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 24 Apr 2026 is acknowledged. Claims 1-25 are currently pending. Of those, claims 1-2 are currently amended, and no claims are new. Claims 3-23 are withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention. The election was made without traverse in the reply filed on 9 Dec 2025 and the provisional species election made by telephone was affirmed in the reply filed 24 Apr 2026. No claims are cancelled. Claims 1-2 will be examined on the merits herein.
Response to Arguments
The Applicants’ arguments filed 24 Apr 2026 are acknowledged. For clarity, in this action, said arguments will be referred to as “Remarks” and the Non-Final Office Action mailed 6 March 2026 will be referred to as “NFOA.”
References to the specification in this action will use paragraph numbers from the Pre-Grant Publication US-20240096440-A1 in order to avoid ambiguity if the page and line numbers change across versions of the specification.
Priority
Applicant did not address the priority finding from the NFOA. The effective filing dates used in this action are not changed.
Objection(s) and Rejection(s) Withdrawn
The objection to the specification (NFOA par. 11) is withdrawn in view of the amendments.
The rejection of claims 1-2 under 35 U.S.C. 112(b) (NFOA par. 12-13) is withdrawn in view of the claim amendments and arguments.
Rejection(s) Maintained
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejections - 35 USC § 101
Claim 2 remains rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural product without significantly more.
The claim recites “A composition for benefiting the health of an animal or a human, the composition comprising i) one or more carriers or excipients and ii) one or more biologically pure cultures, wherein each biologically pure culture consists of a single bacterial species, and wherein said species is selected from the group consisting of: Megamonas funiformis, Megamonas hypermegale, Acidaminococcus intestini, Bacteroides massiliensis, Bacteroides stercoris, Barnesiella intestinihominis, Faecalibacterium prausnitzii, Subdoligranulum variabile, Anaerostipes caccae, Anaerostipes hadrus, Clostridium symbiosum, Clostridium bolteae, Blautia hydrogenotrophica, Marvinbryantia formatexigens, Clostridium scindens, Blautia producta, and Akkermansia muciniphila.” The species election was that the bacteria are the combination of Bacteroides stercoris, Blautia producta, and Akkermansia muciniphila. The instant specification teaches that the bacterial species are isolated from the human gut [0200-0201]. However, the examiner has not found evidence of a human simultaneously having all three species of bacteria in their gut naturally. So, the combination has been analyzed for markedly different characteristics relative to the natural species. See MPEP 2106.04(c): “In Myriad, the Supreme Court made clear that not all changes in characteristics will rise to the level of a marked difference, e.g., the incidental changes resulting from isolation of a gene sequence are not enough to make the isolated gene markedly different. Myriad, 569 U.S. at 580, 106 USPQ2d at 1974-75.” Like in Myriad, any incidental changes from isolating the bacteria into a biologically pure culture do not rise to the level of a marked difference, particularly because the claimed composition is not required to be biologically pure and can be mixed with any number of other species like in the natural microbiome context. The instant specification does not teach any modifications to the bacteria relative to their natural states; instead the specification teaches that the desired functionalities were already present in the bacteria isolated from the gut microbiome [0201]. The specification teaches that for the full GUT-103 bacterial combination, the combination of strains has different properties because “the GUT-103 consortium model does indeed predict growth for the GUT-103 consortium in minimal medium, without the need to include additional nutrients, even though none of the GUT-103 consortium strains alone are predicted to be capable of growing in this medium” [0209]. However, this markedly different property was not found for the elected species of Bacteroides stercoris, Blautia producta, and Akkermansia muciniphila. For example, Table 6 teaches that Bacterioides stercoris must consume L-histidine, but the producing species of Blautia hydrogenica is not present in the elected composition. Also, the other elements of the claim (“comprising (i) one or more carriers or excipients” and the preamble “for benefiting the health of an animal or a human”) does not make the bacterial composition markedly different because the carrier could be only water, which has the benefit of being hydrating, and which is already naturally present in combination with the bacterial strains in the gut. Therefore, the elected species that the bacteria are the combination of Bacteroides stercoris, Blautia producta, and Akkermansia muciniphila is not markedly different from the natural species individually, and the claim recites a natural product.
This judicial exception is not integrated into a practical application because the composition itself is not markedly different from a natural product; there are no additional elements that could integrate the judicial exception. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because the composition itself is not markedly different from a natural product; there are no additional elements that could integrate the judicial exception.
Response to Arguments
Applicant argues (Remarks pg. 17-18) that “If the specific combination of B. stercoris, B. producta, and A. muciniphila does not occur together in nature, then the claimed composition is not a "product of nature" within the meaning of the judicial exception. A composition that has been assembled by human intervention from individually isolated and cultured bacteria, combined with pharmaceutical carriers and excipients, is a man-made product that does not occur in nature in that form.” The arguments point to Diamond v. Chakrabarty, which held that a bacterium with characteristics not found in nature was patent-eligible.
