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
The amended claim set filed 9 Feb 2022 is acknowledged. Claims 1-12 are currently pending. Of those, claims 3-8 are currently amended, and no claims are new or withdrawn. No claims are cancelled. Claims 1-12 will be examined on the merits herein.
Priority
The applicant’s priority claim to provisional application 62/887,790 is acknowledged. The instant application is a 371 of PCT/IB2020/056846. The effective filing date for claims 1-12 is 16 Aug 2019.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 7 Apr 2022 was filed in compliance with the provisions of 37 CFR 1.97, except as discussed here.
The IDS has a typographical error. Applicant submitted a copy of JP-H06113823-A, but the IDS reads JP-H06223823-A. Applicant did not submit a copy of JP-H06223823-A, so that reference has not been considered. The Examiner has considered the reference JP-H06113823-A that was submitted, and this reference has been listed on the PTO-892 form.
Copies were not submitted for the foreign references WO-2013080561-A1 and WO-2011151941-A1 as required by 37 CFR 1.98. Nevertheless, the references have been considered; the reference is listed on the PTO-892 form and a copy is enclosed with this action.
Accordingly, the information disclosure statement has been considered by the examiner. A signed copy of the statement is attached with this action.
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. 37 CFR 1.823(b)(1)(iii) and 37 CFR 1.77(b)(5)(i) require the size of the file be listed in bytes, not KB. For Applicant’s convenience, Office’s measurement of the size in bytes for the most recent sequence listing is reproduced below.
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Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
References to the specification in this action will use paragraph numbers taken from Pre-Grant Publication US-20250270498-A1 in order to avoid ambiguity caused by different page and line numbers in different versions of the specification.
The disclosure is objected to because of the following informalities: at [0020], the specification states “The disclosed subject matter may be understood more readily by reference to the following detailed description taken in connection with the accompanying figures, which form a part of this disclosure.” (emphasis added). However, there are no accompanying figures. Appropriate correction is required.
The use of the term HY-Peptone in the specification, such as at [0093], [0099], [0195], which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 1, 3-5, and 9-11 are objected to because of the following informalities: the genus Clostridium should be italicized to be consistent with conventions in the field. Appropriate correction is required.
Claims 4 and 10 are objected to because of the following informalities: the claims are incomplete because they reference Table 1 in the specification. See MPEP 2173.05(s): “Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience." Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted).” Appropriate correction is required.
Claims 5 and 11 are objected to under 37 CFR 1.75 as being a substantial duplicate of claims 4 and 10, respectively. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m). Table 1 in the specification shows that the strains listed in Table 1 have rDNA fragments with SEQ ID NOs: 1-17, so the groups of bacterial strains claimed are identical between the two claims despite being claimed in different language.
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.
Claims 1-12 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.
Regarding claim 1, 3-5, 7, and 9-11, claim 1 which requires the media be “for culturing a bacterial strain belonging to Clostridium genus.” However, it is unclear how the term “Clostridium genus” is defined in the context of the claim. The generally accepted use of the term “Clostridium genus” refers to bacteria where “Clostridium” is the genus name in their scientific name. For example, Salvetti et al. (2011; PTO-892) teaches that Lactobacillus catenaformis and Lactobacillus vitulinus are within the Clostridia rRNA cluster XVII and should be reclassified into new genera as Eggerthia catenaformis and Kandleria vitulina, respectively (Abstract). Using the generally accepted definition, these bacteria are not within the Clostridium genus despite being within the Clostridia rRNA cluster because their genus is Eggerthia or Kandleria.
