DETAILED ACTION
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 .
Claim Status
Claims 41 and 52-70 are pending.
Claims 52-56 and 61-70 are withdrawn.
Claims 41 and 57-60 are under examination.
Election/Restrictions and Response to Remarks
Applicant argues that claim 52 is not a separate invention (pg. 11) and requests rejoinder (pg. 12).
In response, Applicant’s remarks and arguments are acknowledged. Applicant is reminded that as noted in the previous office action, Applicant’s election of Group IV, claim 41, without traverse in the reply filed on 8th, December, 2025 was acknowledged. The Examiner acknowledged claims 57-60 are also part of the elected Group IV.
Claims 52-56 and 62-70 were identified as directed to an invention that Lacks Unity with the elected invention for the reasons set forth previously.
Withdrawn Objections to Drawings
The objection to the drawings because they do not conform to sequence rules as set forth in the previous office action is withdrawn in view of Applicant’s amendments.
Withdrawn Objections to Specification
Browser Executable Code
The objection to the specification because it contains an embedded hyperlink and/or other form of browser-executable code as set forth in the previous office action is withdrawn in view of Applicant’s amendments.
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 the applicant regards as his invention.
Claim 60 is 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 (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 60 recites “the first heterogeneous population of prokaryotic cells is found in: a mammal's gastrointestinal tract, a human's microbiome, a non-human animal's microbiome, soil, a hot spring, an ocean, a marshland, a swamp, wastewater, agricultural runoff, a fermentation that relies on a mixed community of cells to produce beverages or food, a rhizosphere, a plant microbiome, an industrial process that relies on a community of microorganisms, an industrial wastewater treatment process that relies on a community of microorganisms, or a bioreactor used for bioremediation of wastes.” It is unclear whether the recited limitation “is found in” refers to an active method step of the location of the species during the method, an active method step of finding the population of prokaryotic cells during the method, or whether this describes the natural location of the prokaryotic bacteria which is a characteristic of the bacteria. Further, it is unclear how prokaryotic cells could be contacted with a library of nucleic acids in the recited locations.
Claim Interpretation
Due to the 112b issues identified above, for the sake of compact prosecution, the claims identified with 112 issues above are being examined against the prior art and double-patenting as follows:
Claim 60 is interpreted as the first heterogeneous population of prokaryotic cells is sampled from (or is otherwise normally present in) the recited locations. This is in light of the instant specification which states that “target prokaryotic cells include prokaryotic cells found in a natural environment such as the gastrointestinal tract of a mammal (e.g., a human); the microbiome of a human; the microbiome of a non-human animal soil; hot springs; oceans; marshland; swamps; etc. Target prokaryotic cells include prokaryotic cells found in wastewater, agricultural runoff, and the like.
Target prokaryotic cells include prokaryotic cells involved in food processing (e.g., fermentations to produce beverages or food that rely on a mixed community of cells such as with
kimchi, soy sauce, or kombucha)” (para. [0099]).
Maintained Claim Rejections - 35 USC § 102
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.
Claims 41 and 57-58 stand rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wetmore et al. (mBio. 2015 May 12;6(3):e00306-15.; henceforth “Wetmore”).
Regarding claim 41, Wetmore discloses a method comprising:
a) contacting the first population of prokaryotic cells with a library of nucleic acids, wherein each member of the library comprises:
(i) a nucleotide sequence that is operably linked to a promoter and encodes a non-targeted transposase (transposon vectors);
(ii) a nucleotide sequence encoding a first transposon flanked by recognition sites that are cleaved by the non-targeted transposase (IRs);
and (iii) a unique (primers used in included unique 8-bp indexes that were sequenced “in line” with the random DNA bar code which means the barcodes were also unique; pg. 12 col. 1 2nd para.; see also “No. of strains with unique bar codes” Table 1 and “the strains have unique bar codes” pg. col. 1 2nd para.) nucleotide sequence barcode that identifies the first transposon and/or the promoter
thereby generating genetically modified prokaryotic cells comprising the first transposon inserted into the genome; and
b) sequencing the junction between the first transposon and genomic DNA (TnSeq) and/or by sequencing the nucleotide sequence barcode (BarSeq) (“both the DNA bar code and the transposon insertion site are identified in a single 150-nucleotide Illumina sequencing read” Figure 1).
