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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 11/17/2025 has been entered.
Election/Restrictions
Applicant's election with traverse of Group I (i.e., claims 1, 3, 5, 6, 9, 13 and 19; drawn to a composition comprising a supernatant from a Clostridia consortium), and Species A (i.e., single and specific composition indicating: single and specific combination of bacterial strains including whether the composition further comprises one or more bacterial strains from Table 1, and if so, a single and specific additional bacterial strain or combination thereof, Applicant’s Election: Clostridia anaerovorax, Clostridium XIVa, Clostridium IV and Lachnospiraceae spp. and Eisenbergiella), in the reply filed on 12/11/2024 is acknowledged. The traversal is on the grounds that the Examiner has not shown that a serious burden would result if all of the claims are examined together (see Remarks, filed on 12/11/2024, pg. 6). This is not found persuasive because undue search burden is not a criteria for election/restriction purposes under 35 USC §121 and 35 USC § 372.
The requirement is still deemed proper and is therefore made FINAL.
Claims 10, 14, 25-26, 29-34, 36 and 41 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/11/2024.
Please note that claims 10 and 14 were inadvertently withdrawn in the action mailed on 04/21/2025. Claims 10 and 14 are hereby rejoined and fully examined.
Status of Claims
Claims 1-44 were originally filed on 01/10/2022.
The amendment filed on 07/11/2022, cancelled claims 2, 4, 7-8, 11-12, 15-16, 18, 20-24, 27-28, 35, 37-40 and 42-44; and amended claims 1, 3, 5, 6, 9-10, 13-14, 17, 19, 25, 29-34, 36, and 41.
The amendment filed on 12/11/2024, amended claim 19.
The amendment filed 07/07/2025, canceled claim 17.
The amendment filed on 11/17/2025, cancelled claim 13 and amended claims 1, 10 and 25.
Claims 1, 3, 5-6, 9-10, 14 and 19 are currently pending and under consideration.
Priority
The present application claims status as a 371 (National Stage) of PCT/US2020/042578 filed July 17th 2020, and claims the benefit under 35 U.S.C 119 (e) to U.S. Provisional Application No. 62/875,194 filed July 17th 2019. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C 119 (e) or under 35 U.S.C 120, 121, or 365 (c ) is acknowledged.
Claim /Sequence Interpretation
For purposes of applying prior art, the claim scope has been interpreted as set forth below per the guidance set forth at MPEP § 2111. If Applicant disputes any interpretation set forth below, Applicant is invited to unambiguously identify any alleged misinterpretations or specialized definitions in the subsequent response to the instant action. Applicant is advised that a specialized definition should be properly supported and specifically identified (see, e.g., MPEP § 2111.01(IV), describing how Applicant may act as their own lexicographer).
For claim 1, regarding the scope of “a Clostridia consortium, consisting of Clostridia anaerovorax, Clostridium XIVa, Clostridium IV and Lachnospiraceae spps.” It is noted that the instant specification does not teach an identification number (i.e., Accession Number or NRRL number) for Clostridia anaerovorax. Pursuant to MPEP 2111.01, under a broadest reasonable interpretation, words of the claim must be given their plain meaning, unless such meaning is inconsistent with the specification. The plain meaning of a term means the ordinary and customary meaning given to the term by those of ordinary skill in the art at the time of the invention. The Midas Field Guide describes the genus Anaerovorax as belonging to the family Anaerovoracaceae, class Clostridia, phylum Firmicutes (see Midas Field Guide, Genus: Anaerovorax, pp. 1-3, latest update July 6, 2024, available online at https://www.midasfieldguide.org/guide/fieldguide/genus/anaerovorax, accessed on 04/11/2025) (herein after “Midas”). Additionally, Midas also discloses that the only described species of the Genus Anaerovorax is Anaerovorax odorimutants (see Midas, pg. 1). As such, the Examiner is interpreting the scope of “Clostridia anaerovorax” as any strain belonging to the class Clostridia, phylum Firmicutes, genus Anaerovorax and comprises an amino acid sequence having at least 98% identity to SEQ ID NO: 1.
