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 .
Priority
This application is a 371 of PCT/EP2021/051912 filed 01/28/2021. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign based on EPO 20154679.3 filed 01/30/2020. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 12/04/2025 complies with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of the Claims
Claims 1-17 are pending. Claims 1, 2, 4-8 and 15-17 are amended. Claims 7, 8, 12, 16 and 17 were withdrawn.
Claims 1-6, 9-11 and 13-15 (claim set filed 02/13/2026) are examined on the merits herein.
Withdrawal of Rejections
The response and amendment filed on 02/13/2026 are acknowledged. All of the amendment and arguments have been thoroughly reviewed and considered.
For the purposes of clarity of the record, the reasons for the Examiner's withdrawal and/or maintaining if applicable, of the substantive or essential claim rejections are detailed directly below and/or in the Examiner's response to arguments section.
The previous claims 1, 2, 4-6 and 15 objections have been withdrawn necessitated by amendment of claims 1, 2, 4-6 and 15.
The previous claims 2 and 3 rejection under 35 U.S.C. 112 (b) have been withdrawn necessitated by amendment of claim 2.
The previous claims 1-6, 9-11 and 13-15 rejection under 35 U.S.C. 101 has been withdrawn necessitated by amendment of claim 1 and Applicant’s arguments which are persuasive. Applicant argues that: “Claimed method is directed to the physical production of a fermented food product through sequential bacterial culturing - not to an abstract mental process. … Even if the selection step were characterized as a mental process, the claims integrate any such exception into a practical application by: (1) providing an improvement to food fermentation technology; (2) effecting a transformation of a food product into a fermented food product; and (3) applying the selection in a meaningful way that is constrained by specific technical requirements and results in the physical act of subsequently culturing the food product.” These arguments are persuasive and therefore 35 U.S.C. 101 has been withdrawn.
Maintained/Modified Rejections
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, 4, 9, 14 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Klaenhammer (US 5593885 A).
Regarding claims 1, 4, 9, 14 and 15, Klaenhammer teaches a phage defense rotation strategy for use in the successive fermentation of a substrate in a fermentation plant (Abstract). The substrate is a food substrate (claim 10). Klaenhammer discloses that the method can be applied to fermentation for production of different food products, such as different cheese, yogurt or wine (column 7, lines 8-12). Klaenhammer describes the successive fermentation method as fermenting a substrate with a first bacterial culture comprising a bacterial strain capable of fermenting the substrate and carrying a first phage defense mechanism and then fermenting the substrate with a second bacterial culture, comprising a second bacterial strain isogenic with the first bacterial strain, wherein the second strain carries a second phage defense mechanism different from the first phage defense mechanism (column 2, lines 20-30). Since Klaenhammer used isogenic bacterial strains, they have common bacteriophage sensitivity. However, the defense mechanism of the second strain different from that for the first strain will further decrease common bacteriophage sensitivity. Klaenhammer teaches that the fermentation can be continued with the third culture comprising a third bacterial strain isogenic with the first and second strains and carrying the phage defense mechanism different from the first and the second phage defense mechanism (column 2, lines 31-37). The isogenic strains are derived from the same parental strain and have the same capability to ferment the substrate (column 3, lines 51-54). The isogenic strains are compatible and differ in sensitivity to bacteriophages due to the different phage defense mechanisms. Klaenhammer describes that isogenic strains carrying different phage defense mechanisms maintained activity over 9 cycles in the presence of commercial phage composites (column 10, lines 26-29). Klaenhammer mentions that the same host background (column 10, lines 18-20) improves consistency of fermentation such as cheesemaking and decreases phage diversity (column 10, lines 33-37).
Klaenhammer teaches detection and identification of bacteriophages in the samples and determination of bacteriophage titers by plaque assay (column 13, lines 45-59). Additionally, Klaenhammer describes evaluation of bacterial activity by lowering pH (column 13, lines 36-37) since fermentation by lactic bacteria used by Klaenhammer (columns 6-8, Fermentative Microorganisms) produces lactic acid. Klaenhammer describes that the timing of rotation can occur as needed depending on conditions of the process and that the choice of timing can be made based on empirical studies or phage monitoring programs (column 6, lines 34-40). Klaenhammer mentions that rotation strategy is used to avoid phage attacks on fermentations or to reestablish a fermentation after phage attack (column 5, lines 58-61). Klaenhammer describes that rotation sequences terminated when strains fail to lower the milk pH below 6.0 and had high levels of phage are detected (108-109 PFU/ml) (column 13, lines 37-39) that correspond to the predetermined threshold of the value indicative for a number of bacteriophages.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the Klaenhammer method of consecutive culturing of isogenic strains carrying different defense mechanisms and having different sensitivity to bacteriophages to decrease bacteriophage contamination during production of fermented food and start the second culture after bacteriophage titers reach the predetermined threshold. One would have been motivated to do that since Klaenhammer provides examples of maintenance of fermentation activity over 9 cycles of bacterial culture rotations in the presence of commercial phage composites. A skilled artisan would have reasonably expected success in application of fermentation technique described by Klaenhammer following the description of the prior art. Thus, Klaenhammer teaching renders claims 1, 4, 9, 14 and 15 obvious.
Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Klaenhammer (US 5593885) as applied to claim 1 above, and further in view of Cairns (Cairns et al. PLoS Pathogens, 2008, 5, e1000253, 1-10).
The teaching of Klaenhammer has been set forth above.
Klaenhammer does not teach predicted value at the predetermined critical time point based on determination of the number of bacteriophages at plurality of time points.
Cairns teaches a quantitative models of in vitro bacteriophage-host dynamics (Abstract). Cairns combined experimental and modeling approaches to study kinetics of interaction of Campylobacter jejuni and virulent phage. The model was fit to time series data in order to estimate thresholds and rate constants directly (Abstract). The samples were taken every 2 hours for 24 hours (p. 4, 4th paragraph). Figure 3 demonstrate the exponential growth of bacteria followed after some time by rapid phage proliferation, the crash in bacterial population and slowing of phage growth (p. 5, left column, 2nd paragraph and Figure 3). Cairns mentions that fitted models match very well to the observed phage and bacterial concentrations (p. 5, left column, 2nd paragraph). Cairns discloses that the model allows to predict the outcomes of the joint population dynamics and determine the inundation and proliferation thresholds (p. 3, right column, 3rd paragraph). The inundation threshold is defined as the minimum phage concentration above which the bacterial population declines (p. 2, right column, 1st paragraph).
The threshold is defined in the specification as: “A threshold of a bacteriophage number has been determined in advance, for which it is known that bacterial fermentation will become too inefficient because of the large number of bacteriophages (p. 2, lines 35- 37). Therefore, the predetermined critical time point can correlate with the time when the inundation threshold in Cairns teaching is reached and bacterial populations starts to decline and hence the bacteriophage concentrations at that point can be predicted based on the models.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use model of bacteriophage-host interaction dynamics described by Cairns to predict the concentration of bacteriophage to start rotation of bacterial cultures in method of consecutive culturing to decrease bacteriophage numbers during production of fermented food as described by Klaenhammer. One would have been motivated to do that since Cairns teaches that models match very well to the observed phage and bacterial concentrations and predict outcomes of the joint population dynamics. A skilled artisan would have reasonably expected success in that combination because Klaenhammer and Cairns teach interaction of bacteria and bacteriophage. Thus, Klaenhammer and Cairns teachings render claim 2 obvious.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Klaenhammer (US 5593885) in view of Cairns (Cairns et al. PLoS Pathogen, 2008, 5, e1000253, 1-10) as applied to claims 1 and 2 above, and further in view of Oladunjoye (Oladunjoye et al. LWT – Food Science and Technology, 2017, 76, 9-17).
The teachings of Klaenhammer and Cairns have been set forth above.
Klaenhammer and Cairns do not teach prediction based on an artificial intelligence.
Oladunjoye teaches prediction of relationship between Listeria monocytogenes and bacteriophage using artificial neural network (ANN) (Abstract). Oladunjoye describes that: “Mathematical models were developed using a linear regression and sigmoid (hyperbolic and logistic) activation functions. Data sets (120) were trained using Back propagation ANN containing one hidden layer with four hidden neurons.” (Abstract). Oladunjoye mentions that the prediction showed the highest positive correlation between predicted and observed values and ANN offered better prediction (Abstract). Oladunjoye states that: “ … application of ANN-based approach with logistic activation function offered more accurate prediction than hyperbolic tangent activation function and linear regression's models, wherein a better relationship between the predicted and the actual data was enhanced.” (p. 16, left column, 3rd paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Oladunjoye guidance and add artificial intelligence modeling such as ANN to model of bacteriophage-host interaction dynamics described by Cairns to predict the concentration of bacteriophage to start rotation of bacterial cultures in method of consecutive culturing to decrease bacteriophage contamination during production of fermented food as described by Klaenhammer. One would have been motivated to do that since Oladunjoye teaches that ANN modeling offers more accurate prediction of the bacteriophage-bacterial host interaction. A skilled artisan would have reasonably expected success in that combination because Klaenhammer, Cairns and Oladunjoye teach interaction of bacteria and bacteriophage. Thus, Klaenhammer, Cairns and Oladunjoye teachings render claim 3 obvious.
