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 .
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10/22/2025 has been entered.
DETAILED ACTION
Claims 1-4, 6-14, and 16-22 are pending and under examination on their merits.
Claim Objection
Claims 1 and 12 are objected to because of the following informalities:
In claim 1, bacteriophage insensitive mutant should be bacteriophage-insensitive mutant.
In claim 12, “BIMS” rather than “BIMs.” Since the letter “s” is not part of the acronym “bacteriophage insensitive mutant,” it should not be capitalized.
Appropriate correction is required.
Response to Arguments
Applicant's arguments filed 10/22/2025 have been fully considered but they are not persuasive.
Applicant argues against the rejection of claims 1-4, 6-7, and 16-20 under 35 U.S.C. 103 over Kouwen '233 in view of Hynes on the grounds that Kouwen ‘233 does not teach or suggest attaining BIMs with enhanced acidification profile determined “in milk without the presence of a bacteriophage, wherein acidification profile is the time for the milk without the presence of a bacteriophage to reach pH of 5.2 after five hours of fermentation at 42 °C.” Applicant argues that the number of cycles is not a results-effective variable for attaining BIMs with an improved acidification profile as claimed. Thus, Applicant submits that the results are unexpected (Arguments, paragraph 2 on page 8).
In response, these arguments are unpersuasive because there is no nexus between the evidence of unexpected results and the invention as claimed. Claim 1 is indefinite due to the limitations d(iii) and e(iii). Claim 1 step e(iii) recites that the acidification profile, as determined in d(iii), is improved when compared to the acidification profile of the parent strain. However, it is unclear how the acidification profile is determined in step d(iii) because the wherein clause recites both the time to reach a pH of 5.2 as well as five hours. Furthermore, it is unclear whether the acidification profile of the parent strain is also as determined in d(iii).
Applicant argues against the rejection of claims 10-14 and 21-22 under 35 U.S.C. 102(a)(1) or in the alternative 35 U.S.C. 103 on the grounds that Kouwen ‘468 does not teach a method for obtaining a non-CRISPR bacteriophage-insensitive mutant (BIM) from a lactic acid bacterium parent strain comprising growing surviving lactic acid bacteria for at least 15 cultivation cycles in milk in the presence of said at least one bacteriophage which expresses a gene encoding an anti-CRISPR protein upon infection of a host cell, leading to BIMs with an increased acidification profile as recited in amended claim 1 (Arguments, paragraph 3 on page 9).
In response, this argument is not persuasive because claims 10-14 and 21-22 require a BIM obtained by the method of claim 1, which is a product-by-process limitation. As such, the method steps are only given weight insofar as they limit the structure of the claimed product (MPEP 2113(I)). Here, the structure of the product is a non-CRISPR bacteriophage insensitive mutant with the ability to acidify milk. Note that the process of claim 1 only defines the acidification performance of the BIM relative to the parent strain, which is any lactic acid bacterium. Kouwen ‘468 teaches a non-CRISPR BIM with the ability to acidify milk: Kouwen ‘468 teaches bacteriophage insensitive mutant BIM100-E-DlA-L-5 with the parent strain S. thermophilus 100-E ([0066] and Table 13 on page 13), the BIM has non-CRISPR phage resistance (see Kouwen ‘468 [0066], last line), and is capable of acidifying milk ([0084]).
No new arguments were raised by Applicant with respect to the nonstatutory double patenting rejections of record. The same reasoning applied above in response to the arguments made against the rejections of claims under 35 U.S.C. 103 also applies to the arguments made against the nonstatutory double patenting rejections of record.
Claim Rejections - 35 USC § 112
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.
Claims 1-4, 6-14, and 16-22 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 (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites “A method for obtaining a non-CRISPR bacteriophage insensitive mutant.” It is unclear whether the bacteriophage or the BIM lactic acid bacterium is “non-CRISPR” based upon the placement of the modifier, non-CRISPR, directly before bacteriophage. Applicant may consider amending to “a non-CRISPR and bacteriophage-insensitive mutant.”
Claim 1 is further indefinite for step d)i) exposing said isolated BIM to at least two different bacteriophage to determine the spectrum of bacteriophage insensitivity. Exposing the BIM to two bacteriophages does not immediately result in a spectrum of insensitivity. Therefore, the method step is discordant with the desired result (the spectrum of bacteriophage insensitivity).
Claim 1 is further indefinite for step d)ii) testing the stability of the acquired bacteriophage resistance of said at least one isolated BIM. This limitation is vague as it does not recite an active method step or specify how the stability is tested.
Claim 1 recites in step d)iii) determining an acidification profile of said isolated BIM in milk without the presence of a bacteriophage, wherein acidification profile is the time for the milk without the presence of a bacteriophage to reach a pH of 5.2 after five hours of fermentation at 42 °C. This limitation further renders claim 1 indefinite for several reasons. First, it is unclear whether the step of “determining an acidification profile of said isolated BIM in milk without the presence of a bacteriophage” is limited to the time for the milk without the presence of a bacteriophage to reach a pH of 5.2. It is further unclear whether the time is five hours or any time. Lastly, the definition of acidification profile within the wherein clause does not include the BIM, only the bacteriophage, thus it is further unclear what is subject to the fermentation conditions (the BIM or the bacteriophage).
Claim 1 is further indefinite for the use of subjective terminology in step e)iii), which recites selecting a BIM which has an acidification profile which is improved when compared to the acidification profile of the parent strain. This relative term does not specify the parameter used to measure the improved acidification profile. In addition, it is unclear whether the acidification profile of the parent strain is as determined in step d)iii) or only the acidification profile of the isolated BIM is as determined instep d)iii).
Claim 12 recites “A process for production of a dairy product comprising acidifying a starter culture composition with one or more of the BIMs as obtained by the method of claim 1,” which is indefinite because it is unclear what is being acidified. The ingredients of the starter culture composition are not recited. The only ingredient in claim 12 is the BIMs obtained by the method of claim 1. BIMs cannot acidify themselves to produce a dairy product. Applicant may consider amending to: “A process for production of a dairy product, comprising acidifying milk by adding a starter culture composition comprising one or more of the BIMs as obtained by the method of claim 1.”
Claims 2-4, 6-14, and 16-22 are rejected for depending from a rejected base claim and not rectifying the sources of indefiniteness described above.
Claim Rejections - 35 USC § 102 and 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 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.
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 absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4, 6-7, and 16-20 are rejected under 35 U.S.C. 103 as being unpatentable over Kouwen ‘233 (US 2017/0196233 A1; cited in the Non-Final Action mailed on10/13/2023) in view of Hynes et al. (Nature microbiology 2.10 (2017): 1374-1380; cited in the Non-Final Action mailed on 10/13/2023).
The effective filing date of the instant application is 12/18/2018. Kouwen ‘233, published July 13, 2017, is available as prior art under 35 U.S.C. 102 (a)(1). No grace period exceptions apply since Kouwen ‘233 was published more than one year before the effective filing date of the instant application.
“Cultivation cycle” in claim 1 is interpreted as a single incubation of lactic acid bacteria in milk with the bacteriophage. Two “cycles” is interpreted as one incubation of lactic acid bacteria in milk with the bacteriophage in a first culture, followed by inoculating from the first culture into a fresh culture and a performing a second incubation of the lactic acid bacteria in milk with the bacteriophage in a second culture.
