The human microbiome: A very active area for academic research, with Europe as a clear leader

Following our three first chapters on “The human microbiome: a promising research area with multiple applications”, this article is comparing the emergence of the human microbiome field with the rise of human genomics through a review on how academic research on microbiome has progressed in the last 10 years in the USA and Europe.

  ucsf.edu

 The emergence of human genome analysis can be divided into three waves. The first wave coincides with the initial discovery of human DNA by academic groups in the 1950s. The second phase initiated by private investors with the beginning of the first clinical studies and the emergence of biotechs. The last phase corresponds to the commercialisation of products derived from genome analysis.

The transition from academia to private projects occurred very quickly, largely driven by the seeking of patent for the genes protection. Despite, the announcement of President Clinton in March 2000 that the genome sequence could not be patented, private investments continued leading to the first clinical trials mid 2000s on genetic diseases and oncology. In the meantime, private companies developed new technologies for faster and cheaper DNA sequencing (~$100M in 2000s versus $1k in 2015 per human genome) and all major central labs now have DNA sequencers.

 Concerning the microbiome market, it is still emerging, but it has been following a similar trajectory as the human genome market. It is currently at the beginning of the third wave. The first clinical trial mentioning the microbiome was launched in Europe as early as 2000, compared to 2006 for the USA and 2009 for China (1). Interestingly, after being a pioneer, Europe still leads the way in academic research(Figure 1) (2). At the same time, China is quickly catching up with a growth rate of microbiome publications around +60% p.a. from 2008-16.  

 Fig 1: Number of publications on microbiome (PubMed)

The picture is slightly different tough, when looking at large, academic research programs.

First of the series, the American Human Microbiome Project was launched in the 2000's with around 160M€. 126M€ were allocated to the first part of the project over the period 2008-13. The objective was to characterize the microbiome of healthy volunteers, which led to the creation of a microbiome database and the definition of standardized protocols. It was immediately followed by a second phase running up to the end of 2018 with a budget of 34M€. It has been concentrating on understanding the microbiome evolution of three groups of persons: pregnant women and preterm birth, patients suffering from Irritable Bowel Diseases (IBD), and people at risk of type 2 diabetes. 

 A second major American project, the National Microbiome Initiative, was launched in 2016 by the White House under the Obama administration. It is a consortium with the objectives of supporting interdisciplinary research, developing platform technologies, and expanding the microbiome workforce. Overall budget is near 420M€. While federal contributions to the project remain unclear due to the change of administration, 75% of the budget is from private institutions such as the Bill and Melinda Gates Foundation, the C3 Jian, the Jackson Laboratory, or the Gordon and Betty Moore Foundation.

 In Europe, national research programs on microbiome are less ambitious. MetaHIT  was the first European program, launched in 2008 and completed in 2012. The allocated budget was 21M€, order of magnitude smaller compared to the American equivalent: Human Microbiome Project. MyNewGut is the second major European project (2013-2018) with an estimated budget around 13M€ and it is focusing on the relation between gut microbiome, brain development, and diet-related disorders.  

Conclusion

 In microbiome academic research, despite the large American projects, Europe started earlier and is still leading the way today, ahead of North America. China is quickly catching up with a significant increase in microbiome publications and state-funded programs.

In the next chapters, we will focus on the diversity of private company players ranging from biotechs to dedicated microbiome platforms, with the ongoing development of therapeutic solutions for the Food, Pharma, and Cosmetics industries.

Marc-Olivier Bévierre (Cepton Strategies), Etienne Casal (Biofortis – Mérieux NutriSciences), Murielle Cazaubiel (Biofortis – Mérieux NutriSciences), Françoise Le Vacon (Biofortis – Mérieux NutriSciences), Charles Savoie (Cepton Strategies), Alessandra De Martino (Biofortis – Mérieux NutriSciences)