However, the term “Clostridium genus” is indefinite because the specification and claims indicate that the term is used more broadly than the art-accepted definition, but do not provide a clear, limiting definition for the term. The specification states at [0042] that: “the cluster of “bacteria belonging to the genus Clostridium” can be identified, for example, as follows. Specifically, the bacteria belonging to the genus Clostridium are classified by PCR using a primer set consisting of SEQ ID NOs 18 and 19 (for Clostridium spp. belonging to the cluster XIVa) or a primer set consisting of SEQ ID NOs 20 and 21 (for Clostridium spp. belonging to the cluster IV). In addition, the bacteria belonging to the genus Clostridium are classified by sequencing of 16S rRNA gene amplified using a primer set consisting of SEQ ID NOs 22 and 23.” The use of “for example” means that this definition is only an example of how to identify Clostridium bacteria and is not a limiting definition.
Claims 3-5 and 9-11 limit the “bacterial strain belonging to Clostridium genus”, but the groups listed include bacteria that do not all belong to the Clostridium genus. See Table 1 in the specification, which includes both Clostridium and non-Clostridium genus bacteria, and indicates that these species have the claimed rDNA sequences. Also, Guo et al. (2020; PTO-892) teaches that Clostridium cluster IV and XIVa both comprise non-Clostridium genus bacteria: “Clostridium cluster IV, also called C. leptum group, have 4 members, namely C. leptum, C. sporosphaeroides, C. cellulosi and Faecalibacterium prausnitzii (F. prausnitzii). Clostridium cluster XIVa, also known as Clostridium coccoides group, consists of 21 species. Except Clostridium spp., Acetitomaculum ruminis, Roseburia cecicola, Coprococcus eutactus, Ruminococcus torques, Streptococcus hansenii and Eubacterium cellulosolvens are also included in Clostridium species [5, 12]”. The references cited are both published before the effective filing date, indicating that they were available to one of ordinary skill in the art at the time of filing.
Therefore, claim 1 is rejected as indefinite because it is unclear how the term “Clostridium genus” is defined, and claims 2-12 are also rejected because they do not resolve this ambiguity. Also, claims 3-5, 7, and 9-11 are also rejected as indefinite because it is unclear whether these claims are limited to bacteria from the claimed groups that also have Clostridium as the genus name, or whether the claims are broader and include the species of the group that do not have Clostridium as the genus name. In the interest of compact prosecution, in this action, the term “Clostridium genus” is interpreted broadly as being within the Clostridium rRNA gene cluster, including those that do not have the genus name Clostridium and those that do not match the primer sets disclosed in the specification.
Regarding claims 1 and 2, each of these claims recite “a medium comprising:” and then a list of ingredients (a) through (e), but there is no “and” or “or” before the final ingredient (e). Therefore, the bounds of the claim are unclear because the medium might only need to comprise one of (a)-(e) (i.e. “or”) or the medium might need to comprise all of (a)-(e) (i.e. “and”). This grounds of rejection also applies to claims 2-12 because they depend from claim 1 and do not resolve this ambiguity. For the sake of compact prosecution, in this action, the claim is interpreted as requiring all elements (i.e. “and), in view of the specification’s teaching of media comprising all ingredients (Example 10).
Regarding claim 6, the claim recites “the medium is maintained in anaerobic conditions.” The claim does not clearly indicate whether this is a intended use for the medium (i.e. the medium must be capable of being maintained in these conditions, see MPEP 2111.02, MPEP 2111.04 and In re Schreiber), or whether this is a structural limitation of the medium (i.e. the medium must have “a substantially oxygen-free culture condition”, see definition at [0035]). If the “anaerobic conditions” are structurally limiting, then the term “substantially” in the definition is a relative term that renders the claim indefinite. The term “substantially” is not defined in the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. One of ordinary skill would not be able to identify whether or not media comprising a small amount of oxygen meets the claimed requirement of being “substantially oxygen-free.” Therefore, the claim is indefinite. For the sake of compact prosecution, in this action, the limitation is interpreted as a non-limiting intended use.