Claim 1 is interpreted as requiring that step d)iii) is limited to determining the acidification of said isolated BIM in milk without the presence of a bacteriophage. The wherein clause is interpreted as exemplary language. Step e)iii) is interpreted as requiring that the acidification profile of the isolated BIM is as determined in step d)iii) but not requiring that the acidification profile of the parent strain is as determined in step d)iii).
Kouwen ‘233 teaches a method for the isolation of a bacteriophage-insensitive mutants from a Streptococcus thermophilus parent strain comprising: a) inactivating the CRISPR resistance mechanism of the parent strain, b) exposing the parent strain obtained in step a) to a bacteriophage, c) isolating bacteriophage insensitive mutants, d) comparing the CRISPR loci of the parent strain with the CRISPR loci of the bacteriophage insensitive mutants, and e) selecting bacteriophage-insensitive mutants of which the CRISPR loci is identical to the CRISPR loci of the parent strain (Kouwen ‘233 claim 1). Kouwen ‘233 teaches that non-CRISPR resistance mechanisms are preferred to CRISPR resistance because phage can rapidly evolve to overcome CRISPR-mediated resistance ([0023]). Kouwen ‘233 teaches inactivating the CRISPR resistance mechanism of the parent strain by introducing a DNA construct encoding anti-sense RNA to the cas gene ([0014]). The antisense RNA subsequently binds to the target cas mRNA thereby silencing the cas gene ([0014]).
Kouwen ‘233 teaches a step of characterizing at least one isolated BIM by exposing the isolated BIM to at least two different bacteriophages to determine the spectrum of bacteriophage insensitivity and testing the stability of the acquired bacteriophage resistance of the isolated BIM: Table 6 on page 9 shows the relative efficiencies of plaquing of BIMs derived from Streptococcus thermophilus 100-E. BIM100-E-D1A-L5 has a relative efficiency of plaquing that approaches zero for all four tested phages compared the parent strain. Therefore, BIM100-E-D1A-L5 is insensitive to more bacteriophages compared to the parent strain. Kouwen ‘233 teaches that BIM100-E-D1A-L5 has improved stability of acquired bacteriophage resistance when compared to the parent strain: Table 12 on page 11 indicates that BIM100-E-D1A-L5 is stable over at least 3 cycles of the Heap Lawrence and also confirms that the mechanism of phage resistance is non-CRISPR. Therefore, BIM100-E-D1A-L5’s acquired phage resistance is more stable than that of the parent strain, which had no phage resistance. The Heap Lawrence assay ([0060] of ‘233) is a test of how many cycles are required for a phage to overcome the strain’s phage resistance, which is indicated by the inability of the strain to acidify milk. Therefore, Kouwen ‘233 teaches determining the acidification profile of the isolated BIM in milk.
Kouwen ‘233 does not teach determining the acidification profile of the isolated BIM in milk without bacteriophage.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to test the ability of the isolated BIM to acidify milk (“determining an acidification profile”) without bacteriophage for industrial applicability. The person of ordinary skill in the art would have had a reasonable expectation of success in determining the acidification profile of the isolated BIM without bacteriophage. Relative to the parent strain, the isolated BIM would have necessarily had an improved acidification profile without the presence of a bacteriophage compared to the acidification profile of the parent strain with bacteriophage because the parent strain is not bacteriophage insensitive.
Kouwen ‘233 does not teach exposing the parent strain to at least one virulent bacteriophage that expresses a gene encoding an anti-CRISPR protein.
Kouwen ‘233 does not teach growing surviving lactic acid bacteria for at least 15 cultivation cycles in milk in the presence of the at least one bacteriophage that expresses a gene encoding an anti-CRISPR protein.
Hynes teaches challenging S. thermophilus strain CRISPR-immunized against a set of virulent phages (Abstract). The anti-CRISPR (Acr) protein encoded by the phage completely abolishes CRISPR-mediated immunity (Abstract). In other words, Hynes teaches exposing S. thermophilus to a virulent phage that abolishes CRISPR immunity.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the step of inactivating the CRISPR resistance mechanism of the parent strain taught by Kouwen ‘233 by introducing a virulent phage encoding an anti-CRISPR protein in order to abolish CRISPR-mediated immunity, as suggested by Hynes. One of ordinary skill in the art would have had a reasonable expectation of success given that Hynes taught virulent phages of S. thermophilus encoding anti-CRISPR proteins that inactivated CRISPR systems (Hynes Abstract). Kouwen ‘233 taught that non-CRISPR resistance mechanisms were preferred to CRISPR resistance (Kouwen ‘233 [0023]). Therefore, one of ordinary skill in the art would have recognized an alternative way to inactivate CRISPR resistance in S. thermophilus that would not have required introducing a DNA construct into S. thermophilus.
Regarding the limitaiton that the surviving lactic acid bacteria are grown for at least 15 cultivations cycles in milk in the presence of the at least one bacteriophage that expresses a gene encoding an anti-CRISPR protein, Kouwen ‘233 teaches in [0020] growing surviving lactic acid bacteria for a single overnight incubation (i.e. one cycle).
Kouwen ‘233 does not teach growing surviving lactic acid bacteria for at least 15 cycles in milk in the presence of at least one bacteriophage encoding an anti-CRISPR protein. However, it would have been obvious for the person of ordinary skill in the art before the effective filing date of the claimed invention to grow surviving S. thermophilus bacteria (which are lactic acid bacteria, see [0002] of Kouwen ‘233) for at least two cycles in milk with the bacteriophage in order to ensure that non-CRISPR resistance acquired by the bacteria would have been stable over multiple passages (cultivation cycles). It would have been routine experimentation in an optimization process to increase the number of cultivation cycles until the desired phenotype (stable non-CRISPR resistance) would have been observed. A person of ordinary skill would have had a reasonable expectation of success as the phenotype of non-CRISPR resistance would have been observed based on the teaching of Hynes (see Hynes Abstract).
Regarding claim 2, Kouwen ‘233 teaches a phage resistance robustness assay with the steps of growing cells of BIMs for 1 hour in 10% RSM (milk), adding phage lysate, incubating the strain and the phage, harvesting supernatant containing phages (“obtained bacteriophages”), mixing supernatant 1:1 with phage lysate (“newly added bacteriophage” in the instant claim) in a new tube, incubating the BIM and phage, and repeating the procedure for many cycles, thereby allowing the phages to adapt to overcome the strain’s phage resistance ([0060]). Kouwen ‘233 teaches that monitoring the number of cycles it takes for phage to become virulent is an indication of the phage robustness ([0060]). Table 12 on page 11 of Kouwen ‘233 indicates that the cycles are repeated at least 4 times. Therefore, Kouwen ‘233 teaches steps A-D of the instant method. Note that phage robustness of BIMs is a measure of stability of insensitivity.
Regarding claim 3, the lactic acid bacterium parent strain is Streptococcus thermophilus in the method of Kouwen ‘233 (Kouwen ‘233 claim 1). Therefore, the lactic acid bacterium parent strain in the method of Kouwen ‘233 modified by Hynes would also have been Streptococcus thermophilus.
Regarding claim 4, Kouwen ‘233 teaches that the lactic acid bacterium parent strain is mutagenized by chemical mutagenesis or irradiation with UV light (Kouwen ‘233 [0020]). Therefore, it would have been obvious to include a step of mutagenesis in the method of Kouwen ‘233 modified by Hynes. One of ordinary skill in the art would have recognized that mutagenesis would have increased the chances of the parent strain acquiring a non-CRISPR resistance mechanism.
