DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group II claims and election of species: claims 2-9, 12, and 14-17, drawn to methods of treating and/or preventing gastrointestinal inflammation and/or a disease, disorder, or condition associated with gastrointestinal inflammation, of claims amendment filed 9/29/2023, in the reply filed on 1/15/2026 is acknowledged.
After reconsideration, the restriction requirement between inventions regarding methods of treating of Group II and methods of preventing of Group III, and the election of species requirement as set forth in the Office action mailed on 11/19/2025, is hereby withdrawn and claims 2(b)-9(b), 12(b), and 14(b)-17(b) are hereby rejoined and fully examined for patentability under 37 CFR 1.104. Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Claims status
The amendment filed 1/15/2026 has been entered.
Claims 2-12 and 14-18 are pending.
Claims 10-11 and 18 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group of invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 1/15/2026. Claims 2(a)-9(a), 12(a), and 14(a)-17(a) are elected. Claims 2(b)-9(b), 12(b), and 14(b)-17(b) are rejoined.
Therefore, claims 2-9, 12, and 14-17 are under examination.
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed on 09/29/2023. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
The instant application is a 371 of PCT/EP2022/058442, filed 03/30/2022, which claims priority to foreign application EP21165818.2, filed 03/30/2021. The effective filing date is 03/30/2021, which is the filing date of the foreign application.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 3/20/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being
considered by the examiner.
Claim Objections
Applicant is advised that should claim 9 be found allowable, claim 14 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. 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).
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 2-3 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 2-3 recite a method comprising of deposited Cyberlindnera jadinii or Kluyveromyces lactis strains “or a strain having all of the identifying characteristics" of these deposited strains. The alternative option of “a strain all of the identifying characteristics” of the deposited strains is indefinite because it is unclear how this alternative is different from the claimed deposited Cyberlindnera jadinii or Kluyveromyces lactis strains. In other words, if a strain has “all of the identifying characteristics” of the claimed deposited strains, then it would be the deposited strain, and if it differed from strain, then it would not have all “of the identifying characteristics” of that strain.
Additionally, the specifications provide a definition for "identifying characteristics" that may be a genome sequence percentage identity and/or functional behavior, wherein the genome sequence percentage identity could be at least 70% (page 15, lines 4-8), but does not provide a definition for what particular functional behaviors is a characteristic versus an identifying characteristic for this claimed strain. The disclosure is further silent on what metabolic activity, functional pathways, protein expression, or protein secretion function is a characteristic versus an identifying characteristic for this claimed strain. The disclosure is further silent on what encompasses the scope of "all" identifying characteristics and how to reconcile this with the disclosure that identifying characteristics may be genome sequence percentage identity "and/or" functional behavior, implying the option to choose between genome sequence percentage identity and functional behavior. One skilled in the art would not be able to resolve what combination of genome sequence percentage identity and functional behavior constitute "all identifying characteristics" of the deposited strain. Therefore, the claim fails to particularly point out and distinctly claim the subject matter which the inventor(s) regards as the invention.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Written Description
Claims 2-3 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 2 encompasses a method comprising of the Cyberlindnera jadinii strain deposited as DSM 33763, as well as method comprising a strain having all of the identifying characteristics of the Cyberlindnera jadinii strain deposited as DSM 33763, wherein the strain is used in the method of treating and preventing of parent claim 12.
Claim 3 encompasses a method comprising of the Kluyveromyces lactis strain deposited as DSM 33763, as well as method comprising a strain having all of the identifying characteristics of the Kluyveromyces lactis strain deposited as DSM 33763, wherein the strain is used in the method of treating and preventing of parent claim 12.
The specification discloses the biological deposit of strains identified as DSM 33763 and DSM 33764 (page 43) and exemplary embodiments and results comprising of these deposited strains. The specification discloses that identifying characteristics may be defined by a genome sequence percentage identity and/or functional behavior, wherein the genome sequence percentage identity could be at least 70%, and the functional behavior may metabolic activity, functional pathways, protein expression, or protein secretion (page 15, lines 4-8).
As such, claims 2-3 encompass strains that have at least 70% genome sequence percentage identity to the respective deposited strain and/or have identifying functional behavior relevant to the respective deposited strain.
The specification reduces to practice only the exact Cyberlindnera jadinii strain deposited as DSM 33763 and exact Kluyveromyces lactis strain deposited as DSM 33764. Therefore, written description is met for the method comprising of the exact Cyberlindnera jadinii strain deposited as DSM 33763 and exact Kluyveromyces lactis strain deposited as DSM 33764.