Claims 5 and 6 are rejected under 35 U.S.C. 103 as being unpatentable over Klaenhammer (US 5593885) as applied to claim 1 above, and further in view of Garneau (Garneau and Moineau Microbial Cell Factories, 2011, 10, S20, 1-10).
The teaching of Klaenhammer has been set forth above.
Klaenhammer does not teach determination of the value indicative of bacteriophage number by DNA quantification method and by qPCR.
Garneau teaches detection of Lactobacillus, Lactococcus and Streptococcus bacteriophages by classic PCR method. Garneau mentions that these methods can be used directly on milk or whey samples and report the lowest detection limit of 103 PFR/ml (p. 3, right column, last paragraph). Garneau describes that while the classic PCR methods can take several hours, the qPCR can overcome this limitation and be performed in real time during fermentation (p. 3, right column, last paragraph). Garneau provides examples of qPCR application for detection of bacteriophages and mentions that: “qPCR methods provide a fast, specific, and highly sensitive technique to detect phage contamination.” (p. 4, left column, 1st paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add PCR and more specifically qPCR method for detection of bacteriophages as described by Garneau to method of consecutive culturing of isogenic bacterial strains to decrease bacteriophage contamination during production of fermented food as described by Klaenhammer. One would have been motivated to do that since Garneau teaches that qPCR methods is a fast, specific, and highly sensitive technique to detect phage contamination and provides examples of detection. A skilled artisan would have reasonably expected success in that combination because Klaenhammer and Garneau teach detection of bacteriophages. Thus, Klaenhammer and Garneau teachings render claims 5 and 6 obvious.
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Klaenhammer (US 5593885) as applied to claim 1 above, and further in view of Gao (Gao et al. Nucleic Acid Research, 2018, 46, D700-D707).
The teaching of Klaenhammer has been set forth above.
Klaenhammer does not teach determination of the sensitivity of bacterial cultures to bacteriophages by accessing a database.
Gao teaches a microbe-phage interface database MVP (Microbe Versus Phage) the purpose of which is to provide a comprehensive catalog of microbe-phage interactions (Abstract), Gao describes clustering of 50782 viral sequences and identification of 26572 interactions between 18608 viral clusters and 9245 procaryotes (bacteria and archaea). The interactions were established based on the published datasets, databases and re-analysis of genomic and metagenomic sequences. Gao mentions that MVP is freely available and is equipped with a modern, responsive and intuitive interface (Abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Gao guidance and select bacterial cultures for consecutive culturing to decrease bacteriophage contamination during production of fermented food as described by Klaenhammer based on determination of sensitivities of bacterial cultures to bacteriophages using database described by Gao. One would have been motivated to do that since Gao provides freely accessible database of 26572 interactions between microbes and bacteriophages with modern and intuitive interface. A skilled artisan would have reasonably expected success in that combination because Klaenhammer and Gao teach bacteriophage-bacterial host interactions. Thus, Klaenhammer and Gao teachings render claim 10 obvious.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Klaenhammer (US 5593885) as applied to claim 1 above, and further in view of Collins (Collins Appl. Microbiol., 1955, 3, 145-148).
The teaching of Klaenhammer has been set forth above.
Klaenhammer does not teach a compatibility matrix for the plurality of bacterial strains based on bacteriophage sensitivity.
Collins teaches establishing sensitivity patterns towards bacteriophages for various commercial bacterial cultures to study selection and rotation of cultures (p. 145, left column, 2nd paragraph). Collins describes cross-lysis determination for 37 bacteria-bacteriophage combinations isolated from 14 commercially used cultures and whey from cottage cheese plant (p. 145. right column, 3rd paragraph). Table 1 (p. 146) shows the results of cross-reactions for 22 strains of Streptococcus divided into 4 groups versus 22 bacteriophages. Based on the presented matrix bacterial strains with different sensitivity versus bacteriophages can be selected for rotation cultures.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add compatibility matrix as described by Collins for selection of bacterial cultures for consecutive culturing to decrease bacteriophage contamination during production of fermented food as described by Klaenhammer. One would have been motivated to do that since compatibility matrix provides information allowing to select bacteria for consecutive fermentation with higher accuracy and efficiency. A skilled artisan would have reasonably expected success in that combination because Klaenhammer and Collins teach rotation of bacterial cultures during fermentation to prevent bacteriophage contamination. Thus, Klaenhammer and Collins teachings render claim 11 obvious.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Klaenhammer (US 5593885) as applied to claim 1 above, and further in view of Farmer (US 20170107477 A1).