Regarding claim 6, Kouwen ‘233 teaches testing the stability of the acquired bacteriophage resistance of the isolated BIM for at least 4 cycles (Table 12 on page 11), which approaches at least 5 cycles. Therefore, a prima facie case of obviousness exists. See MPEP 2144.05.
Regarding claim 7, Kouwen ‘233 and Hynes do not teach exposing a parent strain to at least two virulent bacteriophages, wherein at least one encodes an anti-CRISPR protein.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to expose a parent strain to two virulent bacteriophages, wherein one encodes an anti-CRISPR protein. One of ordinary skill in the art would have been motivated to simultaneously inactivate the CRISPR resistance mechanism of the parent strain as well as apply selective pressure to the parent strain via the introduction of a second virulent phage. One of ordinary skill in the art would have had a reasonable expectation of success in the combination of two steps, each of which would have had predictable results: (1) inactivating the CRISPR resistance mechanism of the parent strain and (2) selecting for phage resistance mechanisms in the host.
Regarding claim 18, Kouwen ‘233 does not teach testing the stability of the acquired bacteriophage resistance of the at least one isolated BIM by obtaining bacteriophages from milk and growing said isolated BIM in milk in the presence of newly added bacteriophage and obtained bacteriophage for at least a total of 15 cultivation cycles. However, Kouwen ‘233 teaches that the Heap Lawrence Assay procedure was repeated for many cycles, thereby allowing the phage to adapt to overcome the strain’s phage resistance ([0060]). By monitoring the number of cycles it takes for a phage to become virulent (indicated by the inability of the strain to acidify milk), an indication of the phage robustness is obtained ([0060]). It would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to repeat the number of cycles as many times as it would have taken for the phage to become virulent, which Kouwen ‘233 indicates would have been many cycles. It would have been routine optimization to arrive at the number of cultivation cycles (at least 15 cultivation cycles).
Regarding claims 16-17 and 19-20, Kouwen ‘233 does not teach growing surviving lactic acid bacteria for at least 20 cultivation cycles (claims 16 and 19), or at least 25 cultivation cycles (claims 17 and 20) in milk in the presence of at least one bacteriophage encoding an anti-CRISPR protein.
However, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to grow surviving S. thermophilus bacteria (which are lactic acid bacteria, see [0002] of Kouwen ‘233) for at least two cycles in milk with the bacteriophage in order to ensure that non-CRISPR resistance acquired by the bacteria would have been stable over multiple passages (cultivation cycles). It would have been routine optimization to increase the number of cultivation cycles until the desired phenotype would have been observed (stable non-CRISPR resistance) and the person of ordinary skill in the art would have had a reasonable expectation of success that the phenotype of non-CRISPR resistance would have been observed based on the teaching of Hynes (see Hynes Abstract).
Claims 8-9 are rejected under 35 U.S.C. 103 as being unpatentable over Kouwen ‘233 (US 2017/0196233 A1; cited in the Non-Final Action mailed on10/13/2023) in view of Hynes et al. (Nature microbiology 2.10 (2017): 1374-1380; cited in the Non-Final Action mailed on10/13/2023), as applied to claims 1-4, 6-7 and 16-20 above, further in view of Kouwen ‘468 (US 2017/0218468 A1; cited in the Non-Final Action mailed on10/13/2023) and as evidenced by Carvalho et al. (International Dairy Journal 14.10 (2004): 835-847; cited in the Non-Final Action mailed on10/13/2023).
See discussion of Kouwen ‘233 and Hynes above, which is incorporated into this rejection as well.
Regarding claims 8-9, Kouwen ‘233 and Hynes do not teach that the method further comprises adding a cryoprotectant to the BIM or freeze-drying the BIM.
Kouwen ‘468 teaches a method for the construction of a bacteriophage insensitive mutant (Kouwen ‘468 claim 1).
Regarding claim 8, Kouwen ‘468 teaches a step of adding a cryoprotectant to the BIM (Kouwen ‘468 claim 6).
Regarding claim 9, Kouwen ‘468 teaches a step of freeze-drying the BIM (Kouwen ‘468 claim 7).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Kouwen 233 and Hynes by adding a step of adding a cryoprotectant and a step of freeze-drying the BIM, per the teaching of Kouwen ‘468. One of ordinary skill in the art would have been motivated to preserve the BIM. One of ordinary skill in the art would have had a reasonable expectation of success given that freeze-drying with a cryoprotectant is commonly used to preserve bacteria as evidenced by Carvalho (Abstract and 5. Drying medium, right column, first paragraph, page 840).
Claims 10-14 and 21-22 are rejected under 35 U.S.C. 102(a)(1) as anticipated by or, in the alternative, under 35 U.S.C. 103 as obvious over Kouwen ‘468 (US 2017/0218468 A1; cited in the Non-Final Action mailed on 10/13/2023).
Claims 10-14 and 21-22 contain product-by-process limitations because they define the claimed BIM by how they are made, not by describing their structure. When the prior art discloses a product which reasonably appears to be either identical with or only slightly different than a product claimed in a product-by-process claim, a rejection based alternatively on either section 102 or section 103 of the statute is eminently fair and acceptable. As a practical matter, the Patent Office is not equipped to manufacture products by the myriad of processes put before it and then obtain prior art products and make physical comparisons therewith. Once the examiner provides a rationale tending to show that the claimed product appears to be the same or similar to that of the prior art, although produced by a different process, the burden shifts to applicant to come forward with evidence establishing a nonobvious difference between the claimed product and the prior art product. See MPEP 2113.
Kouwen ‘468 teaches bacteriophage insensitive mutant BIM100-E-DlA-L-5 with the parent strain S. thermophilus 100-E ([0066] and Table 13 on page 13). The BIM is resistant to at least two different phages because the relative efficiencies of plaquing approach zero. In other words, no phage grows so the bacteria is resistant. Furthermore, the BIM has non-CRISPR phage resistance (see Kouwen ‘468 [0066], last line). The BIMs show acidification activity in milk ([0076] and [0084]).
The BIM of Kouwen ‘468 appears to be either identical with or only slightly different than the claimed BIM, so Applicant now bears the burden of coming forward with evidence establishing a nonobvious difference between the claimed BIM and the BIM of Kouwen ‘468.
Therefore claims 13-14 are anticipated by or obvious over Kouwen ‘468.
Regarding claim 10, Kouwen ‘468 teaches a starter culture composition suitable for inoculation of a medium to be fermented on an industrial scale comprising a BIM (Kouwen ‘468 claim 12). The BIM has non-CRISPR phage resistance because it was produced by a method that selected for CRISPR loci identical to the parent strain (see Kouwen ‘468 claim 4 and [0012] step (d)). The BIM shows acidification activity in milk ([0076] and [0084]).
Regarding claim 11, Kouwen ‘468 teaches a starter culture composition comprising a BIM that is frozen, freeze-dried or in liquid form (Kouwen ‘468 claim 13).
Therefore, the starter culture composition of Kouwen ‘468 comprising a BIM necessarily has the same characteristics as Applicant’s starter culture composition comprising a BIM: both BIMs have non-CRISPR phage resistance, although the BIMs were obtained by different methods. The BIMs show acidification activity in milk ([0076] and [0084]). The BIM of Kouwen ‘468 appears to be either identical with or only slightly different than the claimed BIM, so Applicant now bears the burden of coming forward with evidence establishing a nonobvious difference between the claimed starter culture composition comprising a BIM and the starter culture composition comprising a BIM of Kouwen ‘468.
