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 .
Claims status
Claims 1-20 are pending in the application and are presently considered on the merits.
Priority
The present application is a continuation (CON) of PCT/IL2022/051369, filed on 12/21/2022, which claims the benefit of a U.S. provisional application. Applicant’s claim for benefit under 35 U.S.C. 119 (e) of Provisional application No. 63/292,545 filed 12/22/2021 is acknowledged. The present application and all claims are being examined with the earliest effective filing date of 12/22/2021.
Information Disclosure Statement
The Information Disclosure Statements (IDS) filed 08/26/2024 and 03/12/2026 have been considered by the examiner.
Claim Interpretation
Per MPEP § 2111, During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard:
The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1).
Because applicant has the opportunity to amend the claims during prosecution, giving a claim its broadest reasonable interpretation will reduce the possibility that the claim, once issued, will be interpreted more broadly than is justified. In re Yamamoto, 740 F.2d 1569, 1571 (Fed. Cir. 1984).
Claim 1 recites the phrase “an acidic environment” which is not explicitly defined on record. It is noted that this phrase is disclosed to include culture conditions wherein the pH is, for example, 2.5 to 4 or 3.5 to 6.5, depending on the bacterium (see instant specification at pg. 16, lines 5-7; instant claim 5). Accordingly, the phrase “an acidic environment” is given its broadest reasonable interpretation as including any culture condition wherein the pH is less than 7.0.
Claim 11 recites a method step of (a) culturing a nomadic bacteria in a medium to generate a conditioned medium and a further step of (b) contacting a pathogen with the conditioned medium. The instant specification states: “Conditioned medium is the growth medium of a cell culture following a certain culturing period. The conditioned medium may include metabolites, organic acids, bacteriocins, antimicrobial peptides growth factors and cytokines secreted by the cells in the culture. Such a growth medium can be any medium suitable for culturing the nomadic, bacterial cells.” (see pg. 23, lines 21-23). Hence, the broadest reasonable interpretation of the claim is that the “conditioned medium” is a composition comprising any growth medium and further comprising any bacterial products produced by the bacterium during culturing. See also “Claim Scope” under 35 U.S.C. 112(a) for further discussion.
Claim 16 recites a conditioned medium (product) generated by culturing nomadic bacteria in a medium subjected to at least one stress. This is a product-by-process claim, wherein the claimed product only explicitly requires a “conditioned medium”. Therefore, the broadest reasonable interpretation of the claim is that the “conditioned medium” is any composition comprising any growth medium and further comprising any bacterial products. See also “Claim Scope” under 35 U.S.C. 112(a) for further discussion.
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 1-20 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.
Claims 1-2, 5-9, 11-14, 16-17 and 19-20 each recite or otherwise depend from a claim that recites a “nomadic bacteria” which renders the claims indefinite, because the scope of the term “nomadic bacteria” is unclear in view of the definition provided by the specification, which states: “The term ‘nomadic bacteria’ as used herein refers to bacteria which are capable of thriving in different ecological niches” (see pg. 13, lines 28-29). This fails to clarify the scope of the term, because it is not clear how many niches need to be “thrived” in, what these niches are, or what exactly constitutes “thriving”. The term “thriving” is a relative term and the specification does not provide a standard for ascertaining the requisite degree in which the bacteria must be “thriving”. For example, even bacteria associated with a particular niche may be able to grow under a variety of culture conditions, which reasonably demonstrates their ability to survive in more than one “niche”. Therefore, one may conclude that any bacteria that can be grown after changing some subset of culture conditions is, to some extent, nomadic. On the other hand, one may also recognize that some bacteria are clearly much more nomadic than others and they may only consider some of them to be truly nomadic. Therefore, a person of ordinary skill would not be apprised as to the requisite degree the bacteria must be able to thrive in different ecological niches in order to be included in this scope.
In the interest of compact prosecution, the term “nomadic bacteria” is broadly interpreted as including any bacteria. In the case of claim 1 and its dependents, this would include any bacteria that is capable of forming a biofilm.
The broadest reasonable interpretation of claims 3-4, 10, 15 and 18 is that the nomadic bacteria must be selected from the group consisting of “L. rhamnosus, L. plantarum and L. casei”. Therefore, these claims are not rejected on the basis set forth above.
Claim 1 also recites the limitation, wherein the nomadic bacteria are cultured “in an acidic environment under conditions that promote generation of a V-type structure of the nomadic bacteria” which renders the claim indefinite, because it is unclear whether this limitation requires anything more than an “acidic environment”. The specification states that cone-shaped colonies and V-shaped cell chains were discovered in L. plantarum in response to acidic-pH stress (see pg. 13, lines 7-8), but does not explicitly describe any other conditions that are deemed to be associated with the generation of these structures. Therefore, it could be interpreted that the “acidic environment” is a condition that already promotes generation of this structure and no other conditions are required. However, based on a plain reading of the claim, it could also be interpreted that this requires some additional culture condition. Hence, the metes and bounds have not been clearly set forth.
Furthermore, the phrase “V-type structure” also renders the claim indefinite. The specification states: “The phrase ‘V-type structure’ as used herein refers to a particular type of cell chaining where several (typically four partially separated) cells form a filament with V-shaped curvature. This type of chaining can be identified using either light microscopy or SEM” (pg. 15, lines 19-21). However, the terms “several” and “typically four” are not definite. Furthermore, if a bacteria were to form a linear cell chain of 100 cells, wherein only four cells are “partially separated”, it is unclear whether this would be considered to be a linear structure or a V-type structure in view of the provided definition.
In the interest of compact prosecution, the claim is given its broadest, reasonable interpretation: wherein the “acidic environment” promotes generation of a V-type structure of the nomadic bacteria. For the sake of applying prior art, this limitation requires no further culture condition, and the limitation of “having V-type structure” is presumed to be an inherent property of L. plantarum which is necessarily present in response to being cultured in an acidic environment.
Claim 1 also recites the term, “adherent surface” which renders the claim indefinite, because it is unclear what structures this limitation would effectively exclude. This is because the ability to “adhere” to a surface is a property of the bacteria themselves, and not necessarily the material to which they adhere to. In view of the specification, “Exemplary adherent surfaces on which the culturing can be carried out include a wide range of substrates, ranging from various polymeric materials (silicone, polystyrene, polyurethane, and epoxy resins) to metals and metal oxides (silicon, titanium, aluminum, silica, and gold) and glass” (see pg. 17, lines 1-3). Hence, it could be interpreted that “an adherent surface” may include any solid surface, or perhaps only those composed of certain materials. Furthermore, claim 17 recites a method of culturing that is “effected on a non-adherent surface” which causes further confusion. For example, in view of the examples provided in the specification (i.e., plastics, metals, glass), a person of skill may reasonably interpret the “adherent surface” to be some solid material, as opposed to a liquid solution, such as a broth, or a semi-solid, such as an agar-gel. However, an ordinary artisan would also recognize that bacteria cultured on an agar plate clearly “adhere” (or stick) to the surface of said agar-gel. Hence, it is unclear whether such a culture medium should be interpreted to be “adherent”, “non-adherent”, or somehow both in view of the instant claims.