Regarding claim 41, concerning the recited limitation that the population of prokaryotic cells is heterogenous, because the cell strains exhibited different phenotypes (see Table 1 “No. with significant phenotype” ; Table 1), the strains have phenotypic heterogeneity and therefore are encompassed by the broadest reasonable interpretation of “heterogenous.”
Regarding step b) or claim 41, although Wetmore is silent to a result of “identifying the species of the genetically modified prokaryotic cells” and “identifying said prokaryotic species susceptible to genetic modification” as recited in the thereby clause, the active method step of b) as claimed is “sequencing the junction between the first transposon and genomic DNA and/or by sequencing the nucleotide sequence barcode” which is disclosed by Wetmore as discussed above. Therefore, because Wetmore discloses the active method step of step b), the claimed results of “identifying the species of the genetically modified prokaryotic cells” and “identifying said prokaryotic species susceptible to genetic modification” would inherently follow the recitation of the disclosed steps and therefore the disclosure of Wetmore anticipates the limitations of step b) as claimed.
Regarding the preamble of claim 41, the preamble merely states, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations (see MPEP 2111.02) See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) As discussed above, Wetmore discloses all the active method steps of the instantly claimed method and therefore the method of Wetmore is capable of meeting the intended use identifying, within a first heterogeneous population of prokaryotic cells, a prokaryotic species susceptible to genetic modification using a non-targeted transposon system.
Regarding claim 57, further to the discussion of claim 41 above, Wetmore discloses the non-targeted transposon system is a Tn5 system (abstract; pg. 2 col. 2 2nd para.; Figure 1; Table 1; pg. 9 col. 1 3rd and 4th para.; pg. 10 col. 1; pg. 10 col. 2 2nd para.) or Mariner system (abstract; pg. 2 col. 1 1st para., col. 2 2nd para; Figure 1; Table 1; pg. 9 col. 1 2nd para., col. 2 2nd para.; pg. 10 col. 2 2nd para.).
Regarding claim 58, further to the discussion of claim 41 above, Wetmore discloses sequencing the junction (TnSeq) comprises:
fragmenting DNA obtained from the genetically modified prokaryotic cells (shearing genomic DNA);
ligating adaptor DNA fragments to the fragmented DNA (ligating adapters) (“In TnSeq, genomic DNA is sheared, end repaired, and ligated with Illumina Y adapters”; Figure 1 legend); and
amplifying the junction between the first transposon and the genomic DNA by polymerase chain reaction (PCR) (PCR that amplifies the transposon junction using primers that are complementary to the adapter and to the transposon), using a forward PCR primer that hybridizes to a nucleotide sequence in the first transposon and a reverse PCR primer that hybridizes to a nucleotide sequence in the adaptor DNA (“one primer specific to the Y adapter and a second primer specific to the transposon” ; Figure 1 legend) (pg. 2 col. 2 2nd para.; Figure 1B; see also Table S2).
Accordingly, Wetmore anticipates instant claims.
Response to Arguments
Applicant’s arguments, filed 22nd June, 2026, have been fully considered but are not found persuasive.
Applicant argues “an element of the claims is that a population of prokaryotic cells that is already heterogeneous is contacted with the nucleic acid library” (pg. 13). Applicant further argues “Wetmore discloses only contacting homogeneous populations of bacteria with a mutant library” and “There is no further contacting of a mutated population comprising different phenotypes with another nucleic acid library. Wetmore therefore does not disclose mutagenizing a mixed species bacterial population or mutagenizing a single species population comprising cell strains with different phenotypes. Accordingly, Wetmore does not teach the element of contacting a heterogeneous population of prokaryotic cells with a library of nucleic acids as presently claimed” (pg. 13-14).
In response, this is not found persuasive because the prior art of Wetmore still discloses the methods can be used to “assayed growth in pure culture, pooled mutant fitness assays can also be used to assay growth in cocultures” (pg. 9 col. 1). Since co-cultures are heterogeneous populations, this specific disclosure of coculture of Wetmore also specifically anticipates instant claims.