Regarding claims 12 and 21, Kouwen ‘468 teaches a process for production of a fermented milk or cheese comprising using a BIM of Streptococcus thermophilus (see Kouwen ‘468 claim 15). The BIM of Streptococcus thermophilus acidifies milk ([0084]), thus by using the BIM to produce fermented milk, Kouwen ‘468 is acidifying milk (“starter culture composition”).
Regarding claim 22, Kouwen ‘468 teaches a fermented milk or cheese product derived from a bacteriophage insensitive mutant of Streptococcus thermophilus (Kouwen ‘468 claim 15).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claims because the examined application claim is either anticipated by, or would have been obvious over, the reference claims. See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 10-11 and 13-14 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 4-6 of U.S. Patent No. 10,041,135 (hereafter ‘135). The instant claims 10-11 and 13-14 are anticipated by claims 1 and 4-6 of ‘135. Instant claim 11 is also obvious over conflicting claims 4-6 of ‘135.
Claim 1 of ‘135 recites a method for generating a bacteriophage insensitive mutant of a parent strain of Streptococcus thermophilus suitable for food or feed fermentation. Claim 4 of ‘135 recites the method according to claim 1, further comprising culturing the bacteriophage insensitive mutant in a culture medium and recovering the bacteriophage insensitive mutant from the culture medium to provide a starter culture composition. Claim 5 of ‘135 further limits the method of claim 1 by adding a cryoprotectant to the bacteriophage insensitive mutant. Claim 6 of ‘135 further limits the method of claim 1 by freeze-drying or freezing the bacteriophage insensitive mutant.
Instant claims 13-14 are product-by-process claims. As such, unless an unobvious structural limitation is provided by the process limitation, patentability of a product-by-process claim is based on the product itself. See MPEP 2113 and discussion above in the rejections under 35 U.S.C. 103.
Instant claims 13-14 are unpatentable over claim 1 of ‘135 because the bacteriophage insensitive mutant (BIM) produced by the method of claim 1 of ‘135 has the same characteristics as the product comprising a BIM recited in instant claims 13-14. Namely, the mutant is insensitive to bacteriophages, derived from S. thermophilus (lactic acid bacterium), and is suitable for food or feed fermentation (i.e. is capable of acidification).
Instant claims 10-11 are directed to a starter culture composition comprising the product-by-process. Instant claims 10-11 are anticipated by claims 4-5 of ‘135 because the starter culture composition recited in claim 4 of ‘135 has the same characteristics as the instant starter culture composition: the composition comprises a bacteriophage insensitive mutant derived from S. thermophilus, is suitable for fermentation at an industrial scale (i.e. capable of acidification), and is formulated as a liquid. The embodiment of instant claim 11 in which the starter culture composition is freeze-dried is also unpatentable over claims 4-6 of ‘135 because it would have been obvious to one of ordinary skill in the art to freeze-dry the starter culture composition of claim 4 of ‘135 in order to preserve the composition, as suggested by claims 5-6 of ‘135, which recite freeze-drying the bacteriophage insensitive mutant.
Claims 1-4 and 6-9 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-6 of U.S. Patent No. 10,041,135 (hereafter ‘135) in view of Kouwen ‘233 (US 2017/0196233 A1; hereafter ‘233) and Hynes et al. (Nature microbiology 2.10 (2017): 1374-1380).
Claim 1 of ‘135 recites “A method for generating a bacteriophage insensitive mutant of a parent strain of Streptococcus thermophilus suitable for food or feed fermentation, comprising: a. exposing the parent strain to a bacteriophage to obtain a bacteriophage insensitive mutant; b. optionally isolating single colonies of the bacteriophage insensitive mutant from step a; c. selecting one or more bacteriophage insensitive mutants which, compared to said parent strain suitable for food or feed fermentation has: i. an increased sedimentation rate and/or ii. an increased chain formation; and d. optionally, isolating single colonies of the bacteriophage insensitive mutant from step c.” Claim 2 of ‘135 limits the parent strain to Streptococcus thermophilus. Claim 3 of ‘135 further limits the method of claim 2 by adding a step of comparing the CRISPR loci of the bacteriophage sensitive Streptococcus thermophilus parent strain with the CRISPR loci of the bacteriophage insensitive mutant and selecting one or more bacteriophage insensitive mutant having CRISPR loci which are identical to the CRISPR loci of the parent strain. Claim 4 of ‘135 further limits the method of claim 1 by adding a step of culturing the BIM and then recovering the BIM from culture medium to provide a starter culture composition. Claim 5 of ‘135 recites adding a cryoprotectant to the BIM of step c. Claim 6 of ‘135 recites freeze drying or freezing the BIM of step c.
Claims 1-6 of ‘135 do not recite exposing the parent strain to a virulent bacteriophage encoding an anti-CRISPR protein and growing surviving lactic acid bacteria for at least 15 cultivation cycles in milk in the presence of at least one bacteriophage which expresses a gene encoding an anti-CRISPR protein.
Claims 1-6 of ‘135 do not recite characterizing at least one isolated BIM by exposing the isolated BIM to at least two different bacteriophages to determine the spectrum of bacteriophage insensitivity, testing the stability of the acquired bacteriophage resistance, and determining the acidification profile without bacteriophage.
Claims 1-6 of ‘135 also do not recite selecting a BIM which is insensitive to more bacteriophage compared to the parent strain, has improved stability of acquired bacteriophage resistance, and has an improved acidification profile without bacteriophage when compared to the parent strain.
Kouwen ‘233 teaches that non-CRISPR resistance mechanisms are preferred to CRISPR resistance because phage can rapidly evolve to overcome CRISPR-mediated resistance ([0023]). Kouwen ‘233 teaches inactivating the CRISPR resistance mechanism of the parent strain by introducing a DNA construct encoding anti-sense RNA to the cas gene ([0014]). The antisense RNA subsequently binds to the target cas mRNA thereby silencing the cas gene ([0014]).
Kouwen ‘233 teaches a step of characterizing at least one isolated BIM by exposing the isolated BIM to at least two different bacteriophages to determine the spectrum of bacteriophage insensitivity, testing the stability of the acquired bacteriophage resistance of the isolated BIM: Table 6 on page 9 shows the relative efficiencies of plaquing of BIMs derived from Streptococcus thermophilus 100-E. BIM100-E-D1A-L5 has a relative efficiency of plaquing that approaches zero for all four tested phages compared to the parent strain. Therefore, BIM100-E-D1A-L5 is insensitive to more bacteriophages compared to the parent strain. Kouwen ‘233 teaches that BIM100-E-D1A-L5 as improved stability of acquired bacteriophage resistance when compared to the parent strain: Table 12 on page 11 indicates that BIM100-E-D1A-L5 is stable over at least 3 cycles of the Heap Lawrence and also confirms that the mechanism of phage resistance is non-CRISPR. Therefore, BIM100-E-D1A-L5’s acquired phage resistance is more stable than that of the parent strain, which had no phage resistance. The Heap Lawrence assay ([0060] of Kouwen ‘233) is a test of how many cycles are required for a phage to overcome the strain’s phage resistance, which is indicated by the inability of the strain to acidify milk. Therefore, Kouwen ‘233 teaches determining the acidification profile of the isolated BIM in milk.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of claims 1-6 of ‘135 by adding a step of inactivating the CRISPR resistance mechanism of the parent strain and characterizing the BIM relative to the parent strain based on the teaching of Kouwen ‘233. One of ordinary skill in the art would have been motivated to select for BIM with non-CRISPR phage resistance with enhanced phage insensitivity and stability relative to the parent strain, without compromising the acidification profile of the BIM, which Kouwen ‘233 taught was a property required for milk fermentation ([0030] and bottom of [0060]).