With respect to SEQ ID NO:1, please note that the Examiner is interpreting the scope of the 16S rDNA sequence of Clostridia anaerovorax as a naturally occurring bacterium isolated from a fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice, as recited in para[0058] pg. 13 of the instant specification.
Regarding the scope of “Clostridium XIVa” and “Clostridium IV”, it is noted that the instant specification does not specify which genera of Clostridium XIVa and IV clusters are comprised by the Clostridia consortium comprising two or more strains of bacterium. Pursuant to MPEP 2111.01, under a broadest reasonable interpretation, words of the claim must be given their plain meaning, unless such meaning is inconsistent with the specification. The plain meaning of a term means the ordinary and customary meaning given to the term by those of ordinary skill in the art at the time of the invention. Chun describes that Clostridium clusters XIVa and IV are groups of bacteria that have been known as major players in the human microbiome and the designation of these clusters was proposed by using 16S rRNA phylogeny (see Chun, Taxonomy of Clostridium Clusters XIVa and IV, 2017, pp. 1-5, retrieved from https://help.ezbiocloud.net/taxonomy-of-clostridium-cluster-xiva-iv/ on 04/11/2025 (herein after “Chun”). Chun also describes the list of genera for both clusters (see pp. 1-3), with Clostridium cluster XIVa encompassing 13 different genera, but not all genera in the family Lachnospiraceae, and Clostridium cluster IV encompasses 12 different genera, but not all genera in the family Ruminococcaceae (see pp. 1-3). As such, the Examiner is interpreting the scope of “Clostridium XIVa” and “Clostridium IV” as any of the genera encompassed by Clostridium cluster XIVa and by Clostridium cluster IV, respectively, where the cluster necessarily comprises an amino acid sequence having at least 98% identity to SEQ ID NOs: 2-3, respectively.
With respect to SEQ ID NO:2 and to SEQ ID NO: 3, please note that the Examiner is interpreting the scope of the 16S rDNA sequence of Clostridium XIVa and the 16S rDNA sequence of Clostridium IV, respectively as naturally occurring bacteria isolated from a fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice, as recited in para[0059-0060] pg. 13 of the instant specification.
Similarly, regarding the cope of “Lachnospiraceae spps.” it is noted that the instant specification does not specify which genera of the Lachnospiraceae family are comprised by the Clostridia consortium comprising two or more strains of the species Lachnospiraceae. Pursuant to MPEP 2111.01, under a broadest reasonable interpretation, words of the claim must be given their plain meaning, unless such meaning is inconsistent with the specification. The plain meaning of a term means the ordinary and customary meaning given to the term by those of ordinary skill in the art at the time of the invention. Stackebrandt describes that the family Lachnospiraceae is a phylogenetically and morphologically heterogeneous taxon of the class Clostridia, phylum Firmicutes (see Stackebrandt, E., Chapter 15-The Family Lachnospiraceae in The Prokaryotes Firmicutes and Tenericutes 4th Edition, 2014, pp. 197-201 at pg. 197)(herein after “Stackebrandt”). Stackebrandt adds that the family encompasses 19 genera and the family has been described on phylogenetic grounds, i.e., the position of authentic members of Lachnospiraceae, branching within the radiation of the order Clostridiales, especially associated to members of Clostridium rRNA cluster XIVa (see pg. 197). As such, the Examiner is interpreting the scope of “Lachnospiraceae spps.” as any of the 19 genera belonging to the Lachnospiraceae family where the Lachnospiraceae spps. necessarily comprises an amino acid sequence having at least 98% identity to SEQ ID NO: 4.
With respect to SEQ ID NO:4, please note that the Examiner is interpreting the scope of the 16S rDNA sequence of Lachnospiraceae spps. as a naturally occurring bacterium isolated from a fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice, as recited in para[0061] pg. 14 of the instant specification.
