The microbiome: human medicine and agriculture in a microbial world

John Skehel has provided major insights into the molecular basis of how viruses recognise and infect their host cells. John focusses on the virus that causes influenza, of which there are 3–5 million cases a year worldwide, resulting in up to 500,000 deaths. 

To infect a cell, the influenza virus must bind to a sialic acid-containing receptor on the cell surface, which it achieves through its own haemagglutinin glycoprotein. John was able to isolate, crystallise and subsequently determine the three-dimensional structure of this molecule. He also observed that under conditions of low pH, haemagglutinin changes shape — allowing the virus to fuse with and enter the cell.

John has been a leader in virology research for over thirty years. He headed the WHO Collaborating Centre for Reference and Research on Influenza between 1975 and 1993 and was the Director of the National Institute for Medical Research from 1987–2006. His pioneering research was recognised in 1996 when he received a knighthood.

Richard Flavell is a plant geneticist who has focused much attention on traits important in crop plants. In the last five years he has served as Chief Scientist in two companies in the USA. The first, Indigo, Cambridge, Massachusetts is an agricultural microbiome company. The second, Inari, is an agricultural plant genetics company.

He is currently a consultant for companies and public sector organizations committed to plant improvement, including the International Wheat Yield Partnership.

After his undergraduate degree in microbiology and his PhD in the John Innes Institute and the University of East Anglia, he spent two years of postdoctoral research in Stanford University, California. He then joined the Plant Breeding Institute in Cambridge (UK) where he built up a large Department of Plant Molecular Genetics between 1969 and 1987. He was then appointed as Director of the John Innes Centre (JIC), Norwich and to a chair at the University of East Anglia and oversaw a large expansion of JIC’s activities and impact.

In 1998 he became the Chief Scientific Officer of Ceres, a young plant genomics company in California. This became a public company and was recently bought by a multinational agricultural company.

He is a Fellow of the Royal Society and a Commander of the British Empire for services to science.

Professor Denise Kelly joined Seventure Partners, a European Leader in Venture Capital, in 2015 as an Investment Advisor to the Life Sciences Team and is focused specifically on Human Microbiome investment opportunities across Europe and the USA.

Prior to joining Seventure, Denise was Head of her Research team at the World-renowned Rowett Institute, University of Aberdeen, where she acquired over 20 years experience in gut microbiology and immunology. She was the (former) Founder Director, CEO and CSO of GT Biologics Ltd, one of the first translational spinouts, developing Innovative Microbiome-based Therapies. She is the main inventor on numerous EU and USA patent applications and during her career has collaborated with pharmaceutical and healthcare companies on several translational projects.

Denise holds a BSc and PhD from Queen’s University, Belfast and an Emeritus Professorship from the University of Aberdeen.

Ray Riley recently retired as Senior VP, Product Development at Indigo – a company focused on “Harnessing nature to help farmers sustainably feed the planet”.  Ray started his career at Pioneer Hi-Bred where he served in various roles ranging from Corn Breeder in Iowa to Research Director roles spanning US, Latin America, Africa and Asia. Ray joined Syngenta in 2000 as Global Head of Corn Supply Chain where he focused on improving seed supply chain efficiencies. In the mid-2000’s he oversaw the integration of R&D of several acquired seed companies and established an integrated research team with oversight of Syngenta’s Breeding Strategy and Seed Technology. In 2014 Ray became Head of Computational Biology, integrating Syngenta’s computational biology efforts spanning breeding, trait development (GM and native) and chemistry. In May of 2015 he joined Indigo as Sr VP Product Development.

Dr. Robert Finn has been involved in the field of informatics, particularly protein classification for nearly 20 years. Originally trained in microbiology and biochemistry, Dr. Finn has developed into an expert system architect and software engineer. Since joining the EMBL-European Bioinformatics Institute (EMBL-EBI) in 2014, he has spearheaded the running of key EMBL-EBI resource databases including Pfam, InterPro, Rfam, RNAcentral, and the EBI metagenomics platform, MGnify. In January 2018, Dr. Finn was appointed to a dual Service and Research team position. His research focuses on large-scale meta-analysis of metagenomics datasets, focusing on the recovery of genomes.

Until her recent retirement, Penny Hirsch led a group at Rothamsted Research working on soil microbiology and molecular ecology in an agricultural context, where she continues in an emeritus position.  Over the years, she has worked with fungi and bacteria, on rhizosphere interactions and other microbial activity in soil that supports plant health and productivity, including nitrogen cycling.  This is combined with long experience on the extraction, amplification and bioinformatics analysis of DNA and RNA sequences derived from soil and the rhizosphere.  Recent research has focused on nutrient cycling in arable systems and the relationship between the soil and crop plant microbiomes, applying metagenomics and metatranscriptomics, in addition to more conventional approaches.  The long-term field experiments at Rothamsted have provided valuable resource for applying these techniques to determine agronomic impacts on soil and plant microbiomes.

