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 .
DETAILED ACTION
1. Claims 1-24, 29-43, and 45-48 are currently pending.
Election/Restrictions
2. Applicant’s election without traverse of Group I, claims 1-24, 31-40, and 48 in the reply filed on January 14, 2026 is acknowledged.
Claims 29, 30, and 41-47 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 January 14, 2026.
Claims 1-24, 31-40, and 48 are currently under examination.
Claim Objections
3. Claims 1, 7, 17, and 19-20 are objected to because of the following informalities:
As it pertains to claim 1, ‘Cy steine’ should be ‘cysteine’; ‘Hi stidine’ should be ‘Histidine’; and ‘fiavan-3-ol s’ should be ‘flavan-3-ols’. Applicant is encouraged to review and evaluate all terms within the claims for grammatical errors and make the necessary corrections.
As it pertains to claim 7, line 1, ‘guy’ should be ‘gut’. Appropriate correction is required.
As it pertains to claim 17, the defined microbial strains should be italicized. Also, there is an extra space between Alistipes onderdonkii and Parabacteroides johnsonii. Furthermore, said claim recites Clostridium sp., on multiple occasions. Not only is it a multiple occurrence, those terms are written after the recitation of a specific species of Clostridium. Appropriate correction is required.
Claims 19-20 are objected to for depending upon a rejected based claim. Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
4. Claims 1 and 18 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.
Claim 1 is rendered vague and indefinite by the use of parenthesis. Parenthesis are viewed in the same manner as ‘such as’, which is exemplary language and is not permitted in a claim. The ambiguity of scope is not clear as the Office does not know clearly what is included and what is to be excluded. As written, it is impossible to determine the metes and bounds of the claimed invention.
Additionally, claim 1 is rendered vague and indefinite by the use of the terms “starch (structure 1)” in line 18. It is unclear what constitutes “structure 1”? What core features/structures must be maintained? As written, it is impossible to determine the metes and bounds of the claimed invention.
Claim 18 is rendered vague and indefinite by the use of various terms, for example “Acidaminococcus sp. - - D21”. It is unclear what is meant by said term, as it is not explicitly defined in the specification. What constitutes a “derivative”? What core features/structures must be maintained? As written, it is impossible to determine the metes and bounds of the claimed invention.
Claim 18 is rendered vague and indefinite by the use of the phrase “Sanger 24, Sanger 24”. These terms appear to be the same. As written, it is impossible to determine the metes and bounds of the claimed invention. Additionally, there are a lot of terms that appear vague and indefinite, for example, Marvinbryantia formatexigens 1-52, what does 1-52 represent?
Applicant is strongly encouraged to review all terms and make any necessary changes to identify all of the numbers associated with any cited strain. As written, it is impossible to determine the metes and bounds of the claimed invention.
Claim Rejections - 35 USC § 112
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.
5. Claims 1, 18 and 21 are rejected under 35 U.S.C. 112, first paragraph, as containing 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.
Claim 18 and 21 are drawn in part to the high complexity defined microbial community of claim 1, wherein the defined microbial strains are selected from 2.5 pages of specifically identified strains (see claims for reference).
Because it is not clear that cell lines possessing the properties of all the recited and specific strains as claimed are known and publicly available or can be reproducibly isolated from nature without undue experimentation and because the claims require the use of a suitable deposit for patent purposes a deposit in a public repository is required. Without a publicly available deposit of all the recited and specific strains as claimed, one of ordinary skill in the art could not be assured of the ability to practice the invention as claimed. Exact replication of the cell line is an unpredictable event.
Applicant’s referral to the deposit of all the recited and specific strains as claimed in paragraphs 0180-81 of the specification is an insufficient assurance that all required deposits have been made and all the conditions of 37 CFR 1.801-1.809 have been met.
If the deposit has been made under the provisions of the Budapest Treaty, filing of an affidavit or declaration by applicant or assignees or a statement by an attorney of record who has authority and control over the conditions of deposit over his or her signature and registration number stating that the deposit has been accepted by the International Depository Authority under the provisions of the Budapest Treaty and that all restrictions upon public access to the deposit will be irrevocably removed upon the grant of a patent on this application. These requirements are necessary when deposits are made under the provisions of the Budapest Treaty as the Treaty leaves this specific matter to the discretion of each State. Amendment of the specification to recite the date of the deposit and the complete name and full street address of the depository is required.
