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 .
Information Disclosure Statement
The information disclosure statement (IDS) filed 19 April 2024 is considered, initialed, and attached hereto. Foreign Patent Document Cite Nos. 001-030 and Non-Patent Literature Document Cite Nos. 001-142 in the IDS filed 19 April 2024 were not considered because the IDS did not include copies of these cited documents. MPEP §609.04(a)(II) states:
“In addition to the list of information, each information disclosure statement must also include a legible copy of:
(A) Each foreign patent;
(B) Each publication or that portion which caused it to be listed, other than U.S. patents and U.S. patent application publications unless required by the Office”.
Therefore, foreign patent documents and non-patent literature documents were not considered unless a copy was included with the IDS.
Claim Status
Claims 1-19 are pending and under examination.
Claim Rejections - 35 USC § 112(b) - Indefiniteness
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.
Claim 19 is 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 19 recites the limitation "the metagenomics data" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 19 recites the limitation "the functional metagenomic analysis" in line 3. There is insufficient antecedent basis for this limitation in the claim.
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.
Claims 1-19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. While the claims are directed to a process, and therefore meet step 1 of the subject matter eligibility test (see MPEP §2106.03), the claim(s) recite(s) the abstract ideas of diagnosing the subject as having dysbiosis based on the metagenomics analysis and assessing the effectiveness of the dysbiosis, which are mental processes because they can be done in the human mind looking at data of the metagenomics analysis and/or data from the subject following treatment.
Step 2A of the subject matter eligibility test require a two-pronged analysis. Prong One asks: does the claim recite an abstract idea, law of nature or natural phenomenon? As discussed in MPEP §2106.04(II)(A)(1), the meaning of “recites” is “set forth” or “describes”. That is, a claim recites a judicial exception when the judicial exception is “set forth” or “described” in the claim. In the instant case, the claims describe abstract ideas of diagnosing the subject as having dysbiosis based on the metagenomics analysis and assessing the effectiveness of the dysbiosis.
Prong Two of the analysis under step 2A asks: does the claim recite additional elements that integrate the judicial exception into a practical application of the judicial exception? As discussed in MPEP §2106.04(II)(A)(2):
Because a judicial exception is not eligible subject matter, Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)), if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception, that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, the additional elements (if any) in the claim must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B.
The considerations to be used are set forth in MPEP §2106.04(d)(2) and MPEP §2106.05(a) through (c) and (e) through (h). Turning to those sections of the MPEP:
MPEP §2106.05(a) has to do with improvements to the functioning of a computer or to any other technology or technical field. The claims at issue do not improve the functioning of a computer or improve the technical fields of metagenomics analysis and dysbiosis treatment.
MPEP §2106.05(b) has to do with whether the claims involve the use of a particular machine. In this case, the claims do not involve the use of a particular machine as all materials used in steps of the method are described generically.
MPEP §2106.05(c) has to do with whether the claims involve a particular transformation. Here, the claims do not involve a particular transformation because the claims are for a process.
MPEP §2106.05(e) has to do with “other meaningful limitations”. The additional limitations imposed upon the abstract ideas consist of extracting genetic material, subjecting the extracted genetic material to metagenomics analysis, and preparing and administering to the subject a customized probiotic, prebiotic, enzyme, and/or botanical mixture as recited in steps a), b), and d) of claim 1. These are not meaningful limitations because they generally link the use of the judicial exceptions to the particular technological environment of metagenomics analysis and dysbiosis treatment.
MPEP §2106.04(d)(2) has to do with whether the additional elements apply or use the judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition. While the recited step of “administering to the subject a customized probiotic, prebiotic, enzyme, and/or botanical mixture which is formulated specifically to treat the dysbiosis in the subject” is a treatment, it is not considered particular because how a treatment is customized or formulated specifically is not described with sufficient specificity to be particular. For example, the same treatment could be administered to every patient with dysbiosis and is only customized/specific in that it is not administered to patients not diagnosed with dysbiosis. Additionally, the recited treatments cover a broad variety of treatments for dysbiosis, including any treatment that includes any enzyme, lending further weight to the determination that the treatment recited is not a particular treatment.