In the interest of compact prosecution, the limitation of an “adherent surface” is given its broadest reasonable interpretation: wherein the “adherent surface” is any solid surface (e.g., glass, metal or plastic) or any semi-solid surface (e.g., gel). For the sake of applying prior art, this limitation effectively excludes, for example, a liquid medium (e.g., liquid culture broth).
Claim 8 recites the limitation, “wherein at least 30% of the bacteria have a V-shaped structure” which renders the claim indefinite. First, the plain meaning of the claim is that 30% of the bacteria comprise cells which are “V-shaped” (i.e., as opposed to spheres, rods, or spirals). However, the specification states: “The phrase ‘V-type structure’ as used herein refers to a particular type of cell chaining where several (typically four partially separated) cells form a filament with V-shaped curvature. This type of chaining can be identified using either light microscopy or SEM” (pg. 15, lines 19-21). However, this definition leads to different interpretations.
For example, it is still unclear whether this percentage is based on the number of cells in a chain, the number of cell chains in a sample, or both. In the first case, if a filament of 10 bacteria cells comprises a straight chain, with only three cells positioned to form a “V-shape”, a person of skill may conclude that this meets the limitation of the claim, because 30% of the cells are involved in forming a V-shape. However, another person may reasonably conclude that the overall structure of the filament does not conform to a V-shape at all, because there are merely 1-2 cells that are slightly askew (“partially separated”) compared to the rest of the cells, which otherwise forms what is reasonably linear structure. In the latter case, wherein the percentage is based on the number V-type chains in a sample, it is unclear whether the definition requires the “typically four partially separated” cells, because “several” or “typically” are not definite terms. It should be noted that some bacteria form longer cell chains (100+ cells), and the it would not be apparent whether a chain of such length having only four partially separated cells would comprise a V-shape.
In the interest of compact prosecution, the claim is given its broadest reasonable interpretation, wherein the composition comprises any bacteria capable of forming filaments that have a V-shaped chain structure. For the sake of applying prior art, this is an inherent property of L. plantarum and is necessarily present under certain conditions (i.e., acidic-pH).
Claim 11 recites the limitation “(b) contacting said pathogen with said conditioned medium under conditions that reduce biofilm formation of said pathogen” which renders the claim indefinite. On one hand, it could be interpreted that the “conditions that reduce biofilm formation of said pathogen” are provided by the “conditioned medium” which requires no further action. On the other hand, the plain meaning of the phrase implies that some further culture condition is required. However, the specification does not specify any other conditions, other than the “stress” used to generate the conditioned medium and the presence of bacterial products that may be present in said conditioned medium (see Claim Interpretation above). Hence, the metes and bounds have not been clearly set forth.
In the interest of compact prosecution, the claim is given its broadest, reasonable interpretation: wherein the method step of “contacting said pathogen with said conditioned medium” reduces biofilm formation of said pathogen. For the sake of applying prior art, this limitation requires no further culture condition.
Claim 17 recites a method of culturing that is “effected on a non-adherent surface”. As discussed regarding claim 1, it is unclear what surfaces are considered to be “adherent” and what surfaces are considered to be “non-adherent”. In view of the examples provided in the specification, a person of skill may reasonably interpret the “adherent surface” to be any solid material, as opposed to a liquid solution or an agar-gel (semi-solid). However, one would recognize that bacteria cultured on an agar-gel plate clearly “adhere” (or stick) to the surface of said agar. Hence, it is unclear whether such a culture medium should be interpreted to be “adherent”, “non-adherent”, or somehow both in view of the instant claims.
In the interest of compact prosecution, the limitation of an “non-adherent surface” is given its broadest reasonable interpretation: wherein the “non-adherent surface” is any liquid culture (e.g., broth, juice, milk, etc.) or any semi-solid surface (e.g., gel). For the sake of applying prior art, this limitation effectively excludes, for example, any solid surface (e.g., glass, metal or plastic).
Claims 3-4, 10, 15 and 18 are rejected for depending from an indefinite claim and for failing to fully obviate the basis for the rejection of the claim(s) from which they depend.
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 7-10 are rejected under 35 U.S.C. § 101 because the claims are not directed to patent eligible subject matter. Based upon an analysis with respect to the claims as a whole, these claims do not recite something significantly different than a judicial exception. The rationale for this determination is explained below and is in keeping with the latest guidance regarding analysis of judicially excepted subject matter.
Subject Matter Eligibility Guidance
A three-step inquiry has been established to determine subject matter eligibility under 35 U.S.C. 101, in accordance with MPEP § 2106:
Step 1 – Is the claim directed to a process, machine, manufacture, or composition of matter?
Step 2A – Is the claim directed to a law of nature, natural phenomenon (product of nature), or an abstract idea?
Step 2A, prong 1 – Does the claim recite a law of nature, natural phenomenon, or an abstract idea?
Product of Nature Definition
When a law of nature or natural phenomenon is claimed as a physical product, the courts have often referred to the exception as a "product of nature". See Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 580, 106 USPQ2d 1972, 1975 (2013); University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 758-59, 113 USPQ2d 1241, 1243 (Fed. Cir. 2014). As explained in those decisions, products of nature are considered to be an exception because they tie up the use of naturally occurring things, but they have been labeled as both laws of nature and natural phenomena. See Myriad Genetics, Inc., 569 U.S. at 590-91, 106 USPQ2d at 1979.
The Markedly Different Characteristics Analysis
The first step in the analysis is to select the appropriate counterpart to the nature-based product. When the nature-based product is derived from a naturally occurring thing, then the naturally occurring thing is the counterpart. See MPEP § 2106.04(c)(II)(A).
The second step in the analysis is to identify appropriate characteristics to compare. Appropriate characteristics must be possessed by the claimed product, because it is the claim that must define the invention to be patented. Cf. Roslin, 750 F.3d at 1338, 110 USPQ2d at 1673. See MPEP § 2106.04(c)(II)(B).
The final step in the markedly different characteristics analysis is to compare the characteristics of the claimed nature-based product to its naturally occurring counterpart in its natural state, in order to determine whether the characteristics of the claimed product are markedly different. See MPEP § 2106.04(c)(II)(C).
Step 2A, prong 2 – If the claim recites a judicial exception, does it recite additional elements that integrate the judicial exception into a practical application?
Limitations that are indicative of integration into a practical application include:
Improvements to the functioning of a computer, or to any other technology or technical field. See MPEP § 2106.05(a);
Applying the judicial exception with, or by use of, a particular machine. See MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing. See MPEP § 2106.05(c);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition. See MPEP § 2106.05(d);
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. See MPEP § 2106.05(e).
