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
The preliminary amendment filed 09/13/2024 is entered. Claims 6-7, 9-15, 18-20, 28-30, 32, 34, 39-41, 43, 45 and 47-50 are canceled. Claims 1-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44, and 46 are pending and under consideration in this action.
The instant claims are entitled to an effective filing date of 03/15/2022.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Figure 2 includes 16S RNA sequences with 10 or more specifically defined and enumerated nucleotide residues. However, the 16S RNA sequences in figure 2 are not identified with sequence identifiers in the figure or in the description of the figure.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
To obviate this objection, figure 2 can be replaced and/or the description of figure 2 in the specification (p. 9 para. 3) can be amended so that each 16S RNA sequence in figure 2 is identified by its corresponding sequence identification number: AEDJLFGP_03285 (SEQ ID NO: 3), AEDJLFGP_03323 (SEQ ID NO: 4), AEDJLFGP_03383 (SEQ ID NO: 5), AEDJLFGP_03396 (SEQ ID NO: 6), AEDJLFGP_03473 (SEQ ID NO: 7), AEDJLFGP_03569 (SEQ ID NO: 8), AEJDLFGP_03604 (SEQ ID NO: 9), AEJDLFGP_03813 (SEQ ID NO: 10), and AEJDLFGP_04083 (SEQ ID NO: 11).
Information Disclosure Statement
The listing of references in the specification (pgs. 1-2) is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper."
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on p. 27 paragraphs 2, 4 and 6. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claims 17, 21, 33, 35-36 and 46 are objected to because of the following grammatical errors:
In claim 17, “bacterium (A) express” should be “bacterium (A) expresses”; and the acronym “CAZyme” is misspelled as “CAZome” in line 3 and line 5.
In claim 21, the acronym “CAZyme” is misspelled as “CAZome” in line 2.
In claims 33, and 35-36, “bacterium contain” should be “bacterium contains” in line 2.
In claim 46, “method of production of bioenergy products or metabolites” should be “method of producing bioenergy products or metabolites”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(a)
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.
Claims 1-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44, and 46 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor, at the time the application was filed, had possession of the claimed invention.
The claims are drawn to a genus of marine-derived bacteria that are halotolerant and capable of hydrolyzing at least one carbohydrate. Claims 1-4, 42, 44 and 46 do not limit the structure of the marine-derived bacterium in anyway. Claim 5, 8, and 37 limit the capabilities of the bacterium without further limiting the structure of the bacterium associated with such capabilities. Claims 16-17, 21-22, 27, 31, 33, 35-36, and 38 do not substantially limit the structure of the bacterium, because the claims require the bacterium to express certain genes that are associated with specific metabolic or enzymatic functions, but the claims do not limit the bacterium as a whole. Claim 38 requires the bacterium to have at least 85% identity with SEQ ID NO: 1, from the genus Alkalihalobacillus; at least 85% identity with SEQ ID NO: 2; or have a sequence provided in SEQ ID NO: 2. Although SEQ ID NO: 2 is the genomic DNA of a specific bacterium, claim 38 recites “a sequence provided in SEQ ID NO: 2”, which encompass any subsequence of SEQ ID NO: 2 such that the genetic composition of the bacterium as a whole is not particularly limited. The specification does not disclose a representative number of species of the claimed genus by reduction to practice, and does not provide adequate guidance with regard to the structural features of the marine-derived bacteria that are required to provide the recited properties. Therefore, one of skill cannot immediately envision which bacteria will have the required functional characteristics, and one could not conclude that Applicant was in possession of the claimed genus at the time the filing, as discussed more fully below.