Regarding the steps of exposing the parent strain to at least one virulent bacteriophage that expresses a gene encoding an anti-CRISPR protein, Hynes teaches challenging S. thermophilus strain CRISPR-immunized against a set of virulent phages (Abstract). The anti-CRISPR (Acr) protein encoded by the phage completely abolishes CRISPR-mediated immunity (Abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the step of inactivating the CRISPR resistance mechanism of the parent strain in the method of claims 1-6 of ‘135 modified by Kouwen ‘233 by introducing a virulent phage encoding an anti-CRISPR protein in order to abolish CRISPR-mediated immunity, as suggested by Hynes. One of ordinary skill in the art would have had a reasonable expectation of success given that Hynes taught virulent phages of S. thermophilus encoding anti-CRISPR proteins that inactivated CRISPR systems. Kouwen ‘233 taught that non-CRISPR resistance mechanisms are preferred to CRISPR resistance. Therefore, one of ordinary skill in the art would have recognized an alternative way to inactivate CRISPR resistance in S. thermophilus that would not have required introducing a DNA construct into S. thermophilus.
Claims 1-6 of ‘135 do not recite growing surviving lactic acid bacteria for at least 15 cultivations cycles in milk in the presence of a bacteriophage that expresses a gene encoding an anti-CRISPR protein upon infection of a host cell.
Kouwen ‘233 teaches in [0020] growing surviving lactic acid bacteria for a single overnight incubation (i.e. one cultivation cycle). Therefore, it also would have been obvious to incubate the parent strain with the virulent bacteriophage encoding an anti-CRISPR protein overnight in milk in order to ensure that the anti-CRISPR protein was produced by the parent strain, thus inactivating the CRISPR system of the parent strain.
It would have been further obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to grow surviving S. thermophilus bacteria (which are lactic acid bacteria, see [0002] of Kouwen ‘233) for at least two cycles in milk with the bacteriophage in order to ensure that non-CRISPR resistance acquired by the bacteria would have been stable over multiple passages (cultivation cycles). It would have been routine optimization to increase the number of cultivation cycles until the desired phenotype would have been observed (stable non-CRISPR resistance) and the person of ordinary skill in the art would have had a reasonable expectation of success that the phenotype of stable non-CRISPR resistance would have been observed based on the teaching of Hynes (see Hynes Abstract).
Regarding instant claim 1 steps d)iii) and e)iii), it would have been further obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to test the ability of the isolated BIM to acidify milk (“determining an acidification profile”) without bacteriophage for industrial applicability. The person of ordinary skill in the art would have had a reasonable expectation of success in determining the acidification profile of the isolated BIM without bacteriophage. Relative to the parent strain, the isolated BIM would have necessarily had an improved acidification profile without the presence of a bacteriophage compared to the acidification profile of the parent strain with bacteriophage because the parent strain is not bacteriophage insensitive.
Regarding claim 2, claims 1-6 of ‘135 do not recite steps A-D of the instant method. Kouwen ‘233 teaches a phage resistance robustness assay with the steps of growing cells of BIMs for 1 hour in 10% RSM (milk), adding phage lysate, incubating the strain and the phage, harvesting supernatant containing phages (“obtained bacteriophages”), mixing supernatant 1:1 with phage lysate (“newly added bacteriophage”) in a new tube, incubating the BIM and phage, and repeating the procedure for many cycles, thereby allowing the phages to adapt to overcome the strain’s phage resistance ([0060]). Kouwen ‘233 teaches that monitoring the number of cycles it takes for phage to become virulent is an indication of the phage robustness ([0060]). Table 12 of on page 11 of Kouwen ‘233 indicates that the cycles are repeated at least 4 times. Therefore, Kouwen ‘233 teaches steps A-D of the instant method. Note that phage robustness of BIMs is a measure of stability of insensitivity.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the technique of Kouwen ‘233 to the method of claims 1-6 of ‘135 modified by Kouwen ‘233 and Hynes in order to assess the stability of phage insensitivity of the BIM. One of ordinary skill in the art would have had a reasonable expectation of success given that the method of Kouwen ‘233 was applicable to BIMs.
Regarding claim 3, the lactic acid bacterium parent strain is Streptococcus thermophilus in the method of claims 1-6 of ‘135. Therefore, the lactic acid bacterium parent strain in the method of claims 1-6 of ‘135 modified by Kouwen ‘233 and Hynes would also have been Streptococcus thermophilus.
Regarding claim 4, claims 1-6 of ‘135 do not recite that the lactic acid bacterium parent strain is mutagenized.
Kouwen ‘233 teaches that the lactic acid bacterium parent strain is mutagenized by chemical mutagenesis or irradiation with UV light (Kouwen ‘233 [0020]).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to include a step of mutagenesis in the method of claim 1 of ‘135 modified by Kouwen ‘233 and Hynes. One of ordinary skill in the art would have recognized that mutagenesis would have increased the chances of the parent strain acquiring a phage resistance mechanism. The person of ordinary skill in the art would have had a reasonable expectation of success in this modification.
Regarding claim 6, claims 1-6 of ‘135 do not recite obtaining bacteriophages from milk and growing isolated BIM in the presence of newly added bacteriophage and obtained bacteriophage for at least 5 cycles. Kouwen ‘233 teaches testing the stability of the acquired bacteriophage resistance of the isolated BIM or at least 4 cycles (Table 12 on page 11), which approaches at least 5 cycles. Therefore, a prima facie case of obviousness exists. See MPEP 2144.05. It would have been obvious to apply the teaching of Kouwen ‘233 to the method of claim 1 of ‘135 modified by Kouwen ‘233 and Hynes.
Regarding claim 7, claims 1-6 of ‘135 do not recite and Kouwen ‘233 and Hynes do not teach that exposing a parent strain to at least two virulent bacteriophages, wherein at least one encodes an anti-CRISPR protein.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to expose a parent strain to two virulent bacteriophages, wherein one encodes an anti-CRISPR protein. One of ordinary skill in the art would have been motivated to simultaneously inactivate the CRISPR resistance mechanism of the parent strain as well as put selective pressure on the parent strain via the introduction of a second virulent phage. One of ordinary skill in the art would have had a reasonable expectation of success in the combination of two steps, each of which would have had predictable results: (1) inactivating the CRISPR resistance mechanism of the parent strain and (2) selecting for phage resistance mechanisms in the host.
Regarding claims 8-9, claim 5 of ‘135 recites adding a cryoprotectant to the BIM and claim 6 of ‘135 recites freeze-drying the BIM.
Claims 12-13 and 21-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 of U.S. Patent No. 10,041,135 (hereafter ‘135) in view of Kouwen ‘468 (US 2017/0218468 A1).
See discussion of claims 1-6 of ‘135 above, which is incorporated into this rejection as well.
Regarding claim 12, claims 1-6 of ‘135 do not recite a process for production of a dairy product comprising acidifying a starter culture composition with one or more bacteriophage-insensitive mutants.
Kouwen ‘468 teaches a method for the construction of a bacteriophage insensitive mutant (Kouwen ‘468 claim 1). Kouwen ‘468 also teaches a process for the production of a dairy product comprising adding a bacteriophage insensitive mutant of a bacteriophage sensitive Streptococcus thermophilus parent strain to a medium to be fermented (Kouwen ‘468 claim 15). Kouwen ‘468 teaches that both the parent strain and the BIM acidify milk ([0076] and [0084]).