Step 2B. If the recited judicial exception is not integrated into a practical application, does the claim recite additional elements that amount to significantly different than the judicial exception such that they provide an inventive concept? This step includes evaluation of the same considerations under Step 2A, Prong 2, as well as two additional considerations:
Adding a specific limitation or combination of limitations that are not well-understood, routine, conventional activity in the field, which is indicative that an inventive concept may be present; and
Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, which is indicative that an inventive concept may not be present.
Analysis
Step 1: It must first be determined if the claim is to a statutory category and, if so, proceed to step 2A, prong 1.
In this case, the claims are directed to a composition comprising isolated, nomadic bacteria (claims 8-10) or a biofilm (claim 7) and fall within the statutory category of a composition of matter.
Step 2A. prong 1: Prong 1 requires the Examiner to evaluate whether the claim recites a judicial exception and, if so, proceed to prong 2.
Claim 7, which depends from the method of claim 1, recites a biofilm generated according to the method of claim 1. This is a product-by-process claim.
Per MPEP 2106.04(c), for a product-by-process claim, the markedly different characteristics analysis turns on whether the nature-based product in the claim has markedly different characteristics from its naturally occurring counterpart.
In the instant case, the recited “biofilm” is one generated by a bacterium in response to being cultured in an acidic environment. There is no evidence to suggest that a “biofilm” generated in a culture, particularly one that mimics the conditions of the bacteria’s natural habitat (e.g., the acidic conditions of the stomach), would necessarily result in any new structural and/or functional characteristics of said biofilm. In the case of Applicant’s examples, it is only disclosed that under acidic conditions, L. plantarum was able to form “robust biofilms” at “vigorous” levels (see pg. 34, lines 1-2 and lines 18-21). However, these results appear to relate to the amount of biofilm material produced by the bacteria at a low pH, and do not relate to any new property of the biofilms themselves.
This is similar to In Roslin, where the court concluded that claimed clones of farm animals were products of nature, because they lacked markedly different characteristics from the counterpart farm animals found in nature. In re Roslin Institute (Edinburgh), 750 F.3d 1333, 1337, 110 USPQ2d 1668, 1671 (Fed. Cir. 2014). The inventor created its clones (which included the famous cloned sheep named Dolly) by transferring the genetic material of a donor into an oocyte (egg cell), letting the oocyte develop into an embryo, and then implanting the embryo into a surrogate animal where it developed into a baby animal. The applicant argued that the clones, including Dolly, were eligible because they were created via human ingenuity, and had phenotypic differences such as shape, size and behavior compared to their donors. The court was unpersuaded, explaining that the clones were exact genetic replicas of the donors and thus did not possess markedly different characteristics. The court noted that the alleged phenotypic differences (e.g., the fact that Dolly may have been taller or heavier than her donor) could not make the clones markedly different because these differences were not claimed. 750 F.3d at 1338, 110 USPQ2d at 1672 (Emphasis added). See also Roche Molecular System, Inc. v. CEPHEID, 905 F.3d 1363, 1370, 128 USPQ2d 1221, 1226 (Fed. Cir. 2018) (alleged structural differences between linear primers and their counterparts on a circular chromosome were neither claimed nor relevant to the eligibility inquiry).
In the instant case, the claimed biofilm includes biofilms produced in culture which are not claimed or disclosed as having any markedly different characteristics compared to biofilms produced by the same bacteria in nature (e.g., L. plantarum).
Therefore, claim 7 is directed to the judicial exception of a natural product.
Independent claim 8 recites a composition comprising isolated, nomadic bacteria, wherein at least 30% of the bacteria have a V-shaped structure. As discussed under 35 U.S.C. 112(b), the nomadic bacteria are interpreted to include any bacteria capable of forming any “V-shaped” chain structure, which includes Lactobacillus plantarum, which is a naturally-occurring species of bacteria. Furthermore, the specification discloses that the Lactobacillus plantarum strain used in Applicant’s examples was an “[i]solate from a healthy cow” (see pg. 8, Table 1). Therefore, the claim includes microorganisms isolated from nature which are they themselves natural products.
Per MPEP 2106.04(c), if the nature-based product limitation is naturally occurring, there is no need to perform the markedly different characteristics analysis because the limitation is by definition directed to a naturally occurring product and thus falls under the product of nature exception.
Regarding the bacteria’s capability to form “V-shaped” chain structures, Applicant discloses that the “phenomenon of cone-shaped colonies and V-shaped cell chains were discovered in response to acidic-pH stress” (see pg. 13, lines 7-8; Emphasis added). Therefore, this growth characteristic of the Lactobacillus plantarum strain is a functional characteristic of the naturally-occurring bacterium, whether or not this specific property was previously known (i.e., an inherent property). This recited structure is presumed to be an inherent property of the bacterium, and would necessarily be present in the naturally-occurring bacterium when exposed to acidic-pH stress under the same conditions.
It should be noted that per MPEP 2106.04(b), the courts have identified concepts and products exemplifying laws of nature or natural phenomena to include the qualities of bacteria such as their ability to create a state of inhibition or non-inhibition in other bacteria, Funk Bros., 333 U.S. at 130, 76 USPQ at 281 (Emphasis added).
Therefore, claim 8 is directed to the judicial exception of a natural product.
Claim 9 depends from claim 8 and recites the further limitation, “wherein said isolated, nomadic bacteria are of the Lactobacillus genus”. This genus includes, for example, Lactobacillus plantarum, which, as previously discussed, remains unchanged from its existence in nature and is by definition directed to a naturally occurring product.
Therefore, claim 9 is still directed to the judicial exception.
Claim 10 depends from claim 9 and recites the further limitation, “wherein said isolated, nomadic bacteria are of a species selected from the group consisting of L. rhamnosus, L. plantarum and L. casei”. This genus includes, for example, Lactobacillus plantarum, which, as previously discussed, remains unchanged from its existence in nature and is by definition directed to a naturally occurring product.
Therefore, claim 10 is still directed to the judicial exception.
Step 2A, prong 2: Step 2A, prong 2 requires the Examiner to evaluate whether the claim recites additional elements that integrate the exception into a practical application of that exception and, if not, proceed to step 2B. In order to integrate the recited judicial exception into a practical application, the claim will apply, rely on, or use the judicial exception that imposes a meaningful limit such that the claim is more than a drafting effort to monopolize the judicial exception. Examiners evaluate integration by identifying additional elements in the claim beyond the judicial exception and evaluating those elements individually and in combination to determine whether they integrate the exception in to a practical application. Examples that have been found by the Courts in which the exception was not integrated into a practical application include:
- Mere instructions to implement an abstract idea on a computer
- Adding generic instructions that the judicial exception should be used ("apply it")
-Adding insignificant extrasolution activity to the exception ("mere data gathering")
- Generally linking the use of the exception to a particular technological environment or
field of use
In this case, claims 7-10 recite natural products, without reciting any further elements to evaluate under Step 2A, prong 2. Hence, there are no elements beyond the nature-based products to integrate the judicial exception into a practical application.