For claims drawn to a genus, MPEP § 2163(3)(a)(ii) indicates the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant identifying characteristics, i.e., structure or other physical and/ or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
The instant specification teaches isolating starch-hydrolyzing bacteria from the gut microbiome of sea urchin Tripneustes gratilla as the microbiome contains bacteria which are correlated with starch-rich dietary seaweeds of Ulva or Gracilaria. To enrich the gut with such bacteria, adult sea urchins are fed a mono-specific algal diet of Ulva fasciata during eight weeks prior harvesting the gut. See p. 42 last passage. Bacteria growth and α-amylase activity are measured in cultures at different salinities and temperatures. See p. 43 para. 1. The isolated Alkalihalobacillus is examined in 0, 1, 2, 3 or 4% salinity. A following experiment is performed at different temperatures 25, 30, and 37˚C all at 3% salinity, which was determined to be the optimal salinity for growth. See p. 43 para. 2. The enrichment of heterotrophic-halotolerant bacteria resulted in a single bacterium that presented an activity of polylyases when cultured on an assay plate with the Ulva-polysaccharides extract. See p. 47 para. 2. The phylogenic analysis based on the 16S rRNA gene resulted in high identity of this gene in the isolate to that in the bacterial strain Alkalihalobacillus hwajinpoensis SW-72 (taxonomy ID: 208199; accession No. AF541966). See p. 48 para 1. The whole genome sequence of the Alkihalobacillus sp. (i.e. the isolate) is analyzed and much of the genes were clustered under the metabolism categories of amino acids and derivatives, carbohydrates and protein metabolism. See p. 52 para. 1. The CAZome includes GT4, GT2, GH13, GH32. See p. 52 last passage and table 3.
MPEP 2163(3)(a)(ii) states that “the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are "representative of the full variety or scope of the genus," or by the establishment of "a reasonable structure-function correlation. Such correlations may be established "by the inventor as described in the specification," or they may be "known in the art at the time of the filing date”. Considering the lack of guidance provided in the specification, one would appraise support from the state of the art to extrapolate the correlation between the bacterium structure and its halotolerant and carbohydrate hydrolyzing functions.
With respect to the state of the art on marine-derived halotolerant bacteria, Zhou (Front Microbiol. 2023 Mar 13;14:1111472), a past filing date reference, states that halotolerant microorganisms have developed versatile mechanisms for coping with saline stress. See the abstract. Zhou teaches isolating strains from the Yellow Sea and the surrounding areas, but from diverse salinity environments. The strains selected are from two phylogenetically close genera, Pontixanthobacter and Allopontixanthobacter. Although the strains show similar optimum NaCl concentrations for growth, the strains display different halotoerances. Thus, Zhou suggests that the strains adapt to their diverse habitats. See p. 2 right column para. 1. Furthermore, Zhou states that with the increasing number of isolated halotolerant strains and their genomes being sequenced, analyzing genome-wide co-occurrence between genetic diversity and physiological characteristics would expand the knowledge of the salinity adaptation strategies and provide comprehensive information on how microorganisms adapt to the environment, together with findings at the transcriptomic and proteomic levels. See p. 6 right column first passage. Thus, Zhou illustrates the unpredictability of determining which marine-derived bacteria show halotolerance.
With respect to the state of the art on hydrolyzing at least one carbohydrate, Cantarel (Nucleic Acids Res. 2009 Jan;37) states that due to the extreme variety of monosaccharide structures, to the variety [of] intersugar linkages and to the fact that virtually all types of molecules can be glycosylated (from sugars themselves, to proteins, lipids, nucleic acids, antibiotics, etc.), the large variety of enzymes acting on these glycoconjugates, oligo- and polysaccharides probably constitute one of the most structurally diverse set of substrates on Earth. See p. D233 the sentence spanning the left and right column. Cantarel discloses that as of 2008 the carbohydrate-active enzyme database (CAZy) covers approximately 300 protein families. See p. D233 last passage. Cantarel suggests that the number CAZy sequences are growing. Unfortunately, while sequencing is forever more rapid, progress in structural information and biochemical characterization is much slower. Therefore, Cantarel suggests that this means that the gap is widening between available sequences and biochemically characterized enzymes. See p. D237 first passage. Thus, Cantarel illustrates the unpredictability in the art of carbohydrate hydrolyzing enzymes and, consequently, the unpredictability of determining which marine-derived bacteria would be capable of hydrolyzing at least one carbohydrate.
In view of the prior art, the instant disclosure does not satisfy the written description requirement because the species disclosed do not adequately represent the substantial variation within the claimed genus. As discussed above, the breadth of potential structures embraced by the claims is substantial. As evidenced by Zhou, to date, there is no single ubiquitous structural mechanism in bacteria correlated with halotolerance. The instant specification reduces to practice one marine-derived Alkalihalobacillus isolate, which the specification indicates is halotolerant because it is capable of surviving at 4% salinity despite its optimal growth being at 3% salinity. Furthermore, the specification discloses that Alkalihalobacillus isolate is capable of hydrolyzing carbohydrates because the isolate encodes various carbohydrate active enzymes including carbohydrate-binding modules, carbohydrate esterases, glycoside hydrolases and glycosyltransferases. However, this represents a small fraction of potential carbohydrate-active enzymes. As evidenced by Cantarel, carbohydrates are structurally diverse substrates and the enzymes that act on such substrates are continuously being discovered. Consequently, one of skill in the art could not conclude that Applicant was in possession of the claimed genus at the time the application was filed.