The specification has no reduction to practice of and is silent on methods comprising any strain other than the exact Cyberlindnera jadinii strain deposited as DSM 33763 and the exact Kluyveromyces lactis strain deposited as DSM 33764.
Regarding the functional behavior definition for identifying characteristic, although the specification discloses some effects of the deposited strain in the Results section, it is silent on whether these effects are identifying functional behavior or simply functional behavior, and what the entire scope of all the functional behaviors are.
The state of the art teaches that both a different Kluyveromyces lactis strain and Kluyveromyces marxianus have characteristics taught by the specification for this claimed strain, such as survival in the gastrointestinal environment and the potential to treat gastrointestinal related disorders (e.g. Ceugniez et al, Abstract). Therefore, having a shared function does not necessitate even a shared species, so without knowing the exact and complete combination of identifying characteristics the applicant considers within the scope of these claims, the knowledge of any function is insufficient to provide knowledge of all the identifying characteristics of the claimed deposited strains.
Regarding the genome sequence identify definition for identifying characteristic, although one skilled in the art could envision the applicant is in possession of strains with at least 70% genome sequence identity to the deposited strain, the claim is not limited to structure but also requires the function of this structure in the claimed method.
The specification is silent regarding which 30% of the genome sequence can vary from the genome sequence of the deposited strains and still result in a method that retains the function required for its use in the method of treating and/or preventing gastrointestinal inflammation and/or a disease, disorder, or condition associated with gastrointestinal inflammation. The specification is silent regarding how the strains are enabling the method, and thus one skilled in the art would not know which sequences of the genome are critical to this function and should be avoided. Furthermore, there is no disclosure relating similarity of genomic sequence to conservation of function.
The state of the art regarding these specific deposited strains teaches that Cyberlindnera jadinii strain deposited as DSM 33763 and Kluyveromyces lactis strain deposited as DSM 33764 teaches that they produce an ATP-degrading enzyme (Budinoff et al, WO2025080755A1, published 04/17/2025, paragraph 12). However, it is unclear whether production of this enzyme is necessary and/or sufficient for the producing the instantly claimed method. Furthermore, it is not known what other sequences within the genome would constitute the rest of the genome sequence outside of the sequence encoding the enzyme. As such, the at least 70% genome sequence identity for a strain that meets the instant claim limitations is still unknown.
Of note, the state of the art regarding these specific deposited strains teaches that Cyberlindnera jadinii strain deposited as DSM 33763 and Kluyveromyces lactis strain deposited as DSM 33764 is from a disclosure filed and published before the effective filing date of the instant application and therefore one skilled in the art before the effective filing date of the instant application could not have used this disclosure to support the instant application's possession of the claimed invention. However, it is used to teach the state of the art is still lacking sufficient information to support the instant application's possession of the claimed invention and therefore the applicant could not have been in possession of the invention at the effective filing date.
It follows that without disclosure of the entire scope of the functional behaviors and what guidance on the modification of genome sequence identity to retain function, the entire scope of "all" identifying characteristics is not disclosed. Accordingly, the disclosure of the deposited strain and its genome sequence identity and disclosed functional characteristics are not sufficient to be representative or teach the entire scope of the other strains that could function in the method. In light of the lack of disclosure and art-recognized correlation between structure and function and lack of disclosure and art-recognized identifying characteristic for the particular strains, the specification fails to satisfy the written description requirement with respect to scope of strains in claims 2-3.
Enablement
Claims 2-3 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claims contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention. This is a biological deposit enablement rejection.
It is apparent that the bacterial strains represented by DSM 33763 and DSM 33764 are required in order to practice the invention. Specifically, it is noted that claims 2-3 recite deposited material. The deposit of biological organisms is considered by the Examiner to be necessary for the enablement of the current invention (see 37 CRF 1.808(a)). The examiner acknowledges the deposit of organisms under the ATCC Patent Deposit Numbers PTA-127171, PTA-127172, and PTA-127173 in partial compliance with this requirement. However, said deposits are not in full compliance with 37 CFR 1.803-1.809.
If the deposit is made under terms of the Budapest Treaty, then an affidavit or declaration by Applicants or person(s) associated with the patent owner (assignee) who is in a position to make such assurances, or a statement by an attorney of record over his or her signature, stating that the deposit has been made under the terms of the Budapest Treaty and that all restrictions imposed by the depositor on the availability to the public of the deposited material will be irrevocably removed upon the granting of a patent, would satisfy the deposit requirements. See 37 CFR 1.808.
