September 10, 2017
In this issue, we discuss trends in microbiome-related investment, a new approach to address the critical need for computing power in microbiome data crunching, analysis of recently issued microbiome-related patent claims, and some upcoming microbiome-related webinars and conferences.
We’ve all seen interest in microbiome-related technology surge in recent years. A new report from SVB Analytics titled “Emerging Healthcare: Microbiome Investment Trends” nicely sums up the current state of things. A few key points:
Illumina—logical, given the key role genomic sequencing and bioinformatics has played and will play going forward.
The full report is available here.
One of the most critical needs in translating microbiome research into therapeutic and commercial successes is management and analysis of the massive amount of data related to the various “-omes” involved—genomes, transcriptomes, metabolomes, among others. This takes massive amounts of computing power. A new approach, possibly inspired by that used in the search for extraterrestrial intelligence (e.g., the SETI Institute), crowd sources computing power, and YOU can help!
IBM, the Broad Institute and Massachusetts General Hospital have launched a crowdsourced human microbiome computation project in which anyone can contribute unused computational time to help. Using IBM’s World Community Grid, the goal is to get computer users from all over the globe to donate computational power to the effort. Computer users can download a secure software program that automatically detects when a computer has unused processing power, and uses it to run analyses for the Microbiome Immunity Project. More details are here and here.
U.S. patents directed to microbiome-related technologies are being applied for and issuing at the fastest rate ever. The examples of recently issued claims in the following are highlighted for their coverage of interesting science and for notable prosecution devices or approaches to secure that coverage.
Claims of interest:
These claims are of interest for covering the use of a Lactobacillus strain grown as a biofilm to inhibit microbial growth on a surface, including the skin. Biofilm formation by pathogenic bacteria contributes to antibiotic resistance—it’s interesting from a scientific standpoint to use bacteria grown as a biofilm to inhibit the growth of biofilm-forming pathogens.
The dependent claims indicate that the biofilm-produced composition promotes the growth of commensal bacteria and inhibits the growth of pathogenic bacteria, including MRSA. This activity is supported by working examples in the specification demonstrating that the specified strain has both activities.
The applicants overcame enablement and prior art rejections by amendment to recite the specified strain, which was deposited under the Budapest Treaty.
The applicants obtained accelerated examination under a Petition to Make Special based on applicant’s age, rather than using the Track One procedure—this route is available if any applicant is over 65 years of age.
Claims of interest:
and wherein the engineered nucleic acid sequence does not encode said Cas nuclease that is endogenous to said second species of bacteria;
and optionally the HM-system comprises a tracrRNA sequence or a DNA sequence expressing a tracrRNA sequence;
whereby HM-crRNAs guide endogenous Cas activity to modify host target sequences in host cells, whereby host cells are killed or the host cell population growth is reduced, thereby reducing the proportion of said host cell population and altering the relative ratio of said sub-populations of bacteria in the mixed bacterial population.
Many therapeutic approaches aim to out-compete or replace undesirable microbiota bacteria with probiotic species, sometimes in combination with broad-spectrum antibiotics to pave the way. In contrast, this patent covers a targeted method of killing or reducing growth of a population of microbiota bacteria using CRISPR and harnessing endogenous Cas endonuclease activity in the target microbes to do it.
The noted dependent claim combines the targeting of an antibiotic resistance gene with the administration of an antibiotic, which would overcome the resistance problem.
The application was prosecuted under the Track One accelerated examination procedure.
Claims of interest:
These claims are of interest for covering a method of not only treating, but preventing eczema in a subject by administering a specified strain of L. rhamnosus. It is often difficult to get explicit coverage for prevention in other areas of medicine, but we are seeing a reasonable number of claims issue in the microbiome arena that recite prevention. Such claims nearly always require working examples in at least an animal model to show efficacy, and this patent is no exception—prevention is supported in the Examples by double-blind, placebo-controlled human clinical studies of pregnant mothers and their infants through two years postpartum.
The claims are limited to the specific deposited strain, applicants having overcome an obviousness rejection over another strain of L. rhamnosus on the basis of superior efficacy/surprising results.
Claims of interest:
These method claims are of interest because the independent claim characterizes the subject microbes by function alone, rather than by species or strain of ammonia oxidizing bacteria. The specification is detailed, includes a lengthy Sequence Listing and describes successful placebo-controlled human clinical trials.
While not prosecuted under the Track One accelerated examination procedure, the pendency of this application was under two years and involved only one Office Action. After responding to the Office Action, the applicants conducted an in-person examiner interview that included an inventor. Allowance followed shortly thereafter.
Claims of interest:
1. A method for i) promoting gut barrier regeneration, ii) promoting gut barrier maturation and/or adaptation, iii) supporting gut barrier resistance and/or iv) protecting gut barrier function in a pediatric subject in need thereof, comprising:
administering to the pediatric subject a composition comprising an effective amount of a soluble mediator preparation from a late-exponential growth phase of a Lactobacillus rhamnosus GG (LGG) batch-cultivation process, wherein the soluble mediator preparation is produced by
This claim is of interest as a method of treatment of any of the noted pediatric gut barrier issues, involving administration of a composition prepared from a culture of a specific strain of Lactobacillus bacterium in the late exponential growth phase—that is, a method of treatment with a composition defined as a product-by-process. Some look down upon product-by-process claims, but they serve a purpose where, as here, the exact make-up of the subject composition (culture medium from late-exponential phase growth of L. rhamnosus GG) is not necessarily known, but is defined by the described conditions of culture. In this method of treatment claim, as opposed to a composition claim, the product-by-process language need not necessarily define a composition that distinguishes the prior art. The applicants overcame an obviousness rejection by requiring the removal of all cells from the preparation.
Gut Check: Expanding Your Scope —Patents and the Microbiome
The Microbiome Coalition, Nixon Peabody LLP and Icosa are co-hosting a webinar “Gut Check: Expanding Your Scope—Patents and the Microbiome” on November 7, 2017 from 12:30 to 2:00 p.m. Eastern time. Nixon Peabody patent attorneys Mark FitzGerald and David Resnick will present on strategies for patent protection in the U.S., and Icosa European patent attorney Caroline de Mareuil-Villette will present a European perspective. For more information, please contact Kristen DeCandia at firstname.lastname@example.org.
Microbiome R&D Business Collaboration Forum and 2nd Probiotics Congress
A merger of the Global Engage 5th Microbiome R&D Business Collaboration Forum USA with the 2nd Probiotics Congress USA is set for November 2 and 3 in San Diego, CA. More information is available here.
Microbiome in Human Nutrition conference
Microbiome in Human Nutrition conference, November 14–16, Boston, MA. Speakers include Professor Rob Knight of UCSD, and representatives of Nestle Health Science, Danone Nutricia, Mead Johnson Nutrition, USDA and the Bill & Melinda Gates Foundation, among others. More information is available here.
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