DETAILED ACTION
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 12/23/25 has been entered.
Claims 1-6, 8, 9, 11-13, 15, 16, 18-24 and 26-29 are currently pending.
Claims 9 and 22-24 remain withdrawn for being drawn to a non-elected invention.
Claims 1-6, 9, 11, 13, 15, 16, 18-21 and 26-29 as they apply to the elected strain. Applicants previously elected the Species: Bacillus amyloliquefaciens strain NCIMB 42971 and the 16S rDNA of SEQ ID NO: 1.
Claim Rejections - 35 USC § 112-2nd paragraph
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 1-6, 8, 11, 13, 15, 16, 18-21 and 26-29 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.
Claims 1-6, 8, 11, 13, 15, 16, 18-21 and 26-29 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of the different bacterial strains is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: these bacteria comprise different 16S rDNA sequences and are different strains. They do not comprise the same structure. A search for one would not definitely reveal the other. The section ‘other prior art’ shows that the search for these different bacteria is not coextensive and one piece of art may only reveal a single bacterium.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claims 1-6, 8, 11, 13, 15, 16, 18-21 and 26-29 are also vague and indefinite because it is unclear what structures are encompassed by “extracellular material produced by the microorganism”. The metes and bounds of this language is not readily understood. The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. In bacteria, the extracellular consists of three major components: polysaccharides, proteins, and extracellular DNA. The use of the language “extracellular bacteria produced by the bacteria” does not require the bacteria and is vague. Is this supposed to be the supernatant/bacterial extract or does it encompass individual DNA or proteins? Appropriate clarification and/or correction is required as currently it is unclear what is covered by this description.
Claims 5, 6, 26 and 27 are vague and confusing due to the language “the one or more microorganisms independently comprises a gene…” What is meant by this language? Is this a heterologous gene? Which SEQ ID NO. is for which bacterial strain? For instance, does microorganism with 16S rDNA of SEQ ID NO: 1 have SEQ ID NO: 7, 8. 9 or 10? Are the sequences in claims 26 and 27 related to a particular cell strain, e.g, are the inherent in the particular bacterial strain/cell or are they heterologous?
While the specification can be used to provide definitive support, the claims are not read in a vacuum. Rather, the claim must be definite and complete in and of itself. Limitations from the specification will not be read into the claims. The claims as they stand are incomplete and fail to provide adequate structural properties to allow for one to identify what is being claimed. It appears from the teachings in the specification that the sequences in SEQ ID NOS: 7, 8, 9 and 10 are from the bacteria deposited as NCIMB 42971 which also comprises the 16S rDNA set forth in SEQ ID NO: 1. Accordingly, in order to overcome this rejection, Applicants could limit claim 1 (from which these claims depend) to the B. amyloliquefaciens strains comprising the elected strain, e.g., Bacillus amyloliquefaciens strain NCIMB 42971 and the 16S rDNA of SEQ ID NO: 1. Appropriate clarification and/or correction is required.
Claims 2, 3 and 4 are rejected for being unclear. The structure of these peptides is unclear if these are heterologous peptides or naturally-occurring in the bacterium. Further, are they found in all of the strains, or some in a particular strain type and one in another, etc.? For instance, would a strain with 16SrDNA of elected SEQ ID NO:1 possess a peptide from all of these families? It is very unclear. If they inherently are part of the claimed bacterium/bacteria, it does not appear that they are needed. Applicants have argued in the response of 4/28/25 that one of skill in the art, along with knowledge in the prior art, that these peptides are generally known and may encompass different structures as recited in paragraphs [0039]-[0044] of the instant specification. This has been fully and carefully considered but it is still unclear how they relate to each individual bacteria, e.g, are they related to a particular cell strain, e.g, are the inherent in the particular bacterial strain/cell, and if so, which ones are found in a strain that is Bacillus amyloliquefaciens strain NCIMB 42971 and the 16S rDNA of SEQ ID NO: 1 (or SEQ IDN O. 2-6) or are they heterologous? This description in the claims does not adequately make clear the structure of the bacteria claimed.
Further claims 2-4 broadly recite the two or more non-ribosomal proteins as being selected from a broad Family, or an ‘three or more non-ribosomal proteins”. The mere recitation of a name, i.e., a member of the Fengycin family or any ‘non-ribosomal protein”, to describe the invention is not sufficient to satisfy the Statute's requirement of adequately describing and setting forth the inventive concept. The claim should provide any structural properties, such as the amino acid sequence of the protein or the actual protein (not just any of a hundred, etc.), which would allow for one to identify the protein without ambiguity. The mere recitation of a name does not adequately define the claimed protein(s).
Appropriate clarification and/or correction is required.
Response to Applicants’ arguments:
The arguments to the 112 paragraph rejections have been addressed in the body of the rejections set forth above. With respect to the former prior art rejections, Applicants’ arguments have been rendered moot due to the new grounds of rejections set forth below:
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-6, 8, 11, 12, 13, 15, 16, 18 and 28 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by of Nelson et al (WO 2019/152791; 8/8/19) in light of Sas et al (US 2008/0057047).