The teaching of Klaenhammer has been set forth above.
Klaenhammer does not teach bacterial cultures identified by a readable code in or on the packaging.
Farmer teaches a fermentation system and its elements and methods to assist in the operation of a batch process bioreactor to optimize microbiological growth of a selected microorganism (Abstract, paragraph 0003). Farmer describes that bacterial batch is presented with an identification code to prevent selecting an incorrect bacterium (with a similar sounding name) (paragraph 0028). The identification code is readable and can be provided to the user with the provided materials (e.g. the starter culture and nutrient media) or can be read off one or more of the containers or packaging elements (paragraph 0028).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add labeling of bacterial cultures with the readable identification code as described by Farmer to method of consecutive culturing of isogenic bacterial strains to decrease bacteriophage numbers during production of fermented food as described by Klaenhammer. One would have been motivated to do that since providing readable code to bacterial cultures will prevent selection of incorrect bacterial culture. A skilled artisan would have reasonably expected success in that combination because Klaenhammer and Farmer teach fermentation by bacterial cultures. Thus, Klaenhammer and Farmer teachings render claim 13 obvious.
Response to Arguments
Applicant's arguments filed 02/13/2026 have been fully considered but they are not persuasive.
Applicant argues (addressing p. 18-23 of the Remarks) that Klaenhammer requires isogenic strains with the same bacteriophage binding characteristics which is the opposite of the claimed invention. Applicant continues that instant invention selects bacterial cultures with different bacteriophage sensitivities and that Klaenhammer relies on defense mechanisms to protect the bacteria after phage binding occurs rather than selecting strains that the phages cannot bind. Applicant further argues that Klaenhammer does not teach threshold-based selection of the next culture and describes reactive termination while instant claims use predetermined threshold to proactively select the next culture before fermentation failure occurs. Applicant argues that Klaenhammer teaches away from the claimed invention because his principle is rotating through different internal defense mechanism while maintaining the same external binding characteristics and modifying Klaenhammer to use non-isogenic strains with different bacteriophage sensitivities would fundamentally change the nature of Klaenhammer invention and render its phage defense mechanism unnecessary. These arguments are not persuasive because:
First, the Specification describes “sensitivity” as: “The terms "sensitivity", "bacteriophage sensitivity", "phage sensitivity" and the like, as used herein, may refer to the ability of a bacterial culture or a bacterial strain to be infected by a specific bacteriophage. .... A bacteriophage attack or bacteriophage infection comprises the insertion of bacteriophage DNA or RNA into its host, here bacteria. Additionally, the bacteriophage DNA or RNA is replicated and translated by the bacterium, resulting in a large amount of said bacteriophage.” (p. 4, lines 4-12). Thus, the sensitivity is not defined by only binding of bacteriophage to the bacteria, but by the whole mechanism of infection including different steps. Besides, instant claims do not require prevention of bacteriophage binding. The strains of Klaenhammer teaching have different defense mechanisms including “prevention of adsorption (Ads), restriction and modification(R/M), and abortive infection (Hsp)” (columns 4, lines 7-10). These mechanisms differently inhibit infection by bacteriophages and hence strains with different defense mechanism have different bacteriophage sensitivity. Rotation of bacterial cultures of isogenic strains with different defense mechanism allows to further reduce common sensitivity to bacteriophages since the second strain with different defense mechanism will inhibit bacteriophages with evolved resistance to the first defense mechanism. Therefore, Klaenhammer rotation of isogenic strains scheme does not require replacement with non-isogenic strains to provide different bacteriophages sensitivities.