Trevor Lawley is the Faculty Group Leader of the Host-Microbiota Interactions Lab (HMIL) at the Wellcome Sanger Institute (WSI), where his research uses advanced metagenomic sequencing, state-of-the art microbial culturing and mouse models to investigate the microbial communities contained on and within host organisms that are associated with health and a range of diseases and syndromes. In addition, Trevor was key to establishing a germ-free facility at the WSI and is developing humanised/gnotobiotic mice models at the Sanger Institute to enable both basic and translational science of the human microbiome.

Trevor began his research at WTSI in 2007 as a Post-Doctoral Fellow in the Microbial Pathogenesis group, having received a Royal Society Fellowship to start a new research programme in C. difficile epidemiology and pathogenesis. During this time, he has worked with a global consortium from over 25 institutes to assemble a comprehensive C. difficile culture collection, now housed within the Sanger Institute.  Prior to joining WTSI, Trevor held a Canadian Institutes of Health Research post-doctoral fellowship, working in the Laboratory of Professor Stanley Falkow and Dr Denise Monack at Stanford University, USA, where he studied the impact of antibiotic treatment on Salmonella disease and transmission.  Trevor gained his first degree from Acadia University, Canada and his PhD from the University of Alberta, Canada, where he pioneered the use of genomics to study the origins and spread of antibiotic resistance in infectious diseases. 

In December 2016, Trevor co-founded Microbiotica, where he is directing the science as Chief Scientific Officer.  Microbiotica has been established to commercialise ground-breaking research, conducted in Trevor’s academic lab (Host-Microbiota Interactions Lab) at the Wellcome Sanger Institute, into the role of the human microbiome in health and disease and its application to medicine. Microbiotica is now a leading biotechnology company that discovers, develops, manufacturers and commercialises medicines to treat patients. Microbiotica has received £8M in seed funding from Cambridge Innovation Capital and IP Group and in June 2018, sealed a $534M deal with Genentech.

Stéphane Hacquard did his PhD in the lab of Dr. F. Martin/Dr. S. Duplessis (INRA Nancy, France) on the identification of rust fungal effectors using a combination of omics approaches. In 2011, he went for a 2-year post-doc at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, in the laboratories of Prof P. Schulze-Lefert and Dr. Richard O’Connell, where he characterized fungal transcriptional signatures linked to pathogenic transitions in Arabidopsis leaves. In 2013, he got the opportunity to develop his own research project on the microbiota of Arabidopsis roots in the group of Prof. Schulze-Lefert. Since January 2017, he leads a research team at the Max Planck Institute for Plant Breeding Research in Cologne, where he studies the fundamental mechanisms that underlie the structure and the functions of multi-kingdom microbial consortia colonizing plant roots. S. Hacquard has published ~25 articles in peer-reviewed journals and recently obtained an ERC starting grant to support his research activities.

Tracy Raines is a Research Director of Trait Discovery at AgBiome, helping to discover many insecticidal proteins with novel modes of action against pests of agricultural significance. Tracy has over 18 years of scientific and leadership experience within industry and academic environments. She began her career in agriculture biotech in 1998 as one of the early team members of Paradigm Genetics. There she helped develop and optimize the high-throughput gene discovery pipeline for the company’s GeneFunction Factory. In 2001, Tracy joined Athenix Corporation where she was responsible for the design and implementation of MiDAS, the high-throughput insecticidal gene discovery system, from its beginning stages. During her time at Athenix, the team discovered and assayed over 30 novel insecticidal-like proteins from soil bacteria, several having activity on pests of agricultural significance.

Tracy received her undergraduate degree in Biology from Virginia Tech in 1998. She earned her Ph.D. in Biology from the University of North Carolina at Chapel Hill in 2014 where she studied the role of cytokinin signaling in Arabidopsis thaliana.

Professor Eran Elinav, M.D., Ph.D. is a professor at the Department of Immunology, Weizmann Institute of Science. His lab focuses on deciphering the molecular basis of host-microbiome interactions and their effects on health and disease, with a goal of personalizing medicine and nutrition. Dr. Elinav completed his medical doctor’s (MD) degree at the Hebrew University of Jerusalem Hadassah Medical Center summa cum laude, followed by a clinical internship, residency in internal medicine, and a physician-scientist position at the Tel Aviv Medical Center Gastroenterology institute. He received a PhD in immunology from the Weizmann Institute of Science, followed by a postdoctoral fellowship at Yale University School of Medicine. 