MPEP §2016.05(f) raises the question as to whether the additional elements recited in the claim represent “mere instructions to apply an exception”. As steps a) and b) gather data that is used in the abstract idea of diagnosing, the abstract idea of diagnosing is applied by administering a treatment, and the administration of a treatment is part of the process of gathering data for the abstract idea of assessing the effectiveness of the treatment, the additional elements represent mere instructions to apply the exceptions.
MPEP §2106.05(g) has to do with whether the additional elements of the claim amount of insignificant extra-solution activity. MPEP §2106.05(g) notes that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra-solution activity. The steps a) and b) are mere gathering of the metagenomics analysis data used in the abstract idea of diagnosing and step e) is mere data gathering as administration of a treatment is necessary for the effectiveness of the treatment to be assessed.
MPEP §2106.05(h) has to do with whether the additional elements amount to more than generally linking the use of a judicial exception to a particular technological environment or field of use. The recitation of the judicial exceptions being applied to metagenomics analysis and dysbiosis treatment represent “field of use” limitations. However, as MPEP §2106.05(h) indicates, such limiting to a particular “field of use” does not confer patentability to otherwise ineligible subject matter.
In addition, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception (as set forth in step 2B of the subject matter eligibility test) because it was known in the prior art to extract genetic material, to subject the extracted genetic material to metagenomics analysis, and to prepare and administer to the subject a customized treatment for dysbiosis, as seen in the prior art of Quay et al. (US 2013/0121968, see 35 U.S.C. 103 rejection of claim 1 below for full mapping of limitations).
Having considered the factors discussed in MPEP §2106.05 as well as the prior art of Quay et al., it is clear that the additional elements recited in the claims, whether considered individually or as a combination, do not integrate the judicial exceptions into a practical application of those exceptions in such a way as to provide meaningful limits on the use of the judicial exception and do not amount to significantly more than the judicial exception. Therefore, claims 1-19 are rejected here under 35 U.S.C. 101.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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.
Claims 1-4, 7, 11, 13-14, and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Quay (U.S. Patent Document Cite No. 055 in IDS filed 19 April 2014)(US 2013/0121968, published 16 May 2013, effectively filed 3 October 2011) in view of Ezendam et al. (“Probiotics: immunomodulation and evaluation of safety and efficacy” Nutr Rev 64(1), pages 1-14 (2006)), herein Ezendam.
Regarding claim 1, Quay teaches a method for preparing and analyzing a sample (“a method of diagnosing a patient” [0144]; “a method of treating a patient diagnosed with a medical condition as described above” [0153]) comprising:
extracting genetic material from a diverse population of microbes present in a sample obtained from a subject, thereby preparing the sample for analysis (“obtaining a fecal sample from a patient, isolating and quantifying at least a portion of 16S rRNA of the sample” [0144]; also [0059] and [0119]);
subjecting the extracted genetic material to metagenomics analysis (“quantifying at least a portion of 16S rRNA of the sample to determine a metagenomic profile of the sample” [0144]; also [0092]-[0115]);
diagnosing the subject as having dysbiosis based on the metagenomics analysis (“combining the metagenomic and metatranscriptome profiles into a multiplex profile […] comparing the multiplex profile of said mammal to a multiplex profile of a population of patients diagnosed with Antibiotic-Induced Dysbiosis to determine the presence or absence of Antibiotic-Induced Dysbiosis” [0144]);
preparing and administering to the subject a customized probiotic, prebiotic, enzyme, and/or botanical mixture which is formulated specifically to treat the dysbiosis in the subject (“restoring or correcting disease- or medical condition-related imbalances in the patient's microbiome, based on the information revealed by the patient's microbiome profile, with culture-conditioned formulations in which the transcriptome activity of the administered organisms is optimized” [0153]; “In one embodiment, probiotic culture is administered to the patient” [0154]; also [0155-0186]).
However, Quay does not explicitly teach assessing the effectiveness of the dysbiosis treatment. This deficiency is made up for in the teachings of Ezendam.
Regarding claim 1, Ezendam teaches that assessing the effectiveness of probiotic treatments is standard practice and provides the advantages of enabling the treatment to pass various approval processes for sale and marketing regulations (Section titled “Assessment of efficacy and safety of probiotics” beginning page 8 right column last paragraph).
Regarding claim 2, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above), and Quay further teaches that the genetic material comprises a nucleic acid molecule (“16S rRNA of the sample” [0144]; also [0059] and [0119]).
