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 .
Status of Claims
Receipt of Arguments/Remarks filed on 10/15/2025 is acknowledged. Claims 1, 2, 4-6, 9, 12, 19, 21, 34, 36, 39, 41, 43, 44, 50, and 53-56 are pending. Claims 1, 12, 43, and 44 were amended. Claims 3, 7-8, 10-11, 13-18, 20, 22-33, 35, 37-38, 40, 42, 45-48, 49, 51, and 52 were canceled. Claims 50 and 53-56 are withdrawn as being directed to nonelected inventions.
Withdrawn objections and rejections
The objections to claims 24 and 49 are withdrawn.
The rejections of claims 12, 43, and 44 under 35 U.S.C. § 112(b) are withdrawn.
The rejections on the grounds of non-statutory double patenting are withdrawn.
New and modified rejections necessitated by amendment
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1, 2, 4-6, 9, 12, 19, 21, 34, and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Leung et al., FEMS microbiology letters; 162(2):227-33 in view of Fraser et al., US 2017/0342131 A1.
Regarding claims 1, 2, and 36, Leung teaches a method of culturing hemoglobin-dependent Prevotella intermedia by incubating the bacterium in a growth medium with a heme-containing peptide, hemoglobin, as a source of iron (Leung Abstract, pg. 228 “Growth Assays”). Leung teaches that the hemoglobin added to the culture medium is human or bovine hemoglobin (Leung Abstract, p. 229 para. 1).
Leung does not teach that the heme-containing protein is a piscine, avian, or non-animal derived protein.
Regarding claim 1, Fraser teaches the production of heme-containing polypeptides in recombinant bacterial cells (Fraser p. 1 para. 2). Fraser teaches that there is a need for methods to produce these proteins at a large scale, and that heme-containing proteins can be difficult to secrete (Fraser p. 1 para. 3-4). Fraser teaches that heme-containing polypeptides can be from mammals, birds, plants, algae, fungi, ciliates, or bacteria (Fraser p. 6 para. 42). Fraser teaches that heme-containing polypeptides can be extracted from the source material e.g., extracted from animal tissue, or plant, fungal, algal, or bacterial biomass, or from the culture supernatant for secreted proteins (Fraser p. 7 para. 49).
Regarding claim 2, Fraser teaches that the polypeptide may be hemoglobin (Fraser p. 2 para. 14).
Regarding claim 4, Fraser teaches that the polypeptide may be leghemoglobin derived from plants, that leghemoglobin is readily available as an unused by-product of commodity legume crops, and that the amount of leghemoglobin in the roots of these crops in the United States exceeds the myoglobin content of all the red meat consumed in the United States (Fraser p. 7 para. 49).
Regarding claim 5, Fraser teaches that the heme-containing polypeptide may be a myoglobin (Fraser p. 2 para. 14).
Regarding claim 6, Fraser teaches that the heme-containing polypeptide sequence may be from fish, i.e. a piscine polypeptide (Fraser p. 8 para. 56).
Regarding claim 9, Fraser teaches that the heme-containing polypeptides can be from birds, i.e. an avian polypeptide (Fraser p. 6 para. 42).
Regarding claim 12, Fraser teaches the production of non-animal derived heme-containing polypeptides in recombinant bacterial cells (Fraser p. 1 para. 2). Fraser teaches that heme-containing polypeptides can be extracted from the culture supernatant for secreted proteins, i.e. purified from bacteria (Fraser p. 7 para. 49). Fraser additionally teaches non-animal-derived polypeptides purified from plants (Fraser p. 1 para. 8) or fungi (Fraser p. 6 para. 42).
Regarding claims 19 and 21, Fraser teaches a polypeptide from Glycine max with a sequence according to SEQ ID NO: 4 (Fraser p. 6 para. 45). SEQ ID NO: 4 of Fraser is 100% identical to instant SEQ ID NO: 4 (see sequence alignment in OA Appendix).