Claim Rejections - 35 USC § 112(b)
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.
Claims 1-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44, and 46 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.
The term “halotolerant” in claim 1 is a relative term which renders the claim indefinite. The term “halotolerant” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Evidentiary reference Zhou (cited above) states that halotolerance is a relative term that refers to the ability to tolerate salt concentrations higher than those necessary for growth, and microorganisms are considered halotolerant if they survive at high salt concentrations but do not require these conditions for growth. See p. 1 last passage. The instant specification does not provide a standard for ascertaining which bacteria are halotolerant within the scope of the instant claims. Therefore, one of ordinary skill in the art cannot ascertain the metes and bounds of the instant claims.
Claims 2-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44, and 46 depend from claim 1 and are rejected for the reason set forth above.
The term “low” in claim 3 is a relative term which renders the claim indefinite. The term “low” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear which abundances in the intestine of a marine urchin can be considered low, because the specification does not provide any examples of low abundances relative to the microbiome in the intestine of a marine urchin as a whole.
Claim 4 depends from claim 3 and is rejected for the reason set forth above.
Claim 5 recites the term “about” in lines 2 and 3, which is a term of approximation. The specification teaches that the term “about” indicates values that may deviate up to 1%, more specifically 5%, more specifically 10%, more specifically 15% and in some cases up to 20% higher or lower than the value referred to. See p. 40 para. 2. “Up to 20%” describes a wide range of variation when the recited value is 3%. This definition is insufficient because it is uncertain which amounts of variation are permissible in claim 5.
Claim 8 recites “optionally” in line 2, which renders the claim indefinite because it is unclear which limitations are optional. Therefore, in one interpretation the claim requires the carbohydrate to be selected from a group that includes (A) a polysaccharide and if the carbohydrate is a polysaccharide, then the polysaccharide is optionally (i) cellulose, (ii) starch, (iii) glycogen, or (iv) any combination thereof. Under an alternative interpretation, every limitation recited after the term “optionally” is optional and not required.
Claim 17 recites “optionally” in line 3, which renders the claim indefinite because it is unclear which limitations are optional. Therefore, in one interpretation the claim requires the bacterium to (A) express gene copies of at least one carbohydrate active enzyme (CAZome), (B) contain at least one CAZome, or (C) produce at least one CAZome; and, if the bacterium (A) expresses CAZome, then the bacterium optionally comprises at least 80 gene copies or optionally at least 90 gene copies of CAZymes. Under an alternative interpretation, every limitation after the term “optionally” is optional and not required.
Claims 21-22, 27, 31, 33, and 35 depend from claim 17 and are rejected for the reason set forth above.
Claim 22 recites the limitation “the at least one bacterium” in lines 1-2. There is insufficient antecedent basis for this limitation in the claim. Since there is no earlier requirement for at least one bacterium, it is unclear which at least one bacterium is being limited in claim 22.
Claims 27, 31, 33, and 35 depend from claim 22 and are rejected for the reason set forth above.
Claim 27 recites “(i) GT4, (ii) GT2, (iii) a combination thereof, optionally” in lines 2-3, which renders the claim indefinite because there is no conjunction between (ii) GT2 and (iii) a combination thereof. Furthermore, claim 27 recites “optionally” three times in lines 3-4, such that it is unclear which limitations are optional and which are required.
Claims 31, 33, and 35 depend from claim 27 and are rejected for the reason set forth above.
Claim 36 recites “listed in Table 3”, which renders the claim indefinite because it is incorporation by reference to a table in the specification. Where possible, claims are to be complete in themselves. To obviate this rejection, all enzymes listed in table 3 can be added in claim 36 to replace the limitation “listed in Table 3”.
Claim 38 recites “wherein said bacterium has at least 85% identity with SEQ ID NO:1, from the genus Alkalihalobacillus”, which is indefinite because SEQ ID NO:1 is inherently from the genus Alkalihalobacillus according to the sequence listing. It is unclear whether the claim is reciting SEQ ID NO: 1 as being from the genus Alkalihalobacillus. Thus, it is uncertain whether the claim is requiring the bacterium to have at least 85% identity with SEQ ID NO: 1 or be from the genus Alkalihalobacillus. To obviate this rejection, claim 38 can be amended to recite “wherein said bacterium has at least 85% identity with SEQ ID NO:1 or 2.”
