed to the environmental site directly, and not the sample collected from the environmental site before any administering occurred. Clarification is requested.
Claim 2 is indefinite for recitation of “…identifying a plurality of sub-pathways…and wherein the product is metabolized by the single microbe”. Claim 1, from which claim 2 depends, recites “a single microbe” in the “identifying a list of partial pollutant degraders” and in the “identifying a plurality of sub-pathways within…” limitations, and thus it is unclear which single microbe is being referenced. For purpose of examination, the limitation will be interpreted to mean “metabolized by a single microbe”. This rejection is previously cited.
Claim 2 is indefinite for recitation of “creating the…(PPOM) using the information on identified degradation pathway(s) for each of one or more identified pollutants…”. It is unclear what information “the information on identified degradation pathway for each of one or more identified pollutants” is referring to (i.e. the identification set of microbes of the pathway, the information on the environmental niche, or both?). It is further noted that the step of creating the PPOM also requires using the set of microbes and the information about the respective environmental niches, in addition to “the information on identified degradation pathway”, suggesting “the information” may be referring to some other information. Clarification is requested. This rejection is previously cited.
Claim 2 is indefinite for recitation of “creating the…(PPOM)…based on literature mining and manual curation about the environmental niche from which the set of microbes are isolated…wherein the PPOM includes…the environmental niche from which the set of microbes are isolated”. There is insufficient antecedent basis for “the respective environmental niche from which the set of microbes are isolated” because claim 2 previously recites “…obtaining information on the environmental niche in which the microbes reside and can be isolated”, but does not require the set of microbes were isolated.
Claim 2 is indefinite for recitation of “employing the literature mining techniques to create the…(DEGB), wherein the DEBG comprises of the information pertaining to the microbe(s) and the respective environmental niches in which the microbe(s) thrive”. T Claim 1, from which claim 2 depends, recites “information about respective environmental niches in which the microbes thrive”, which requires multiple microbes. However, claim 2 refers to “the respective environmental niches in which the microbe(s) thrive”, referring to one or more microbes. As a result, it is unclear if claim 2 is intended to refer to “the information…in which the microbes thrive” of claim 1, or if claim 2 is intending to refer to environmental niches for a at least one of the microbes in claim 2. Clarification is requested.
Claim 2 is indefinite for recitation of “creating a pathway domain map (PDM)…constituting the plurality of sub-pathways that comprise each degradation pathway present in the created PPOM”. However, claim 2 previously recites “creating the…(PPOM) using the information on identified degradation pathway(s)…, the plurality of sub-pathways for the degradation pathway(s)” and then “wherein the PPOM includes identified degradation pathway(s)…”, which are not required to be the identified degradation pathway(s) for which a plurality of sub pathways were identified. As a result, it is not clear which “plurality of sub-pathways” of the identified degradation pathway(s) included in the PPOM are being referenced. To overcome the rejection, claim 2 can be amended to recite “wherein the PPOM includes the identified degradation pathway(s)…”.
Claim 4 is indefinite for recitation of “…wherein the threshold value…, wherein the threshold value…”. Claim 2, from which claim 4 depends, recites “a predefined threshold value” and claim 3, from which claim 4 also depends, recites “a threshold value within a predefined window of genes”, and thus it is not clear if claim 4 intends to refer to the threshold value recited in claim 2 or recited in claim 3. Furthermore, it is noted that none of claims 1-3 recite “a threshold minimum number of domains”. As such, the metes and bounds of claim 4 are unclear.
Claim 4 is indefinite for recitation of “…domains whose presence is required in order to confirm existence of the subpathway within a microbial genome…the total number of domains corresponding to this subpathway in the PDM”. The the metes and bounds of any “domains” that are required, versus not required, to confirm the existence of any subpathway are unclear, nor does Applicant’s specification provide any limiting definitions or examples that would serve to clarify the metes and bounds of the claim. Clarification is requested.
Claim 5 is indefinite for recitation of “…using manual curation …within which the protein domains can be considered…, wherein the genes encoding protein domains forming a sub-pathway occur together on the microbial genome…on the microbial genome”. Claim 3, from which claim 5 depends recites “protein domains corresponding to a sub-pathway” in line 3 and “sub-pathway protein domains” in line 6. Therefore it is not clear which set of protein domains claim 5 is referring to. Furthermore, claim 2, from which claim 5 depends, recites “microbial genomes” and claim 3, from which claim 5 depends” recites “a microbial genome”. Therefore, it is further unclear what microbial genome, “the microbial genome” of claim 5 is referring to.
Claim 6, and claims dependent therefrom, are indefinite for recitation of “the microbial genome” because claim 2 recites “microbial genomes” and therefore it is not clear what genome is being referred to.
