Chairs
Dr Mike Romanos, CEO Microbiotica
Dr Mike Romanos, CEO Microbiotica
Mike is co-founder and CEO of Microbiotica, which is commercialising leading microbiome science from the Wellcome Sanger Institute. He has 30 years’ experience in the biotech and pharma, previously co-founding Crescendo Biologics which he led as CEO and CSO for six years, building a leading discovery platform and pipeline in antibody fragment-based therapeutics. Prior to that he held senior global roles in GlaxoSmithKline over 10 years, during which time he built trans-national innovative R&D organisations which contributed to the company’s platforms and pipeline across therapeutic areas and across multiple product types, latterly as VP for Genomics/Target Discovery.
Mike is highly experienced in biotech translation and commercialisation, serving as a Trustee on the LifeArc Board, and previously Translator in Residence at Imperial College, Venture Partner for UK Innovation and Science Seed Fund, and member for MRC’s Developmental Pathway Funding Scheme panel.
Mike’s academic work included research in influenza virology (MRC, National Institute for Medical Research) and in yeast genetics and biotechnology (University of Leicester). He holds a degree in Natural Sciences from Cambridge University, a PhD in Molecular Virology from Imperial College, and is a Fellow of the Royal Society of Biology.
11:05-11:25
Data driven knowledge discovery applied to the human gut microbiome
Dr Rob Finn, European Bioinformatics Institute
Abstract
Metagenomics, the analysis of the sum of genetic material from an environmental sample, has started to shed light on the huge diversity of micro-organisms that occupy environments such as the human body, soil and the World's oceans. During this talk, I will provide an overview of how metagenomics is being used to identify the different microbes, many of which have not previously been observed before. There are, however, limitations to this approach that differ across biomes. Despite this, metagenomic approaches are beginning to unveil the so call ‘microbial dark matter’ – the previously unknown biological repertoire – which when harnessed will provide many applications to the medical and biotechnology industries.
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Dr Rob Finn, European Bioinformatics Institute
Dr Rob Finn, European Bioinformatics Institute
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.
11:30-11:50
Microbiomes for improving crop production
Professor Penny R Hirsch, Rothamsted Research
Abstract
For decades, the microbial community in soil has been appreciated as very large and diverse, essential for both terrestrial nutrient cycling and plant health, whilst remaining very poorly understood. The recent advances in sequencing technology and bioinformatics have greatly improved our familiarity with soil and plant microbiomes, and the complex relationship between them. Plants encounter bacteria and fungi in soil which, if they are proficient in utilising plant-derived substrates, proliferate in the rhizosphere. They may colonise the rhizoplane and above-ground parts, some becoming endophytes. Not all are beneficial, but the microbiome is reported to inhibit pests and pathogens, modulate plant growth and improve nutrient acquisition. With global pressure to escalate food production whilst minimising fertilizer and agrochemical use, a better understanding of how to maximise the benefits of the plant microbiome becomes increasingly important.
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Professor Penny R Hirsch, Rothamsted Research
Professor Penny R Hirsch, Rothamsted Research
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.
11:55-12:15
Culture-based microbiome analysis in personalised medicine and birth cohort studies
Dr Trevor Lawley, Microbiotica
Abstract
Studies at the Human Microbiota Interactions lab have addressed key bottlenecks in high resolution strain profiling and functional validation of the gut microbiota through the development of reference genome-based analysis approach that vastly increases the precision and efficiency of metagenomic analysis. Our approach is underpinned by mass isolation of bacteria and generation of a large reference genome sequence database. We call this approach “Precision Metagenomics”. Precision metagenomics underpins studies in HMIL and the Wellcome Sanger Institute spinout company Microbiotica, which has industrialised the platform and is using it for biomarker and therapeutic discovery. The platform and its application will be discussed in the context of a major UK Baby Cohort study aiming to find correlates between early life microbiota development and long-term health and disease.
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Dr Trevor Lawley, Microbiotica
Dr Trevor Lawley, Microbiotica
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.
12:20-12:40
Dissecting the role of multi-kingdom microbial consortia on plant health
Dr Stéphane Hacquard, Max Plank Institute for Plant Breeding Research
Abstract
Roots of healthy plants are inhabited by soil-derived bacteria, fungi, and oomycetes that have evolved independently in distinct kingdoms of life. How these microorganisms interact and to what extent those interactions affect plant health are poorly understood. We examined root-associated microbial communities from three Arabidopsis thaliana populations and detected mostly negative correlations between bacteria and filamentous microbial eukaryotes. We established microbial culture collections for reconstitution experiments using germ-free A. thaliana. In plants inoculated with mono- or multi-kingdom synthetic microbial consortia, we observed a profound impact of the bacterial root microbiota on fungal and oomycetal community structure and diversity. We demonstrate that the bacterial microbiota is essential for plant survival and protection against root-derived filamentous eukaryotes. Deconvolution of 2,862 binary bacterial-fungal interactions ex situ, combined with community perturbation experiments in planta, indicate that biocontrol activity of bacterial root commensals is a redundant trait that maintains microbial inter-kingdom balance for plant health.
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Dr Stéphane Hacquard, Max Plank Institute for Plant Breeding Research
Dr Stéphane Hacquard, Max Plank Institute for Plant Breeding Research
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.
12:45-13:05
AgBiome: Harvesting the Plant Microbiome
Dr Tracy Raines, AgBiome
Abstract
AgBiome is a biotechnology company applying advanced knowledge of the plant-associated microbiome to create innovative products for agriculture. Our research platform allows us to efficiently capture and screen the most diverse and unique microbes for agriculturally relevant applications. To drive our discoveries, we use our in-depth knowledge of the crop microbiome and an extensive network of field-sampling partners to build an ever-expanding proprietary strain collection. This collection sources the discovery of new biologicals and trait genes for use in disease and pest control.
Unlike many programs which only use metagenomic surveys, the AgBiome platform is focused on isolated microbial strains and their fully sequenced genomes, which gives us unparalleled insight into the detailed genomic composition of crop-associated microbes. Isolate sequences are used to de-replicate the collection and uncover true microbial diversity at an even deeper level than 16S rRNA identity alone. Microbes from our collection are screened in innovative high-throughput assays against a broad range of fungal pathogens, insect pests, and plant-parasitic nematodes. Successful candidates are tested in field trials and confirmed active biologicals proceed through our fermentation and formulation pipeline. As we continue to integrate sequence data with performance data across multiple assays and field trials, the AgBiome team will improve our ability to quickly identify active leads that are attractive product candidates and will begin to correlate the effect of microbe communities on plant health.
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Dr Tracy Raines, AgBiome
Dr Tracy Raines, AgBiome
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.