If the deposits have not been made under the provisions of the Budapest Treaty, then in order to certify that the deposits comply with the criteria set forth in 37 CFR 1.801-1.809, assurances regarding availability and permanency of deposits are required. Such assurance may be in the form of an affidavit or declaration by applicants or assignees or in the form of a statement by an attorney of record who has the authority and control over the conditions of deposit over his or her signature and registration number averring: (a) during the pendency of this application, access to the deposits will be afforded to the Commissioner upon request; (b) all restrictions upon the availability to the public of the deposited biological material will be irrevocably removed upon the granting of a patent on this application; (c) the deposits will be maintained in the public repository for a period of at least thirty years from the date of deposit or for the enforceable life of the patent of or for a period of five years after the date of the most recent request for the furnishing of a sample of the deposited biological material, whichever is longest; and (d) the deposits will be replaced if they should become nonviable or non-replicable.
In addition, a deposit of biological material that is capable of self-replication either directly or indirectly must be viable at the time of deposit and during the term of deposit. Viability may be tested by the repository. The test must conclude only that the deposited material is capable of reproduction. A viability statement for each deposit of biological material not made under the Budapest Treaty must be filed in the application and must contain: 1) The name and address of the depository; 2) The name and address of the depositor; 3) The date of deposit; 4) The identity of the deposit and the accession number given by the depository; 5) The date of the viability test; 6) The procedures used to obtain a sample if test is not done by the depository; and 7) A statement that the deposit is capable of reproduction. As well as a statement that removes restrictions to provide access to this strain upon granting of a patent has not made, either in the instant Specification, nor in Applicant's Remarks.
One of the critical conditions of Deposit is defined in 37 CFR 1.808 requires that the deposit of biological material be made under two conditions: (A) access to the deposit will be available during pendency of the patent application making reference to the deposit to one determined by the Commissioner to be entitled thereto under 37 CFR 1.14 and 35 U.S.C. 122, and (B) with one exception, that all restrictions imposed by the depositor on the availability to the public of the deposited biological material be irrevocably removed upon the granting of the patent. Upon making this statement, the rejection under 35 USC 112, first paragraph will be withdrawn. This rejection can be obviated through perfection of the Deposit and amendment of the claims to clearly set forth the Deposited strains.
As a possible means for completing the record, applicant may submit a copy of the contract with the depository for deposit and maintenance of each deposit.
If the deposit was made after the effective filing date of the application for patent in the United States, a verified statement is required from a person in a position to corroborate that the all the recited and specific strains as claimed described in the specification as filed is the same as that deposited in the depository. Corroboration may take the form of a showing a chain of custody from applicant to the depository coupled with corroboration that the deposit is identical to the biological material described in the specification and in the applicant’s possession at the time the application was filed.
Applicant’s attention is directed to In re Lundack, 773 F.2d.1216, 227 USPQ (CAFC 1985) and 37 CFR 1.801-1.809 for further information concerning deposit practice.
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.
6. Claim(s) 1-18, 21-24, 31-40 and 48 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Henn et al., WO 2014/145958 A2; Published: 9/18/14.
Independent claim 1 is essentially drawn to a high complexity defined gut microbial community, comprising a plurality of between 40 and 500 defined microbial strains comprising at least 3 to 4 phyla selected from the group consisting of Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria.
Henn discloses that their bacterial compositions comprises two types of bacteria, and typically a large number of bacteria types. For instance, a bacterial composition can comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 1 1 , at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21, 22, 23, 24, 25, 26, 27, 28, 29 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, or at least 40, at least 50 or greater than 50 types of bacteria, as defined by species or operational taxonomic unit (QTU), or otherwise as provided herein. In some embodiments, the bacterial composition includes at least 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, or greater numbers of bacteria types (see paragraph 092; meets claims 1 and 34-35).
