The microbiome is the entire community of microbes within a habitat and the surrounding environmental conditions. It holds arguably the most important and extraordinarily diverse forms of life on the planet, and sustains the biodiversity of life on Earth.
The Microbiology Society’s report ‘Unlocking the Microbiome’ was launched on 15 November 2017. It explores opportunities and challenges for microbiome research identified over the course of the Microbiome Policy Project. It will also provide an opportunity for multidisciplinary networking and knowledge exchange between researchers, funders, learned societies, policy advisers and other stakeholders interested in microbiome research.
The MBA’s contribution to the report through Dr Declan Schroeder (Senior MBA Fellow and member of the expert panel) can be seen in particular in Section 4.3. Environment - highlighting the important role microbes play in our oceans and consequently human health. This led to one recommendation that “Researchers should work with funders to enable support for large-sample and longitudinal studies so that researchers can validate associations, identify biomarkers and assess the long-term implications of human or environmental changes to microbiomes.”
The Microbiome is defined as the entire community of microbes (bacteria, archaea, lower and higher eukaryotes, and viruses) within a habitat and the surrounding environmental conditions. They are often invisible to the human eye (<2 mm in size). There is growing awareness that microbes may be one of the most important components of any ecosystem. Their socio-economic value can be seen in context of their contribution to the world’s primary production; as nearly half of the world’s oxygen supply is generated by microbes through photosynthesis. However, understanding of the complexities within and surrounding this key group of organisms on the scale of a host cell or habitat to its surrounding environment is not matched by their global importance.
There are currently estimated to be between 4 and 6 × 1030 prokaryotes (Bacteria and Archaea) in the biosphere, with around 4 × 1028 in the aquatic environment. The sheer abundance of viruses (~1031) in the aquatic environment results in around 1023 virus infections per second, the consequence of which is the release of gigatonnes of carbon per day from the biosphere. The biogeochemical impact of this ‘viral shunt’ is the diversion of carbon away from the classically understood food web, towards cellular-mediated recycling processes. Viruses also play an important, if not critical role in sustaining the balance and diversity of life in the biosphere.
The vast majority (99%) of microbes cannot be grown under standard laboratory conditions and so are not amenable to study by the classical methods. However, the microbial research community has benefitted greatly from the use of genomic (sequencing of cultures) and metagenomic (sequencing of community and environmental DNA) approaches. For the first time in biology, the new high throughput achieved by second generation sequencing technologies promise to overcome this gap in knowledge by providing information on the genetic diversity and potential function of microbes on an unprecedented scale. New third generation ultra-high-throughput sequencing technologies currently entering the market, promise even cheaper per base prices enticing researchers further to scale up their sequencing efforts.
The overarching goal of Microbiome research in the Schroeder lab is to assign ecosystem function to the Microbiome. To this end, bioinformaticians have already developed statistical tools to position genes on phylogenetic trees and metabolic networks, and to establish correlations between environmental parameters, evolution and global metabolic activities of select populations. But these approaches obviously need now to be extended to other functions such as disease profiling and to a more diverse set of organisms present, i.e., the full Microbiome in biosphere ecosystems, especially viruses (see the paper in the journal Viruses by Flaviani et al. A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater). Over the past 20 years, a completely new form of life termed giant viruses has been discovered, further indicating our ignorance of the true Microbiome community composition and therefore function. Similarly, the extraordinary diversity in the picorna-like virus lineage is changing our view of the role of viromes in for example honey bee health (e.g. Superinfection exclusion and the long-term survival of honey bees in Varroa-infested colonies)