Category: The Emergent Microbiome Series

The Emergent Microbiome: A Revolution for the Life Sciences – Part XIV, Revisiting Immunotherapy and Combination Therapies

Three recent articles in Science discuss how the composition of the gut microbiome affects anti-PD-1 therapy for the treatment of melanoma, metastatic melanoma, and epithelial tumors, further bolstering the idea of gauging immunotherapeutic efficacy based on one’s microbiome composition.  We first reviewed this concept in Part VIII of The Emergent Microbiome Series and are revisiting it here.  Bolded patent documents are further summarized in the table at the end of this installment.

The Emergent Microbiome: A Revolution for the Life Sciences – Part XIII, The Microbiome and Antibiotic Resistance

Antibiotic resistance is a major problem in the United States and is considered by the World Health Organization (WHO) to be one of the largest threats to human health. The top 12 bacterial threats classified by WHO are shown in Table 21. Researchers are going so far as to send antibiotic resistant bacteria into space in order to determine how the bacteria mutate, with the thought being that in space, bacteria will mutate at an accelerated rate, making it easier to study bacterial resistance patterns and, therefore, develop better antibiotics that are active against resistant bacterial forms.

The Emergent Microbiome: A Revolution for the Life Sciences. Part XII: Taking Stock of Livestock

As we have discussed in previous installments of “The Emergent Microbiome,” we have seen a distinct growth in the interest of the microbial communities found in our environment beyond the confines of the human body. Earlier articles in this series have focused on the microbiology of the built environment (See Part VII: The Microbiology of the Built Environment) and the microbial communities of plants that have been characterized and manipulated to maximize their growth and crop yield (See Part XI: Agriculture and the Microbiome). In both circumstances, we noted robust intellectual property activity. Likewise, we have also observed an increased interest in the microbial communities found in livestock animals, and how manipulations of these communities could result in more effective, productive, and sustainable means of food production. Although this area is less well developed than other areas of microbiome research, including that of plant agriculture, we see it as a promising area of development in terms of both the science and the innovation that will inevitably flow from it.

The Emergent Microbiome: A Revolution for the Life Sciences- Part X, The Big Data Component

Research into the human microbiome has resulted in such unprecedented amounts of data that challenges related to both interpretation and management have emerged. Somewhat paradoxically, current statistical methods have made it such that it is more difficult and less likely to identify statistically significant results from large data sets. We see much potential for the expansion of intellectual property protection in the area of big data related to the microbiome, not only as a result of recent research advances and the desire to better and more efficiently handle big data, but also because of several recent Federal Circuit decisions in intellectual property law that provide some promising guidance for protecting software and computing information that may be required for managing and interpreting microbiome-related data. Moreover, the United States Patent and Trademark Office (USPTO) has provided examples for crafting potentially patent eligible claims in this space, a promising step forward in what has become a difficult area for IP protection.

The Emergent Microbiome: A Revolution for the Life Sciences – Part IX, The Microbiome and Immunotherapy II

Given that the majority of the human microbiome is found in the gut, it is not surprising that most microbiome-based therapeutic approaches have been used to treat gastrointestinal disorders, such as inflammatory bowel disease (IBD) and Clostridium difficile infections. However, growing evidence suggests that targeting the microbiome can have broader therapeutic implications, demonstrating the ever-evolving nature of the microbiome field. Specifically, microbiome modulators could be used to either enhance or suppress the immune response and would thus be considered immunotherapy. Part VIII of this Series reviewed how altering the microbiome could be used in combination with checkpoint blockade. As a continuation to Part VIII, this article will explore how microbiome modulators could be used as single agent immunotherapy to treat autoimmune disease, inflammatory disease, and cancer. Bolded patent documents are further summarized in the table at the end of this ins

The Emergent Microbiome: A Revolution for the Life Sciences – Part VIII, The Microbiome and Immunotherapy I