Moreover, said compositions comprise a network ecologies comprising at least two types of isolated bacteria, chosen from the species in Table 1 and preferably more than one of the following: Enterococcus faecalis (previously known as Streptococcus faecalis), Clostridium innocuum, Clostridium ramosum, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaiotaomicron, Escherichia coli, Clostridium bifermentans, and Blautia producia (previously known as Peptostreptococcus productus). In an alternative embodiment, at least one of the preceding species is not substantially present in the bacterial composition (see paragraph 094-95; meets claim 1, 15). Further, the composition comprises Bifidobacterium, Faecalibacterium prausnitzii, Bacteroides fragilis, Bacteroides thetaiotaomicron (see paragraph 097&100; meets claim 1, 13-17). In yet another embodiment, the bacterial composition comprises Anaerosripes and adlercreutzia (see paragraph 098; meets claim 1, 16). Henn discloses Acidaminococcus sp. -D21 (see table 1; meets claim 18, 21).
In the present method, the bacterial composition can be administered enterically, in other words, by a route of access to the gastrointestinal tract. This includes oral administration, rectal administration (including enema, suppository, or colonoscopy), by an oral or nasal tube (nasogastric, nasojejunal, oral gastric, or oral jejunal), as detailed more fully herein (see paragraph 0185; meets claim 10). The bacterial compositions can be administered with other agents in a combination therapy mode, including anti-microbial agents and prebiotics. Administration can be sequential, over a period of hours or days, or simultaneous (see paragraph 0201; meets claim 11).
Moreover, to generate functional annotation from metagenomic or whole genome shotgun sequence data, reads are first clustered and then representative reads are annotated. In all cases, functional pathways are derived from the sequence read annotations based on the mapping of the sequence annotations to a functional database, such as but not limited to KEGG (http://www.genome.jp/kegg), Biocyc (http://biocyc.org), IMG (http://img.jgi.doe.gov), MetaCyc (http://www.metacyc.org), or Reactome (http://www.reactome.org) (see paragraph 0370; meets claim 7).
Henn in their claim 102 discloses a pharmaceutical formulation comprising a purified first bacterial entity and a purified second bacterial entity, wherein the first bacterial entity comprises a first nucleic acid sequence encoding a first polypeptide capable of catalyzing a first chemical reaction, wherein the second bacterial entity comprises a second nucleic acid sequence encoding a second polypeptide capable of catalyzing a second chemical reaction, wherein the pharmaceutical formulation is formulated for oral administration to a mammalian subject in need thereof, wherein the first chemical reaction and the second chemical reaction are capable of occurring in the gastrointestinal tract of the mammalian subject under conditions such that a first product of the first chemical reaction, a substance present within said mammal ian subject, or a combination of said first product with the substance is used as a substrate in the second chemical reaction to form a second product, wherein the second product induces a host cell response (see Henn’s claim 102; meets claim 8-9). In yet another method to generate a metabolic profile of a microbial ecology, characterization of metabolites produced by the ecology are analyzed in tissues or fluids. Samples can include, without limitation, blood, urine, serum, feces, ileal fluid, gastric fluid, pulmonary aspirates, tissue culture fluid, or bacterial culture supernatants (see paragraph 0372; meets claim 6). The resulting culture is sampled at 1 , 2, 4 and 8 hours. The sample is analyzed by HPLC as described above to find organisms with maximal activity (see paragraph 0385; meets claim 3, 5).
Further, a person of ordinary skill in the art can identify the specific hypervariable regions of a candidate 16S rRNA by comparing the candidate sequence in question to a reference sequence and identifying the hypervariable regions based on similarity to the reference hypervariable regions, or alternatively, one can employ Whole Genome Shotgun (WGS) sequence characterization of microbes or a microbial community (see paragraph 058; meets claims 32-33). Nucleic acid sequences are analyzed and annotated to define taxonomic assignments using sequence similarity and phylogenetic placement methods or a combination of the two strategies. Sequence reads (e.g. 16S, 18S, or ITS) are placed into a reference phylogeny comprised of appropriate reference sequences (see paragraph 0272; meets claims 36-38).