Step 2B: Step 2B requires the Examiner to first identify whether there are any additional elements (features/limitations/steps) recited in the claim beyond the judicial exception(s), and then evaluate those additional elements individually and in combination to determine whether they contribute to an inventive concept (i.e., amount to significantly more than the judicial exception(s)).
In this case, claims 7-10 recite natural products without reciting any further elements to evaluate under Step 2B. Hence, there are no elements beyond the nature-based products that amount to significantly more than the judicial exception.
Therefore, claims 7-10 are not patent eligible.
Claim Rejections - 35 USC § 112(a) – Written Description
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 1-2, 5-9, 11-14, 16-17 and 19-20 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 claim(s) contains 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(s), at the time the application was filed, had possession of the claimed invention.
Brief Statement of the Issue(s)
The claims at issue are directed to several genera of products and/or structures (i.e., biofilms, nomadic bacteria, conditioned media) and related methods of making and using said products, wherein each element is recited generically as to encompass a genus that is not commensurate in scope with Applicant’s disclosure. In particular, the claims define a genus of nomadic bacteria and the necessary culture conditions necessary to perform said methods by reciting functional requirements (e.g., “conditions that promote the generation of V-type structure”) that do not clearly correspond to any prior art structures, making it impossible for one to fully envisage the claimed genus of bacteria or the full scope of the claimed invention(s).
Claim Scope
Claims 1, 8, 11 and 16 are representative of the pending claims scope and recite products and methods of using “nomadic bacteria” which are defined at least in part using functional limitations/requirements (i.e., the capability to form V-type structure).
The applicable claim interpretations have been set forth above under 35 U.S.C. 112(a) and in a separate Claim Interpretation section. Those discussions are incorporated herein.
Claim 1 recites a method of generating a biofilm comprising a nomadic bacteria, wherein the bacteria used in said method are interpreted to be any bacteria capable of forming a biofilm. The claim also requires that the bacteria are capable of forming “a V-type structure” and that the first culturing step is “under conditions” that promote generation of said V-type structure.
Claim 8 recites a composition comprising isolated, nomadic bacteria, which are interpreted as comprising any bacteria capable of forming a “V-shaped structure”.
Claim 11 recites a method of reducing biofilm formation of a pathogen comprising a first step of culturing a nomadic bacteria in a medium subjected to at least one stress to generate a “conditioned medium”. It is interpreted that the nomadic bacteria is any bacteria and the conditioned medium comprises any growth medium, as well as any bacterial product produced by said bacteria. As such, the claim is directed to the generation of any conditioned medium (i.e., any medium comprising any bacterial product). The claim recites a second step of contacting said pathogen with said conditioned medium “under conditions that reduce biofilm formation of said pathogen”. Therefore, the conditioned medium must comprise compounds (e.g., bacterial products) that are capable of reducing the biofilm of a pathogen, and the scope of the claim includes any such medium capable of reducing the biofilm of any such pathogen.
Claim 16 recites a conditioned medium that is generated by culturing a nomadic bacteria in a medium subjected to at least one stress to generate a “conditioned medium”. It is interpreted that the nomadic bacteria is any bacteria and the conditioned medium comprises any bacterial product produced by said bacteria. As such, the claim is directed to any conditioned medium (i.e., any medium comprising any bacterial product). In view of the instant specification, it is an object of the invention that the conditioned medium can be used to control biofilm formation (see pg. 1, lines 17-19; pg. 12, lines 30-32), in particular, to reduce the biofilm formation of pathogens (see pg. 23, lines 10-11). Therefore, the scope of the claim includes any such medium capable of reducing the biofilm of any such pathogen.
Hence, it is unclear if the claim scope encompass trillions of species (i.e., any bacteria, any culture condition, any conditioned medium) or perhaps only a few in view of the functional limitations/requirements set forth in the claim(s) (i.e., the capability to generate V-type structure, to form biofilms, or to reduce pathogenic biofilms). Accordingly, the claim scope reasonably appears to be vast and highly varied.
Actual Reduction to Practice
In Example 1, the inventors disclose that L. plantarum (nomadic bacteria), B. subtilis (an additional bacteria for co-culturing), and C. albicans (a pathogenic yeast) were cultured for the experiments (see pg. 28, lines 15-23). The inventors disclose that the “investigation was initiated following the observation of unusual cone-shaped colonies formed by L. plantarum on the MRS air-agar interface, which was triggered by acidic pH” (see pg. 31, lines 26-27). The inventors disclose that this structure was hypothesized to help the cells to improve survivability during subsequent stress (see pg. 32, lines 10-19). The inventors also found that cold stress potentiates L. plantarum cells to release pre-accumulated signals that coordinate cellular aggregation (see pg. 33, lines 14-15). The inventors disclose further experiments relating to the previously known symbiotic relationship of B. subtilis with L. plantarum (see pg. 33, lines 16-30).
The inventors further investigated the morphology of L. plantarum cells during the transition to low pHs, noting that the cells grown at a particularly acidic-pH (pH 3.5) “displayed unique V-shaped cellular structures… though they showed slower growth rates compared to the cells grown at elevated pHs” (see pg. 33, lines 31-34). The inventors disclose that this phenomenon was “demonstrated for at least five strains of L. plantarum” (see pg. 33, line 34 to pg. 35, line 1). The inventors disclose that the low pH grown cells retained their V-shaped structures while forming robust biofilms on polystyrene and glass surfaces, and collectively, these results demonstrate a survival mode of growth with increased resistance, “which could be linked to biofilm formation” (see pg. 34, lines 1-4). The inventors disclose that the V-shaped cells were tested to see whether they could better fight a medically important yeast pathogen, C. albicans using a C. elegans model, comparing the mortality rates of C. elegans previously fed with L. plantarum to C. elegans previously fed with E. coli OP50 (control) in response to an infection by C. albicans (see pg. 34, lines 5-21).
Hence, Applicant’s first example demonstrated that (1) low pH-stressed L. plantarum cells formed V-shaped cell chain structures and (2) low pH-stressed L. plantarum cells increased survivability of a nematode (C. elegans) against an infection by a pathogenic yeast (C. albicans).
In a second set of experiments, the inventors used L. plantarum to prepare probiotic filtrates (postbiotics), from cold-stressed L. plantarum colonies (“CSP”) and unstressed L. plantarum colonies (“UP”) (see pg. 38, lines 1-19). The inventors disclose that postbiotics from both stressed and unstressed L. plantarum had similar effects on the biofilm-forming ability of E. coli and S. aureus, with CSP showing “slightly better activity (marginally significant)” (see pg. 40, lines 1-8). The inventors also disclose that both postbiotics inhibited the “swarming motility” in E. coli, which is described as being “related” to one of the mechanisms controlling biofilm formation, hinting at the ability of the postbiotics to have broad-spectrum antipathogenic effects (see pg. 40, lines 14-23). The inventors disclose that the postbiotics were effectual in preventing the formation of biofilms by C. albicans, but they were not strong enough to disassemble the pre-formed mature biofilms; however, a marginal reduction in mature biofilms was noted when the concentration of postbiotics was doubled (see pg. 40, line 33 to pg. 41, line 2).