This argument has been carefully considered and not found persuasive. Respectfully, the argument that if the specific combination does not occur together in nature, then the composition cannot be a “product of nature” is inconsistent with the Office’s policies laid out in the MPEP. Instead, MPEP 2106.04(c) states: “If the claim includes a nature-based product that does not exhibit markedly different characteristics from its naturally occurring counterpart in its natural state, then the claim recites a "product of nature" exception, and requires further analysis in Step 2A Prong Two … Examiners should keep in mind that if the nature-based product limitation is naturally occurring, there is no need to perform the markedly different characteristics analysis because the limitation is by definition directed to a naturally occurring product and thus falls under the product of nature exception. However, if the nature-based product limitation is not naturally occurring, for example due to some human intervention, then the markedly different characteristics analysis must be performed to determine whether the claimed product limitation is a product of nature exception. … When there are multiple counterparts to the nature-based product, the comparison should be made to the closest naturally occurring counterpart. … When the nature-based product is a combination produced from multiple components, the closest counterpart may be the individual nature-based components of the combination. For example, assume that applicant claims an inoculant comprising a mixture of bacteria from different species, e.g., some bacteria of species E and some bacteria of species F. Because there is no counterpart mixture in nature, the closest counterparts to the claimed mixture are the individual components of the mixture, i.e., each naturally occurring species by itself. See, e.g., Funk Bros., 333 U.S. at 130, 76 USPQ at 281 (comparing claimed mixture of bacterial species to each species as it occurs in nature);”
As required by the MPEP, the nature-based product produced by combining multiple components (B. stercoris, B. producta, and A. muciniphila) was analysed using the markedly different products test to determine whether the mixed composition has markedly different properties from the natural analogue (the natural microbial species individually). Unlike in Diamond but like Funk Bros and Myriad., the analysis did not find any markedly different properties for the strains in the combination compared to the individual natural strains.
Applicant argues (Remarks pg. 18) that “The Office Action dismisses the "one or more carriers or excipients" element on the ground that "the carrier could be only water." However, the claim requires "carriers or excipients," and the specification teaches that the compositions can be formulated as capsules, powders, liquid suspensions, aerosols, or creams. The specification further describes pharmaceutical formulations including enteric-coated pellets, modified release dosage forms, tablets, and gel capsules. These formulated dosage forms are not naturally occurring products. A composition of three rationally selected bacterial species formulated in a capsule with enteric coating and pharmaceutical excipients bears no resemblance to any naturally occurring product. Water in the gut is not a "carrier or excipient" as that term is understood in the pharmaceutical arts.”
This argument has been carefully considered and not found persuasive. The arguments do not point out where the specification defines that the composition must (rather than can) be formulated in the narrower formulation discussed in the argument. If the applicant would like to amend the specification to exclude water as being a “carrier or excipient” within the scope of the claims, or point out where the specification excludes this scope, then the examiner would reassess this argument.
Applicant argues (Remarks pg. 18) that “Unlike the isolated DNA segment at issue in Association for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576 (2013), the claimed composition was not simply extracted from a natural source. The specification describes a systematic computational process in which metabolic models were created for individual strains, integrated into community models, and analyzed using flux balance analysis to identify the optimal combination of strains. The GUT- 103 consortium subset 1 extended (which corresponds to the elected species) was designated as a minimal consortium based on this computational analysis, not by randomly selecting bacteria from a stool sample. The fact that the individual bacterial species can be found in the human gut does not make a rationally designed, computationally optimized composition of those species into a natural product, any more than the presence of individual amino acids in nature makes a synthetic peptide a natural product.”
This argument has been carefully considered and not found persuasive. Arguments about the process of making the product are not relevant to the rejection because the claim is drawn to a product rather than a method of making a product. The claimed product could be made by many different methods, including “randomly selecting bacteria from a stool sample” (Remarks pg. 18). Also, the claimed species of composition is not the GUT- 103 consortium subset 1 extended. The species election was the combination of Bacteroides stercoris, Blautia producta, and Akkermansia muciniphila. The subset was defined in [0013] as also including the non-elected bacterial species of Bacteroides massiliensis, and as being limited to specific isolates from each bacterial species which are not required by instant claim 2.
To clarify the examiner’s position, the examiner agrees that “the presence of individual amino acids in nature [does not make] a synthetic peptide a natural product”; however, in a synthetic peptide the individual amino acids interact with each other via covalent and non-covalent bonds and result in a structure with properties that the individual amino acids do not have (presumably the peptide has some function, or it would fail the utility requirement of 35 U.S.C. 101). Unlike the hypothetical peptide, the claimed composition appears to be a mixture of bacteria that are not disclosed to physically interact with each other or disclosed to have any different properties as a result of the mixing.