If a deposit is not made under the terms of the Budapest Treaty, then an affidavit, or declaration by Applicants or person(s) associated with the patent owner (assignee) who is in a position to make such assurances, or a statement by an attorney of record over his or her signature, stating that the following criteria have been met:
1) during the pendency of the application, access to the deposit will be afforded to one determined by the Commissioner to be entitled thereto;
2) all restrictions imposed by the depositor on the availability to the public of the deposited material will be irrevocably removed upon the granting of a patent; and
3) the deposits will be maintained for a term of at least thirty (30) years from the date of the deposit or for the enforceable life of the patent or for a period of at least five (5) years after the most recent request for the furnishing of a sample of the deposited material, whichever is longest; and
4) a viability statement in accordance with the provisions of 37 CFR 1.807; and
5) the deposit will be replaced should it become necessary due to inviability, contamination or loss of capability to function in the manner described in the specification.
In addition, the identifying information set forth in 37 CRF 1.809(d) should be added to the specification. See 37 CFR 1.803 – 1.809 for additional explanation of these requirements. To fulfill these requirements, Applicant must provide a statement ensuring all restrictions imposed by the depositor on the availability to the public of the deposited material will be irrevocably removed upon the granting of a patent, and provide the address of the depository.
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 4-9, 12, 14-17 are rejected under 35 U.S.C. 103 as being unpatentable over Ghannoum et al (WO2019173763A1, filed 03/08/2019, published 09/12/2019) as evidenced by Rupp et al (The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms, J Biotechnol. 2015 Oct 10;211:20-30, published 2015), in view of Ceugniez et al (Anti-Salmonella activity and probiotic trends of Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 isolated from a French cheese, Tomme d' Orchies, Research in Microbiology 168 (2017) 575-582, published 2017).
Ghannoum et al teaches a method of treating and/or preventing (paragraph 193, treat is defined to include prevent) gastrointestinal inflammation and/or a disease, disorder or condition associated with gastrointestinal inflammation in a subject in need thereof, comprising administering a composition comprising an effective amount of non-pathogenic fungal strains to the subject ((IX) Method of Treating Gut Inflammation, (VI) Methods of disrupting biofilm and treatment, and Table 4), wherein exemplary fungal strains include Kluyveromyces lactis and Pichia jadinii (which is an older and synonymous name for Cyberlindnera jadinii, as evidenced by Rupp et al (Introduction paragraph 1)) (paragraphs 16 and 92), as is relevant to claim 12.
Claims 4-6 and 14-17 depend on claim 12. The teachings of the prior art regarding claim 12 are incorporated in its entirety here and further described below.
Ghannoum et al teaches the fungal strain in the composition is present at about 1 x 10^9 CFU/g to about 5 x 10^10 CFU/g of composition (Table 5 and Table 7), as is relevant to claim 4.
Ghannoum et al teaches the composition is a probiotic (Abstract, Table 4), as is relevant to claim 5.
Ghannoum et al teaches the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and/or excipient (paragraphs 146-150, 159), as is relevant to claim 6.
Ghannoum et al teaches the composition is formulated for oral administration (paragraphs 142-158) or topical administration (paragraphs 159-167), as is relevant to claim 7.
Ghannoum et al teaches the composition is a food product, food ingredient, dietary supplement, or medicament (e.g. (IV) Cooked Food Products, Table 4), as is relevant to claim 8.
Ghannoum et al teaches the disease, disorder, or condition is IBD, IBS, cancer, chemotherapy-induced gastrointestinal inflammation, radiation-induced gastrointestinal inflammation, immunotherapy-induced gastrointestinal inflammation, bacterial infection, viral infection, fungal infection, antibiotic use, aging, dysbiosis, obesity, type 2 diabetes, metabolic syndrome, asthma, atherosclerosis, non- alcoholic fatty liver disease, multiple sclerosis, or skin inflammation (e.g. paragraphs 25, 29, 192), as is relevant to claims 9 and 14; and specifically IBD (e.g. paragraphs 29, 192), as is relevant to claim 15; and specifically ulcerative colitis or Crohn's disease (e.g. paragraphs 29, 192), as is relevant to claim 16; and specifically dysbiosis (e.g. paragraph 25), as is relevant to claim 17.