Regarding claim 3, the combination of Quay and Ezendam teach the method of claim 2 (see 35 U.S.C. 103 rejection of claim 2 above), and Quay further teaches that the nucleic acid molecule is DNA (“As used herein, the term "metagenomics" refers to the application of modern genomics techniques to the study of communities of microbial organisms directly in their environment based on DNA obtained from a sample” [0059]; “the multiplex profile identifies a lower than normal amount of DNA and RNA associated with the phyla associated with the distal gut” [0144]).
Regarding claim 4, the combination of Quay and Ezendam teach the method of claim 2 (see 35 U.S.C. 103 rejection of claim 2 above), and Quay further teaches that the nucleic acid molecule is RNA (“16S rRNA of the sample” [0144]; also [0119]).
Regarding claim 7, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above), and Quay further teaches that extracting genetic material comprises treatment of the sample with one or more buffers (“For example, total RNA can be is isolated using an RNEASY 96.TM. kit and buffers” [0088]).
Regarding claim 11, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above), and Quay further teaches the mechanical treatment of the sample to cause physical lysis of cells (“Extraction of RNA from cells are generally carried out using methods known in the art. Physical and/or chemical cell lysis and affinity column purification is used to extract RNA” [0088]; “RNA is extracted from the resulting mixture by using an RNeasy minikit (Qiagen) following standard instructions and including mechanical disruption of the cells using glass beads” [0119]).
Regarding claim 13, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above), and Quay further teaches that the sample is obtained from a gut of the subject (“obtaining a fecal sample from a patient” [0144], stools are derived from the gut).
Regarding claim 14, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above), and Quay further teaches that the diverse population of microbes comprises one or more of bacteria and archaea (“the term "bacteria" encompasses both prokaryotic organisms and archaea present in mammalian microbiota. The terms "intestinal microbiota", "gut flora", and "gastrointestinal microbiota" are used interchangeably to refer to bacteria in the digestive tract [0050]; “the multiplex profile identifies a lower than normal amount of DNA and RNA associated with the phyla associated with the distal gut including Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, Verrucomicrobia and Clostridiales” [0144]).
Regarding claim 18, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above), and Quay further teaches the identification of a disease or disorder based on the dysbiosis (“the patient is diagnosed with Antibiotic-Induced Dysbiosis” [0144]; see also [0145-0152]).
In view of the advantages taught by Ezendam, one of ordinary skill in the art would be motivated to combine the method Quay with the assessment of efficacy taught by Ezendam (MPEP §2143(I)(G)). One of ordinary skill in the art would have a reasonable expectation of success in this combination because the assessment of efficacy of a treatment would not be expected to negatively impact a method of diagnosing and treating that is performed before the assessment and the diagnosis and treating is a necessary input data for the assessment to be made. Therefore, the invention as a whole of claims 1-4, 7, 11, 13-14, and 18 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 5, 9, and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Quay (U.S. Patent Document Cite No. 055 in IDS filed 19 April 2014)(US 2013/0121968, published 16 May 2013, effectively filed 3 October 2011) in view of Ezendam et al. (“Probiotics: immunomodulation and evaluation of safety and efficacy” Nutr Rev 64(1), pages 1-14 (2006)), herein Ezendam, as applied to claims 1-4, 7, 11, 13-14, and 18 above, and further in view of Smith et al. (U.S. Patent Document Cite No. 045 in IDS filed 19 April 2014)(US 2011/0200983, published 18 August 2011, effectively filed 15 February 2010), herein Smith.
Regarding claim 5, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, neither Quay nor Ezendam teach the extraction of genetic material comprising magnetic bead based nucleic acid purification. This deficiency is made up for in the teachings of Smith.
Regarding claim 5, Smith teaches extracting genetic material using magnetic bead based nucleic acid purification (“sample can be subjected to a standard nucleic acid extraction technique such as those described elsewhere (e.g., Sambrook and Russell, (2001) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Press) or a nucleic acid extraction technique that includes the use of magnetic beads. For example, the blood sample can be contacted with magnetic beads that bind nucleic acid, the beads can be removed, and bound nucleic acid can be eluted into an appropriate buffer to form a processed sample for further analysis” [0082]).
