Health and the Human Microbiome

Around 35 trillion tiny, unseen organisms live in and on the surface of our bodies. These microorganisms (or microbes) include many different types of bacteria, viruses and fungi, and are collectively known as our microbiome. Microorganisms live on and in our body tissues and fluids - like skin, saliva or tears, and in the gastrointestinal tract (gut). Just like different animal species live in diverse habitats all over the world, different microbial communities live on and in various parts of the body.

We call the special collection of microbes that live in our guts the ‘human gut microbiome’. ​​Over 400 species of bacteria are found in the human gut, most of them in the large intestine (colon). The stomach and small intestine are too acidic for bacteria to thrive. The types of bacteria most commonly found in the human gut are Bifidobacterium, Lactobacillus, Clostridium, Escherichia, Streptococcus and Ruminococcus. Some are ‘friendly’ (for example, Bifidobacterium and Lactobacillus). These microbes have a symbiotic relationship with humans as hosts. The intestine provides microbes with nutrition and a warm living environment. In return, the gut microbiome plays an important part in the way food is digested and metabolised. Other types can be harmful (for example, some species of Escherichia are pathogenic).

To identify the many different types of bacteria that colonise various parts of our bodies, scientists have relied on culturing (growing) the bacteria in the laboratory, staining them to make them easier to see, and studying them under powerful microscopes. Some bacteria, for example, E. Coli, can be easily cultured, however, most microbes can’t be grown in this way. New technologies like DNA sequencing are becoming faster, cheaper and easier. This means that microbiome research has developed at an exponential rate within the past five years.

Scientists have discovered that the gut microbiome can be manipulated (altering or changing the number and type of microorganisms in the gut). For example, antibiotics might kill some types of bacteria that live in the gut, while a laxative or enema might clean the gut right out. We often eat probiotic or prebiotic foods. Probiotics such as yoghurt contain ‘good’ or helpful bacteria. Prebiotic foods like garlic, onions, and leeks feed the good bacteria that already live in our gut. One way of manipulating the gut microbiome is to transfer faecal material (poo) from one person to another. This is because (perhaps not surprisingly), faecal matter contains much of the same microorganisms as the human gut. An ancient and effective Chinese treatment for a nasty diarrhoea illness called Clostridioides (formerly clostridium) difficile was to give the sick person “yellow soup”. This soup was made from the faeces of a healthy person and helped to improve the balance of ‘good’ gut bacteria. 

In humans, the types of microbes that dominate the guts of lean people are different and more diverse than the gut microbes of people who are affected by obesity.  People with diabetes or bowel disease also have different gut bugs to healthy people. It might be tempting to say that the gut bugs have influenced their conditions. The gut bugs are different, and therefore that has caused the issues with obesity or made their condition worse. However, these are association studies only - and an association or correlation between two factors do not prove a cause and effect relationship.

Knowing this, do gut bugs influence obesity? Will replacing ‘bad’ gut microbes with ‘good’ gut microbes help people living with obesity to improve their health and well being? No one yet knows exactly how the gut microbes interact with the body’s complex metabolic pathways and digestion processes. The only way to know for sure is to conduct an experimental trial that proves a causal link between gut microbiota and the condition of obesity in humans.