Regarding claim 34, Fraser teaches that heme-containing polypeptides (such as the leghemoglobin according to SEQ ID NO: 4) may be isolated from, or expressed in, fungi including Pichia pastoris (Fraser p. 6 para. 42).
It would have been obvious to a skilled artisan, before the effective filing date, to combine the teachings of these references and substitute the heme-containing polypeptides of Leung with a piscine, avian, or non-animal-derived heme-containing polypeptide as taught by Fraser. Leung teaches heme polypeptides from multiple sources, human or bovine, that are added to a culture medium for culturing Prevotella. A substitution of a hemoglobin from one species, such as human hemoglobin, for hemoglobin from a different species, such as piscine, avian, or non-animal-derived hemoglobin, would be considered a simple substitution of one known element for another of the same function, and a skilled artisan would have a reasonable expectation of success in substituting the human hemoglobin in the Prevotella culture medium for another hemoglobin polypeptide. As Leung teaches that multiple heme-containing polypeptides can serve as an iron source for Prevotella, (hemoglobin, hemin, catalase), it would have been obvious to substitute other heme-containing polypeptides, such as leghemoglobin or myoglobin as taught by Fraser, in a Prevotella culture medium.
Further, a non-animal-derived polypeptide includes any heme-containing polypeptide that is recombinantly produced by a microorganism, including a polypeptide that is recombinantly expressed from a sequence that encodes an animal polypeptide (specification p. 15 para. 49). Thus, as Fraser teaches the recombinant production of heme-containing polypeptides by microorganisms, a skilled artisan would have found it obvious to recombinantly express a sequence encoding a human or bovine heme-containing polypeptide in bacteria, resulting in a non-animal-derived polypeptide. It would have been obvious, with a reasonable expectation of success, to utilize a hemoglobin polypeptide produced in this manner in place of the hemoglobin polypeptides taught by Leung.
Regarding the use of leghemoglobin in a culturing method of Leung, a skilled artisan would have been motivated to substitute the hemoglobin of Leung with leghemoglobin because leghemoglobin is readily available as an unused by-product of commodity legume crops, and there is an excess of leghemoglobin the United States (Fraser p. 7 para. 49). Fraser additionally teaches that it is beneficial to produce heme-containing polypeptides on a large scale and that they can be difficult to produce, and thus it would be considered advantageous to utilize a heme-containing polypeptide such as leghemoglobin which is readily available as an unused byproduct in a bacterial culturing method. Further, a skilled artisan would have been motivated to obtain a non-human-derived heme-containing polypeptide via recombinant expression in a bacterial host cell, as taught by Fraser, for use in a method of culturing a heme-dependent bacteria, as this is an efficient way to obtain large quantities of heme-containing polypeptides for industrial use (Fraser p. 1 para. 3-4).
Claims 39, 41, 43, and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Leung in view of Fraser as applied to claims 1, 2, 4-6, 9, 12, 19, 21, 34, and 36 above, and further in view of Suzuki et al., Anaerobe; 18(3):350-6, Downes et al., International journal of systematic and evolutionary microbiology; 58(8):1788-91, and Murray et al., (US 10,555,975 B2).
Leung and Fraser teach the method of claim 36 as set forth above. Leung and Fraser do not teach Prevotella Strain B 50329 or Prevotella Strain C as recited in claims 39 and 41; Prevotella comprising a protein selected from SEQ ID NOs: 45-85 as recited in claim 43, or Prevotella free of a protein having SEQ ID NOs: 86-113 as recited in claim 44.
Regarding claim 39, Suzuki teaches that Prevotella intermedia and other Prevotella sp. such as Prevotella melaninogenica are found in the oral cavity, require iron for growth, and produce hemolysins (Suzuki pg. 350 “Introduction”). Suzuki teaches that iron is limited in the oral cavity and is contained within heme-containing proteins such as hemoglobin and myoglobin, which can be released from red blood cells via hemolysins (Suzuki pg. 350 “Introduction”).