Regarding claim 9, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Smith teaches extracting genetic material using a heat shock treatment (“a sample can be heated […] to release nucleic acid from cells present in the sample” [0079]; “a sample can be homogenized and treated to disrupt cells including microbial cells that are present in the sample. For example, a mucus sample […] can be subjected to high temperature” [0082]).
Regarding claim 12, the combination of Quay and Ezendam teach the method of claim 11 (see 35 U.S.C. 103 rejection of claim 11 above). Smith teaches extracting genetic material using mechanical treatment of the sample to cause physical lysis of cells wherein mechanical treatment comprises bead mixing or bead mill homogenization (“a sample can be homogenized and treated to disrupt cells including microbial cells that are present in the sample. For example, a mucus sample can be subjected to high speed mechanical homogenization with glass/silica/zirconium/stainless steel beads” [0082]).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the method of extraction of genetic material using magnetic beads taught by Smith for extraction of genetic material taught generally and not limited to any specific method of extraction in the method of the combination of Quay and Ezendam (MPEP §2143 I. B.). One of ordinary skill in the art could have performed this substitution and would have found the results of this substitution predictable because both serve the same purpose of extracting genetic material from a sample. Therefore, the invention as a whole of claims 5, 9, and 12 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 6-8 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Quay (U.S. Patent Document Cite No. 055 in IDS filed 19 April 2014)(US 2013/0121968, published 16 May 2013, effectively filed 3 October 2011) in view of Ezendam et al. (“Probiotics: immunomodulation and evaluation of safety and efficacy” Nutr Rev 64(1), pages 1-14 (2006)), herein Ezendam, as applied to claims 1-4, 7, 11, 13-14, and 18 above, and further in view of Ley et al. (U.S. Patent Document Cite No. 064 in IDS filed 19 April 2014)(US 2015/0050293, published 19 February 2015, effectively filed 5 March 2012), herein Ley, and as evidenced by Davis et al. (“A dose dependent impact of prebiotic galactooligosaccharides on the intestinal microbiota of healthy adults” Int J Food Microbiol 144(2), pages 285-292 (2010)), herein Davis, and as evidenced by Qiagen (Safety Data Sheet for Buffer ASL, downloaded from the Qiagen website on 19 June 2026).
Regarding claim 6, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, neither Quay nor Ezendam teach that extracting genetic material comprises phenol-chloroform-alcohol extraction. This deficiency is made up for in the teachings of Ley.
Regarding claim 6, Ley teaches a method of extracting genetic material from a sample wherein extracting genetic material comprises phenol-chloroform-alcohol extraction (“DNA was extracted from gnotobiotic fecal pellets as described previously (Davis et al., Int. J. Food Microbiol. 144:285 (2010)), but with five phenol-chloroform-isoamyl alcohol extractions” [0085]).
Regarding claim 7, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Ley teaches, as evidenced by Davis, extracting genetic material from a sample wherein extracting genetic material comprises treatment of the sample with one or more buffers (“DNA was extracted from gnotobiotic fecal pellets as described previously (Davis et al., Int. J. Food Microbiol. 144:285 (2010)” Ley [0085]; “2.4 DNA Extraction […] Buffer ASL (1.6 mL) from the QIAamp DNA Stool Mini Kit (Qiagen, Hilden, Germany) was added to each sample after the samples were homogenized” Davis page 286 right column last paragraph).
Regarding claim 8, the combination of Quay, Ezendam, and Ley teach the method of claim 7 (see 35 U.S.C. 103 rejection of claim 7 above) and Ley further teaches, as evidenced by Davis and Qiagen, that the one or more buffers comprise a detergent (“DNA was extracted from gnotobiotic fecal pellets as described previously (Davis et al., Int. J. Food Microbiol. 144:285 (2010)” Ley [0085]; “2.4 DNA Extraction […] Buffer ASL (1.6 mL) from the QIAamp DNA Stool Mini Kit (Qiagen, Hilden, Germany) was added to each sample after the samples were homogenized” Davis page 286 right column last paragraph; “Components […] sodium dodecyl sulphate” Qiagen page 3 Section 3).