Additionally, in order to complete the art of record and rebut Applicant’s arguments, Applicant is additionally directed to the art of Austin et al. (Antonie Van Leeuwenhoek. 2017 Oct;110(10):1247-1256. Epub 2017 Feb 6.; henceforth “Austin”). Austin evidences that pure culture does not necessarily contain clones of identical bacteria, but that there may be variation in the genetic potential of the component cells, i.e. the cells are not homogeneous (pg. 1247 col. 1). Therefore the pure cultures disclosed by Wetmore also encompass phenotypic and genetic heterogeny and are encompassed by the broadest reasonable interpretation of “heterogeneous.”
Applicant is reminded that preferred embodiments or working examples are not the only teaching of a reference. “The use of patents as references is not limited to what the patentees describe as their own inventions or to the problems with which they are concerned. They are part of the literature of the art, relevant for all they contain.” In re Heck, 699 F.2d 1331, 1332-33, 216 USPQ 1038, 1039 (Fed. Cir. 1983) (quoting In re Lemelson, 397 F.2d 1006, 1009, 158 USPQ 275, 277 (CCPA 1968)). A reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill the art, including nonpreferred embodiments. Merck & Co. v. Biocraft Laboratories, 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989). In the instant case, both of these embodiments (the pure cultures that are evidenced to have phenotypic and genetic heterogeny and the specifically taught co-culture) disclosed by Wetmore meet instant claims for the reasons set forth above and therefore Applicant’s arguments are not found persuasive.
Maintained Claim Rejections - 35 USC § 103
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.
Claims 59-60 stand rejected under 35 U.S.C. 103 as being unpatentable over Wetmore et al. (mBio. 2015 May 12;6(3):e00306-15.; henceforth “Wetmore”) in view of Rey et al. (Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13582-7. Epub 2013 Jul 29.; henceforth “Rey”).
The teachings of Wetmore above are hereby incorporated in their entirety.
Regarding claim 59, although Wetmore teaches the method can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data (abstract), and Wetmore teaches pooled mutant fitness assays can also be used to assay growth in cocultures, growth in mice, motility, or survival, or to identify strains with altered morphology after separation with a cell sorter (pg.9 col. 1 4th para.) Wetmore is silent to performing the method on a first heterogenous population of cells that comprises at least 5 different species of prokaryotic cells.
Nevertheless, regarding claim 59, Wetmore cites Rey (pg.9 col. 1 4th para.; citation 29). Rey teaches a method comprising performing transposon mutagenesis on samples from mice colonized with 9 bacterial species (pg. 13583 col. 1; see also “Nine-Member Artificial Community” SI results pg. 1 col. 1) to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common Sulfate-reducing bacteria in a surveyed cohort of healthy US adults (abstract).
Therefore, regarding claim 59, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention or practice the method of Wetmore, and combine the known prior art element of the target population of 9 bacterial species of Rey to obtain the predictable result of a method to assay fitness. One of ordinary skill would have been motivated to do so as taught by Rey to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common Sulfate-reducing bacteria in a surveyed cohort of healthy US adults (abstract). Regarding the reasonable expectation of success, Wetmore evidences performing the transposon sequencing method on populations of prokaryotic bacteria (abstract; Figure 1; Table S1).
Regarding claim 60, further to the discussion of claim 41 above, the target bacteria suggested by Rey above (see claim 59 rejection above), are sampled from a mammal’s (mouse) gastrointestinal tract and are normally found in a humans gastrointestinal tract (pg. 13583 col. 1; see also “Nine-Member Artificial Community” SI results pg. 1 col. 1).
Hence, the claimed invention as a whole was prima facie obvious.
Response to Arguments
Applicant’s arguments filed 22nd, June, 2026, have been fully considered but are not found persuasive.
Applicant argues “Wetmore does not disclose contacting a heterogeneous population of prokaryotic cells with a library of nucleic acids as presently claimed. Wetmore also does not suggest this element because Wetmore teaches different methods for mutagenizing different bacterial species (see, e.g., "Transposon mutant library construction" pg. 10).
In response, as set forth above in the response to arguments, above, Wetmore still anticipates the claims because Wetmore discloses the methods can be used to “assayed growth in pure culture, pooled mutant fitness assays can also be used to assay growth in cocultures” (pg. 9 col. 1). Since co-cultures are heterogeneous populations, this specific disclosure of coculture of Wetmore also anticipates instant claims.
Applicant argues “it would not be possible to perform these different methods in a mixed species population” (pg. 15).