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 3-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44 and 46 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 3-5, 8, 16-17, 21-22, 27, 31, 33, and 35-38 fail to include all of the limitations of the claim upon which they depend. Claims 3-5, 8, 16-17, 21-22, 27, 31, 33, and 35-38 depend from claim 1, which requires a “marine-derived halotolerant bacterium”. However, claims 3-5, 8, 16-17, 21-22, 27, 31, 33, and 35-38 recite “The bacterium” in line 1, which is broader in scope compared to the marine-derived halotolerant bacterium of claim 1. To obviate this rejection the claims can be amended to replace “The bacterium” with “The marine-derived halotolerant bacterium”.
Claim 16 has a different scope of the bacterium required in claim 1, from which claim 16 depends. Claim 1 requires the bacterium to be capable of hydrolyzing at least one carbohydrate. Claim 16 recites “wherein said bacterium expresses genes capable of metabolizing (i) amino acid and derivatives, (ii) carbohydrate, (iii) protein metabolism or (iv) a combination thereof. Claim 16 fails to include all of the limitations of claim 1, because claim 16 does not require the bacterium to hydrolyze a carbohydrate.
Claims 42 and 44 recite “a bacterium of claim 1” (lines 1-2 of claim 42 and line 3 of claim 44) and claim 46 recites “the bacterium of claim 1” in line 2. Claims 42, 44 and 46 broaden the scope of the bacterium required in claim 1 because ‘a bacterium’ and ‘the bacterium’ are broader recitations compared to the recitation in claim 1 that requires a “marine-derived halotolerant bacterium”. To obviate this rejection, “a bacterium of claim 1” and “the bacterium of claim 1” can both be amended to recite “the marine-derived halotolerant bacterium of claim 1”.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44 and 46 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural product without significantly more. Each step described below is in reference to the subject matter eligibility test for products and processes (MPEP 2106).
Claim 1 recites a “marine-derived halotolerant bacterium ” in line 1. Claim 2 recites a “consortium” in line 1. Claim 42 recites a “bacterial culture”. Therefore, claims 1-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, and 42 are directed to a composition of matter statutory category. Claims 44 and 46 recite a “method”, so claims 44 and 46 are directed to the method statutory category. (Step 1:Yes)
The instant specification teaches isolating starch-hydrolyzing bacteria from the gut microbiome of sea urchin Tripneustes gratilla. See p. 42 last passage. The isolate shows >99.5% similarity with Alkalihalobacillus hwajinpoensis SW-72 (taxonomy ID: 208199; accession No. AF541966) based on 16S rRNA phylogenic analysis. See p. 48 para. 1. As evidenced by Yoon (Int J Syst Evol Microbiol. 2004 May;54(Pt 3):803-808; cited in the IDS filed 08/04/2026) strain SW-72 (accession no. AF541966) can be isolated from sea water of the East Sea in Korea. Compared to closest naturally occurring counterpart, there is no structural difference between the natural product (i.e. the isolate that shares >99.5% similarity with A. hwajinpoensis SW-72) and the instantly claimed product. Because there is no indication in the record that the instantly claimed product has a markedly different characteristic in structure, function, or other properties as compared to its natural counterpart (i.e. the isolate), the claims are directed to a natural-product, which is a judicial exception (Step 2A Prong 1: Yes).
Claims 1 and 2 do not recite any additional elements besides the natural product that could integrate it into a practical application.
Claim 3 requires the bacterium to be present at a low abundance in intestine of a marine urchin. Claim 4 requires the bacterium to be present in Tripneustes gratilla elatensis (i.e. a marine urchin). Claims 3 and 4 cannot integrate the judicial exception into a practical application, because the claims merely describe the source of the natural product.
Claim 5 requires the bacterium to be capable of (i) growing in a solution comprising about 3% saline, (ii) growing at 30˚C or (iii) growing at 30˚C in a solution comprising about 3% saline. Claim 8 requires the bacterium to be capable of hydrolyzing a carbohydrate that is a polysaccharide including starch, amylopectin, carrageenan, agar, cellulose, alginate, laminarin, fucoidan, ulvan, chitin, xylan, rhamnan sulfate, chrysolaminarin, or any combination thereof. As such, claims 5 and 8 merely describe characteristics of the natural product, so the claims cannot integrate the judicial exception into a practical application.