It is noted that claim 1 does not recite a function associated with the Clostridia consortium consisting of Clostridia anaerovorax, Clostridium XIVa, Clostridium IV, and Lachnospiraceae spps; As such, given the disclosure of SEQ ID NOs: 1-4, (see instant specification, Table 1, pg. 16), and combined with the pre-existing knowledge in the art regarding the genetic code and its redundancies, an ordinary skilled artisan would have put one in possession of the genus of a Clostridia consortium comprising two or more strains of bacterium encoded by a base DNA sequence set forth in SEQ ID NOs: 1-4 . With the aid of a computer, an ordinary skilled artisan could have identified all of the bacteria strains as claimed. Thus, an ordinary skilled artisan would conclude that the Applicant was in possession of the claimed genus (i.e., Clostridia consortia) at the time the application was filed.
Response to Arguments
1. Applicant's arguments filed 11/17/2025, with respect to the Specification, have been fully considered but are not persuasive. The objection to the specification (i.e., pg. 13, para[0058]) has been maintained.
2. Applicant's arguments filed 11/17/2025, with respect to the Specification, have been fully considered but are not persuasive. The objection to the specification (i.e., pg. 4, para[0019]) has been maintained.
4. Applicant's arguments filed 11/17/2025, with respect to the Specification, have been fully considered and persuasive. The objection to the specification (i.e., pg. 5, para[0022]) has been withdrawn.
5. Applicant's arguments filed 11/17/2025, with respect to the Drawings, have been fully considered and persuasive. The objection to the drawings (i.e., Fig. 20D-20E) has been withdrawn.
6. Applicant’s arguments, filed 11/17/2025, with respect to the 35 U.S.C. 102(a)(2) as being anticipated by US 11,395,838 B2 Date of Patent Jul. 26, 2022, with Provisional Application No. 62/400,372, filed on Sep. 27, 2016 (herein after “Wargo et al.”), as evidenced by Chun. J. Taxonomy of Clostridium Clusters XIVa and IV, 2017, pp. 1-5, retrieved from https://help.ezbiocloud.net/taxonomy-of-clostridium-cluster-xiva-iv/ on 04/11/2025 (herein after “Chun”); have been fully considered and are persuasive. The 35 U.S.C. 102(a)(2) rejection of claims 1, 3, 5-6, 9, 13 and 19 has been withdrawn.
Maintained/Modified Objections
Specification
The disclosure is objected to because of the following informalities: missing information. It is noted that pages 13, paragraph [0058], recite NRRL or ATCC Accession number; however the Accession number for Clostridia anaerovorax is not provided. Appropriate correction is required.
The disclosure is objected to because of the following informalities: Incorrect Figure Description. It is noted that page 4, paragraph [0019] describes Fig. 3C and Fig. 3D and refers to the genera with enriched relative abundance in WT animals as shaded in blue and in T-Myd88-/- animals as shaded in red. However, the patent or application file does not contain any figure/drawing executed in color. Appropriate correction is required.
Additionally, the amendment filed 11/17/2025 is objected to under 35 U.S.C. 132(a) because it introduces new matter into the disclosure. 35 U.S.C. 132(a) states that no amendment shall introduce new matter into the disclosure of the invention. The added material which is not supported by the original disclosure is as follows: at pg. 2 of 12 of the amendment filed 11/17/2025, paragraph [0019], at lines 6-7, recites “Genera with enriched relative abundance in WT animals are shown by the bottom symbols, genera with enriched relative abundance in T-Myd88-/- animals are shown by the top symbols”. However, the specification does not provide support for symbols, additionally it is noted that the figure corresponding to the amended description (i.e., Fig. 3C) does not include a symbol key.
Applicant is required to cancel the new matter in the reply to this Office Action.
The disclosure is objected to because of the following informalities: editing mistakes. Paragraph [0129] at pg. 37 of the specification filed on 01/10/222, describes Example 1. However the first word in the paragraph is “Abstract”. Similarly, paragraph [0130] at pg. 38 recites “Introduction” as the starting word in the first sentence of the paragraph. Appropriate correction is required.