Regarding claim 7, the claim is rejected because it contains a Markush group but recites the phrase “16S rDNA sequences selected from the group: SEQ ID NO: 1…”. The instant claim should instead contain closed language (i.e., it should recite “selected from the group consisting of”). See MPEP 2173.05(h), which states “A Markush grouping is a closed group of alternatives, i.e., the selection is made from a group ‘consisting of’ (rather than ‘comprising’ or ‘including’) the alternative members. Abbott Labs., 334 F.3d at 1280, 67 USPQ2d at 1196. If a Markush grouping requires a material selected from an open list of alternatives (e.g., selected from the group ‘comprising’ or ‘consisting essentially of’ the recited alternatives), the claim should generally be rejected under 35 U.S.C. 112(b) as indefinite because it is unclear what other alternatives are intended to be encompassed by the claim. If a claim is intended to encompass combinations or mixtures of the alternatives set forth in the Markush grouping, the claim may include qualifying language preceding the recited alternatives (such as ‘at least one member’ selected from the group), or within the list of alternatives (such as ‘or mixtures thereof’).”
Regarding claim 8, like claims 1-2, claim 8 recites a list (a)-(c) of method steps; however, there is no “and” or “or” before the final step (c). Therefore, the claim is indefinite because one of ordinary skill in the art would not be able to determine whether only one of the claimed steps is required (“or”) or whether all steps are required (“and”). This rejection also applies to claims 9-12 because they depend from claim 8 and do not resolve the ambiguity. For the sake of compact prosecution, in this action, the claim is interpreted as requiring all elements (i.e. “and).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-6, 8, and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Salvetti et al. (2011; PTO-892) as evidenced by FDA “BAM Media M24: Brain Heart Infusion (BHI) Broth and Agar (Equivalent media are available from Difco and BBL)” (2001; PTO-892) in view of Zhou et al. (CN-109097310-A; PTO-892), Jung et al. (US-20110091937-A1; PTO-892), Kim et al. (KR-20030063960-A; PTO-892), and Van Dien et al. (WO-2010141920-A2; PTO-892).
Regarding claims 1-2, Salvetti teaches a peptone medium comprising 20 g/L phytone peptone, 20 g/L proteose peptone, 12.5 g/L yeast extract (5 g normal + 7.5 mL freshly prepared), and 5 g/L of K2HPO4, and 20 g/L of BHI broth (pg. 2521 col. 1 par. 1). The instant specification teaches that M9 salts comprise: 33.9 g/L Na2HPO4, 15 g/L KH2PO4, 5 g/L NH4Cl, and 2.5 g/L NaCl [0079-0083]. The FDA provides evidence that BHI broth comprises NaCl, Na2HPO4, and dextrose/glucose (Table 1). Salvetti teaches the use of this media to grow Lactobacillus catenaformis and Lactobacillus vitulinus, which are placed within the Clostridia rRNA cluster XVII (Abstract).
Regarding the intended uses of claims 3-5, MPEP 2111.04 is clear that “Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure.” See MPEP 2111.02: “To satisfy an intended use limitation which is limiting, a prior art structure which is capable of performing the intended use as recited in the preamble meets the claim. See, e.g., In re Schreiber, 128 F.3d 1473, 1477, 44 USPQ2d 1429, 1431 (Fed. Cir. 1997).” There is no evidence of record to suggest that the Salvetti media, which is capable of growing one Clostridia species, would not be capable of growing at least one bacteria from the claimed groups for at least some small level of growth.
Regarding claim 8, Salvetti teaches growing the bacteria in the broth medium and describes the incubation conditions (pg. 2521 col. 1 par. 1), so it inherently teaches providing a container (i.e. bioreactor), mixing the culture and bacteria, and incubating the mixture.
Regarding claims 6 and 12, Salvetti teaches bacterial growth in anaerobic conditions (pg. 2521 col. 1 par. 1). So, Salvetti also teaches that the medium is capable of being in those conditions.
Salvetti does not teach the media comprises NH4Cl, and does not teach the exact ingredient ratios of claims 1-2.
