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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 09/17/2025 has been entered.
Status of the Claims
Claims 1-21, 23, 25, 26 and 28 are pending in the response of 09/17/2025. Claims 1-19, 23, 25, 26 have been withdrawn and thus claims 20, 21 and 28 are being examined.
Withdrawn objection/ rejections:
Applicant's amendments and arguments filed 09/17/2025 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
The following rejection and/or objection are either reiterated or newly applied. They constitute the complete set of rejection and/or objection presently being applied to the instant application.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Level of Ordinary Skill in the Art
(MPEP 2141.03)
MPEP 2141.03 (I) states: “The “hypothetical ‘person having ordinary skill in the art’ to which the claimed subject matter pertains would, of necessity have the capability of understanding the scientific and engineering principles applicable to the pertinent art.” Ex parte Hiyamizu, 10 USPQ2d 1393, 1394 (Bd. Pat. App. & Inter. 1988). The level of skill is that of a medical/pharmaceutical prebiotics/probiotics research scientist, as is the case here, then one can assume comfortably that such an educated artisan will draw conventional ideas from medicine, pharmacy, physiology and chemistry— without being told to do so.
In addition, the prior art itself reflects an appropriate level (MPEP 2141.03(II)).
Claims 20-21 and 28 are rejected under 35 U.S.C. 103(a) as being unpatentable over US2016/0199424A1 (inventors: Berry, Afeyan, Kaplan and Rahman, hereinafter “Berry”) in view of US2018/0264053A1 (inventors: Lynch, Kimes, Lin, Valladares and Fujimura, hereinafter “Lynch”) and further in view of Li et al., “Degradation of marine algae-derived carbohydrates by Bacteroidetes isolated from human gut microbiota”, Marine Drugs, 2017, pp. 1-12.
Applicant claims the below claim 20 filed on 09/17/2025:
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Determination of the scope and content of the prior art
(MPEP 2141.01)
Berry teaches probiotic and prebiotic composition and methods of use thereof for modulation of the microbiome (title); specifically, this prior art teaches a method for detection and correction of a dysbiosis in a human subject in need thereof ([0060]) wherein the symptom of dysbiosis includes overgrowth of an undesired pathobiont or pathogen, reduced representation of key bacterial taxa such as the Bacteroidetes or Firmicutes or genera or species thereof, or reduced diversity of microbial species compared to a healthy individual, or reduced overall abundance of anaerobic bacteria ([0810]); and Berry teaches when the normal intestinal microbiota has been disturbed due to use of broad-spectrum antibiotics and antibiotic resistance is an emerging public health issue ([0005]-[0006]), and to mimic the condition of dysbiosis, the subject can receive an antibiotic treatment that can cause incidence of dysbiosis because antibiotic treatment can crease taxonomic richness, diversity, and evenness of the community, including a reduction of abundance of a significant number of bacterial taxa ([0892]), and therefore, Berry teaches/suggests a method for reducing antibiotics-induced microbiome dysbiosis in an individual; the method for detection and correction of a dysbiosis comprising the steps of: providing a fecal sample from the human subject comprising a plurality of bacterial entities and contacting the fecal sample with a first detection moiety capable of detecting a first bacterial entity present in a network; detecting the absence of the first bacterial entity in the fecal sample, thereby detecting a dysbiosis in the human subject ([0060]-[0062]) and further this prior art teaches detecting, quantifying and characterizing signatures of the microbial network ([0973]) and administering to the human subject a microbial composition comprising an effective amount of the first bacterial entity ([0060]-[0062] and [00973])) which reads on the claimed administering step (b); the intestinal microbiota plays a significant role in the pathogenesis of many diseases and disorders, including a