Regarding claim 12, the combination of Quay and Ezendam teach the method of claim 11 (see 35 U.S.C. 103 rejection of claim 11 above). Ley teaches, as evidenced by Davis, that the mechanical treatment comprises bead mixing or bead mill homogenization (Davis et al., Int. J. Food Microbiol. 144:285 (2010)” Ley [0085]; “2.4 DNA Extraction […] the samples were homogenized in a MiniBeadbeater-8” Davis page 286 right column last paragraph).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the method of extracting genetic material taught by Ley for the method of extracting genetic material in the method taught by the combination of Quay and Ezendam (MPEP §2143 I. B.). One of ordinary skill in the art could have performed this substitution and would have found the results of this substitution predictable because both serve the same purpose of extracting genetic material. Therefore, the invention as a whole of claims 6-8 and 12 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Quay (U.S. Patent Document Cite No. 055 in IDS filed 19 April 2014)(US 2013/0121968, published 16 May 2013, effectively filed 3 October 2011) in view of Ezendam et al. (“Probiotics: immunomodulation and evaluation of safety and efficacy” Nutr Rev 64(1), pages 1-14 (2006)), herein Ezendam, as applied to claims 1-4, 7, 11, 13-14, and 18 above, and further in view of Bastian et al. (U.S. Patent Document Cite No. 011 in IDS filed 19 April 2014)(US 6,180,778, published 30 January 2001), herein Bastian.
Regarding claim 8, the combination of Quay and Ezendam teach the method of claim 7 (see 35 U.S.C. 103 rejection of claim 7 above), and Quay further teaches the use a lysozyme in the extraction of genetic material (“RNA is isolated from the resulting cell pellet by applying an enzymatic cell lysis using mutanolysin and lysozyme” [0119]). However, neither Quay nor Ezendam teach that the one or more buffers comprise a lysozyme, a detergent, a chelator, a chaotropic agent, a protease, or any combination thereof. This deficiency is made up for in the teachings of Bastian.
Regarding claim 8, Bastian teaches the extraction of nucleic acid from a microbe comprising treatment with a buffer comprising a lysozyme (“For the isolation of whole RNA from bacteria, an additional step is inserted before performing the standard protocol in order to lyse the cell walls of the bacteria. The cell pellet is resuspended in 400 µg/ml lysozyme in TE” col 11 lines 30-33).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the method of extracting nucleic acid from microbes taught by Bastian for the method of extracting nucleic acid from microbes in the method taught by the combination of Quay and Ezendam (MPEP §2143 I. B.). One of ordinary skill in the art could have performed this substitution and would have found the results of this substitution predictable because both serve the same purpose of extracting genetic material from microbes. Therefore, the invention as a whole of claim 8 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 10 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Quay (U.S. Patent Document Cite No. 055 in IDS filed 19 April 2014)(US 2013/0121968, published 16 May 2013, effectively filed 3 October 2011) in view of Ezendam et al. (“Probiotics: immunomodulation and evaluation of safety and efficacy” Nutr Rev 64(1), pages 1-14 (2006)), herein Ezendam, as applied to claims 1-4, 7, 11, 13-14, and 18 above, and further in view of Maron et al. (U.S. Patent Document Cite No. 034 in IDS filed 19 April 2014)(US 2007/0015177, published 18 January 2007, effectively filed 15 October 2003), herein Maron.
Regarding claim 10, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, neither Quay nor Ezendam teach that extracting genetic material comprises treatment of the sample to induce germination of bacterial spores and/or fungal spores present in the sample. This deficiency is made up for in the teachings of Maron.
Regarding claim 10, Maron teaches a method for extracting nucleic acids from microorganisms ([0019]) wherein the yield of DNA from collected spores in a sample is improved by treating the sample to induce germination of the bacterial spores to their vegetive form (“The results obtained show that the spores are reluctant to be lysed. […] To improve these yields, a protocol including a prior step of taking up the sporulated forms into culture in a TS liquid medium (soy trypticase) for 2 hours at 37° C. was tested. This incubation allows the sporulated forms to change to vegetative forms. […] This protocol was tested on two strains of Bacillus globigii” [0229]).