However, Ghannoum et al teaches Saccharomyces boulardii as a heavily used and studied yeast in probiotics, and uses Saccharomyces boulardii in their example compositions. Although Ghannoum et al does teach exemplary fungal strains in the compositions include Kluyveromyces lactis and Cyberlindnera jadinii, it does not explicitly teach Cyberlindnera jadinii or Kluyveromyces lactis in the exemplary embodiments disclosed, as is relevant to claim 12 and its dependent claims.
However, Ceugniez et al teaches that Kluyveromyces lactis is safe (Introduction paragraph 3; section 2.4. Safe Properties), has potential as a probiotic, and displayed inhibitory activities against human bacterial infection (Abstract), and compared it to Saccharomyces boulardii, as is relevant to reference Ghannoum et al, and differentiated it from the pathogenic Candida albicans, as is relevant to the instant specification. Ceugniez et al further teaches Kluyveromyces lactis' capacity to survive in vitro gastrointestinal conditions (Discussion paragraph 4), has antagonistic activity against bacterial and fungal human pathogens (Discussion paragraph 1).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, to substitute the Saccharomyces boulardii explicitly taught in the methods of Ghannoum et al with Cyberlindnera jadinii, as taught in Ghannoum et al, or Kluyveromyces lactis, in light of the teachings of Ghannoum et al and Ceugniez et al. Although Ghannoum et al teaches an extensive list of exemplary non-pathogenic fungal strain that could be appropriate for their method in their specification (e.g. paragraphs 16 and 92), they explicitly claim the non-pathogenic fungal strain in the method is selected from a narrower list comprising of Cyberlindnera jadinii and Saccharomyces boulardii in Claim 20 of Ghannoum et al. As such, it would have been obvious to one skilled in the art, before the effective filing date of the instant application, that Ghannoum et al explicitly teaches Cyberlindnera jadinii as an alternative to Saccharomyces boulardii. Ghannoum et al further teaches that Saccharomyces boulardii was chosen for its ability to reduce virulence of the human pathogenic Candida fungus, which can invade the gastrointestinal epithelial mucosa (paragraph 234). Ceugniez et al teaches they corroborated Kluyveromyces lactis antagonistic properties against Candida albicans (Discussion paragraph 1). Additionally in light of the Ghannoum et al already teaching Kluyveromyces lactis as an exemplary non-pathogenic fungus for their methods, it would have been obvious to one skilled in the art, before the effective filing date of the instant application, that Kluyveromyces lactis could be a suitable substitute for Saccharomyces boulardii.
Ceugniez et al further teaches that recent research regarding non-Saccharomyces yeasts have expanded interest in developing these yeast as probiotic candidates. In light of these interests and teachings of the suitability of Cyberlindnera jadinii and Kluyveromyces lactis as substitutes for a commonly known fungal strain in probiotics and food additives for gastrointestinal health, Saccharomyces boulardii, one skilled in the art, before the effective filing date of the instant application, would be motivated to also develop these beneficial fungal strains to treat gastrointestinal infection and inflammation.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success because these Cyberlindnera jadinii and Kluyveromyces lactis have already been taught as alternatives to Saccharomyces boulardii in methods for treating gastrointestinal inflammation, disease, disorders, or conditions in a subject in need thereof, comprising of administering this yeast to the subject.
KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 398, (2007), discloses that a simple substitution of one known element for another to obtain predictable results is obvious. In this case, the prior art contained a method which differed from the claimed method by the fungus used in the method, Saccharomyces boulardii instead of the instantly claimed Cyberlindnera jadinii and Kluyveromyces lactis. However, the prior art also teaches the instantly claimed fungi as suitable alternatives to Saccharomyces boulardii, arriving at the claimed invention. The prior art teaches the motivation to focus on Cyberlindnera jadinii and Kluyveromyces lactis. The prior art teaches that the substituted fungus and their functions were known in the art relative to Saccharomyces boulardii. One skilled in the art, before the effective filing date of the instant application, could have substituted one fungus for another and the results of the substitution would have been predictable in light of teachings that Cyberlindnera jadinii is a suitable alternative for Saccharomyces boulardii and that Kluyveromyces lactis has the same functions that underlies the motivation for using Saccharomyces boulardii.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BONIRATH CHHAY whose telephone number is (571)272-0682. The examiner can normally be reached Mon-Thu 8AM-5PM EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Daniel Kolker can be reached at (571) 272-3181. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/B.C./
Examiner, Art Unit 1645
February 18, 2026
/DANIEL E KOLKER/Supervisory Patent Examiner, Art Unit 1645