Prevotella Strain B and Strain C as instantly claimed are Prevotella histicola strains (specification pg. 10-11). Downes teaches that Prevotella histicola sp. are also found in the oral cavity (Downes pg. 1788 para. 1-3; pg. 1790 Fig. 2). Downes teaches P. histicola strain N12-20 (Downes pg. 1788 para. 2).
Murray teaches the use of Prevotella histicola for treating autoimmune conditions. Murray teaches P. histicola with NRRL accession number B 50329, having a 16S rRNA sequence according to SEQ ID NO: 1 (Murray Fig. 10, col. 2 lines 44-46). Murray further teaches the P. histicola strain N12-20, with a 16S rRNA sequence according to SEQ ID NO: 2 (Murray Fig. 10, col. 5 lines 35-37). Murray teaches that the 16S rRNA sequences of strain 50329 and N12-20 are 99% identical (Murray Fig. 10).
It would have been obvious to a skilled artisan, before the effective filing date, to combine the teachings of these references, using Prevotella histicola strain B 50329 in the culturing method taught by Leung. Prevotella strains are known in the art as heme-dependent bacteria of the oral cavity, including P. histicola. It would have been obvious to a person having ordinary skill in the art to use P. histicola N12-20 as taught by Downes, which has a 16S rRNA sequence that is 99% identical to strain B 50329 as taught by Murray, because N12-20 is an oral mucosal strain which are known to be hemoglobin-dependent (Downes pg. 1788 para. 2; Suzuki pg. 350 “Introduction”).
A skilled artisan would have a reasonable expectation of success in substituting the Prevotella intermedia strain taught by Leung with a P. histicola strain according to claim 39, given the known hemoglobin-dependency of Prevotella strains from the oral cavity. As P. histicola and P. intermedia share significant phylogenetic similarity and are both found in the oral cavity (Downes pg. 1790 Fig. 2), a skilled artisan could substitute one known Prevotella strain for another to achieve predictable results.
Regarding claim 41, the 16S rRNA or CRISPR sequence of Prevotella histicola Strain C (PTA-126140) is not provided in the specification and does not appear to be publicly available. However, it would have been obvious to a skilled artisan, given the teachings set forth above, to use P. histicola strain C in a method of culturing as taught by Leung. As P. histicola strain B 50329 is obvious in view of the prior art, it would similarly be obvious to use a different strain of the same species in the method of culturing hemoglobin-dependent bacteria.
Regarding claim 43, a P. histicola strain according to claims 39 and 41 would be expected to have at least one protein from Table 1. Instant SEQ ID NO: 45, Uniprot ID G6ADE1, is an outer membrane protein SusF/SusE-like C-terminal domain-containing protein in P. histicola strain F0411. The 16S rRNA sequence of strain F0411 (GenBank: HM596283.1) is 99.6% identical to the 16S rRNA sequence of strain B 50329. Thus, it would have been obvious to a skilled artisan to use a Prevotella strain such as P. histicola having at least the protein represented by SEQ ID NO: 45.
Regarding claim 44, it would be obvious for a skilled artisan to use a Prevotella strain that is substantially free of a protein listed in Table 2. For example, SEQ ID NO: 93, Uniprot ID P19579, corresponds to Bacillus anthracis capsule biosynthesis protein CapA (GenBank: AAA22288.1). An NCBI BLAST search of this amino acid sequence results in no significant similarity found for Prevotella histicola (taxid:470565), indicating that P. histicola does not have this protein. Therefore, a P. histicola strain used in the culturing method of claim 1 would be free of at least one protein, SEQ ID NO: 93, listed in Table 2.