Second, Klaenhammer teaches that: (i) the timing of rotation can be variable; (ii) the choice of timing can be made based on empirical studies or phage monitoring programs (column 6, lines 34-40); (iii) describes methods of detection and quantification of bacteriophages (column 13, lines 36-37, 45-59); (iv) mentions that rotation strategy allows to avoid bacteriophage attacks or to re-establish fermentation after attack (column 5, lines 58-61) and (v) provides example of terminating rotation sequence when strains fail to lower the milk pH below 6.0 and had high levels of phage are detected (108-109 PFU/ml) (column 13, lines 37-40). Thus, these parameters can be considered predetermined threshold after which fermentation needs to be re-established by rotating the bacterial culture. The instant claim 1 requires selecting the second bacterial culture when the value indicative of bacteriophage number is larger than the predetermined threshold and Specification (as mentioned by the Applicant) describes: “In the worst case, the food producer will determine that the value is larger than a predetermined threshold, for example the value for which is known that fermentation is severely hampered and a change of bacterial culture is necessary.” (p. 4, lines 27-29). That is very similar to Klaenhammer teaching and therefore, Klaenhammer teaches the threshold for selection of the next culture.
Regarding claim 2, Applicant argues (addressing p. 23-24 of the Remarks) that Cairns is directed to phage therapy, i.e. using bacteriophages to kill bacteria which is the opposite purpose of the instant claims and threshold in Cairns is the phage concentration needed to kill bacteria and not at which fermentation becomes inefficient. These arguments are not persuasive because:
Although Cairns is directed to phage therapy, Cairns teaches models of bacteriophage-host dynamics (Abstract) that can be applied to bacteriophage-bacterial host interaction during fermentation. Cairns describes that model allows to predict the outcomes of the joint population dynamics and determine inundation and proliferation threshold (p. 3, right column, 3rd paragraph) providing motivation to use Cairns models to predict the bacteriophage concentration at the predetermined critical time point to start second culture when the predicted value is larger than the predetermined threshold.
Regarding claim 3, Applicant argues (addressing p. 25-26 of the Remarks) that Oladunjoye is directed to a completely different field of food safety and not fermentation and used bacteriophages to kill bacteria which is opposite to instant goal. These arguments are not persuasive because:
Although Oladunjoye is directed to a food safety, Oladunjoye teaches prediction of interaction of bacteriophage with bacterial host using artificial neural network (ANN) (Abstract) that can be applied to bacteriophage-bacterial host interaction during fermentation. Oladunjoye showed highest positive correlation between predicted and observed values and indicated that ANN offered more accurate prediction than hyperbolic tangent activation function and linear regression's models (p. 16, left column, 3rd paragraph) providing motivation to add artificial intelligence modeling such as ANN to model of bacteriophage-host interaction dynamics described by Cairns to predict the concentration of bacteriophage to start rotation of bacterial cultures in method of consecutive culturing to decrease bacteriophage contamination during production of fermented food as described by Klaenhammer.
Regarding claim 10, Applicant argues (addressing p. 27-28 of the Remarks) that Gao database is designed to select phages to target and eliminate microbes that is opposite to the instant purpose. These arguments are not persuasive because:
Gao provides a comprehensive catalog of phage-microbe interactions that can assist users to select phage that target specific microbes (Abstract) and since it contains phage-microbe interaction information the catalog can also provide necessary information for the sensitivity of bacterial hosts. Gao database is freely accessible, contains 26572 interactions between microbes and bacteriophages and has modern and intuitive interface providing motivation to use database described by Gao to determine sensitivities of bacterial cultures to bacteriophages during selection of bacterial cultures for consecutive culturing during production of fermented food as described by Klaenhammer.
Regarding claim 11, Applicant argues (addressing p. 28-29 of the Remarks) that Collins teaches pre-planning rotation schemes based on historical sensitivity data and not for real-time selection based on current bacteriophage measurements. These arguments are not persuasive because:
In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., real-time selection) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). In instant case, claim 11 is directed to accessing a compatibility matrix, however, does not indicate the timing of accessing, whether accessing a compatibility matrix is performed prior to fermentation as pre-planning or during fermentation. Therefore, one would have been motivated to add compatibility matrix as described by Collins for selection of bacterial cultures for consecutive culturing described by Klaenhammer since compatibility matrix provides information allowing to select bacteria for consecutive fermentation with higher accuracy and efficiency.
Regarding claims 5, 6 and 13, Applicant arguments (addressing p. 26-27 and 29-30 of the Remarks) are based on arguments against Klaenhammer teaching that were addressed above.
Therefore the 35 U.S.C. 103 rejected is maintained and modified necessitated by amendment of claims.
Conclusion
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 LIOUBOV G KOROTCHKINA whose telephone number is (571)270-0911. The examiner can normally be reached Monday-Friday: 8:00-5:30.
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/L.G.K./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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