In response, this is not found persuasive because Wetmore evidences performing the transposon sequencing method on populations of prokaryotic bacteria (abstract; Figure 1; Table S1), and Rey evidences performing the transposon sequencing methods on a mixed population of bacteria (pg. 13583 col. 1; see also “Nine-Member Artificial Community” SI results pg. 1 col. 1). The combined teachings of both references provide a reasonable expectation of success in performing the suggested method in a heterogeneous population of prokaryotic cells that includes at least 5 species as claimed.
Furthermore, Applicant is reminded that conclusive proof of efficacy is not required to show a reasonable expectation of success. OSI Pharm., LLC v. Apotex Inc., 939 F.3d 1375, 1385, 2019 USPQ2d 379681 (Fed. Cir. 2019) ("To be clear, we do not hold today that efficacy data is always required for a reasonable expectation of success. Nor are we requiring ‘absolute predictability of success.’"); Acorda Therapeutics, Inc. v. Roxane Lab., Inc., 903 F.3d 1310, 1333, 128 USPQ2d 1001, 1018 (Fed. Cir. 2018) ("This court has long rejected a requirement of ‘[c]onclusive proof of efficacy’ for obviousness." (citing to Hoffmann-La Roche Inc. v. Apotex Inc., 748 F.3d 1326, 1331 (Fed. Cir. 2014); PharmaStem Therapeutics, Inc. v. ViaCell, Inc., 491 F.3d 1342, 1364 (Fed. Cir. 2007); Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1364, 1367–68 (Fed. Cir. 2007) (reasoning that "the expectation of success need only be reasonable, not absolute")).
Lastly, Applicant is directed to MPEP 2141.03 (I) which states that "A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton." KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 421, 82 USPQ2d 1385, 1397 (2007). "[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle." Id. at 420, 82 USPQ2d 1397. Office personnel may also take into account "the inferences and creative steps that a person of ordinary skill in the art would employ." Id. at 418, 82 USPQ2d at 1396. In the instant case, a person of ordinary skill would employ creative steps to combine the disclosure of Wetmore to fit the teachings of Rey to be usable in a population with multiple species with a reasonable expectation of success.
Applicant argues “Rey does not make up for the deficiency of Wetmore. While Rey teaches that "mice were colonized with D. piger GOR1 and eight other sequenced human gut bacterial species" (emphasis added), transposon mutagenesis was performed on only D. piger. As described in "Transposon Mutagenesis Identifies Key Determinants for D. piger Fitness in Vivo" on pg. 13583, "An isogenic library composed of ~30,000 unique inter- and intragenic transposon insertion mutants of D. piger was constructed", which, following administration to the mice, "revealed mutations in 262 and 321 0. Piger genes [respective to different diets] that produced a significant reduction in invasiveness/fitness". In the Supporting Information, Rey describes only "Transposon Mutagenesis of D. piger GOR1" (pg. 2). Rey is completely silent with respect to mutagenesis of any of the other eight bacterial species. Thus, Rey discloses performing transposon mutagenesis in only a single, homogeneous population of bacteria. Accordingly, Rey does not teach or suggest that the heterogeneous population to be modified comprises at least 5 different species of prokaryotic cells. Rey also does not teach or suggest the element of contacting a heterogeneous population of prokaryotic cells with a library of nucleic acids, and as such, Rey does not make up for the deficiencies of Wetmore with respect to independent claim 41” (pg. 16).
In response, the arguments concerning the Wetmore reference with respect to independent claim 41 are addressed above.
In response, this is not found persuasive because Applicant is not appreciating the broadest reasonable interpretation of instant claims. Instant claims only recite “contacting the first heterogeneous population of prokaryotic cells with a library of nucleic acids” and therefore, the claim only requires that the population is contacted and does not require that each and every species of the population is subjected to mutagenesis. Because Rey teaches this above, this element is met by the suggested combination of art and falls within the broadest reasonable interpretation of instant claims.
Conclusion
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.
No claim is allowable.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIANA N EBBINGHAUS whose telephone number is (703)756-4548. The examiner can normally be reached M-F 9:30 AM to 5:30 PM ET.
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/BRIANA N EBBINGHAUS/Examiner, Art Unit 1632
/EMILY A CORDAS/Primary Examiner, Art Unit 1632
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