Claim Rejections - 35 USC § 103
Claim 2 remains rejected under 35 U.S.C. 103 as obvious over Cook et al. (US-20160317653-A1; hereafter Cook; PTO-892).
Cook teaches compositions useful for treatment of immune system disorders [Title] that contain a carrier [0028]. Cook states: “In some embodiments, the composition comprises or consists essentially of species selected from the group consisting of … Akkermansia muciniphila, … Bacteroides stercoris, … [and] Blautia producta” [0053]. Therefore, Cook teaches compositions comprising each bacterial species individually present, see MPEP 2131.02: “when the species is clearly named, the species claim is anticipated no matter how many other species are additionally named. See Ex parte A, 17 USPQ2d 1716 (Bd. Pat. App. & Inter. 1990)”.
One of ordinary skill in the art at the time of filing would consider it prima facie obvious to modify the Cook compositions comprising the bacteria individually by combining the compositions, thereby arriving at the claimed invention, because "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. compositions comprising each bacteria individually) were known in the art. In addition, combining these elements yields a 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. Specifically, the result of producing the mixed composition that is claimed would be predictable. Also, there is no evidence of record that the combination of Bacteroides stercoris, Blautia producta, and Akkermansia muciniphila leads to a composition having any unexpected results when being produced or used. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Response to Arguments
Applicant argues (Remarks pg. 19) that “A reference that teaches both the inclusion and the exclusion of a particular component does not provide clear direction to a person of ordinary skill in the art to include that component in a therapeutic composition. To the contrary, a reference that teaches exclusion of a species from compositions teaches away from the claimed invention. See MPEP 2141.02.”
This argument has been carefully considered but is not found persuasive. First, it is noted that both Cook and the instant application teach both the inclusion and exclusion of all bacterial species listed, because they teach multiple alternative compositions. MPEP 2141.02.IV states: “However, "the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004).” See also MPEP 2123: “A reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill in the art, including nonpreferred embodiments. Merck & Co. v. Biocraft Labs., Inc. 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir. 1989), cert. denied, 493 U.S. 975 (1989).” Cook does not teach away from a composition consisting essentially of Bacteroides stercoris because it specifically discloses compositions either comprising or not comprising Bacteroides stercoris.
Applicant argues (Remarks pg. 19) that “The Office Action does not identify any teaching, suggestion, or rationale in Cook for selecting the specific combination of B. stercoris, B. producta, and A. muciniphila from among the hundred- plus species listed. No passage in Cook identifies these three species as having any particular synergy, complementary function, or therapeutic advantage when combined. Without such guidance, selecting this specific 3-species combination from over one hundred candidates requires the exercise of impermissible hindsight reconstruction. See MPEP 2143.01; KSR, 550 U.S. at 421.”
This argument has been carefully considered but is not found persuasive. The examiner agrees that Cook does not teach the specific combination of B. stercoris, B. producta, and A. muciniphila; therefore, this rejection is a 103 rejection instead of a 102 rejection. Instead, Cook is relied upon to teach “compositions useful for treatment of immune system disorders… comprising each bacterial species individually present” (par. 21 above).
Respectfully, applicant is incorrect that an obviousness rejection lacking an explicit teaching, suggestion, or rationale from the art “requires the exercise of impermissible hindsight reconstruction.” In KSR, the court rejected that an explicit teaching, suggestion, or motivation is required. See MPEP 2141: “The Supreme Court in KSR reaffirmed the familiar framework for determining obviousness as set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), but stated that the Federal Circuit had erred by applying the teaching-suggestion-motivation (TSM) test in an overly rigid and formalistic way. KSR, 550 U.S. at 404, 82 USPQ2d at 1391. Specifically, the Supreme Court stated that the Federal Circuit had erred in four ways: … (4) by overemphasizing "the risk of courts and patent examiners falling prey to hindsight bias" and as a result applying "[r]igid preventative rules that deny factfinders recourse to common sense" (Id.).”
In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, the motivation to combine the references is derived from each composition comprising the individual bacteria being disclosed in the art as being useful for the same purpose, and the predictable outcome that mixing the three individual compositions would result in a composition comprising all three bacteria that would have the use that all three bacteria are individually taught to have.
Applicant argues (Remarks pg. 19-20) that “Kerkhoven involved two fungicidal agents, each individually known to be effective for the same purpose, where combining them for the same purpose was straightforward. Here, Cook teaches a single massive Markush group of species that could be included in compositions for treating immune system disorders, but Cook does not teach that B. stercoris, B. producta, or A. muciniphila are individually effective as therapeutic compositions for the same purpose. Cook lists them as potential ingredients among many, while also teaching (at [0063]) that B. stercoris should be excluded from some embodiments. This is fundamentally different from the Kerkhoven situation. The Kerkhoven rationale is inapplicable.”