Regarding claim 14, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Maron teaches the extraction of nucleic acids from a microbes including bacteria, archae, fungi, protozoa, spores, and algae (“The nucleic acid extraction method is suitable for extracting nucleic acids from any type of prokaryotic or lower eukaryotic microbial population, including bacteria, protozoa, single celled algae, archaebacteria or fungi” [0045]; [0229]).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the method of extracting genetic material taught by Maron for the method of extracting genetic material in the method taught by the combination of Quay and Ezendam (MPEP §2143 I. B.). Additionally, one of ordinary skill in the art would be motivated to combine the teachings of Maron with the method of Quay and Ezendam in order to improve the method of Quay and Ezendam with the advantage of improved yields from spores as taught by Maron. One of ordinary skill in the art could have performed this substitution and would have found the results of this substitution predictable because both serve the same purpose of extracting genetic material from microbes. Therefore, the invention as a whole of claims 10 and 14 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 15-17 are rejected under 35 U.S.C. 103 as being unpatentable over Quay (U.S. Patent Document Cite No. 055 in IDS filed 19 April 2014)(US 2013/0121968, published 16 May 2013, effectively filed 3 October 2011) in view of Ezendam et al. (“Probiotics: immunomodulation and evaluation of safety and efficacy” Nutr Rev 64(1), pages 1-14 (2006)), herein Ezendam, as applied to claims 1-4, 7, 11, 13-14, and 18 above, and further in view of Turnbaugh et al. ("The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice" Sci Transl Med 1(6):6ra14 (2009)), herein Turnbaugh.
Regarding claim 15, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, neither Quay nor Ezendam teach that the metagenomics analysis identifies one or more food stuffs the subject has consumed and/or one or more macronutrients the subject has consumed. This deficiency is made up for in the teachings of Turnbaugh.
Regarding claim 15, Turnbaugh teaches that differences in diet, including consumed macronutrients, is identified by metagenomics analysis (“The recipient mice were maintained on a standard low-fat, plant polysaccharide–rich (LF/PP) diet in separate cages within a gnotobiotic isolator. Fecal samples were collected from these animals 1 day, 1 week, and 1 month after colonization, at which point half of the mice were switched to a high-fat, high-sugar Western diet” page 2 left column paragraph 2; “Administration of the Western diet to mice 4 weeks after colonization resulted in a shift in gut community structure that was evident after a single day and that stabilized by 7 days” page 2 right column paragraph 2). Therefore, it would be prima facie obvious to one of ordinary skill in the art that the consumption of a macronutrient, such as fat, can be identified in the metagenomics analysis of the method of Quay and Ezendam.
Regarding claim 16, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). In view of Turnbaugh’s teaching that the metagenomics analysis can distinguish between subjects consuming a low fat, healthier diet and those consuming a high fat, less healthy diet (see 35 U.S.C. 103 rejection of claim 15 above), it would have been prima facie obvious to one of ordinary skill in the art (e.g. a healthcare provider) to provide dietary guidance, such as recommending the healthier diet, to subjects identified as having the less healthy diet.
Regarding claim 17, the combination of Quay, Ezendam, and Turnbaugh teach the method of claim 16 (see 35 U.S.C. 103 rejection of claim 16 above). As the claim and specification do not provide any limiting definition of “food stuff”, the broadest reasonable interpretation of “food stuff” used is anything consumed for nutrition. As any dietary guidance includes the consumption of food stuff (consumption of sources of nutrition is required to sustain life), the recommendation discussed in the rejection of claim 16 above made based on the determination of a dietary guidance inherently includes treating the subject with a food stuff.
In view of Turnbaugh’s teaching that a metagenomics analysis can differentiate healthy low fat diets from unhealthy high fat diets, leading to dietary recommendations, one of ordinary skill in the art (e.g. a healthcare provider) would be motivated to combine Turnbaugh’s teachings with the method of the combination of Quay and Ezendam that generates a metagenomics analysis to improve the metagenomics analysis with the ability to use it for dietary recommendations. One of ordinary skill in the art would have a reasonable expectation of success because including an additional interpretation of the metagenomics analysis would not be expected to prevent the method taught by Quay and Ezendam from functioning. Therefore, claims 15-17 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Quay (U.S. Patent Document Cite No. 055 in IDS filed 19 April 2014)(US 2013/0121968, published 16 May 2013, effectively filed 3 October 2011) in view of Ezendam et al. (“Probiotics: immunomodulation and evaluation of safety and efficacy” Nutr Rev 64(1), pages 1-14 (2006)), herein Ezendam, as applied to claims 1-4, 7, 11, 13-14, and 18 above, and further in view of Vernocchi et al. (“Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health” Front Microbiol 7:1144 (2016)), herein Vernocchi.