It would have been obvious to add the BIM of claim 1 of ‘135 to a medium to be fermented (“starter culture composition”) in order to produce a dairy product such as fermented milk or cheese, per the teaching of Kouwen ‘468. One of ordinary skill in the art would have had a reasonable expectation of success given that the BIM of claim 1 of ‘135 is derived from a Streptococcus thermophilus parent strain and is suitable for fermentation.
Regarding claims 13 and 21-22, claims 1-6 of ‘135 do not recite a fermented milk or cheese dairy product comprising a bacteriophage insensitive mutant.
However, Kouwen ‘468 teaches a fermented milk or cheese dairy product comprising a bacteriophage insensitive mutant derived from a Streptococcus thermophilus parent strain (see Kouwen ‘468 claims 10-11), which is a lactic acid bacterium.
Therefore, it would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to acidify a starter culture composition with the BIM produced by the method of claims 1-6 of ‘135 in order to produce a fermented milk or cheese dairy product per the teaching of Kouwen ‘468. The person of ordinary skill in the art would have had a reasonable expectation of success in acidifying the starter culture composition given that claims 1-6 of 135 require that the BIM is suitable for food fermentation.
Claims 10-14 and 21-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4-5, 8-10, and 19-20 of U.S. Patent No. 10,519,519 (hereafter ‘519). Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims 10-11, 13-14, and 22 are anticipated by claims 1, 4-5, 8-10, and 19-20 of ‘519 and instant claims 12 and 21 are obvious over conflicting claims 12 and 21.
Claim 1 of ‘519 recites a bacteriophage insensitive mutant of a parent strain of Streptococcus thermophilus. Claim 4 of ‘519 recites a starter culture composition suitable for inoculation of a medium to be fermented on an industrial scale comprising the bacteriophage insensitive mutant (BIM) according to claim 1. Claim 5 of ‘519 recites the starter culture composition according to claim 4 wherein the starter culture composition is frozen, freeze-dried or in liquid form. Claim 8 of ‘519 is drawn to a bacteriophage insensitive mutant. Claim 9 of ‘519 recites that the BIM of claim 8 has a bacteriophage sensitive parent strain. Claim 10 of ‘519 recites the bacteriophage insensitive mutant of claim 9 wherein the mutant has CRISPR loci which are identical to the CRISPR loci of the sensitive Streptococcus thermophilus strain. Claims 19-20 of ‘519 are drawn to a fermented milk product or cheese comprising a starter culture composition comprising a bacteriophage insensitive mutant.
Instant claims 10-11 are anticipated by claims 4-5 of ‘519. Instant claims 13-14 are anticipated by claims 1 and 8-10 of ‘519.
Instant claim 22 is anticipated by claims 19-20 of ‘519.
Regarding instant claims 12 and 21, claims 1, 4-5, 8-10, and 19-20 of ‘519 do not recite a process for production of a fermented milk product or cheese comprising acidifying a starter culture composition with one or more of the BIMs.
Since claim 19 of ‘519 is drawn to a fermented milk product or cheese comprising a starter culture composition suitable for inoculation of a medium to be fermented, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to ferment (“acidify”) the starter culture composition of claim 4 of ‘519 comprising a BIM, per its intended use (inoculating a medium to be fermented) in order to produce a fermented milk product or cheese. The person of ordinary skill in the art would have had a reasonable expectation of success.
Claims 10-11, 13-14, and 22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7 and 11 of U.S. Patent No. 10,244,771 (hereafter ‘771). Although the claims at issue are not identical, they are not patentably distinct from each other because instant claims 13-14 are anticipated by claim 7 of ‘771 and claims 10-11 and 22 are obvious over conflicting claim 11 of ‘771.
Claim 7 of ‘771 recites a bacteriophage-insensitive mutant of a Streptococcus thermophilus parent strain wherein the CRISPR loci of the bacteriophage-insensitive mutant are identical to the CRISPR loci of the parent Streptococcus thermophilus. Claim 11 of ‘771 recites a process for production of a dairy product optionally a fermented milk product or cheese comprising adding the bacteriophage-insensitive mutant of the Streptococcus thermophilus parent strain as defined in claim 7 to a milk product.
Claims 13-14 are anticipated by claim 7 of ‘771.
Claims 10-11 and 22 are unpatentable over claim 11 of ‘771 because the outcome of adding the BIM to a milk product, as recited in claim 11 of ‘771, is a liquid starter culture composition. Regarding the instant claim 11, fermented milk products such as yogurt are liquids.
Claims 1-4 and 6-7 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 10,244,771 (hereafter ‘771) in view of Kouwen ‘233 (US 2017/0196233 A1; hereafter ‘233) and Hynes et al. (Nature microbiology 2.10 (2017): 1374-1380).
Claim 1 of ‘771 recites a method for the isolation of bacteriophage-insensitive mutants from a Streptococcus thermophilus parent strain comprising: (a) inactivating the CRISPR resistance mechanism of the parent strain, (b) exposing the parent strain obtained in step (a) to a bacteriophage to obtain bacteriophage insensitive mutants, (c) isolating the bacteriophage insensitive mutants, (d) comparing the CRISPR loci of the parent strain with the CRISPR loci of the bacteriophage insensitive mutants and (e) selecting bacteriophage insensitive mutants of which the CRISPR loci are identical to the CRISPR loci of the parent strain.
Claim 1 of ‘771 does not recite exposing said parent strain to at least one virulent bacteriophage that expresses a gene encoding an anti-CRISPR protein.
Claim 1 of ‘771 does not recite characterizing the isolated BIM by exposing the BIM to at least two different bacteriophages to determine the spectrum of bacteriophage insensitivity, testing the stability of the acquired bacteriophage resistance, and determining the acidification profile of the isolated BIM in milk without the presence of a bacteriophage.
Claim 1 of ‘771 does not teach selecting a BIM which when compared to the parent strain is insensitive to more bacteriophages, has improved stability of acquired bacteriophage resistance, and has an acidification profile without the presence of a bacteriophage which is improved when compared to the parent strain.
Regarding the steps of characterizing and selecting the BIM, Kouwen ‘233 teaches a step of characterizing at least one isolated BIM by exposing the isolated BIM to at least two different bacteriophages to determine the spectrum of bacteriophage insensitivity and testing the stability of the acquired bacteriophage resistance of the isolated BIM: Table 6 on page 9 shows the relative efficiencies of plaquing of BIMs derived from Streptococcus thermophilus 100-E. BIM100-E-D1A-L5 has a relative efficiency of plaquing that approaches zero for all four tested phages compared to the parent strain. Therefore, BIM100-E-D1A-L5 is insensitive to more bacteriophages compared to the parent strain. Kouwen ‘233 teaches that BIM100-E-D1A-L5 has improved stability of acquired bacteriophage resistance when compared to the parent strain: Table 12 on page 11 indicates that BIM100-E-D1A-L5 is stable over at least 3 cycles of the Heap Lawrence and also confirms that the mechanism of phage resistance is non-CRISPR. Therefore, BIM100-E-D1A-L5’s acquired phage resistance is more stable than that of the parent strain, which had no phage resistance. The Heap Lawrence assay ([0060] of Kouwen ‘233) is a test of how many cycles are required for a phage to overcome the strain’s phage resistance, which is indicated by the inability of the strain to acidify milk. Therefore, Kouwen ‘233 teaches determining the acidification profile of the isolated BIM in milk.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of claim 1 of ‘771 by adding a step of characterizing the BIM relative to the parent strain based on the teaching of Kouwen ‘233. One of ordinary skill in the art would have been motivated to select for BIM with enhanced phage insensitivity and stability relative to the parent strain, without compromising the acidification profile of the BIM, which Kouwen ‘233 taught was a property required for milk fermentation ([0030] and bottom of [0060]).
