Networking microbiome science

An entire ecosystem of microorganisms (bacteria, archaea, eukaryotes, and viruses), their genomes, and the surrounding environmental conditions (proteins, metabolites, environmental data, etc). This is the frontier of 21st century science.

The microbiome has a critical role to play in our personal health as well as the health of our planet. Your microbiome strongly influences your immune system, metabolic health, perhaps even your mood, while environmental microbiomes influence ecosystem diversity, agricultural success, and even climate change. Understanding and harnessing the microbiome will provide the mechanism to improve health and wellness across the globe.

The applications of microbiome science are vast: some examples include functional foods and nutritional supplements, consumer goods like cosmetics and personal hygiene products, biofertilizers for healthy soils, improved diets for livestock, and living therapeutics for diseases. Use cases are rapidly increasing as our understanding of the microbiome grows.

Applying microbiome science to product design can have a variety of benefits, including safety (not disrupting your natural microbiome), increased functionality (designing a product that actually enhances some aspect your microbiome), personalization (specifically designed for your microbiome), and product sustainability (improved value chains and natural alternative ingredients).

Traditionally, R&D works to create new products or improve existing ones through efficacy, safety, etc. Microbiome science provides a novel mechanism for innovation by reinventing traditional processes in ingredient production, safety evaluation, and health management. For example, microbiome-driven innovation can enable the identification of new food supplements that promote health by altering bacterial species in the gut; the discovery of new proteins that can be used in ingredient manufacturing; or the detection of new biosynthetic gene clusters that produce particular chemicals.

Microbiome research typically involves sampling from a specific environment (a ‘biome’), which can be a particular geographical area, such as a field or a lake, or a body site, such as the gut or scalp. Genomic material extracted from the samples is then sequenced. This can involve the targeting of taxonomic marker genes, whole genome shotgun (WGS) metagenomic sequencing, and RNA-seq metatranscriptomic sequencing to study diversity, composition and function. Microbial assembled genomes (MAGs) can also be reconstructed for genomic studies of novel organisms.

The term ‘microbiome’ refers to the environment that is sampled, including the microbial community. In addition to sequencing data, a range of other measurements can also be taken, depending on the environment sampled. These can include the temperature or pH of soil or water, or gene expression measurements relating to the host organism.

Network science involves the study of patterns of connections in complex networks. The study of the microbiome involves networks of interacting microbes connected to wide constellations of other data. These include the array of metabolites that microbes produce, which may in turn interact with host systems, such as the immune system. The holistic approach offered by network science is therefore the only way to reliably and fully understand the microbiome.

There are in the order of 10,000+ human diseases alone, and it is increasingly clear that the microbiome is implicated in many of them. Similar challenges and opportunities exist in animals, plants and other ecosystems. The ability to optimize for platform condition/disease fit will differentiate winners and losers in the emerging bio-economy. 

Eagle Genomics is enabling a new era of collaborative, data-driven innovation. Our robust analytical platform fuses network science, AI and graph technology, creating a trusted data fabric for life science research. The e[datascientist] empowers scientists to exploit multi-omics data, discover biological connections, formulate and test valuable hypotheses and generate knowledge to tackle the world’s grand challenges.