Hence, Applicant’s second example demonstrated the effects of postbiotics (i.e., bacterial products produced in culture) from a cold-stressed L. plantarum strain against the biofilms of E. coli, S. aureus, and C. albicans.
In view of Applicant’s examples, there is no “nomadic bacteria” other than L. plantarum that has been shown to respond to acidic culture conditions by generating “V-type” or “V-shaped” structure. Furthermore, there is also no reduction to practice that demonstrates this structure to have any superior effect, other than the inventors’ hypothesis that it may be an underlying mechanism of L. plantarum’s survival under certain stress-causing conditions and “could be” linked to biofilm formation. Nonetheless, this structure has only been demonstrated in a single species.
Furthermore, the inventors showed that postbiotics (i.e., bacterial products) from L. plantarum may reduce the biofilm formation in E. coli, S. aureus and C. albicans, but the inventors report that there was only a marginal improvement when using postbiotics from a cold-stressed strain of L. plantarum compared to the unstressed strain. While the inventors demonstrate that the feeding of low pH-stressed L. plantarum cells to a nematode (C. elegans) increased its survival against a pathogenic yeast strain (C. albicans), this was not demonstrated using a “conditioned medium” (i.e., postbiotics) or shown to reduce biofilm formation.
Assessment of whether disclosed species are representative of the claimed genus
MPEP § 2163 states that a “representative number of species” means that the species which are adequately described are representative of the entire genus (see, e.g., MPEP § 2163(II)(3)(a), MPEP §2163.03(V)). Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
In this case, the claims encompass an essentially infinite number of potential products and methods but, at best, only one was fully reduced to practice for each of the claimed inventions (e.g., the generation of a biofilm by L. plantarum in support of the method of claim 1, the prevention of biofilm formation using the products produced by a cold-stressed L. plantarum strain in support of the method of claim 11 and the product of claim 16).
Although the MPEP does not define what constitutes a sufficient number of representative species, the Courts have indicated that claims directed to a functionally defined genus of structures may not be supported by a disclosure that only described one type of similar structures. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that "only describe[d] one type of structurally similar antibodies" that "are not representative of the full variety or scope of the genus.").
Furthermore, the disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us]." See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) ("[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.") (Emphasis added).
Finally, satisfactory disclosure of a "representative number" depends on whether one of skill in the art would recognize that the inventor was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See, e.g., Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
In the instant case, the disclosure of one embodiment of the claimed invention does not provide sufficient disclosure to satisfy the written description requirement for the instantly claimed genus without the further disclosure of a reasonable structure-function relationship.
Identifying characteristics of the genus
In the absence of a reduction to practice of a representative number of species, the written description requirement for a claimed genus may be satisfied by disclosure of relevant, identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.
The specification defines the term “nomadic bacteria” as any bacteria which are capable of thriving in different ecological niches (see pg. 13, para. 28-29). According to a preferred embodiment, the nomadic bacteria belong to the genus Lactobacillus, and exemplary species of nomadic Lactobacillus that are contemplated include but are not limited to L. rhamnosus, L. plantarum and L. casei (see pg. 14, lines 4-7). However, there is zero discussion as to which nomadic bacteria would be expected to generate the same V-type morphology observed in L. plantarum when exposed to particular stresses.
The specification states that the conditioned medium may include metabolites, organic acids, bacteriocins, antimicrobial peptides growth factors and cytokines secreted by the cells in the culture (see pg. 23, lines 22-23) and “[f]ollowing accumulation of adequate factors in the medium, the conditioned medium is separated from the nomadic bacterial cells and collected” (see pg. 24, lines 15-16). The specification states that L. plantarum is known to secrete diverse volatile compounds, which were shown to possess antibacterial and/or antifungal activities (see pg. 41, lines 17-18). However, there is zero discussion as to which bacteria produce which compounds (“factors”) that would be expected to reduce biofilms, or which pathogens each possible embodiment may specifically be able to address.
Accordingly, the claimed limitations of “V-type or V-shaped structure” and “conditioned medium” are only utilized as a vague attempt to capture unknown and undisclosed structures, sufficient to achieve some functional result that Applicant desires the disclosed invention to achieve. However, the disclosure does not meaningfully disclose an unambiguous structure/function relationship permitting an artisan to identify, a priori, which exact structures do or do not satisfy the functional limitations at issue.
Predictability in the Art
According to Nguyen, et al. (Exopolysaccharide production by lactic acid bacteria: the manipulation of environmental stresses for industrial applications. AIMS Microbiol. 2020 Nov 17;6(4):451-469; cited in the IDS filed 03/12/2026), exopolysaccharides (EPSs) are biological polymers secreted by microorganisms including Lactic acid bacteria (LAB) to cope with harsh environmental conditions and are one of the main components involved in the formation of extracellular biofilm matrix to protect microorganisms from adverse factors such as temperature, pH, antibiotics, host immune defenses, etc. (see Abstract). Nguyen teaches that under environmental stresses, LAB have different adaptation mechanisms (see pg. 457, para. 4), and while low pH was found to enhance biofilm formation in L. rheuteri strains, it was also found to significantly decrease biofilm formation in L. rhamnosus GG (see pg. 458, para. 3). Regarding osmotic stress, high NaCl concentration enhances EPS production in Leuconostoc mesenteroides/speudomesnteroides, while the inhibition of EPS production by NaCl was recorded in L. helveticus (see 459, para. 1). See also Table 1 on pg. 461 which shows the impact of various stress conditions on the EPS synthesis of different lactic acid bacteria.
Serra, et al. ("Stress Responses Go Three Dimensional - The Spatial Order of Physiological Differentiation in Bacterial Macrocolony Biofilms", Environmental Microbiology, 16(6): 1455-1471, 13 April 2014; cited in the IDS filed 08/26/2024) is an extensive review (citing more than 140 publications) relating to the many links between stress responses and biofilm physiology that have emerged over the past years (see pg. 1456, col. 2, para. 3). Serra teaches that in natural habitats, bacteria often occur in multicellular communities characterized by a robust extracellular matrix of proteins, amyloid fibres, exopolysaccharides and extracellular DNA, and these biofilms show pronounced stress resistance including a resilience against antibiotics that causes serious medical and technical problems. Serra teaches that recent studies have revealed clear spatial physiological differentiation, complex supracellular architecture and striking morphology in macrocolony biofilms. Serra teaches that microcolony biofilms also exhibit striking macroscopic morphological patterns of ridges, rings and wrinkles, a phenotype that has been termed ‘wrinkled’, ‘rugose’ or ‘rdar’ (‘rough, dry and red’, with ‘redness’ depending on the use of the dye Congo Red), although these simple designations do not adequately reflect the complexity and diversity of these structures (see pg. 1466, col. 2). Serra states that it will be a major challenge for future research to characterize the underlying morphogenetic molecular mechanisms, i.e. how distinct matrix components, the network of multiple c-di-GMPcontrolling DGCs and PDEs, the asymmetric expression of these components in different biofilm strata established by long-range nutrient and oxygen gradients as well as the role of additional stress signal input contribute to the microarchitecture and macroscopic morphology of biofilms (see pg. 1466, col. 2).