Please note that the specification has not been checked to the extent necessary to determine the presence of all possible error. Applicant’s cooperation is required in correcting any errors of which applicant may become aware in the specification. See MPEP 608.01.
New Rejections in light of Amendment
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
1. Claims 1, 3, 5-6, 9-10, 14 and 19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a nature-based product (i.e., a supernatant from a Clostridia consortium) without significantly more. As discussed in the “Claim/Sequence Interpretation” section above, the Examiner is interpreting the scope of the 16S rDNA sequence of Clostridia anaerovorax, the 16S rDNA sequence of Clostridium XIVa, the 16S rDNA sequence of Clostridium IV, and the 16S rDNA sequence of Lachnospiraceae spps as naturally occurring bacteria isolated from the fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice (see instant specification, pg. 13, para[0058]). Therefore, the claimed composition comprising a supernatant wherein the Clostridia consortium consists of Clostridia anaerovorax having a 16S rDNA sequence comprising SEQ ID NO: 1, Clostridium XIVa having a 16S rDNA sequence comprising SEQ ID NO: 2, Clostridium IV having a 16S rDNA sequence comprising SEQ ID NO: 3, and Lachnospiraceae spps. having a 16S rDNA sequence comprising SEQ ID NO: 4 is directed to a product, which is one of the statutory categories of invention.
Regarding step 2A, Prong One, of the patent eligible subject analysis, the claims recite a judicial exception of a nature-based product. Claims 1, 10 and 14 are drawn to a composition comprising a Clostridium consortium, wherein the consortium consists of Clostridia anaerovorax having a 16S rDNA sequence comprising SEQ ID NO: 1, Clostridium XIVa having a 16S rDNA sequence comprising SEQ ID NO: 2, Clostridium IV having a 16S rDNA sequence comprising SEQ ID NO: 3, and Lachnospiraceae spps. having a 16S rDNA sequence comprising SEQ ID NO: 4. Claims 3, 5, 6, 9 and 19 are directed to properties of the composition comprising the claimed Clostridium consortium. These limitations therefore encompass nature-based products of the Clostridia anaerovorax having a 16S rDNA sequence comprising SEQ ID NO: 1, Clostridium XIVa having a 16S rDNA sequence comprising SEQ ID NO: 2, Clostridium IV having a 16S rDNA sequence comprising SEQ ID NO: 3, and Lachnospiraceae spps. having a 16S rDNA sequence comprising SEQ ID NO: 4. The claims thus encompass bacteria (i.e., a Clostridia consortium) that are identical (i.e., no difference in structural and/or functional characteristics) to naturally occurring Clostridia. Moreover, there is no indication in the specification nor the claims that isolating a Clostridia consortium from the fecal pellet, and luminal content from the lower small intestine of CD4-Cre+ wild type mice; markedly changes the structure and/or function of the claimed bacteria consortium. Similarly, there is no indication that the claimed composition imparts a structural and/or functional characteristic distinct from the naturally occurring Clostridia consortium found in a fecal pellet and luminal content of the lower small intestine of CD4-Cre+ wild type mice.
Since there is no difference between the naturally occurring Clostridia consortium and the claimed Clostridia anaerovorax having a 16S rDNA sequence comprising SEQ ID NO: 1, Clostridium XIVa having a 16S rDNA sequence comprising SEQ ID NO: 2, Clostridium IV having a 16S rDNA sequence comprising SEQ ID NO: 3, and Lachnospiraceae spps. having a 16S rDNA sequence comprising SEQ ID NO: 4. The claimed composition does not have markedly different characteristics, and thus is a “product of nature” exception. In re Roslin Institute (Edinburgh), 750 F.3d at 1338-39, 110 USPQ2d at 1672-73 (Fed. Cir. 2014). Since the claimed Clostridia consortium (i.e., Clostridia anaerovorax having a 16S rDNA sequence comprising SEQ ID NO: 1, Clostridium XIVa having a 16S rDNA sequence comprising SEQ ID NO: 2, Clostridium IV having a 16S rDNA sequence comprising SEQ ID NO: 3, and Lachnospiraceae spps. having a 16S rDNA sequence comprising SEQ ID NO: 4) does not result in a markedly different structural and/or functional characteristic of the naturally occurring Clostridia consortium, it would then follow that a supernatant that results from the claimed Clostridia consortium is also a natural composition without evidence to the contrary.