Regarding the step of exposing the parent strain to at least one virulent bacteriophage that expresses a gene encoding an anti-CRISPR protein, Hynes teaches challenging S. thermophilus strain CRISPR-immunized against a set of virulent phages (Abstract). The anti-CRISPR (Acr) protein encoded by the phage completely abolishes CRISPR-mediated immunity (Abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the step of inactivating the CRISPR resistance mechanism of the parent strain in the method of claim 1 of ‘771 modified by Kouwen ‘233 by introducing a virulent phage encoding an anti-CRISPR protein in order to abolish CRISPR-mediated immunity, as suggested by Hynes. One of ordinary skill in the art would have had a reasonable expectation of success given that Hynes taught virulent phages of S. thermophilus encoding anti-CRISPR proteins that inactivated CRISPR systems. Kouwen ‘233 taught that non-CRISPR resistance mechanisms were preferred to CRISPR resistance. Therefore, one of ordinary skill in the art would have recognized an alternative way to inactivate CRISPR resistance in S. thermophilus that would not have required introducing a DNA construct into S. thermophilus.
Claim 1 of ‘771 does not recite growing surviving lactic acid bacteria for at least 15 cultivation cycles in milk in the presence of at least one bacteriophage that expresses a gene encoding an anti-CRISPR protein.
Kouwen ‘233 already taught that in a preferred embodiment exposing the parent strain to a bacteriophage is carried out in milk overnight or until clotting is observed ([0020]). Thus, Kouwen ‘233 teaches one cultivation cycle.
Kouwen ‘233 does not teach growing surviving lactic acid bacteria for at least 15 cycles in milk in the presence of at least one bacteriophage encoding an anti-CRISPR protein.
However, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to grow surviving S. thermophilus bacteria (which are lactic acid bacteria, see [0002] of Kouwen ‘233) for at least two cycles in milk with the bacteriophage in order to ensure that non-CRISPR resistance acquired by the bacteria would have been stable over multiple passages (cultivation cycles). It would have been routine optimization to increase the number of cultivation cycles until the desired phenotype would have been observed (stable non-CRISPR resistance) and the person of ordinary skill in the art would have had a reasonable expectation of success that the phenotype of non-CRISPR resistance would have been observed based on the teachings of Hynes (see Hynes Abstract).
Regarding instant claim 1 step d)iii) and e)iii), it would have been further obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to test the ability of the isolated BIM to acidify milk (“determining an acidification profile”) without bacteriophage for industrial applicability. The person of ordinary skill in the art would have had a reasonable expectation of success in determining the acidification profile of the isolated BIM without bacteriophage. Relative to the parent strain, the isolated BIM would have necessarily had an improved acidification profile without the presence of a bacteriophage compared to the acidification profile of the parent strain with bacteriophage because the parent strain is not bacteriophage insensitive.
Regarding claim 2, claim 1 of ‘771 does not recite steps A-D of the instant method. Kouwen ‘233 teaches a phage resistance robustness assay with the steps of growing cells of BIMs for 1 hour in 10% RSM (milk), adding phage lysate, incubating strain and phage, harvesting supernatant containing phages (“obtained bacteriophages”), mixing supernatant 1:1 with phage lysate (“newly added bacteriophage”) in a new tube, incubating the BIM and phage, and repeating the procedure for many cycles, thereby allowing the phages to adapt to overcome the strain’s phage resistance ([0060]). Kouwen ‘233 teaches that monitoring the number of cycles it takes for phage to become virulent is an indication of the phage robustness ([0060]). Table 12 of on page 11 of Kouwen ‘233 indicates that the cycles are repeated at least 4 times. Therefore, Kouwen ‘233 teaches steps A-D of the instant method. Note that phage robustness of BIMs is a measure of stability of insensitivity. It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the technique of Kouwen ‘233 to the method of claim 1 of ‘771 modified by Kouwen ‘233 and Hynes in order to assess the stability of phage insensitivity of the BIM.
Regarding claim 3, the lactic acid bacterium parent strain is Streptococcus thermophilus in the method of claim 1 of ‘771. Therefore, the lactic acid bacterium parent strain in the method of claim 1 of ‘771 modified by Kouwen ‘233 and Hynes would also have been Streptococcus thermophilus.
Regarding claim 4, claim 1 of ‘771 does not recite that the lactic acid bacterium parent strain is mutagenized.
Kouwen ‘233 teaches that the lactic acid bacterium parent strain is mutagenized by chemical mutagenesis or irradiation with UV light (Kouwen ‘233 [0020]).
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to include a step of mutagenesis in the method of claim 1 of ‘771 modified by Kouwen ‘233 and Hynes. One of ordinary skill in the art would have recognized that mutagenesis would have increased the chances of the parent strain acquiring a non-CRISPR resistance mechanism. The person of ordinary skill in the art would have had a reasonable expectation of success in this modification.
Regarding claim 6, claim 1 of ‘771 does not recite obtaining bacteriophages from milk and growing isolated BIM in the presence of newly added bacteriophage and obtained bacteriophage for at least 5 cycles.
Kouwen ‘233 teaches testing the stability of the acquired bacteriophage resistance of the isolated BIM or at least 4 cycles (Table 12 on page 11), which approaches at least 5 cycles. Therefore, a prima facie case of obviousness exists. See MPEP 2144.05.
It would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to apply the teaching of Kouwen ‘233 to the method of claim 1 of ‘771 modified by Kouwen ‘233 and Hynes. The person of ordinary skill in the art would have had a reasonable expectation of success in this modification.
Regarding claim 7, claim 1 of ‘771 does not recite and Kouwen ‘233 and Hynes do not teach that exposing the parent strain to at least two virulent bacteriophages, wherein at least one encodes an anti-CRISPR protein.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to expose a parent strain to two virulent bacteriophages, wherein one encodes an anti-CRISPR protein. One of ordinary skill in the art would have been motivated to simultaneously inactivate the CRISPR resistance mechanism of the parent strain as well as put selective pressure on the parent strain via the introduction of a second virulent phage. One of ordinary skill in the art would have had a reasonable expectation of success in the combination of two steps, each of which would have had predictable results: (1) inactivating the CRISPR resistance mechanism of the parent strain and (2) selecting for phage resistance mechanisms in the host.
Claims 8-9 rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 10,244,771 (hereafter ‘771) in view of Kouwen ‘233 (US 2017/0196233 A1; hereafter ‘233) and Hynes et al. (Nature microbiology 2.10 (2017): 1374-1380), as applied to claims 1-4 and 6-7 above, further in view of Kouwen ‘468 (US 2017/0218468 A1) and as evidenced by Carvalho et al. (International Dairy Journal 14.10 (2004): 835-847; cited in the Non-Final Action mailed on10/13/2023)..
See discussion of claim 1 of ‘771, Kouwen ‘233, and Hynes above, which is incorporated into this rejection as well.
Regarding claims 8-9, claim 1 of ‘771 does not recite and Kouwen ‘233 and Hynes do not teach that the method further comprises freeze-drying the BIM.
Kouwen ‘468 teaches a method for the construction of a bacteriophage insensitive mutant (Kouwen ‘468 claim 1).