Zhou teaches an “inorganic salt medium composed of NaCl 24g/L, KCl 0.7g/L, MgSO4*7H2O 7g/L, NH4Cl 1g/L, NaNO3 0.5g/L, KH2PO4 2g/L, Na2HPO4 3g/L” (claim 3), and teaches that this medium can be used to grow and screen for Clostridium sp. LZ25 (claims 2-3). This medium comprises all salts from the M9 salt mixture.
Jung teaches the amounts of glucose, yeast extract, phytone peptone, and other ingredients in each media described above may be within the range of 0.2 wt % to 3 wt %, respectively, based on total weight of the media [0016], which corresponds with 2-30 g/L of ingredients. Jung teaches specific examples where phytone peptone is 1% (10 g/L) and 0.5% glucose (5 g/L) [Table 1], and 1% glucose (10 g/L) [0049]. Jung teaches this media is useful for growing Clostridium bacteria [Title, Abstract].
Kim teaches amounts of proteose peptone can be 10 g/L and glucose can be 10 g/L, and that the media is grown anaerobically to cultivate gastrointestinal contents (Example 1); Kim teaches the probiotic microorganism can be Clostridium (pg. 7 par. 5).
Van Dien teaches M9 minimal medium comprises 6.78 g/L Na2HPO4, 3.0 g/L KH2PO4, 0.5 g/L NaCl, and 1.0 g/L NH4Cl (pg. 90 ln. 14-15). This is more than the claimed quantities of 0.39 g/L Na2HPO4 (11.4 g/L of an ingredient at 33.9 g/L), 0.17 g/L KH2PO4 (ingredient at 15 g/L), 0.06g/L NH4Cl (ingredient at 5 g/L) and 0.03 g/L NaCl (ingredient at 2.5 g/L).
One of ordinary skill in the art at the time of filing would consider it prima facie obvious to modify the Clostridium media of Salvetti by combining with the Clostridium media of Zhou and optimizing within the concentration ranges disclosed in the art collectively cited here, thereby arriving at the claimed invention, because all ingredients were known in the art at the time of filing and were known to be useful to grow Clostridium. The modification could have been performed with a reasonable expectation of success because the modification only requires mixing known compositions. "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art." In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980) (citations omitted).
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case all elements (i.e. the Salvetti and Zhou media; or alternately, proteose peptone, phytone peptone, yeast extract, Na2HPO4, KH2PO4, NH4Cl, NaCl, and glucose; and methods of using these media to grow Clostridium bacteria) were known in the art. In addition, combining these elements yields a method/composition wherein each element merely performs the same function as it does separately; thus the results of the combination would be recognized as predictable to one of ordinary skill in the art.
Although the concentrations of Salvetti and Zhou differ from the concentrations of instant claims 1-2, the claimed concentrations are within the ranges disclosed in the art collectively cited here. See MPEP section 2144.05 II, which states: “Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. ‘[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.’ In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (Claimed process which was performed at a temperature between 40°C and 80°C and an acid concentration between 25% and 70% was held to be prima facie obvious over a reference process which differed from the claims only in that the reference process was performed at a temperature of 100°C and an acid concentration of 10%.); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (‘The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages.’)” The selection of specific nutrient concentrations would have been a routine matter of optimization on the part of the artisan of ordinary skill, said artisan recognizing that bacterial viability may be affected by these concentrations. There is no evidence of record that these concentrations are critical because the instant specification only disclosed that Clostridium strains grow on this media and did not compare with media lacking the ingredients or media with concentrations outside of the claimed ranges (see Example 10 in the instant specification).
Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMELIA NICOLE DICKENS whose telephone number is (571)272-0381. The examiner can normally be reached M-R 8:30-4:30, and every other F 8:30-4:30 (EDT/EST).
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/AMELIA NICOLE DICKENS/Examiner, Art Unit 1645
/GARY B NICKOL/Supervisory Patent Examiner, Art Unit 1645