At the time of filing, the prior art of record appears to be silent regarding “V-type” or “V-shaped” structure in bacteria, let alone any significance of this particular structure as it may relate to the claimed invention. Therefore, there are no prior art teachings that a person of skill could rely upon to identify which bacteria are capable of generating this structure in accordance with the claims.
Although the level of skill in the art is high, the predictability in the art is low due to the complexity of biological systems, biochemistry, and the diversity of bacteria and their functions. Specifically, an artisan would not be able to predict or identify, a priori, and in the absence of any guidance or consensus structures exactly what bacteria would be capable of generating V-type structure and could be used in accordance with the claims to achieve the results desired by the inventors.
Accordingly, in the absence of sufficient structure/function teachings identifying particular bacteria capable of forming V-type structures, biofilms, and/or bacterial products which can be used according to the full scope of the claims, an artisan would not reasonably conclude that Applicant possessed the full scope of the broad and highly varied claim scope.
Conclusion
The description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736 F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming rejection because the specification does "little more than outlin[e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate.").
The Federal Circuit has explained that a specification cannot always support expansive
claim language and satisfy the requirements of 35 U.S.C. 112 "merely by clearly describing one
embodiment of the thing claimed." LizardTech v. Earth Resource Mapping, Inc., 424 F.3d 1336,
1346, 76 USPQ2d 1731, 1733 (Fed. Cir. 2005). See also Tronzo v. Biomet, 156 F.3d at 1159, 47
USPQ2d at 1833 (Fed. Cir. 1998)(holding that the disclosure of a species in a parent application
did not provide adequate written description support for claims to a genus in a child application
where the specification taught against other species).
This is pertinent because, in the instant case, Applicants have claimed a broad and highly varied genus comprising an unknown number of species defined by reference to one or more functional limitations; however, the originally filed disclosure has failed to identify any common structure/function relationship sufficient to permit an artisan to identify what structures are included or excluded by the claim scope. This also means that the skilled artisan cannot envisage what structures infringe or do not infringe upon the pending claim scope.
In conclusion, for the reasons discussed above, the skilled artisan would not reasonably conclude that the inventor(s), at the time the application was filed, had possession of the full scope of the claimed invention.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 16-20 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Markkinen, et al. (Impact of malolactic fermentation with Lactobacillus plantarum on volatile compounds of sea buckthorn juice. Eur Food Res Technol 247, 719–736 (2021); cited on Form 892), hereafter, “Markkinen”.
Regarding claim 16, Markkinen teaches that malolactic fermentation using sea buckthorn juice as raw material was performed with six different strains of Lactobacillus plantarum, and increasing juice pH from 2.7 to 3.5 or adapting cells to low pH (i.e., acclimation) prior to inoculation allowed malolactic fermentation with all tested strains. Markkinen teaches that microbial activity increased the levels of acetic acid, free fatty acids, ketones, and alcohols with fruity descriptors (see Abstract). Markkinen teaches that exposure of L. plantarum cells to sub-optimal pH and L-malic acid prior to inoculation to sea buckthorn (i.e., acclimation) likely led to activation of genes related to acid stress (see pg. 730, col. 2, para. 5). Markkinen discloses that the increase in acid content was due to production of acetic acid by L. plantarum and increased hydrolysis of fatty acid-derived esters (see pg. 734, col. 1, para. 4). Markkinen discloses that 2-Undecanone (fruity aroma) was the only compound that was detected solely in fermented samples (see pg. 730, col. 2, para. 2), and the formation of 3-hydroxybutan-2-one, butane-2,3-dione and 2-undecanone explained the increase in the ketone content of the culture (see pg. 734, col. 1, para. 4).
As discussed under Claim Interpretation, the broadest reasonable interpretation of the claim, which is directed to a product-by-process, is that the conditioned medium is any composition comprising any growth medium and any bacterial products. Per MPEP 2113, the patentability of a product does not depend on its method of production, unless there is some change in structure implied by the product-by-process steps. In the instant case, the prior art product (i.e., sea buckthorn fermentation juice comprising acetic acid produced by L. plantarum), as well as the method used to obtain said product, are both within the scope of the claim.
Thus, Markkinen teaches a conditioned medium, comprising a growth medium (i.e., sea buckhorn juice) and bacterial products (i.e., acetic acids), which are disclosed as being produced by L. plantarum in said growth medium after exposure to a pH stress, which meets the claim.
Regarding claim 17, Markkinen teaches the culturing was performed in sea buckhorn juice. As discussed under 35 U.S.C. 112(b), a non-adherent surface is interpreted as including any liquid culture medium, including “juice”.
Regarding claim 18, Markkinen teaches the cultured bacteria was of the species L. plantarum, as discussed above.
Regarding claim 19, Markkinen teaches the L. plantarum was exposed to pH stress, as discussed above, which meets the limitation of an “acid stress”.
Regarding claim 20, Markkinen discloses that the fermented samples contained 2-undecanone, as discussed above.
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.
Claim(s) 1-10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Shemesh, et al. (US 2019/0216124 A1; cited on Form 892), hereafter, “Shemesh”, and further in view of Nguyen, et al. (Response of Lactobacillus plantarum VAL6 to challenges of pH and sodium chloride stresses. Sci Rep. 2021 Jan 14;11(1):1301; cited on Form 892), hereafter, “Nguyen”.
Regarding claim 1, Shemesh teaches a method of preparing a bacterial composition comprising (a) in vitro co-culturing beneficial bacteria with biofilm-producing bacteria in a growth substrate under conditions that generate a biofilm which comprises said beneficial bacteria and said non-pathogenic bacteria and (b) isolating said biofilm from said growth substrate, thereby preparing the bacterial composition (see claim 1). Shemesh teaches the method wherein said probiotic bacteria are of the Lactobacillus plantarum species (see claims 7 and 9). Shemesh teaches the method, wherein said conditions comprise a pH of about 6.5-8 (see claim 15).