Regarding claim 8, Kouwen ‘468 teaches a step of adding a cryoprotectant to the BIM (Kouwen ‘468 claim 6).
Regarding claim 9, Kouwen ‘468 teaches a step of freeze-drying the BIM (Kouwen ‘468 claim 7).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify the method of claim 1 of ‘771 modified by Kouwen 233 and Hynes by adding a step of adding a cryoprotectant and a step of freeze-drying the BIM, per the teaching of Kouwen ‘468. One of ordinary skill in the art would have been motivated to preserve the BIM. One of ordinary skill in the art would have had a reasonable expectation of success given that freeze-drying with a cryoprotectant is commonly used to preserve bacteria as evidenced by Carvalho (Abstract and 5. Drying medium, right column, first paragraph, page 840).
Claims 12-13 and 21-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 10,244,771 (hereafter ‘771) in view of Kouwen ‘468 (US 2017/0218468 A1).
See discussion of claim 1 of ‘771 above, which is incorporated into this rejection as well.
Regarding claim 12, claim 1 of ‘771 does not recite a process for production of a dairy product comprising acidifying a starter culture composition with one or more bacteriophage-insensitive mutants.
Kouwen ‘468 teaches a process for the production of a dairy product comprising adding a bacteriophage insensitive mutant of a bacteriophage sensitive Streptococcus thermophilus parent strain to a medium to be fermented (Kouwen ‘468 claim 15). The BIM acidifies milk ([0084]). Kouwen ‘468 teaches that the parent strain and the BIM acidify milk ([0076] and [0084]).
It would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to add the BIM to a medium to be fermented (“starter culture composition”) in order to produce a dairy product by acidifying the medium, per the teaching of Kouwen ‘468. One of ordinary skill in the art would have had a reasonable expectation of success given that the BIM of claim 1 of ‘771 is derived from a Streptococcus thermophilus parent strain.
Regarding claims 13 and 21-22, claim 1 of ‘771 does not recite a fermented milk or cheese dairy product comprising a bacteriophage insensitive mutant.
However, Kouwen ‘468 teaches a fermented milk or cheese dairy product comprising a bacteriophage insensitive mutant derived from a Streptococcus thermophilus parent strain (see Kouwen ‘468 claims 10-11).
Therefore, it would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to use the BIM produced by the method of claim 1 of ‘771 in a starter culture composition to produce a fermented milk or cheese dairy product per the teaching of Kouwen ‘468. The person of ordinary skill in the art would have had a reasonable expectation of success in the modification.
Suggested Claim Amendment
Applicant may consider amending claim 1-2 as follows in order to obviate the rejections of claim 1 under 35 U.S.C. 112(b) and 35 U.S.C. 103.
A method for obtaining a non-CRISPR and bacteriophage-insensitive
mutant (BIM) from a lactic acid bacterium parent strain comprising:
a) exposing said parent strain to at least one virulent bacteriophage which
expresses a gene encoding an anti-CRISPR protein upon infection of said parent strain
b) growing surviving lactic acid bacteria for at least 15 cultivation cycles in milk in
the presence of said at least one bacteriophage which expresses a gene
encoding an anti-CRISPR protein upon infection of the growing lactic acid bacteria
c) isolating at least one BIM[[s]] resulting from b;
d) characterizing the at least one isolated BIM by:
i) exposing said at least one isolated BIM to at least two different bacteriophages
ii) testing the stability of the acquired bacteriophage resistance of said at
least one isolated BIM by:
A) growing the at least one isolated BIM in milk in the presence of a bacteriophage;
B) obtaining bacteriophages from the resulting milk of A;
C) growing said at least one isolated BIM in milk in the presence of newly added bacteriophage and the bacteriophages obtained in B; and
D) repeating obtaining bacteriophages from the resulting milk and growing of said at least one isolated BIM in milk in the presence of newly added bacteriophage and the obtained bacteriophages for at least a total of 3 cultivation cycles to determine the number of cultivation cycles of survival of the at least one isolated BIM as a measure for stability of insensitivity in batch cultures with evolving bacteriophage present;
iii) fermenting the at least one isolated BIM in milk at 42 °C without the presence of a bacteriophage while monitoring the pH and determining the time for the BIM-fermented milk to reach pH 5.2
e) characterizing the parent strain by:
i) exposing said parent strain to at least two different bacteriophages;
ii) testing the stability of any bacteriophage resistance of said parent strain by:
A) growing the parent strain in milk in the presence of a bacteriophage;
B) obtaining bacteriophages from the resulting milk of A;
C) growing the parent strain in milk in the presence of newly added bacteriophage and the bacteriophages obtained in B; and
D) repeating obtaining bacteriophages from the resulting milk and growing of said parent strain in milk in the presence of newly added bacteriophage and the obtained bacteriophages for at least a total of 3 cultivation cycles to determine the number of cultivation cycles of survival of the parent strain;
iii) fermenting the parent strain in milk at 42 °C without the presence of a bacteriophage while monitoring the pH and determining the time for the parent strain-fermented milk to reach pH 5.2;
f) and selecting a BIM from the at least one isolated BIM which:
i) when compared to the parent strain is insensitive to more bacteriophages as determined in d[[ ]](i) and e(i);
ii) when compared to the parent strain has an improved stability of the
acquired bacteriophage resistance as determined in d(ii) and e(ii); and
iii) ferments the milk at 42 °C without the presence of a bacteriophage to a pH of 5.2 in less time than the parent strain
(Cancelled)
The following is a statement of reasons for the indication of allowable subject matter: the prior art does not teach the required steps in a method for selecting a non-CRISPR and bacteriophage-insensitive mutant (BIM) lactic acid bacterium, which ferments milk to a pH of 5.2 at 42 °C without the presence of a bacteriophage in less time than the parent strain.
Although Kouwen ‘233 teaches a method for selecting a non-CRISPR and bacteriophage-insensitive mutant of a lactic acid bacterium (Kouwen ‘233 claim 1), Kouwen ‘233 does not teach the acidification profile without bacteriophage of the resulting BIM. Likewise, although Kouwen 468 teaches a method for selecting a non-CRISPR and bacteriophage-insensitive mutant (Kouwen ‘468 claim 4), the method results in a BIM with similar acidification activities to the parent strain ([0084]).
Mills (Journal of microbiological methods 70.1 (2007): 159-164) teaches a method for the generation of BIM (Title). Mills’s method also requires 20-25 passages in milk (left column, step 3 on page 161), which is analogous to step b) of the claimed method (“growing surviving lactic acid bacteria for at least 15 cultivation cycles in milk”). However, Mills’s method results in BIMs with similar acidification activity to the parent strain: “all BIMs retained the starter activity profile of their respective parent strains, indicating that their acid-producing capabilities had not been compromised in any way during the acquisition of phage resistance” (page 163, right column, paragraph 3). Thus, Mills does not teach that the BIMs ferment milk to a pH of 5.2 at 42 °C, without the presence of a bacteriophage, in less time than the parent strain. In addition, Mills’s method does not select for non-CRISPR resistance.
Therefore, the person of ordinary skill in the art would have been unable to predict that a non-CRISPR and bacteriophage-insensitive mutant obtained in step c) of the claimed method is capable of fermenting milk to a pH of 5.2 at 42 °C without the presence of bacteriophage in less time than the parent strain.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CANDICE LEE SWIFT whose telephone number is (571)272-0177. The examiner can normally be reached M-F 8:00 AM-4:30 PM (Eastern).
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, Louise Humphrey can be reached at (571)272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657
Prosecution Insights