Cancer immunotherapy or immuno-oncology (I-O) has gone mainstream. You may have heard about these topics in the media. Along with having surgery and radiation therapy, Former President Jimmy Carter was treated with the monoclonal antibody pembrolizumab (Keytruda®) that stimulated his immune system to fend or fight off melanoma that had metastasized to his brain. His remarkable response has highlighted the power of immunotherapy. After his son Beau succumbed to brain cancer, Vice President Joe Biden helped spearhead the Cancer Moonshot, a national initiative to cure cancer, one of the main goals of which is furthering immunotherapy research. The White House has dedicated $1 Billion to this initiative. This article will introduce you to immunotherapy and how it is now beginning to intersect with the microbiome. Recent patent filings suggest that intellectual property protection will be an important part of the research efforts in this field. Bolded patent documents are further summarized in the table at the end of this installment.

The Emergent Microbiome: A Revolution for the Life Sciences – Part VII, The Microbiology of the Built Environment

Many research efforts into the microbiome have focused primarily on the human microbiome, i.e. microorganisms within and on the body, and how changes in these microbial communities correlate with changes in health and disease. Less attention, however, has been paid to the microbial communities external to humans and how changes in these communities can affect health. These communities have a broad range, from the microbiome of indoor spaces, also called the microbiology of the built environment (MoBE), to microbial communities found outdoors. Microbial communities that give certain foods, such as San Francisco sour dough bread, various wines, beers, and even cheeses, characteristic qualities like taste and texture are also examples of external microbiomes. As with the human microbiome, scientists do not yet fully understand how changes in external or indoor microbiomes could alter human health, but we see plentiful possibilities for further research and intellectual property protection of subsequent innovation, especially with regards to the MoBE. This article concludes with a sampling of some of the patenting activity in this area.

The Emergent Microbiome: A Revolution for the Life Sciences – Part VI, Diagnostics

With the passage of the Patient Protection and Affordable Care Act (PPACA) in 2010, preventive medicine – services that focus on disease prevention, rather than disease treatment – became a major focus of healthcare and the market for medical diagnostics expanded to meet a growing demand. During the same time, faster and less expensive next-generation DNA sequencing (NGS) and improvements in cloud storage, which facilitated the analysis of sequence data, boosted the development of microbiome-based diagnostics.

The Emergent Microbiome: A Revolution for the Life Sciences – Part V, Patents Relating to Obesity and Metabolic Disorders

This is the fifth installment in a series on advancements in microbiome research and development. This article will summarize issued U.S. microbiome-based patents that describe therapies relating to obesity and other metabolic disorders. It is a follow-up to the fourth part of the series, which reviewed important research and development in this subject area. The patents reviewed herein are neatly summarized in the table at the end of this installment.

The diet and nutrition industry is big business: the industry brings in over $60 billion dollars from the nation’s 100 million-plus dieters. Yet, years of R&D have failed to produce a blockbuster weight loss drug. Clearly, there is a big incentive to develop new and effective therapies for this area, particularly considering the risks and adverse events that have plagued previous prescription therapies, and companies are looking to the untapped potential of the microbiome for an elusive wonder drug.

The Emergent Microbiome: A Revolution for the Life Sciences – Part IV, Obesity and other Metabolic Disorders

Some of the earliest evidence for the relationship between the microbiome and obesity came from studies of antibiotics and their association with weight gain in livestock, which pointed to a link between microbiome composition and weight maintenance. A 2006 study from the laboratory of the prominent researcher Jeffrey Gordon uncovered a mechanism by which some gut bacteria trigger obesity. Lead author Peter Turnbaugh and his colleagues noted that obese mice had different microbiomes than their lean littermates. The same was true of lean and obese human twins. When Gordon’s team characterized this phenomenon, they found that the microbiomes in obese mice and humans obtain more calories from food as compared to the microbiomes of their lean counterparts. In addition, when the researchers transferred the gut bacteria of an obese mouse to a germ free one, the formerly germ free mouse became obese.