• Organism

Human Microbiome

Did you know, the cells that make up your microbiota outnumber the cells in your body by a ratio of 3:1?


The human microbiome describes all the DNA, including genes, contained within the human microbiota - all of the microbes which live in and on the human body. This mostly consists of bacteria, although there are also viruses, archaea, and fungi present. Whilst some of these microbes can be pathogenic, or cause problems when they are present in high volumes or the wrong area of the body, many are beneficial and absolutely vital for a healthy functioning body. For example, ‘friendly’ bacteria in your body can outcompete other, pathogenic ones, protecting you from disease.

Each person has a unique microbiota. This is thought to be determined by both genetics and environment - for example, those which you receive from your mother during birth and breastfeeding and those in the food you consume. The microbiota generally stabilizes around the age of three although it does undergo changes throughout your life. 

There seems to be a correlation between diet and gut microbiota composition, and therefore variations between people eating a Western diet high in fat and protein, and those for example in Africa, whose diet is higher in carbohydrates. 

Scientific significance.

Due to the sheer size of the microbiota, its composition can affect many things: from your mood, how effective medicines are and how well you digest food to how susceptible you are to certain diseases. The importance of the microbiota in such a breadth of health areas has caught the interest of the scientific community, who are certain that understanding and looking after it may be the key to solving many health issues.

What Earlham Institute is doing.

We analyse what microbe species are present in healthy and diseased guts, as well as the interactions between gut microbes and our own cells, because we know that disrupting a healthy microbiota leads to the development of various diseases.

One such disorder is Inflammatory Bowel Disease (IBD), which includes conditions such as Crohn’s Disease (CD). We use systems biology and machine-learning to classify disease subtypes, discover drug-targets and predict drug responses, with the aim of developing microbial therapeutic approaches with minimal side-effects and maximal benefits tailored to fit each patient.

Such data integration techniques (combining machine learning and systems biology) are also used to analyse the relationship between the microbiome and ageing. In collaboration with BenevolentAI, we are developing a workflow to identify prognostic indicators of healthy ageing and age-related disorders, with an approach based on metagenomics and metatranscriptomics data.

We are also developing a bioinformatics pipeline (based on ‘omics data and network biology) to predict host-microbiome interactions in the scalp and oral cavity, in collaboration with Unilever.

Moreover, we also analyse human microbiome interactions with experimental approaches, using mice, human cell lines and organoids (‘mini guts’) from patients. This helps us to decipher the mechanisms by which microbes modulate host cellular function in health and disease.