USF Initiative on Microbiomes

USF Initiative on Microbiomes

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The microbiota (the community of microbes) and microbiome (the interplay between the microbiota and the environment) offer a novel paradigm for modern science. Microbiome research encompasses the study of human and animal health and nutrition, as well as the wider environment that includes marine and soil microbiota communities. Indeed the microbiota and microbiome have major implications when it comes to intervention in environmental and health processes, and they are also a fine illustration of the impact of technological progress in science.

In human health, while the importance of the microbiome in the lungs and airways, skin and vagina is increasingly recognized, it is the gut microbiome that has received the most attention to date. It is now clear that gut dysbiosis is linked to several diseases, including metabolic disorders (such as obesity and diabetes), cardiovascular diseases and stroke, inflammatory bowel diseases and colon cancer, non-alcoholic fatty liver disease (NAFLD) and chronic respiratory disorders such as asthma. Numerous studies have also emphasized the importance of the microbiome in perinatology, potentially shaping the future of newborns and influencing the health outcome of the mother in the post-partum phase. Some studies also suggest that gut dysbiosis influences neurodegenerative conditions (Parkinson’s and Alzheimer’s disease) and possibly also psychiatric disorders. The impact of the microbiota in cancer patients is doubtless one of the most stimulating areas of research for therapy. Not only has gut dysbiosis been demonstrated in various forms of cancer, but microbiome composition has been shown to interfere with the efficacy of chemotherapy and immunotherapy. The interplay between the gut and lung microbiomes and infectious diseases – such as in Clostridium difficile infection, norovirus and malaria – is also notable. The number of medical disorders potentially associated with microbiome imbalance is constantly on the rise. Moreover, the role played by the insect gut microbiota in mosquitoes’ ability to transmit viruses such as Zika and dengue opens a fascinating new avenue for investigation, raising the possibility of future strategies in this field.

Moreover this is now an area where medical interventions can be contemplated. Probiotics is still a controversial area but with major promises; the efficacy of fecal microbiota transplantation has been clearly established for the treatment of Clostridium difficile infection and is currently being evaluated for several other medical conditions. Finally, there is now some evidence that determining bacterial and/or metabolite signatures may be a way of predicting susceptibility to disease and response to therapy. In fact the microbiome analysis can be integrated into prospective longitudinal deep molecular and physiological profiling which may provide important tools for precision health. Thus the microbiome can now be considered as part of a precision medicine strategy.

In this context it comes as no surprise that the microbiome is currently a major focus of research worldwide for both academics and pharmaceutical companies, whether for environmental or health purposes. The global human microbiome market is expected to reach $1,197.08 Million in 2025 up from $257.30 Million in 2017; it is estimated to grow with a CAGR of 21.8% from 2018-2025. Public and private investment in the microbiome industry are estimated to be $1.5 billion to date, with significant dollars flowing from Europe, USA, Canada and Asia; at least 200 companies have some level of interest in microbiomes.

Regarding academic funding research agencies $215 M have been invested in the NIH’s Human Microbiome Project (HMP) program between FY07-16 and $728 M in NIH extramural human microbiome research activities outside of the HMP between FY12-16 . 21 of 27 NIH Institutes and Centers currently fund this area through their extramural research programs.

Finally, only in the US, at least 30 centers or initiatives focused on microbiome investigation have been launched.

However, there are several major challenges that need to be addressed:

  1. Microbiota taxonomy is still evolving, with much yet to be discovered; studies have mainly relied on 16S RNA sequencing, whereas whole metagenome sequencing is required to accurately describe bacterial populations;
  2. The microbiota includes not only bacteria but also viruses (mostly phages) as well as fungi, archaea and parasites, and this may have resulted in erroneous interpretations in studies which overlooked these aspects;
  3. Geographical differences, involving environment, nutrition and human genetics, may have a major impact on the results of these studies;
  4. Most research has been descriptive, and there is a genuine need for functional studies; and
  5. The real efficacy of medical procedures, including probiotics or fecal microbiota transplantation, has not been clearly demonstrated.

These challenges can only be overcome through a combination of scientific and medical expertise, and through translational efforts including basic and technological science and top-quality clinical research, and robust infrastructures and equipment comprising omics (genomics, proteomics and metabolomics) and germ-free animal facilities. This approach will also be greatly improved by incorporating disciplines such as synthetic biology, chemistry and nanotechnology; and it goes without saying that data analysis capabilities are vital for any major microbiome research initiative.

USF Microbiome Initiative

It is against this backdrop, that we propose a USF-wide project, the “USF Microbiome Initiative.” This initiative should encompass the whole spectrum of expertise at USF, including the College of Arts and Science, the College of Engineering and the Department of Computer Science and Engineering, and others to be determined, in addition to USF Health. It will be based on close academic-industry partnerships. It will also be part of a wider effort in the State of Florida through partnerships with other universities such as the Universities of Florida and Miami, and it will establish a network of international partnerships.

The strategy will be based on eight interlinked objectives:

  1. Determining a strategy for USF and Moffitt Cancer Center and identifying research areas where we can be competitive
  2. Recruitment of High-level scientists
  3. Engaging the community and sharing expertise and projects; developing a scientific and medical strategy: we created the Microbiome Club as a first step of the USF Initiative in identifying, engaging and pooling the work of talented investigators in this area and enabling them to share their viewpoints and needs. This is also the aim of the Microbiome Award (Annex x), which will provide seed funding for the early phases of novel, interdisciplinary projects involving several departments. The Microbiomes Initiative will also offer mentoring for junior investigators. It will work closely with the colleges of Medicine, Pharmacy and Nursing as well as with undergraduate programs to provide effective training for early career scientists. The USF Microbiome Initiative will develop an effective strategy for communication and data sharing, with an online forum, joint workshops, mentoring and support for grant applications.
  4. Strengthening technologies, infrastructure, expertise and coordination mechanisms
  5. Fostering entrepreneurship and partnerships with industry
  6. Fundraising
  7. Partnerships with universities in Florida
  8. International collaboration

In conclusion: This microbiota and microbiome initiative represents a major opportunity for USF, fully aligned with the USF System Research (2017-2021) Strategic Plan, ensuring that the university and the Moffitt Cancer Center play a key part in one of the most promising scientific and medical revolutions in recent times. It will also enable USF and Moffitt to pool the expertise of their colleges and departments, which will provide a solid basis for tackling other research challenges to come; it will strengthen cooperation between universities in Florida; and finally it will offer an excellent topic to help foster entrepreneurship and academic-industry partnerships in Tampa and Florida.

This web site will allow to foster this initiative by providing all necessary information on its different components. It will ensure communication and exchange of ideas between the scientists. It will also aim to generate interactions with our various academic and industrial partners as well as lay people.