Regarding claim 19, the combination of Quay and Ezendam teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, neither Quay nor Ezendam teach that further metabolomic data can be determined from the metagenomics data or that the sample can be further tested for metabolites to determine a functional metagenomic analysis. This deficiency is made up for in the teachings of Vernocchi.
Regarding claim 19, Vernocchi teaches that various bacteria that may be in the detected in the metagenomics analysis (page 8 Table 2 column 2) produce metabolites (page 8 Table 2 column 2), thereby teaching that metabolomic data can be determined from the metagenomics analysis. Vernocchi also teaches that various metabolites produced by gut microbiota are associated with disease in the subject, so the determination of metabolomic data about these metabolites from the metagenomics analysis advantageously provides information on disease in the subject (section titled “Biological action of the gut microbiota in healthy and diseased subjects” starting on page 11 left column).
In view of Vernocchi’s teaching that a metagenomics analysis can provide information on disease-associated metabolites in a subject, one of ordinary skill in the art (e.g. a healthcare provider) would be motivated to combine Vernocchi’s teachings with the method of the combination of Quay and Ezendam that generates a metagenomics analysis to improve the metagenomics analysis with the ability to provide healthcare providers with information on disease-associated metabolites in the subject. One of ordinary skill in the art would have a reasonable expectation of success because including an additional interpretation of the metagenomics analysis would not be expected to prevent the method taught by Quay and Ezendam from functioning. Therefore, claim 19 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 16-17 of U.S. Patent No. 10,428,370, herein ‘370, in view of Quay; Ezendam; Smith; Ley as evidenced by Davis and Qiagen; Bastian; Maron; Turnbough; and/or Vernocchi. Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding instant claim 1, claim 1 of ‘370 recites language largely equivalent to steps a), b), c), d), and e) of instant claim 1 (the recited modified probiotic in claim 1 of ‘370 being equivalent to the customized probiotic of step d) of instant claim 1). Though claim 1 of ‘370 does not recite the preparing action in step d) of claim 1, this is taught by Quay as discussed in the 35 U.S.C. 103 rejection of claim 1 above. The additional limitations of claim 1 of ‘370 only further limit its scope and therefore claim 1 of ‘370, modified by Quay, is a species of instant claim 1. As Quay teaches a similar process of metagenomic analysis and treatment of dysbiosis, this would merely constitute combining prior art elements via known methods that perform the same function in combination as they do separately (the preparation of the treatment of Quay is still functioning to prepare a treatment for administration in the combination)(MPEP §2143(I)(A)). One of ordinary skill in the art would have a reasonable expectation of success due to the close similarities between the methods of claim 1 of ‘370 and Quay. Therefore, instant claim 1 is not patentably distance from claim 1 of ‘370.
Regarding instant claims 14 and 18, depending on instant claim 1, claims 16 and 17 of ‘370 recite identical or equivalent language to instant claims 14 and 18, respectively, and depend on claim 1 of ‘370. Therefore, instant claims 14 and 18 are not patentably distinct from claims 16-17 of ‘370.
Regarding instant claims 2-13, 15-17, and 19, the limitations of these claims are not recited in the claims of ‘370, but are all obvious variants of instant claim 1. The limitations of instant claims 2-13, 15-17, and 19 are taught in the references of Quay; Ezendam; Smith; Ley as evidenced by Davis and Qiagen; Bastian; Maron; Turnbough; and/or Vernocchi as discussed in the 35 U.S.C. 103 rejections relating to instant claims 2-13, 15-17, and 19 above. As it is obvious to combine ‘370 with Quay, it will therefore be obvious to combine ‘370 and Quay with the other references for the same reasons it was obvious to combine the respective references with Quay as discussed in the 35 U.S.C. 103 rejections relating to instant claims 2-13, 15-17, and 19 above. Therefore, instant claims 2-13, 15-17, and 19 are not patentably distance from claim 1 of ‘370.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 11-12, and 14 of U.S. Patent No. 10,837,046, herein ‘046, in view of Quay; Ezendam; Smith; Ley as evidenced by Davis and Qiagen; Bastian; Maron; Turnbough; and/or Vernocchi. Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding instant claim 1, claim 1 of ‘046 recites language largely equivalent to steps a), b), c), d), and e) of instant claim 1. The additional limitations of claim 1 of ‘046 only further limit its scope and therefore claim 1 of ‘046 is a species of instant claim 1. Therefore, instant claim 1 is not patentably distance from claim 1 of ‘046.