Elected Claim 1: (Currently Amended) A composition comprising 1. (i) one or more microorganisms selected from Bacillus amyloliquefaciens (also known as or reclassified as Bacillus velezensis) strains deposited as NCIMB 42971 or a strain comprising the 16S rDNA of SEQ ID NO: 1 or a sequence having more than 98% sequence identity thereto and/or extracellular material produced by the microorganism and one of more food grade ingredients.
Nelson teaches a B. amyloliquefaciens strain with 99.94% sequence identity (see SEQ ID NO: 10) to Applicants’ SEQ NO: 1. Nelson teaches a B. amyloliquefaciens strain with 99.94% sequence identity (see SEQ ID NO: 10) to Applicants’ SEQ NO: 1, (additionally, 99.87% identical to present SEQ ID NO: 3 and 100% identical to present SEQ NOs: 5 and 6). See sequence alignment in Public pair. Bacterial strains among the same Genus species, generally have 16S rDNA within a strains within the same species differ by <1% (i.e., >99% identity), as demonstrated by the Nelson reference. Nelson teaches this strain in a feed composition, e.g., one or more feed grade ingredients. The bacteria would inherently produce the two or more non-ribosomal proteins because Bacillus bacteria are known to produce non- ribosomal lipopeptides (e.g. surfactins, iturins or fengycins, par. 33 of in light of reference Sas et al). The term “animal feed” is defined by Nelson to refer to any compound, preparation, or mixture suitable for, or intended for intake by an animal. Animal feed for a production animal comprises concentrates as well as for example vitamins, minerals, enzymes, amino acids and/or other feed ingredients (such as in a premix). The animal feed may further comprise forage. The term “composition” refers to a composition comprising a carrier and at least one bacterial strain as described herein. The compositions described herein may be mixed with an animal feed(s) to obtain a “mash feed”, extruded or pressed feed pellets, or liquid feed.
The instant claims are drawn to a product. A recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim. Additionally, a patent for a new method/use of a known product may be obtained, but a patent cannot be obtained for a known product, e.g., when the prior art device is the same as a device described in the specification for carrying out the claimed method, it can be assumed the device will inherently perform the claimed process. In re King, 801 F.2d 1324, 231 USPQ 136 (Fed. Cir. 1986). The discovery of a new use for an old structure based on unknown properties of the structure might be patentable to the discoverer as a process of using. In re Hack, 245 F.2d 246, 248, 114 USPQ 161, 163 (CCPA 1957). However, when the claim recites using an old composition or structure and the "use" is directed to a result or property of that composition or structure, then the claim is anticipated. In re May, 574 F.2d 1082, 1090, 197 USPQ 601, 607 (CCPA 1978) (Claims 1 and 6, directed to a method of effecting nonaddictive analgesia (pain reduction) in animals, were found to be anticipated by the applied prior art which disclosed the same compounds for effecting analgesia but which was silent as to addiction. The court upheld the rejection and stated that the applicants had merely found a new property of the compound and such a discovery did not constitute a new use. The court went on to reverse the rejection of claims 2-5 and 7-10 which recited a process of using a new compound. The court relied on evidence showing that the nonaddictive property of the new compound was unexpected.). See also In re Tomlinson, 363 F.2d 928, 150 USPQ 623 (CCPA 1966) . "While the references do not show a specific recognition of that result, its discovery by appellants is tantamount only to finding a property in the old composition." 363 F.2d at 934, 150 USPQ at 628 (emphasis in original).). Since Nelson teaches the identical bacteria, e.g., Bacillus amyloliquefaciens strain having a sequence more than 98% identical to Applicants’ SEQ ID NO: 1, it meets the structural limitations of the claims.
Additionally, Nelson recites: Concentrates: The term “concentrates” means feed with high protein and energy concentrations, such as fish meal, molasses, oligosaccharides, sorghum, seeds and grains (either whole or prepared by crushing, milling, etc. from, e.g. , corn, oats, rye, barley, wheat), oilseed press cake (e.g., from cottonseed, safflower, sunflower, soybean (such as soybean meal), rapeseed/canola, peanut or groundnut), palm kernel cake, yeast derived material and distillers grains (such as wet distillers grains (WDS) and dried distillers grains with solubles (DDGS)). In a preferred embodiment, the composition comprises one or more bacterial strains described herein, wherein the bacterial count of each of the bacterial strains is between 1x104 and 1x1012 CFU/kg of composition, preferably between 1x107 and 1x1011 CFU/kg of composition, more preferably between 1x108 and 1x1010 CFU/kg of composition and most preferably between 1x109 and 1x1010 CFU/kg of composition. In a preferred embodiment, the bacterial count of each of the bacterial strains in the composition is between 1x104 and 1x1012 CFU/kg of dry matter, preferably between 1x107 and 1x1011 CFU/kg of dry matter, more preferably between 1x108 and 1x1011 CFU/kg of dry matter and most preferably between 1x108 and 1x101° CFU/kg of dry matter. In a more preferred embodiment, the bacterial count of each of the bacterial strains in the composition is between 1x109 and 1x101° CFU/kg of dry matter
In a preferred embodiment, Nelson teaches that the composition has a bacterial count of each Bacillus spore between 1x103 and 1x1013 CFU/animal/day, preferably between 1x105 and 1x1011 CFU/animal/day, more preferably between 1x106 and 1x1010 CFU/animal/day and most preferably between 1x107 and 1x109 CFU/animal/day. It is also taught the Bacillus strain can be prepared by freezing a mixture of Bacillus solution with a bulking agent such as ground soybean meal, and then lyophilizing the
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 19-21 and 29 is/are rejected under 35 U.S.C. 103 as being unpatentable over Nelson et al (WO 2019/152791; 8/8/19) in light of Sas et al (US 2008/0057047) in view of Wilson et al (Infect. Immun., ASM US. 56(1): 2610-2614; October 1, 1988).