This argument has been carefully considered but is not found persuasive. The examiner respectfully disagrees that Cook does not teach that B. stercoris, B. producta, or A. muciniphila are individually effective as therapeutic compositions for the same purpose. As cited above, Cook states: “In some embodiments, the composition comprises or consists essentially of species selected from the group consisting of … Akkermansia muciniphila…” [0053], which is a teaching that A. muciniphila is individually effective. Similarly, Cook states: “In some embodiments, the composition comprises or consists essentially of species selected from the group consisting of … Bacteroides stercoris …” [0053], which is a teaching that Bacteroides stercoris is individually effective. Also, Cook states: “In some embodiments, the composition comprises or consists essentially of species selected from the group consisting of … Blautia producta …” [0053], which is a teaching that Blautia producta is individually effective. The individual compositions are clearly named, despite the presence of other species. Cook also teaches that these compositions are useful for treatment of immune system disorders, as cited above, which is the same function for all three individual compositions, like in Kerkhoven.
Applicant argues (Remarks pg. 20) that “The Office Action asserts that combining these species would yield "predictable results." However, the interactions among gut bacteria in a consortium are complex and not predictable from knowledge of the individual species. The instant specification describes extensive computational modeling, including flux balance analysis and auxotrophy profiling, that was required to identify functional consortia. The specification teaches that the GUT-103 consortium strains exhibit metabolic interdependencies, with each strain dependent on at least one other strain for growth. These interactions cannot be predicted merely from knowing that the species exist in the gut.”
This argument has been carefully considered but is not found persuasive. The elected species of composition is not the GUT-103 consortium (which is defined in the instant specification as an 18-strain combination found in Table 4); the elected species of composition is the combination of B. stercoris, B. producta, or A. muciniphila. The evidence of the specification is not persuasive because the effect disclosed in the specification requires features (specifically, the presence of certain microbial species) that are not claimed in the species of composition currently under examination.
The arguments not related to the specification are not persuasive because they do not provide any evidence that there actually is any unexpected result from combining the three species or that the three combination of the three species would actually fail to have the predictable result that is disclosed in Cook for all three individual compositions. See MPEP 716.01(c): “Arguments presented by the applicant cannot take the place of evidence in the record. In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965) and In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984). Examples of statements which are not evidence and which must be supported by an appropriate affidavit or declaration include statements regarding unexpected results, … [and] inoperability of the prior art…” Arguments related to secondary considerations will be considered when evidence, commensurate in scope to what is claimed, is presented to support the argument.
Therefore, the claim remains rejected for the reasons of record and the reasons above.
Allowable Subject Matter
Claim 1 is allowed. The following is a statement of reasons for the indication of allowable subject matter: The closest prior art to claim 1 is Berry and Kaplan (US-20160143962-A1; hereafter Berry; PTO-892), which teaches pharmaceutical compositions comprising one or at least two types of bacteria found in Tables 1, 1A, 1B, 1C, 1D, 1E, and 1F [0226-0227]; these pharmaceutical compositions are useful for correcting or treating a distal dysbiosis (i.e. benefitting the health of an animal or human). All bacterial species mentioned in claim 1 are present in at least one of these tables, and many of the bacterial species are also disclosed by name in other locations in the specification. However, there is no teaching in Berry to combine all the claimed species such as by specifically pointing out the bacteria in the instant claim- note that Example 2 used a different set of bacterial species that overlaps with but does not comprise those in the instant claims [Figures 2-10, 0364]. There also is no teaching in Berry to combine all disclosed bacterial species into a single composition, similar to a fecal microbiome transfer. Therefore, Berry does not anticipate claim 1. The subject matter of claim 1 is also not obvious over Berry in view of the art because the combination of these specific bacterial strains had unexpected effects on a mouse model of IBD (combination called GUT-103 in the spec, defined in Table 4 and [219], data in Example 8). The unexpected result from the specific combination of bacteria points away from obviousness because the results from combining the claimed strains would not have been predictable to one of ordinary skill in the art at the time of filing, so claim 1 is also non-obvious. The combination of claimed strains is also markedly different from the natural product of each individual strain because each individual strain is auxotrophic but the combination of strains can grow on minimal media [Example 8].
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMELIA N DICKENS whose telephone number is (571)272-0381. The examiner can normally be reached M-F 8:30-4:30 (EDT/EST).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Samira Jean-Louis can be reached at (571) 270-3503. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMELIA NICOLE DICKENS/Examiner, Art Unit 1645
/SAMIRA J JEAN-LOUIS/Supervisory Patent Examiner, Art Unit 1642
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