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Why microbes?

Updated: Oct 26, 2022

FindingPheno has taken on the challenging task of analysing omics data from the full holobiont, i.e. both the plant or animal host and its associated microbiome, all taken together. This clearly makes things harder for us, so why include the microbiome in our studies?


The key aim for FindingPheno is to understand the biological mechanisms that give rise to phenotypic variance. In other words, we want to know how what is going on inside a plant or animal can cause its physical outcomes – because once we understand it, we can change it for the better. To do this we are developing a new framework for analysing multi-omic data sets, i.e. information about all the different genetic and molecular processes within an organism, to find the causal relationships within. However, in recent years, it has become increasingly clear that we must also consider the complex interactions between the organism and its associated microbiome in order to fully understand this phenotypic variation. There is a multi-way flow of information and biological effect between all the different players within this system, host and microbiome, meaning that the microbiome is a critical part of why a host turns out the way it does and should not be ignored.

What is microbiome research?

Microbiome research involves characterising the genetic, species or metabolic diversity of all of the microbes (e.g. bacteria, viruses, fungi, protozoa) present within a defined environment. In FindingPheno we are particularly interested in microbes that are associated with a macrobiotic host, e.g. living in the gut of an animal or on the roots of a plant. The rise of microbiome research has been driven by the ongoing development of metagenomics sequencing tools such as 16s profiling or shotgun sequencing, along with microbe-specific versions of other omics such as metatranscriptomics, etc.

There are two main ways to look at the microbiome. The first is cataloguing species diversity, i.e. working out which microbes are in a given sample and in what proportions. This diversity both influences and is influenced by the host genetics and environment, and can give insights into the health or growth status of the overall system. The second is to consider the metabolic capacity of the microbiome regardless of which exact microbes are providing this capacity, with a focus on the functional genes and proteins present rather than the exact species profile. While the latter approach is more complex and computationally difficult, it may be more informative for understanding the phenotypic outcomes.

Application areas

The most researched model for microbiome-host interactions is the human, with studies starting as far back as the 1680s when Antonie van Leewenhoek compared the diversity of his oral and faecal microbiota. The rise in metagenomic technology in the past 15 years has dramatically increased interest in human microbiome research, with an exponential increase in publications and funding in this area (see also the figure below). These studies are providing increasing support for the importance of the microbiome in a wide array of human health phenotypes, with examples ranging from diseases such as obesity, colitis, diabetes, and heart health to more unexpected areas such as behaviour, antibiotic tolerance, and response to chemotherapy.

Given that we have now incorporated the microbiome as a central part of human health related studies, it is only natural to expect that the microbiome plays a similarly significant role in non-human-health related fields, such as agriculture and aquaculture. Early successes in this area have included the use of probiotic interventions to improve feed conversion efficiency for animals or provide germination or growth advantages in crops. It is also likely that having a better understanding of the microbiome could be used to reduce antibiotic use or increase drought tolerance in food production systems. Although the role of the microbiome is now universally acknowledged to be important in these systems, there has been little research investigating the interaction between the microbiome, the host genome and the host gut environment within food production species. By including the microbiome data in our project and working to analyse this web of hologenomic interactions, we can begin to see what is really going on.

Written by Shelley Edmunds