Dr. Elinav has published more than 120 publications in leading peer-reviewed journals, including major recent discoveries related to the effects of host genetics, innate immune function and environmental factors, such as dietary composition and timing, on the intestinal microbiome and its propensity to drive multi-factorial disease. His honors include multiple awards for academic excellence including the Claire and Emmanuel G. Rosenblatt award from the American Physicians for Medicine (2011), the Alon Foundation award (2012), the Rappaport prize for biomedical research (2015), the Lindner award (2016) and the Levinson award for basic science research (2016). Since 2016 he is a senior fellow at the Canadian Institute For Advanced Research (CIFAR), and since 2017 he’s an international scholar at the Howard Hughes Medical Institute (HHMI)  and the Bill & Melinda Gates Foundation.

Professor Dame Fiona Powrie is Director of the Kennedy Institute of Rheumatology, University of Oxford, a Fellow of the Royal Society and the Academy of Medical Sciences and a Governor of the Wellcome Trust. 

She gained a PhD in immunology at the University of Oxford and then moved to the DNAX Research Institute in Palo Alto, before returning to Oxford in 1996 as a Wellcome Trust Senior Research Fellow. Prior to her appointment to the Kennedy Institute, Fiona Powrie was the Sidney Truelove Professor of Gastroenterology and Head of the Translational Gastroenterology Unit, Oxford (2009- 2014). 

Her research examines the relationship between the intestinal microbiome and the host immune system and how this mutualistic relationship breaks down in inflammatory bowel disease, arthritis and cancer. 

Fiona Powrie has received numerous prestigious prizes and awards, including the Louis Jeantet Prize for Medicine in 2012. She was elected an international member of the National Academy of Sciences in 2020 and was appointed Deputy Chair of the Wellcome Board of Governors and Dame Commander of the Most Excellent Order of the British Empire (DBE), for services to Medical Science, in 2022.

Roeland Berendsen is a senior scientist in the Plant-Microbe Interactions group at Utrecht University. His research is focused on the functioning of the rhizosphere microbiome in maintaining plant health. He aims to find out how plants are able to recruit protective microorganisms, and enhance the microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production.

Prof John Wallace held a personal chair in the Gut Health group at the Rowett Institute of Nutrition and Health at the University of Aberdeen until 2016, and is now Emeritus Professor at the University.  He specializes in the microbiology of animal and human digestive tracts, most recently focussing on how the ruminal microbiome and metagenome determine the amounts of methane emitted by beef and dairy cattle.  Prof Wallace was coordinator of three major research consortia funded by the European Commission, named ‘Rumen-up’, ‘REPLACE’ and ‘RuminOmics’, the last of which aimed to understand the relations between the ruminal microbiome, the host genome, and emissions of methane and nitrogen from dairy cows.  Prof Wallace was awarded the DSM Nutrition Award in 2007 'in recognition of his pioneering research in animal nutrition.'  He has published >200 peer-reviewed papers in international journals. He is a member of the FEEDAP (feed additives) panel of the European Food Safety Authority (EFSA). 

David Cook is the Executive Vice President of R&D and Chief Scientific Officer of Seres. He has over 20 years of experience as a scientist and entrepreneur and has held senior operating and management positions in the biotechnology industry throughout his career. Prior to joining Seres, he served as the Chief Operating Officer for the International AIDS Vaccine Initiative (IAVI), a global R&D organization. Prior to IAVI, Dr. Cook was the founding CEO at Anza Therapeutics, a biotechnology startup that focused on developing a microbial vaccine platform to induce cellular immune responses. 

Before launching Anza, Dr. Cook held positions of increasing responsibility at the biotechnology corporations Cerus and Eligix, overseeing R&D, program management, manufacturing, and clinical and regulatory affairs. He has led teams in the development and commercialization of several biotech products and has been directly responsible for obtaining marketing authorization from the European Union for four medical products. Dr. Cook is also a co-inventor on more than 25 patents. He earned his undergraduate degree from Harvard College and his Ph.D. in chemistry from the University of California, Berkeley.

Ian returned to the UK from Australia where he was Director of the ithree institute, University of Technology, Sydney to take up his role as Director of the Quadram Institute Bioscience (formerly Institute of Food Research) and Founding Director of the Quadram Institute in May 2015.

Ian has over 30 years’ experience in academic and commercial research.  His academic career has included being a founding member of The Wolfson Institute for BioMedical Research at University College London, one the UK’s first institutes of translational medicine. He has worked in the pharmaceutical industry at Glaxo Wellcome, and has founded biotech companies in the area of infectious disease, including Arrow Therapeutics, sold to AstraZeneca in 2007, and Auspherix, a venture capital backed company founded in 2013.  He is also a Non-Executive Director for Genus plc.

Ian is an internationally recognised scientist and has expertise in infectious diseases, the microbiome, and its impact on health and wellbeing, genomics and metagenomics.