Claim 9 is indefinite for recitation of “the desired intermediate product or products…”. There is insufficient antecedent basis for this limitation in the claim because claim 1 does not refer to desired intermediate product or products. Furthermore, term “desired” is a relative term which renders the claim indefinite. The term “desired” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claim 16 is indefinite for recitation of “the information from the knowledgebase…”. The knowledgebase includes “information of the identified one or more pollutants”, “information pertaining to complete degradation pathways”, information about respective environmental niches”, “a list of microbes…”, “a pollutant pathway organism matrix (PPOM), a…(GPE) map, a…(GPM), and a database of abundant environmental microbes (DEBG)”. Therefore it is unclear if “the information” is referring to only the information pertaining one or more of “information of the identified one or more pollutants”, “information pertaining to complete degradation pathways”, information about respective environmental niches”, or if “the information” is referring to all the information/data stored in the knowledgebase, such as the list of microbes, PPOM, etc.
Claim 16 is indefinite for recitation of “the microbes from a GPE matrix having value 1”. It is not clear what microbes “the microbes” are referring to given the GPE matrix does not refer to any previous claim element associated with a particular set of microbes.
Claim 16 is indefinite for “an environment from where the organism had been isolated and thrives in”. It is not clear which organism, “the organism” is referring to because claim 16 previously recites “organisms”.
Response to Arguments
Applicant's arguments filed 23 Jan. 2026 regarding 25 U.S.C. 112(b) have been fully considered but they are not persuasive.
Applicant remarks, regarding the GPM, that Applicant acknowledges the Examiner’s interpretation of GPM as explained in claim 2 and therefore the rejection is addressed (Applicant’s remarks at pg. 16, para. 5 to pg. 17, para. 1).
This argument is not persuasive. The interpretation provided in the previous Office action was provided to facilitate compact prosecution. However, it is improper to import limitations from the specification into the claims. If Applicant intends for the GPM to be interpreted as explained in claim 2, claim 1 should be amended to similarly define the metes and bounds of the GPM as in claim 2.
Applicant remarks that the rejection regarding the term “abundant” is addressed based on the amendment of “wherein microbe(s) found in abundance…are curated..” (Applicant’s remarks at pg. 17, para. 2-3).
This argument is not persuasive because “found in abundance” also uses relative terminology and it is not clear how many microbes are required to be found to be considered “in abundance”. The phase “in abundance” is not any clearer than “abundant”, and does not serve to clarify the metes and bounds of the claim.
Applicant remarks that the single microbe being reference in claim 2 is referring to “a single microbe” in the same limitation of claim 2, and therefore the rejection is addressed (Applicant’s remarks at pg. 24, para. 3-4).
This argument is not persuasive because Applicant has not amended claim 2 to make clear that the single microbe of claim 2 does not refer to the single microbe of claim 1. As presently recited, the claim is indefinite.
Applicant remarks that Applicant clarifies the step of creating the PPOM requires the use of the set of microbes, the information about respective environmental niches, and “the information on identified degradation pathway”, and in view of the amendment the rejection is addressed (Applicants’ remarks at pg. 24, para. 5 to pg. 25, para. 2).
This argument is not persuasive because the metes and bounds of “the information on identified degradation pathway(s) is indefinite for the same reasons previously discussed. As explained above, it is unclear what information “the information on identified degradation pathway for each of one or more identified pollutants” is referring to (i.e. the identification set of microbes of the pathway, the information on the environmental niche, or both?). Applicant appears to suggest the set of microbes and the information about respective environmental niches are not part of the information on degradation pathway(s) which further raises confusion what information “the information on identified degradation pathway(s)” is referring to.
Applicant remarks that claim 4 is amended to be dependent from claim 3, and therefore the rejection regarding “the threshold value” is addressed (Applicant’s remarks at pg. 31, para. 4-5).
This argument is not persuasive because both claims 2 and 3, from which claim 4 depends, recite a threshold value, and therefore it is still not clear what threshold value is being referenced.
Applicant’s remaining arguments have been considered, but they do not pertain to the new grounds of rejection set forth above under 35 U.S.C. 112(b).
Claim Rejections - 35 USC § 112(d)
The rejection of claims 12-15 under 35 U.S.C. 112(d) in the Office action mailed 05 Nov. 2025 has been withdrawn in view of the cancellation of these claims received 23 Jan. 2026.
Conclusion
No claims are allowed.
Claims 1-9, 11, and 16 are patent eligible for the reasons discussed in the Office action mailed 05 Nov. 2025.
Claims 1-9, 11, and 16 appear free of the prior art for the reasons discussed in the Office action mailed 05 Nov. 2025.
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 (37 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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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685