The teachings of Nelson are set forth above. However, they do not particularly exemplify the compositions further comprise glucosamine.
Regarding claims 19-21 and 29, Wilson discloses that gut microorganisms compete more efficiently than C. difficile for monomeric glucose, N-acetyl-glucosamine, and sialic acid found in the colonic contents (see Abstract). Therefore, in view of Wilson, when looking for further compounds capable of ameliorating C. difficile infection it would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to include the use of an additional nutrient, e.g., N-acetyl-glucosamine as a supplement to B. subtilis or B. amyloliquefaciens (when starting from the teachings of Nelson).
Claim(s) 26 and 27 s/are rejected under 35 U.S.C. 103 as being unpatentable over Nelson et al (WO 2019/152791; 8/8/19) in light of Sas et al (US 2008/0057047).
in view of Borriss, R. (WO 2004/111240 A2).
The teachings of Nelson are set forth above. However, they do not particularly exemplify the nucleic acid sequences recited in claims 26 and 27.
Borriss describes the DNA and amino acid sequences for the Bacillomycin D-Operons and the use of the sequences for the biosynthesis of antibiotically effective lipopeptides and methods for the production thereof.
B. amyloliquefaciens SEQ ID NO: 2 of Borriss is 96.25% identical to Applicants’ SEQ ID NO: 9; and B. amyloliquefaciens SEQ ID NO: 3 of Borris is 97.61% (98%) identical to Applicants’ SEQ NO: 10. B. amyloliquefaciens SEQ ID NO: 1 of Borriss is 97.54% (98%) identical to Applicants’ SEQ ID NO: 8.
The instant specification teaches that these sequences are inherently part of B. amyloliquefaciens strain NICMB 42971 with the 16S rDNA set forth in SEQ ID NO: 1. Claims 26 and 27 recite at least 95% identical to SEQ ID Nos: 7, 8, 9 or 10.
These nucleic sequences are found in naturally occurring B. amyloliquefaciens so would inherently be found in the Bacillus amyloliquefaciens strains taught by Nelson.
Prior art not presently relied upon:
AU 2011 227 226, 2/176/17 discloses the use of B. subtilis QST713 cells or spores for treating Clostridium difficile associated infection and gastrointestinal disorder (par. 22, claim 9), as an effective probiotic (par. 15), also when it is incorporated in food or drink or in the form of capsules or tablets (par. 29). The metabolites of B. subtilis QST713 is disclosed to include lipopeptides, such as iturins, surfactins and other antibacterial compounds (par. 23).
B. amyloliquefaciens SEQ ID NO: 3 of WO 2019/152791 is 99.94% identical to present SEQ ID NO: 2;
B. subtilis SEQ ID NO: 2 of WO 2107/147130 is 100% identical to present SEQ ID NO: 4;
B. amyloliquefaciens SEQ NO: 1 of DE 10 2004 061385 A1 is 96.67% identical to present SEQ ID NO: 7;
B. amyloliquefaciens SEQ ID NO: 1 of WO 2004/111240 A2 is 97.54% (98%) identical to present SEQ ID NO: 8;
B. amyloliquefaciens SEQ ID NO: 2 of WO 2004/111240 A2 is 96.25% identical to present SEQ ID NO: 9; and B. amyloliquefaciens SEQ ID NO: 3 of WO 2004/111240 A2 is 97.61% (98%) identical to present SEQ NO: 10).
Correspondence regarding this application should be directed to Group Art Unit 1645. Papers related to this application may be submitted to Group 1600 by facsimile transmission. Papers should be faxed to Group 1600 via the PTO Fax Center located in Remsen. The faxing of such papers must conform with the notice published in the Official Gazette, 1096 OG 30 (November 15,1989). The Group 1645 Fax number is 571-273-8300 which is able to receive transmissions 24 hours/day, 7 days/week.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jennifer E. Graser whose telephone number is (571) 272-0858. The examiner can normally be reached on Monday-Thursday from 8:00 AM-6:30 PM.
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/JENNIFER E GRASER/Primary Examiner, Art Unit 1645 1/26/26