Henn discloses that OTUs can be defined either by full 16S sequencing of the rRNA gene (Table 1), by sequencing of a specific hypervariable region of this gene, or by sequencing of any combination of hypervariable regions from this gene. The bacterial 16S rDNA is approximately 1500 nucleotides in length and is used in reconstructing the evolutionary relationships and sequence similarity of one bacterial isolate to another using phylogenetic approaches. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most microbes (see paragraph 0108; meets claims 38-39). MALDI-TOF-mass spectrometry can also be used for species identification (see paragraph 0279; meets claim 40).
Moreover, Henn discloses that engraftment of OTUs from the ethanol- treated spore preparation treatment into the patient as well as the resulting augmentation of the resident microbiome led to a significant decrease in and elimination of the carnage of pathogenic species other than C. difficile in the patient, 16S-V4 sequencing of primary stool samples demonstrated that at pretreatment, 20%o of reads were from the genus Klebsiella and an additional 19% were assigned to the genus Fusobacterium (see paragraph 0339; meets claim 7). To test the potential of a bacterial composition's ability to treat obesity, 8-9 week old GF C57BL/6J mice can be conventionalized by introducing by oral gavage a) the bacterial composition, b) fecal samples from an obese female twin discordant for obesity (obese control), or c) fecal samples from the paired lean female twin (lean control). One gnotobiotic isolator is used per microbiota sample and each recipient mouse is individually caged within the isolator. The obese twin donors must have BMI > 30 kg/m2 and the donating pair must have a sustained multi-year BMI difference of at least 5.5 kg/m2. Recipient mice are fed a low fat (4% by v/eight) high in plant polysaccharide (LF- HPP), autoclaved mouse chow (see paragraph 0427).
To prepare the fecal samples for gavage into the GF mice, fecal samples provided by donors are frozen immediately after production, stored at -80°C. Samples are homogenized by mortar and pestle while submerged in liquid nitrogen and a 500 mg aliquot of the pulverized material is diluted in 5 mL of reduced PBS (PBS supplemented with 0.1 % Resazurin (w/v), 0.05% L-cysteine-HCl) in an anaerobic Coy chamber (atmosphere, 75% N2, 20% C02, 5% H2) and then vortexed for 5 min at room temperature. The suspension is settled by gravity for 5 min, and then the clarified supernatant transferred to an anaerobic crimped tube that is transported to a gnotobiotic mouse facility (see paragraph 0428, meets claim 1, 3-5). Once a mouse develops diabetes it is gavaged with the microbial composition, and blood glucose, urine glucose, and insulin serum levels are evaluated (see paragraph 0438; meets claim 12)
The invention also includes a pharmaceutical formulation comprising a purified bacterial population comprising a plurality of bacterial entities, wherein the bacterial entities are present in an amount effective to induce the formation of a functional bacterial network in the gastrointestinal tract in a mammalian subject in need thereof to whom the formulation is administered (see paragraph 067; meeting claim 48). The bacterial composition is generated for oral or gastric administration (see paragraph 0144; meets claim 4).
Lastly, with regard to claims 2, 3, 9, 24 the defined gut microbial community as claimed is the same disclosed in the prior art, metabolization or the production of a metabolite can necessarily be determined by culturing or determined by the administration of the defined gut microbial, absent evidence to the contrary.
As it pertains to claims 22-23 and 31, the defined gut microbial community as claimed is the same disclosed in the prior art, the community stability is necessarily characterized by the appearance of up to 10% of new strains, as well as characterized by metagenomic analysis of a fecal sample, absent evidence to the contrary.
Since the Office does not have the facilities for examining and comparing applicants’ composition with the composition of the prior art, the burden is on applicant to show a novel or unobvious difference between the claimed product and the prior art. See In re Best, 562 F.2d 1252, 195 USPQ 430 (CCPA 1977) and In re Fitzgerald et al., 205 USPQ 594.
Conclusion
7. No claim is allowed.
8. Any inquiry concerning this communication or earlier communications from the examiner should be directed to LAKIA J JACKSON-TONGUE whose telephone number is (571)272-2921. The examiner can normally be reached Monday-Friday 930AM-530PM.
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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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/LAKIA J JACKSON-TONGUE/Examiner, Art Unit 1645 February 20, 2026
/BRIAN GANGLE/Primary Examiner, Art Unit 1645