Claim 16 requires the bacterium to express genes capable of metabolizing amino acid and derivatives, carbohydrate, protein metabolism or a combination thereof. Claim 17 requires the bacterium to express gene copies of at least one carbohydrate active enzyme (CAZome). Claim 21 limits the CAZome to at least one glycoside hydrolase (GH) enzyme, at least one glycosyltransferase (GT) enzyme, at least one polysaccharide lyases (PLs) enzyme, at least one carbohydrate esterases (CEs) enzyme, at least one carbohydrate-binding modules (CBM) enzyme, at least one auxiliary activity (AAs) enzyme or any combination thereof. Claim 22 requires the gene copies of at least one CE enzyme, at least one CBM enzyme, at least one AA enzyme, at least one PL enzyme, at least one GT enzyme, or at least one GH enzyme. Claim 27 requires the at least one GT enzyme to be at least one of (i) GT4, (ii) GT2, (iii) a combination thereof. Claim 31 requires said GH enzyme is GH4 or at least one of (i) GH13, (ii) GH32, (iii) GH31, (iv) GH16 or (v) a combination thereof. Claim 33 requires said bacterium to contain at least 6 GH13 gene copies. Claim 35 requires said bacterium to contain at least 6 GH32 gene copies. Claim 36 requires said bacterium to contain at least one enzyme listed in table 3. The instant specification discloses the CAZymes genes of the isolated bacterium (i.e. natural product) in table 3 (p. 52), which includes 9 copies of GH13, 9 copies of GH32, 16 copies of GT4 and 9 copies of GT2. Therefore, claims 16-17, 21-22, 27, 31, 33, and 35-36 do not include additional elements that could integrate the judicial exception into a practical application, because the claims merely describe characteristics of the natural product. At best these limitations serve to generally link the judicial exception to its field of use.
Claim 37 requires the bacterium to be capable of hydrolyzing a carbohydrate into at least one of (i) amino sugars and nucleotide sugars, (ii) D-glucose, (iii) D-glucose-6p, or combinations thereof. The specification discloses that the isolated bacterium allows a complete metabolism of starch into either D-glucose, D-glucose 6P, or UDP-glucose. See p. 40 para. 1 last sentence. Claim 38 requires the bacterium to have at least 85% identity with SEQ ID NO: 1, from the genus Alkalihalobacillus; have at least 85% identity with SEQ ID NO: 2 or has a sequence as provided in SEQ ID NO: 2. SEQ ID NO: 1 is DNA of Alkalihalobacillus hwajinpoensis SW-72 and SEQ ID NO: 2 is the genomic DNA of the isolate bacterium. Therefore, the limitations of claims 37 and 38 merely describe characteristics of the natural product, and at best serve to generally link the natural product to its field of use.
Claim 42 is drawn to a bacterial culture comprising a biomass composition and the natural product. However, the biomass element is recited at a high level of generality such that it encompasses any collection of cells including the gut microbiome of Tripneustes gratilla. This provides insufficient specificity to add anything of significance to the judicial exception because at best the claim merely implies that the composition can contain additional elements besides the judicial exception.
Claims 44 and 46 cannot integrate the natural product judicial exception into a practical application because the claims themselves are directed to separate judicial exceptions. Claim 44 requires a method of hydrolyzing carbohydrate, the method comprises contacting a biomass, biomass derivatives or compositions comprising biomass or any derivative thereof with the bacterium of claim 1 with a biomass. Claim 46 is drawn to a method of production of bioenergy products or metabolites comprising contacting a biomass or biomass derivatives with the bacterium of claim 1. MPEP 2106.04(I) indicates that it is sufficient to identify that the claimed concept aligns with at least one judicial exception. Claims 44 and 46 require the natural product judicial exception identified above. Besides the identified natural product, the preamble of claim 44 recites “hydrolyzing carbohydrate” and the preamble of claim 46 recites “production of bioenergy products or metabolites”. These preamble recitations in claims 44 and 46 are merely attempts to generally link the natural product judicial exception to its field of use. Furthermore, the contacting steps recited in claim 44 and claim 46 are recited with a high level of generality, such that the claims encompass any contact between a biomass or a derivative thereof with the natural product. As such, the insignificant limitations of claim 44 and 46 do not integrate the natural product into a practical application because at best the claim merely implies that the natural product can be in contact with additional elements besides the judicial exception.