Shemesh teaches that the co-culture may be carried out on a solid surface (see pg. 9, para. [0137]). Shemesh teaches that exemplary solid surfaces on which the culturing can be carried out include a wide range of substrates, ranging from various polymeric materials (silicone, polystyrene, polyurethane, and epoxy resins) to metals and metal oxides (silicon, titanium, aluminum, silica, and gold) (see pg. 9, para. [0138]). In view of the instant specification, exemplary “adherent surfaces on which the culturing can be carried out include a wide range of substrates, ranging from various polymeric materials (silicone, polystyrene, polyurethane, and epoxy resins) to metals and metal oxides (silicon, titanium, aluminum, silica, and gold)” (see pg. 17, lines 1-3). Therefore, the “solid surface” taught by Shemesh meets the claimed limitation of an “adherent surface”.
Therefore, Shemesh teaches a method of generating a biofilm comprising a nomadic bacteria (L. plantarum), the method comprising culturing the nomadic bacteria on an adherent surface, thereby generating the biofilm comprising the nomadic bacteria.
Shemesh does not explicitly teach culturing the bacteria in an acidic environment prior to culturing on an adherent surface.
Nguyen teaches that Exopolysaccharides (EPS) are high molecular weight biological polymers synthesized extracellularly by various microorganisms (archaea, bacteria, fungi or algae) and applied in a variety of industries such as food and pharmaceuticals, and teaches the function of exopolysaccharides (EPS) is to protect bacterial cells from the negative effects of the environment, such as dehydration, antibiotics, phagocytosis and phage attacks by forming biofilms (see pg. 1, paras. 1-2). To investigate the effect of environmental stresses on exopolysaccharide biosynthesis, Nguyen discloses that after 24 hours of culturing at 37 °C and pH 6.8, without sodium chloride, Lactobacillus plantarum VAL6 was exposed to different stress conditions, including pH (pHs of 3 and 8), as well as high sodium chloride concentration treatments (see Abstract). Nguyen discloses that the Lactobacillus plantarum VAL6 exposed to stress at pH 3 for 3 hours gave the highest exopolysaccharide yield (50.44 g/L) which is 6.4 fold higher than non-stress (see Abstract).
Therefore, Nguyen teaches culturing Lactobacillus plantarum in an acidic environment (i.e., pH 3), which increases the production of EPSs the bacterium uses to produce biofilms.
Regarding the limitation of “under conditions that promote generation of a V-type structure”, as discussed under 35 U.S.C. 112(b), this limitation is interpreted to only require the bacteria to be cultured in an acidic environment. Furthermore, the capability of the bacterium to generate this structure is presumed to an inherent property of L. plantarum itself and does not require, or otherwise imply, any further method step.
It would have been obvious at the time of filing to have arrived at the claimed invention by combining the teachings of Shemesh and Nguyen, because Nguyen teaches that culturing Lactobacillus plantarum in an acidic environment for 3 hours resulted in the bacterium producing a high yield of EPS, which is used to form biofilms. A person of skill would have been motivated to do so, because Nguyen teaches that EPS has a variety of uses in the food and pharmaceutical industries and is a key component of biofilms. One would have recognized that exposing the L. plantarum taught by Shemesh to an acidic culture condition prior to co-culture with an additional bacterium on a solid surface would have effectively triggered the bacterium to increase the production of EPS which would be expected to result in a more effective method to produce a biofilm. Furthermore, it is well within the ordinary skill in the art to add additional method steps when culturing bacteria in order to condition said bacteria to enhance the production of desirable products by said bacteria. There would have been a reasonable expectation of success when modifying the method taught by Shemesh, because the prior art of Nguyen teaches the expectation that culturing L. plantarum at a low pH would increase EPS yield. Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Regarding claim 2, Shemesh and Nguyen teach the bacteria is Lactobacillus plantarum, as discussed above.
Regarding claim 3, Shemesh and Nguyen teach the bacteria is Lactobacillus plantarum, as discussed above.
Regarding claim 4, Nguyen teaches the L. plantarum was cultured in an acidic environment of pH 3, as discussed above.
Regarding claim 5, Shemesh teaches co-culturing beneficial bacteria with biofilm-producing bacteria, as discussed above.
Regarding claim 6, Shemesh teaches the co-culture, wherein the bacteria are Lactobacillus rhamnosus and Bacillus subtilis (see claims 8 and 9).
Regarding claim 7, Shemesh teaches a bacterial composition comprising a biofilm produced by the method discussed above (see claim 1(b) and claim 22).
Regarding claim 8, Shemesh teaches a composition comprising bacteria, as discussed above. Regarding the limitation, “wherein at least 30% of the bacteria have a V-shaped structure”, this is presumed to be an inherent property of L. plantarum that does not require, or otherwise imply, any further method step. In view of the instant specification, the “phenomenon of cone-shaped colonies and V-shaped cell chains were discovered in response to acidic-pH stress” in L. plantarum (see pg. 13, lines 7-8). Therefore, this recited structure is presumed to be an inherent property of L. plantarum, and would necessarily be present in a composition comprising L. plantarum subjected to the acidic-pH stress taught by Nguyen.
Regarding claim 9, Shemesh and Nguyen teach the bacteria is Lactobacillus plantarum, as discussed above.
Regarding claim 10, Shemesh and Nguyen teach the bacteria is Lactobacillus plantarum, as discussed above.
Claim(s) 11 and 13-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Nguyen and further in view of Mahdhi, et al. (Use of extracellular polysaccharides, secreted by Lactobacillus plantarum and Bacillus spp., as reducing indole production agents to control biofilm formation and efflux pumps inhibitor in Escherichia coli. Microb Pathog. 2018 Dec; 125: 448-453; cited on Form 892), hereafter, “Mahdhi”.
Regarding claim 11, Nguyen teaches that Exopolysaccharides (EPS) are high molecular weight biological polymers synthesized extracellularly by various microorganisms (archaea, bacteria, fungi or algae) and applied in a variety of industries such as food and pharmaceuticals, and teaches the function of exopolysaccharides (EPS) is to protect bacterial cells from the negative effects of the environment, such as dehydration, antibiotics, phagocytosis and phage attacks by forming biofilms (see pg. 1, paras. 1-2). To investigate the effect of environmental stresses on exopolysaccharide biosynthesis, Nguyen discloses that after 24 hours of culturing at 37 °C and pH 6.8, without sodium chloride, Lactobacillus plantarum VAL6 was exposed to different stress conditions, including pH (pHs of 3 and 8), as well as high sodium chloride concentration treatments (see Abstract). Nguyen discloses that the Lactobacillus plantarum VAL6 exposed to stress at pH 3 for 3 hours gave the highest exopolysaccharide yield (50.44 g/L) which is 6.4 fold higher than non-stress (see Abstract).
Nguyen does not explicitly teach a method of reducing biofilm formation of a pathogen comprising culturing the nomadic bacterium “to generate a conditioned medium” and “contacting said pathogen with said conditioned medium”.