variety of pathogenic infections distal to the gastrointestinal tract, and for instance, subjects become more susceptible to pathogenic infection ([0005]), and the loss or reduction of intestinal barrier function is recognized to occur during bacterial dysbiosis or in the shift in one or more microbiotal populations that give rise to the dysbiosis and the antibiotic therapy removes the existing microflora in a target niche, while newly administered or recruited bacteria populate (or repopulate) the target niche and therefore the probiotic composition can prevent or treat such loss or reduction of barrier function, restoring the normal microbiotal components ([0985] and Example 26), and thus the composition treats dysbiosis, e.g., gastrointestinal dysbiosis such that the bacterial population is effective to modulate or augment the microbiota diversity present in the mammalian recipient ([0088], [0201] and [0645]), and the prior art teaches a method for detection and correction of a dysbiosis in a human subject in need thereof comprising providing a fecal sample from the human subject comprising a plurality of bacterial entities; contacting the fecal sample with a first detection moiety capable of detecting a first bacterial entity present in a network; detecting the absence of the first bacterial entity in the fecal sample, thereby detecting a dysbiosis in the human subject; and administering to the human subject a composition comprising an effective amount of the first bacterial entity ([0060]), and accordingly this prior art teaches or suggests administration of the said composition reduces antibiotics-induced gut dysbiosis which leads to the loss of microbiota diversity resulting from prior antibiotic treatment and reads on the claimed step (b). The prior art method further includes e.g., using 16S profiling to determine whether administering the composition has resulted in population by one or more administered bacteria in the gastrointestinal tract and as quantitative assessments colony counting can be used ([0895]), and the probiotic composition comprises isolated population in an amount sufficient to alter microbiome at a distal site of administration (claim 37) wherein the composition comprises a species of bacteria that is deficient at the site of the distal dysbiosis and a species of bacteria present in the probiotic composition is augmented at the site of the distal dysbiosis (claims 37-39 of prior art), and see the teachings of entire documents including [0005]-[0006], [0060]-[0062], [0088], [0201], [0645], [0892]-[0895], [0943], [0948], [0976], [0985], [0973] and claims 37-39 of Berry read on the claimed steps (a)-(b); and the probiotic composition comprises a species of bacteria and the bacterial compositions may be prepared comprising one or at least two types of isolated bacteria, among others, e.g., Bacteroides uniformis, Bifidobacterium bifidum, Bifidobacterium pseudolongum, Faecalibacterium prausnitzii, Roseburia inulinivorans, Ruminococcus bromii, Ruminococcus torques, and Subdoligranulum variabile, all of these bacterial species would be used for probiotic composition (e.g., [0669], Table 1, 1A, 1B, 1D, 1F, claim 7 of prior art etc.); bacteria contained in the probiotic composition can correct dysbiosis by promoting translocation of other gut commensals to the distal site, or by modifying the microenvironment of the distal site to create conditions that restore a healthy microbiome and thus administering of the said probiotic composition restores intestinal barrier integrity and (e.g., [0976] and [0983]-[0984]), and according to Example 26, the subject suffering from recurrent bouts of C.difficle was treated with an antibiotic and then bacterial composition is administered and as a result, the presence of C.difficile is reduced to at least 95%, which means the microbiota diversity would be restored to a state that existed before administration of the prior antibiotic treatment (instant claims 20-21 and 28, in part).
However, Berry does not expressly teach selecting the claimed specific selected microorganism of instant claims 20 and 28 for treating antibiotic-induced dysbiosis. The deficiency is cured by Lynch.