Therefore, claims 1-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44 and 46 separately and as a whole do not integrate the judicial exception into a practical application (Step 2A Prong 2: No).
The additional elements fail to amount to an inventive concept. Masasa (Animal microbiome, 3(1), 79, 2021) teaches assigning Tripneustes gratilla elatensis to feeding trials. See p. 2 methods section para. 1. The experimental diet is comprised solely of Ulva fasciata. See p. 2 methods section para. 2. Masasa teaches sampling DNA from the gut regions of the sea urchins. See p. 3 para. 1. The genomes of the bacteria are analyzed in the carbohydrate-active enzymes database to identify annotated genes that encode carbohydrate-active enzymes of carbohydrate binding, carbohydrate esterases, glycoside hydrolases and glycoside transferases. See p. 4 para. 1. Yoon (cited above) teaches isolating Bacillus hwajinpoensis SW-72 (accession number AF541966) from sea water of the East Sea. See p. 804 first passage. Furthermore, Yoon discloses that SW-72 hydrolyzes starch (i.e. a carbohydrate). See table 1. As evidenced by BacDrive, Bacillus hwajinpoensis SW-72 is halotolerant, because the strain is disclosed as being capable of surviving in 4% salinity, which is above the disclosed optimum salinity. See the halophily section on p. 2. Peking (BioSample: SAMN21557940; Sample name: KcN21-2; submitted 2021-09-22) teaches a Guptibacillus hwajinpoensis KcN21-2 strain, which is of the same species as Yoon’s Bacillus hwajinpoensis SW-72. CAZy (bacteria, 2026 Cazy.Org) discloses that Guptibacillus hwajinpoensis encodes 9 copies of GH13, and 6 copies of GH32. See pgs. 1-2. Furthermore Yoon teaches obtaining cell biomass of strain SW-72 and Bacillus SW-93 from cultures in marine broth (i.e. contacting). Yoon teaches the acid production from carbohydrates. See p. 804 para. 1 and table 1 for the acids produced. Thus, the additional limitations in the claims fail to amount to an inventive concept (Step 2B: No).
For all of these reasons, claims 1-5, 8, 16-17, 21-22, 27, 31, 33, 35-38, 42, 44 and 46 are not patent eligible.
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.
Claims 1-2, 5, 8, 38 and 42 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yoon (Int J Syst Evol Microbiol. 2004 May;54(Pt 3):803-808; cited in the IDS filed 08/04/2026), with evidence from BacDive (Dsmz.De 2026) and Yoon2002 (NCBI accession no. NR_025264.1, submitted 28-AUG-2002)
Regarding claims 1-2, Yoon teaches isolating Bacillus hwajinpoensis SW-72 (accession number AF541966) from sea water of the East Sea. See p. 804 first passage. Furthermore, Yoon discloses that SW-72 hydrolyzes starch (i.e. a carbohydrate). See table 1.
As evidenced by BacDrive, Bacillus hwajinpoensis SW-72 is halotolerant, because the strain is disclosed as being capable of surviving in 4% salinity, which is above the disclosed optimum salinity. See the halophily section on p. 2.
Regarding claim 5, Yoon teaches cultivating SW-72 on plates at 30˚C. See p. 804 para. 1.
Regarding claim 8, Yoon discloses that SW-72 hydrolyzes starch (i.e. a carbohydrate). See table 1.
Regarding claim 38, Yoon discloses that the 16S rDNA sequence of strain SW-72 is GenBank accession number AF541966. See p. 803 the footnote in the left column.
Yoon2002 is the NCBI reference sequence NR_025264.1 derived from SW-72 (accession number AF541966). The sequence is a 100% identity match to instant SEQ ID NO: 1. See the alignment provided in the office action appendix.
Regarding claim 42, Yoon teaches obtaining cell biomass of strain SW-72 (i.e. the marine-derived and halotolerant bacterium) and Bacillus SW-93 from cultures in marine broth. See p. 804 para. 1.
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.
Claims 16-17, 37, 44 and 46 are rejected under 35 U.S.C. 103 as being unpatentable over Yoon (Int J Syst Evol Microbiol. 2004 May;54(Pt 3):803-808, IDS 08/04/2026).
The teachings of Yoon 1-2, 5, 8, 38 and 42 are discussed above and incorporated herein.
Regarding claim 16, Yoon discloses that Bacillus hwajinpoensis SW-72 (accession number AF541966) hydrolyzes starch (i.e. a carbohydrate) and casein (i.e. a protein). See table 1.