Regarding instant claims 7-8 and 12-14, depending on instant claim 1, claims 2, 2, 11, 11, 12, and 14 of ‘046 recite either identical language to or are more limited species of instant claims 7, 8, 11, 12, 13, and 14, respectively, and depend on claim 1 of ‘046. Therefore, instant claims 7-8 and 11-14 are not patentably distinct from claims 2, 11-12, and 14 of ‘046.
Regarding instant claims 2-6, 9-11, and 15-19, the limitations of these claims are not recited in the claims of ‘046, but are all obvious variants of instant claim 1. The limitations of instant claims 2-6, 9-11, and 15-16 are taught in the references of Quay; Ezendam; Smith; Maron; Turnbough; and/or Vernocchi as discussed in the 35 U.S.C. 103 rejections relating to instant claims 2-6, 9-11, and 15-16 above. As Quay teaches a similar process of metagenomic analysis and treatment of dysbiosis (see 35 U.S.C. 103 rejection of claim 1 above), it would be obvious to combine Quay with claim 1 of ‘046 because the combination would merely constitute combining prior art elements via known methods that perform the same function in combination as they do separately (MPEP §2143(I)(A)). One of ordinary skill in the art would have a reasonable expectation of success due to the close similarities between the methods of claim 1 of ‘046 and Quay. As it is obvious to combine ‘046 with Quay, it will therefore be obvious to combine ‘046 and Quay with the other references for the same reasons it was obvious to combine the respective references with Quay as discussed in the 35 U.S.C. 103 rejections relating to instant claims 2-6, 9-11, and 15-19 above. Therefore, instant claims 2-6, 9-11, and 15-19 are not patentably distinct from claim 1 of ‘046.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 3-14 of U.S. Patent No. 11,959,125, herein ‘125, in view of Quay; Ezendam; Smith; Ley as evidenced by Davis and Qiagen; Bastian; Maron; Turnbough; and/or Vernocchi. Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding instant claim 1, claim 1 of ‘125 recites language largely equivalent to steps a), b), c), d), and e) of instant claim 1. The additional limitations of claim 1 of ‘125 only further limit its scope and therefore claim 1 of ‘125 is a species of instant claim 1. Therefore, instant claim 1 is not patentably distance from claim 1 of ‘125.
Regarding instant claims 5-6, 9-13, and 15-19, depending on instant claim 1, claims 3-14 of ‘125 recite either identical or equivalent language to instant claims 5-6, 9-13, and 15-19, respectively, and depend on claim 1 of ‘125. Therefore, instant claims 5-6, 9-13, and 15-19 are not patentably distinct from claims 3-14 of ‘125.
Regarding instant claims 2-4, 7-8, and 14, the limitations of these claims are not recited in the claims of ‘125, but are all obvious variants of instant claim 1. The limitations of instant claims 2-4, 7-8, and 14 are taught in the references of Quay; Ezendam; and/or Ley as evidenced by Davis and Qiagen as discussed in the 35 U.S.C. 103 rejections relating to instant claims 2-4, 7-8, and 14 above. As Quay teaches a similar process of metagenomic analysis and treatment of dysbiosis (see 35 U.S.C. 103 rejection of claim 1 above), it would be obvious to combine Quay with claim 1 of ‘125 because the combination would merely constitute combining prior art elements via known methods that perform the same function in combination as they do separately (MPEP §2143(I)(A)). One of ordinary skill in the art would have a reasonable expectation of success due to the close similarities between the methods of claim 1 of ‘125 and Quay. As it is obvious to combine ‘046 with Quay, it will therefore be obvious to combine ‘125 and Quay with the other references for the same reasons it was obvious to combine the respective references with Quay as discussed in the 35 U.S.C. 103 rejections relating to instant claims 2-4, 7-8, and 14 above. Therefore, instant claims 2-4, 7-8, and 14 are not patentably distinct from claim 1 of ‘125.
Conclusion
Claims 1-19 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jeffrey Lawrence Bellah whose telephone number is (571)272-1024. The examiner can normally be reached M-Th, 7:30-5 ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JEFFREY BELLAH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
Prosecution Insights