Response to Arguments
Applicant’s arguments, filed 10/15/2025, have been fully considered, and in light of amendments to the claims, the rejections under 35 U.S.C. § 102 have been withdrawn. However, upon further consideration, new grounds of rejection of claims 1, 2, 4-6, 9, 12, 19, 21, 34, 36, 39, 41, 43, 44, and 49 are made under 35 U.S.C. § 103 as set forth above. Given these new grounds of rejection, the arguments presented regarding claims rejected under 35 U.S.C. § 102, or claims rejected under 35 U.S.C. § 103 over Noya and Yingling or Noya and Leung are moot. However, responses to pertinent arguments are provided below.
Applicant argues: Leung teaches or suggests that growth of certain bacteria can be supported by human hemoglobin (Abstract). However, Leung also emphasized that non-globin heme-containing molecules such as hemin, catalase, and cytochrome C would not provide the same success in culture (Abstract, Fig. 4). A person of skill, reading Leung, would therefore understand that Leung teaches or suggests that human hemoglobin supports growth, but that the teachings of Leung cannot be further extended to piscine, avian, or non-animal-derived polypeptides.
In response to this argument, it is noted that Leung teaches: “Human Hgb (Sigma), hemin, and bovine catalase (Sigma) could each serve as a source of iron for the growth of iron-limited P. intermedia” and “(2 μM of heme-equivalent or above) of bovine hemoglobin promoted the growth of iron-restricted P. intermedia” (Leung p. 229 col. 2 para. 1). Therefore, Leung expressly teaches that other heme-containing polypeptides, including bovine-derived hemoglobin, can support the growth of P. intermedia in culture in addition to human hemoglobin. A skilled artisan could reasonably expect that other heme-containing polypeptides, especially other hemoglobin polypeptides, such as piscine, avian, or non-animal derived hemoglobin as taught by Fraser, could be added to a Prevotella culture medium.
Applicant argues: Leung does not teach or suggest the technical advantages achieved by methods as recited in the present claims. For example, Example 6 shows that, growth of a
Prevotella strain in media supplemented with a heme-containing polypeptide as recited was restored to levels similar to when cultured with animal-sourced hemoglobin or spirulina (see, e.g., FIG. 1). Example 7 likewise show that the growth of a Parabacteroides strain, a Bacteroides strain, and an Alistipes Strain in media comprising a heme-containing polypeptide as recited was all restored to the similar levels as animal source hemoglobin (see e.g., Figs. 3, 4, 5). The higher concentration of heme-containing polypeptide as recited even exceeded the growth with animal sourced hemoglobin for the Parabacteroides strain (see e.g., Fig. 3).
In response to this argument, it is noted that the present claims are directed to a method of culturing bacteria with a heme-containing polypeptide added to the growth medium. The claims do not require a specific amount of growth as a result of the method, just that the bacteria are cultured. Thus, the technical advantages regarding amount of growth in media supplemented with heme-containing polypeptides compared to animal-sourced hemoglobin are not relevant to the instant claims, which only require the recited method steps of culturing bacteria by incubating the bacteria in a growth medium with a heme-containing polypeptide.
Regarding the rejections of claims 1, 2, 4-6, 9, 12, 19, 21, 34, 36, 39, 41, 43, 44, and 49 on the grounds of non-statutory double patenting, these rejections are withdrawn. The claims of co-pending 17/632,449 are directed to a method of culturing hemoglobin-dependent bacteria by a method comprising adding algae or cyanobacterial biomass to a culture medium. The claims of copending ‘449 do not recite a heme-containing polypeptide of piscine, avian, or non-animal origin in a culture medium.
Conclusion
Claims 1, 2, 4-6, 9, 12, 19, 21, 34, 36, 39, 41, 43, and 44 are rejected. No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILY F EIX whose telephone number is (571)270-0808. The examiner can normally be reached M-F 8am-5pm ET.
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/EMILY F EIX/Examiner, Art Unit 1653
/JENNIFER M.H. TICHY/Primary Examiner, Art Unit 1653