Although Yoon does not teach that the bacterium expresses genes capable of metabolizing carbohydrate or protein, it would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention that the carbohydrate and protein hydrolysis capabilities of SW-72 taught by Yoon are only possible due to an expression of genes capable of metabolizing carbohydrate and protein.
Regarding claim 17, Yoon discloses that Bacillus hwajinpoensis SW-72 (accession number AF541966) hydrolyzes starch (i.e. a carbohydrate). See table 1.
Although Yoon does not teach said bacterium expresses gene copies of at least one carbohydrate active enzyme (CAZome), it would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention that Yoon’s starch-hydrolyzing SW-72 strain expresses at least one CAZome.
Regarding claim 37, Yoon discloses that Bacillus hwajinpoensis SW-72 (accession number AF541966) hydrolyzes starch (i.e. a carbohydrate). See table 1.
Yoon does not teach said bacterium is capable of hydrolyzing a carbohydrate into at least one of (i) amino sugars and nucleotide sugars, (ii) D-glucose, (iii) D-glucose-6P or (iv) a combination thereof.
The instant specification discloses that Alkalihalobacillus sp., consist various carbohydrate-active enzymes (CAZymes) in its genome including those of a-amylases that enables the bacterium to degrade starch through a potential complete metabolism of this polysaccharide into D-glucose monosaccharide. See p. 2 para. 5.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention that Yoon’s starch-hydrolyzing SW-72 strain is capable of hydrolyzing carbohydrate into D-glucose because Yoon’s SW-72 (accession number AF541966) is identical to the Alkalihalobacillus hwajinpoensis SW-72 (taxonomy ID: 208199; accession No. AF541966) disclosed in the instant specification on p. 48 in para. 1.
Regarding claim 44, Yoon teaches obtaining cell biomass of strain SW-72 (i.e. the marine-derived and halotolerant bacterium) and Bacillus SW-93 from cultures in marine broth (i.e. contacting). Furthermore, Yoon teaches determining hydrolysis of starch. See p. 804 para. 1 and table 1 for the starch hydrolysis.
Although Yoon does not explicitly teach contacting a biomass, biomass derivatives or compositions comprising biomass or any derivative thereof with the marine-derived halotolerant bacterium, it would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention that Yoon’s SW-72 is being contacted with biomass including the biomass formed by the cells of SW-72.
Regarding claim 46, Yoon teaches obtaining cell biomass of strain SW-72 and Bacillus SW-93 from cultures in marine broth (i.e. contacting). Furthermore, Yoon teaches the acid production from carbohydrates. See p. 804 para. 1 and table 1 for the acids produced.
Although Yoon does not explicitly teach producing bioenergy products or metabolites, it would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention that the acids produced by Yoon’s SW-72 are products or metabolites resulting from contacting the SW-72 with carbohydrates.
Claims 21, 22, 27, 31, 33 and 35-36 are rejected under 35 U.S.C. 103 as being unpatentable over Yoon (Int J Syst Evol Microbiol. 2004 May;54(Pt 3):803-808), as applied to claims 16-17, 37, 44 and 46 above, and further in view of Peking (BioSample: SAMN21557940; Sample name: KcN21-2; submitted 2021-09-22) with evidence from CAZy (bacteria, 2026 Cazy.Org).
Regarding claim 21, Yoon teaches Bacillus hwajinpoensis SW-72 (accession number AF541966). See p. 804 first passage.
Yoon does not teach wherein said CAZome comprises at least one glycoside hydrolase (GH) enzyme, at least one glycosyltransferase (GT) enzyme, at least one polysaccharide lyases (PLs) enzyme, at least one carbohydrate esterases (CEs) enzyme, at least one carbohydrate-binding modules (CBM) enzyme, at least one auxiliary activities (AAs) enzyme or any combination thereof.
Peking teaches a Guptibacillus hwajinpoensis KcN21-2 submission in 2021. See p. 1. Guptibacillus hwajinpoensis is synonymous with Bacillus hwajinpoensis. As evidenced by CAZy (p. 1), Guptibacillus hwajinpoensis encodes glycoside hydrolase (GH), glycosyltransferase (GT), polysaccharide lyase (PL), carbohydrate esterase (CE) and carbohydrate binding module (CBM) enzymes.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention that Yoon’s Bacillus hwajinpoensis SW-72 necessarily encodes GT, GH, PL, CE and CBM, because Peking and evidentiary reference CAZy teach a bacterium of the same species as Yoon that encodes such enzymes.