Since there is no difference between the claimed composition comprising a supernatant from a Clostridia consortium wherein the Clostridia consortium consists of Clostridia anaerovorax having a 16S rDNA sequence comprising SEQ ID NO: 1, isolated from the fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice; Clostridium XIVa having a 16S rDNA sequence comprising SEQ ID NO: 2, isolated from the fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice; Clostridium IV having a 16S rDNA sequence comprising SEQ ID NO: 3, isolated from the fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice; and Lachnospiraceae spps. having a 16S rDNA sequence comprising SEQ ID NO: 4, isolated from the fecal pellet and luminal content from the lower small intestine of CD4-Cre+ wild type mice; and the naturally occurring clostridia Consortium, the claimed supernatant does not have markedly different characteristics, and thus is a “product of nature” exception. In re Roslin Institute (Edinburgh), 750 F.3d at 1338-39, 110 USPQ2d at 1672-73 (Fed. Cir. 2014). Accordingly, the claims are directed to an exception (i.e., nature-based products). Thus, the answer to step 2A, Prong One is YES.
Regarding Step 2A, Prong Two, of the patent eligible subject analysis, the claims do not integrate the judicial exception into a practical application. The judicial exception is not integrated into a practical application because the claims fail to recite a practical application of the nature-based product. Although claim 14 further encompasses a pharmaceutically acceptable carrier, the incorporation of a carrier is recited at a high level of generality and would be considered a nominal or tangential addition to the claims. In other words, claim 14 recites additional elements beyond the judicial exception (i.e., a pharmaceutically acceptable carrier), however this limitation does not provide any additional information regarding any markedly changes to the structure and/or function of the claimed bacteria consortium. Instead the claim covers any pharmaceutically acceptable carrier that the relevant audience (i.e., a scientist) decides to employ, without indicating that such carrier imparts a distinct structural and/or functional characteristic to the Clostridium consortium.
Moreover, although the claim is directed to additional/further components (i.e., pharmaceutically acceptable carrier), such recitation of additional components tell the relevant audience about which parameters to modify, and at most adds a suggestion that the scientist take those parameters into account when preparing a composition comprising a Clostridium consortium. As such, the limitations of the claim recite a high level of generality without any specificity, and are nothing more than an attempt to generally link the judicial exception to a particular technological environment. Therefore, the answer to step 2A, Prong Two, is NO.
Regarding step 2B of the patent eligible subject analysis, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the composition comprising a supernatant from a Clostridia consortium of the claimed invention is directed to non-statutory subject matter. Although claims 14 encompasses a pharmaceutically acceptable carrier, this limitation is routine and conventional in the art. Similarly, the limitations recited in claims 3, 5-6, 9-10 and 19 are routine and conventional as they encompass well-known members of the Clostridiaceae and Lachnospiraceae families. Therefore, the claim as a whole adds nothing significantly more to the “products of nature” themselves. Thus, the claims do not amount to significantly more than the judicial exception itself and the answer to Step 2B is NO.
Accordingly, the claimed invention is directed to ineligible patent subject matter.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CLAUDIA E ESPINOSA whose telephone number is (703)756-4550. The examiner can normally be reached Monday-Friday 9:30-5:30 EST.
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/CLAUDIA ESPINOSA/Patent Examiner, Art Unit 1654
/LIANKO G GARYU/Supervisory Patent Examiner, Art Unit 1654