The microbiome – will legal question marks stop progress? Part three – patents

Our understanding of the microbiome is developing rapidly. The systematic collection and analysis of human microbiome samples is generating an increasing – and fascinating - body of data. Based on this data, researchers and clinicians are now also recognising new potential for understanding human disease and developing treatments. What are the legal issues that could stand in the way of progress? In this article we consider issues around patenting of microbiome-based therapies.

Challenges around securing patent protection.

In earlier parts of this series we considered privacy issues that arise from the collection and analysis of microbiome samples, and regulatory uncertainty for microbiome-based therapies. In this part, we consider patenting.

As with any other biotechnology development, it is important to consider what forms of intellectual property (IP) protection can be obtained to protect investment and innovation and support future plans. Patents deliver the strongest form of protection.

It is also important to consider how a new development may be impacted by rights already applied for or obtained by third parties.

A crowded landscape?

Research into the microbiome has seen real focus over a number of years and there has been a rapid increase in the number of patent filings in the area year on year, an increase that outstrips many other biotechnological areas. There is clearly opportunity for businesses to develop valuable patent portfolios in new research areas but clearly there is also an imperative, given an increasingly crowded landscape, for businesses to understand what may block or hinder future plans.

It is interesting to note that new filings (e.g. for medicinal products using live bacteria) are not dominated by established pharmaceutical filers but are increasingly being made by new entrants to biotechnology markets. 

Getting the scope right

As with other biotechnology inventions, it is important to invest time at the outset thinking strategically about what should be protected and how practicable it will be to obtain useful patent protection (see below for further thoughts).  

An invention may make use known products in the microbiome but can patent protection be sought for the treatment of a new disease? Is the mode of administration or dosage regimen novel? How is the analysis then impacted by restrictions in particular patent systems (such as the US) around the patentability of naturally occurring products.

Current systems provide real options and flexibility and should be explored to ensure that innovation and investment value is captured, and can be maintained.

Are there specific challenges applicable to patenting in the microbiome space?

The microbiome field remains relatively new for legal systems, and is new when compared with other biotechnological areas. There is limited case law to rely upon and patent examiners (particularly outside of the main patent jurisdictions) remain inexperienced when considering applications referencing bacteria. Whilst there is a ”first mover” advantage, the immaturity of the market causes uncertainty for businesses applying for and prosecuting patent applications, and may require some “fleetness of foot”.

The lack of clinical data to support whether a therapy is going to work effectively may also present another challenge for an innovator. When should you file? Do you wait until you have more supporting data or delay and risk the chance that someone may get there first.

All the usual good practice steps around maintaining confidentiality until filing apply in the microbiome space and are possibly more acute when there is such a clamour from the research community for publication. A focus on confidentiality will be key for businesses entering into research collaborations with other organisations.


Traditional life sciences licensing models may not be appropriate for microbiome technologies and licensing structures will need careful consideration. In particular, how will the licensing agreement deal with:

  • licensor and licensee improvements be dealt with (recognising the probable dynamic nature of technologies in this field),
  • what is licensed outside of the patent,
  • manufacturing and sourcing of product, and
  • royalty structures.  

Will these challenges hinder or prevent progress?

No, this is an exciting area with real opportunities for those with innovative technologies. As with other areas, the key to managing risk is careful preparation and planning, but also being flexible in the overall objective of securing valuable protection.


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Every piece of content we create is correct on the date it’s published but please don’t rely on it as legal advice. If you’d like to speak to us about your own legal requirements, please contact one of our expert lawyers.

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