Regarding claim 22, CAZy discloses that Guptibacillus hwajinpoensis encodes the following carbohydrate esterases: CE14, CE4 and CE9. It encodes the following carbohydrate binding modules: CBM34, CBM38, and CBM4. See p. 1. It encodes the polysaccharide lyase PL17. See p. 2. It encodes the following glycosyltransferases: GT1, GT119, GT2, GT28, GT4, GT5, GT51, and GTnc. See p. 2. It encodes the following glycoside hydrolases: GH1, GH123, GH13, GH15, GH16, GH171, GH193, GH23, GH25, GH3, GH31, GH32, GH42, GH52, GH68, GH88 and GHnc. See pgs. 1-2.
Regarding claim 27, CAZy discloses that Guptibacillus hwajinpoensis encodes 14 copies of GT4 and 9 copies of GT2. See p. 2.
Regarding claim 31, CAZy discloses that Guptibacillus hwajinpoensis encodes GH13, GH31, and GH32. See pgs. 1-2.
Regarding claim 33, CAZy discloses that Guptibacillus hwajinpoensis encodes 9 copies of GH13, which is at least 6 copies as instantly required. See p. 1.
Regarding claim 35, CAZy discloses that Guptibacillus hwajinpoensis encodes 6 copies of GH32. See pgs. 1-2.
Regarding claim 36, the instant specification lists CE14, CE4, CE9, GH1, GH31, GH32, GH42, GH52, GH68, GT2, GT28, GT4, GT5. See p. 53-54 of the instant specification. CAZy discloses that Guptibacillus hwajinpoensis encodes the following carbohydrate esterases: CE14, CE4, CE9, GH1, GH31, GH32, GH42, GH68, GT2, GT28, GT4, and GT5. See pgs. 1-2.
Claims 1-4 are rejected under 35 U.S.C. 103 as being unpatentable over Masasa, (Animal microbiome, 3(1), 79, 2021).
Regarding claim 1-2, Masasa teaches assigning Tripneustes gratilla elatensis to feeding trials. See p. 2 methods section para. 1. The experimental diet is comprised solely of Ulva fasciata. See p. 2 methods section para. 2. Masasa teaches sampling DNA from the gut regions of the sea urchins. See p. 3 para. 1. The genomes of the bacteria are analyzed in the carbohydrate-active enzymes database to identify annotated genes that encode carbohydrate-active enzymes of carbohydrate binding, carbohydrate esterases, and glycoside transferases. See p. 4 middle passage. A heat-map of the copies of polysaccharide lyase (PL), glycoside hydrolases (GH) genes in the genome of the key microbes are shown in figure 6.
Masasa does not teach a halotolerant bacterium. However, Masasa teaches marine-derived bacteria that are capable of hydrolyzing at least one carbohydrate.
The instant specification states that the gut microbiome of sea urchin Tripneustes gratilla was selected for isolation of starch-hydrolyzing bacteria as it contains bacteria which were correlated with starch-rich dietary seaweeds of Ulva or Gracilaria. To enrich the gut with such bacteria, sea urchins are fed a mono-specific algal diet of Ulva fasciata. See p. 42 last passage. The enrichment of heterotrophic-halotolerant bacteria resulted in a single bacterium that presented an activity of polylyases when cultured on an assay plate with Ulva-polysaccharides extract. See p. 47 para. 2.
It would have been obvious to a person of ordinary skill in the art prior to the effective filing date of the instantly claimed invention that halotolerant bacteria are necessarily present in the Tripneustes gratilla elatensis gut microbiome taught by Masasa. MPEP 2112.01(I) states “[w]here the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established”.
Regarding claims 3-4, Masasa teaches taxonomic phyla identified in the sea urchin digestive tract. In figure S4(a), Masasa teaches the cumulative abundance of all OTUs of each phylum. The right column represents the intestines of Tripneustes gratilla elatensis fed exclusively Ulva. Low bacterial abundances include (from top to bottom of figure S4) Chloroflexi, Cloacimonetes, Lentisphaerae, Tenericutes, Thaumarchaeota, and Thermotogae.
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Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KIMBERLY C BREEN whose telephone number is (571)272-0980. The examiner can normally be reached M-Th 7:30-4:30, F 8:30-1:30 (EDT/EST).
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/K.C.B./Examiner, Art Unit 1657
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