David Cook is the Executive Vice President of R&D and Chief Scientific Officer of Seres. He has over 20 years of experience as a scientist and entrepreneur and has held senior operating and management positions in the biotechnology industry throughout his career. Prior to joining Seres, he served as the Chief Operating Officer for the International AIDS Vaccine Initiative (IAVI), a global R&D organization. Prior to IAVI, Dr. Cook was the founding CEO at Anza Therapeutics, a biotechnology startup that focused on developing a microbial vaccine platform to induce cellular immune responses. 

Before launching Anza, Dr. Cook held positions of increasing responsibility at the biotechnology corporations Cerus and Eligix, overseeing R&D, program management, manufacturing, and clinical and regulatory affairs. He has led teams in the development and commercialization of several biotech products and has been directly responsible for obtaining marketing authorization from the European Union for four medical products. Dr. Cook is also a co-inventor on more than 25 patents. He earned his undergraduate degree from Harvard College and his Ph.D. in chemistry from the University of California, Berkeley.

Ray Riley recently retired as Senior VP, Product Development at Indigo – a company focused on “Harnessing nature to help farmers sustainably feed the planet”.  Ray started his career at Pioneer Hi-Bred where he served in various roles ranging from Corn Breeder in Iowa to Research Director roles spanning US, Latin America, Africa and Asia. Ray joined Syngenta in 2000 as Global Head of Corn Supply Chain where he focused on improving seed supply chain efficiencies. In the mid-2000’s he oversaw the integration of R&D of several acquired seed companies and established an integrated research team with oversight of Syngenta’s Breeding Strategy and Seed Technology. In 2014 Ray became Head of Computational Biology, integrating Syngenta’s computational biology efforts spanning breeding, trait development (GM and native) and chemistry. In May of 2015 he joined Indigo as Sr VP Product Development.

Professor Denise Kelly joined Seventure Partners, a European Leader in Venture Capital, in 2015 as an Investment Advisor to the Life Sciences Team and is focused specifically on Human Microbiome investment opportunities across Europe and the USA.

Prior to joining Seventure, Denise was Head of her Research team at the World-renowned Rowett Institute, University of Aberdeen, where she acquired over 20 years experience in gut microbiology and immunology. She was the (former) Founder Director, CEO and CSO of GT Biologics Ltd, one of the first translational spinouts, developing Innovative Microbiome-based Therapies. She is the main inventor on numerous EU and USA patent applications and during her career has collaborated with pharmaceutical and healthcare companies on several translational projects.

Denise holds a BSc and PhD from Queen’s University, Belfast and an Emeritus Professorship from the University of Aberdeen.

Until her recent retirement, Penny Hirsch led a group at Rothamsted Research working on soil microbiology and molecular ecology in an agricultural context, where she continues in an emeritus position.  Over the years, she has worked with fungi and bacteria, on rhizosphere interactions and other microbial activity in soil that supports plant health and productivity, including nitrogen cycling.  This is combined with long experience on the extraction, amplification and bioinformatics analysis of DNA and RNA sequences derived from soil and the rhizosphere.  Recent research has focused on nutrient cycling in arable systems and the relationship between the soil and crop plant microbiomes, applying metagenomics and metatranscriptomics, in addition to more conventional approaches.  The long-term field experiments at Rothamsted have provided valuable resource for applying these techniques to determine agronomic impacts on soil and plant microbiomes.

Philip Poole was Professor of Microbial Physiology at the University of Reading until he moved to the John Innes Centre in Norwich in 2007. In 2013, he took up a personal chair as Professor of Plant Microbiology at the University of Oxford. His group studies the physiology of bacterial growth and survival in the rhizosphere, colonisation of roots and how bacteria establish symbiotic interactions with plants. A further focus of his research is the physiology and biochemistry of nitrogen fixation in legume nodules. Recently he has developed new methods to study how plants control the plant root microbiome.

Richard Flavell is a plant geneticist who has focused much attention on traits important in crop plants. In the last five years he has served as Chief Scientist in two companies in the USA. The first, Indigo, Cambridge, Massachusetts is an agricultural microbiome company. The second, Inari, is an agricultural plant genetics company.

He is currently a consultant for companies and public sector organizations committed to plant improvement, including the International Wheat Yield Partnership.

After his undergraduate degree in microbiology and his PhD in the John Innes Institute and the University of East Anglia, he spent two years of postdoctoral research in Stanford University, California. He then joined the Plant Breeding Institute in Cambridge (UK) where he built up a large Department of Plant Molecular Genetics between 1969 and 1987. He was then appointed as Director of the John Innes Centre (JIC), Norwich and to a chair at the University of East Anglia and oversaw a large expansion of JIC’s activities and impact.

In 1998 he became the Chief Scientific Officer of Ceres, a young plant genomics company in California. This became a public company and was recently bought by a multinational agricultural company.

He is a Fellow of the Royal Society and a Commander of the British Empire for services to science.