Data driven knowledge discovery applied to the human gut microbiome
Dr Rob Finn, European Bioinformatics Institute
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.
Microbiomes for improving crop production
Professor Penny R Hirsch, Rothamsted Research
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.
Culture-based microbiome analysis in personalised medicine and birth cohort studies
Dr Trevor Lawley, Microbiotica
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.
Dissecting the role of multi-kingdom microbial consortia on plant health
Dr Stéphane Hacquard, Max Plank Institute for Plant Breeding Research
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.
AgBiome: Harvesting the Plant Microbiome
Dr Tracy Raines, AgBiome
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.