Lynch discloses microbial consortium and uses thereof for the treatment of dysbiosis wherein dysbiosis comprises a decrease of beneficial microorganisms and/or increase of pathobionts (pathogenic or potentially pathogenic microorganisms) and/or decrease of overall microbiota species diversity, and many factors can harm the beneficial members of the intestinal microbiota leading to dysbiosis, including (but not limited to) antibiotic use which is called “antibiotic-induced dysbiosis” and antibiotic administration is a common and significant cause of major alterations in the normal microbiota ([0087]); thus the subject with dysbiosis or bacterial infection comprises gastrointestinal microbiome that has reduced proportion of Bifidobacteria spp., Kactibacukkys spp., Faecalibacterium spp, etc., compared to a healthy population ([0179](d) and claim 21-(d)); thus, Lynch teaches a method for treating or preventing dysbiosis in a subject in need thereof, wherein the subject has received antibiotic therapy within e.g., 1-10 weeks ([0087]), comprising administering an effective amount of bacterial populations or microbial compositions ([0157]), and specifically, the method comprises administering to the subject an effective amount of a bacterial population comprising Lactobacillus sp., Faecalibacterium sp., Akkermansia sp., Myxococcus sp., and Pediococcus sp. wherein the Faecalibacterium sp., is Faecalibacterium prausnitzii ([0141]-[0142], [0324]-[0325]: Embodiment 1) and the effective amount for administration is effective to increase e.g., the level of e.g., Ruminococcus sp. Bifidobacterium sp., in the subject ([0361](i)), claims 1, 7 12-14, 15, 17, 21, and 22 of prior art); and further, Lynch teaches administering an effective amount of a bacterial population comprising Lactobacillus sp., Faeclibacterium prausnitzil, Bifidobacterium sp. including Bifidobacterium bifidum, Bifidobacterium pseudolongum, Bifidobacterium saeculare, and/or Bifidobacterium subtile for the treatment of dysbiosis, wherein the bacterial population comprises, consists essentially of or consist of 8 or less (e.g., 1-8) bacterial species ([0006] and [0161]) (instant claims 20-21 and 28 – treatment with antibiotic-induced dysbiosis).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to specifically select bacteria e.g., Faeclibacterium prausnitzil, Bifidobacterium spp. as taught by Lynch, among myriads of microorganisms of Berry, and administer it to the patient who has prior antibiotic-induced gut dysbiosis and loss of microbiota diversity (e.g., reduced Faeclibacterium prausnitzil and Bifidobacterium spp.) in order to treat or reduce antibiotics-induced gut microbiome dysbiosis and restore gut microbiota diversity, as taught/suggested by Lynch.
However, Berry in view of Lynch does not expressly teach “the microorganisms are selected for their carbohydrate degradation capability” of instant claim 20. The deficiency is cured by Li.
Li discloses Bacteroidetes isolated from human gut microbiota is capable of degrading carbohydrates, and specifically, polysaccharides, carrageenan, agarose, and their oligosaccharide is degraded by Bacteroides ovatus, Bacteroides uniforms, Bacteroides xylanisolvens (abstract) and in particular, Bacteroides uniforms degrade agarose (AP) (e.g., Fig. 4), and the said oligosaccharides generated from the degradation have the potential to affect the structure of human gut microbiota, and also gut health (see conclusion on page 10) (instant claim 20 – carbohydrate degradation of microbiota).
It would have been obvious to modify the teachings of the Berry in view of Lynch with Bacteroides uniforms that provides carbohydrate degradation in order to affect the structure of human gut microbiota and gut health as taught by Li.
In light of the forgoing discussion, the Examiner concludes that the subject matter defined by the instant claims would have been obvious within the meaning of 35 USC 103(a).
From the combined teachings of the references, it is apparent that one of ordinary skill in the art would have had a reasonable expectation of success in producing the claimed invention. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made, as evidenced by the combined references, especially in the absence of evidence to the contrary.
Response to Arguments
Applicant’s arguments have been fully considered, but are moot in view of new reference of Li disclosing that Bacteroides uniforms is capable of degrading carbohydrates that affect the structure of human gut microbiota and gut health.
Conclusion
All examined claims are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYUNG S CHANG whose telephone number is (571)270-1392. The examiner can normally be reached M-F 8-5.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Yong (Brian-Yong) S Kwon can be reached at 571-272-0581. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KYUNG S CHANG/Primary Examiner, Art Unit 1613