However, Nguyen teaches that culturing Lactobacillus plantarum in a medium subjected to a pH stress (i.e., pH 3) results in a more robust production of EPS, which is a bacterial product. As discussed under Claim Interpretation, the broadest reasonable interpretation of a “conditioned medium” is the medium after the first step of culturing which includes any products produced by the bacterium during said culturing.
Mahdhi teaches that the overuse of antibiotics and biofilm formation ability has led to the emergence of bacterial resistant strains, and the combined use of several antibiotics has been found as an efficient strategy to overcome this resistance. In this study, two exopolysaccharides (EPS) obtained from Lactobacillus plantarum (EPS-Lp) and Bacillus spp. (EPS-B), isolated from a traditional Tunisian food “ricotta cheese” and hypersaline environment respectively, were used to counteract the biofilm formation and efflux pumps activities in Escherichia coli ATCC35218. The obtained results revealed that the tested EPSs can be effective against E. coli at a concentration > 1 mg/ml and were able to modulate biofilm formation by 50%. See Abstract.
Mahdhi teaches that due to their physicochemical properties, EPSs produced by probiotic bacteria have been used in a wide range of applications, and recently it has been revealed that EPSs produced by different lactic acid bacteria (LAB) strains have potential biological activities such as antioxidant, immunomodulating, and antibacterial properties (see pg. 448, col. 2 to pg. 449, col. 1, para. 1). Mahdhi teaches that other studies showed that EPS produced by Lactobacillus plantarum inhibit the biofilm formation of pathogenic bacteria, including E. coli O157:H7, Salmonella Typhimurium ATCC13311, and Staphylococcus aureus CMCC26003 (see pg. 449, col. 1, para. 1).
In Mahdhi’s study, Lactobacillus plantarum and halophilic Bacillus spp. previously characterized for their probiotic properties, especially antibacterial activity, were cultivated and their exopolysaccharides (EPSs) were collected (see pg. 449, col. 1, paras. 3-4). Mahdhi discloses that pathogenic E. coli ATCC35218 was dispensed into each well of 96-well plates containing the EPSs from L. plantarum and Bacillus spp. at different concentrations, and the plates were incubated to allow biofilm development (see pg. 449, col. 2, para. 2). Mahdhi discloses that the tested EPSs displayed a dose dependent inhibitory effect against E. coli biofilm, and in the presence of different concentrations of EPSs, a decrease in biofilm formation (more than 50%) was observed (see pg. 450, col. 1, para. 5). Mahdhi concludes that there are several possible applications of EPSs, such as their use with probiotics to control pathogenic biofilm formation and/or as potential prebiotic agents in therapeutic strategies for bacterial biofilm-associated infections (see pg. 452, col. 1, para. 6).
It would have been obvious at the time of filing for a person of ordinary skill to have arrived at the claimed invention by combining the teachings of Nguyen and Mahdhi, because Mahdhi teaches contacting pathogenetic E. coli with EPS derived from L. plantarum is effective in decreasing biofilm formation. One would have been motivated to have combined these teachings, because Nguyen teaches that low pH stress increases EPS yield in L. plantarum, and Mahdhi teaches that the EPS produced by L. plantarum can be used to control pathogenic biofilm formation. One would have recognized that the method steps of each disclosure could have been combined using known methods and there would have been a reasonable expectation of success, because both disclosures relate to using the same bacterium (i.e., L. plantarum) to produce the same bacterial product (i.e., EPS). Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Regarding claim 13, in view of the instant specification, the “phenomenon of cone-shaped colonies and V-shaped cell chains were discovered in response to acidic-pH stress” in L. plantarum (see pg. 13, lines 7-8). Therefore, the functional limitation of “wherein said culturing promotes a chain structure” requires no further method step and is presumed to be an inherent property of L. plantarum that would necessarily be present when subjecting the L. plantarum strain to acidic-pH stress, as taught by Nguyen.
Regarding claim 14, Mahdhi teaches the pathogen was a pathogenic strain of E. coli, as discussed above.
Regarding claim 15, Nguyen and Mahdhi teach the bacteria is L. plantarum, as discussed above.
Claim(s) 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Nguyen and Mahdhi, as applied to claims 11 and 13-15 above, and further in view of Song, et al. (Cold stress improves the ability of Lactobacillus plantarum L67 to survive freezing. Int J Food Microbiol. 2014 Nov 17;191:135-43; cited on Form 892), hereafter, “Song”.
Regarding claim 12, Nguyen teaches the culturing of Lactobacillus plantarum in a medium subjected to a pH stress (i.e., pH 3), as discussed above, which meets the limitation of a “acidic stress”.
Nguyen does not explicitly teach wherein the stress further comprises a cold stress.
Song teaches that the exposure of L. plantarum cells to low temperatures aids their ability to survive through subsequent freeze–thaw processes and lyophilization (see Abstract). Song teaches that during the manufacture of lactic acid fermented products, bacterial cells are exposed to various environmental stresses such as extreme temperatures, pH, osmotic pressure, oxygen, high pressure and starvation, which may affect the physiological status and the properties of the cells (see pg. 135, col. 2). However, bacterial cells are naturally equipped with a plethora of defense mechanisms to enhance survival in stressful environments, and many research studies have reported the positive effects of the stress response (see pg. 135, col. 2). Song teaches that freezing is generally used to preserve a starter culture for an extensive amount of time while still maintaining its viability and acidification activity, and the freezing resistance of Lactobacillus is enhanced by applying cold stress conditions before freezing (see pg. 136, col. 1, para. 2). Song discloses that many L. plantarum L67 proteins were overexpressed in the cells exposed to low temperatures, and these proteins may interact with each other, resulting in cryotolerance (see pg. 142, col. 1, para. 6).
It would have been obvious at the time of filing for a person of ordinary skill in the art to have arrived at the claimed invention by combining the teachings of Nguyen and Song, because Song teaches that applying a cold stress to L. plantarum enhances its resistance to cold stress conditions. Therefore, a person of skill would have recognized there to be an advantage when subjecting the bacterium to a combination of environmental stresses for the preservation of the cultured bacterium and its production of desired products. For example, one would have recognized that a culture comprising the bacterium could be subjected to a cold stress condition prior to freezing the culture for preservation, and later subjected to an acidic stress after thawing to generate the desired products. Furthermore, any cryopreserved strain has reasonably been exposed to a “cold stress”, and an ordinary artisan would have recognized this to be a common means of preserving bacteria for later use. There would have also been a reasonable expectation of success, because Song teaches that utilizing the stress response of bacterial cells to produce positive effects, such as resistance to certain environmental conditions, are well known in the art. Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DENNIS ARMATO whose telephone number is (703)756-5348. The examiner can normally be reached Mon-Fri 11:00am-7:30pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Melenie Gordon can be reached at (571) 272-8037. 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.
/DENNIS IGNATIUS ARMATO JR/Examiner, Art Unit 1651
/MELENIE L GORDON/Supervisory Patent Examiner, Art Unit 1651
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