All About The Microbiome

Dr Kate Stephens PhD Food and Microbial Sciences; Gut Microbiology (University of Reading), BSc Medical Microbiology

One of the most popular ‘buzz’ scientific words over the past few years has been ‘the microbiome’. We are seeing this in the news, in magazines and newspapers and on the television. But what does the word actually mean?

The microbiome: What does it mean?

I’m sure many of you have watched nature shows, especially some of David Attenborough’s. They take you to many destinations such as coral reefs, rainforests, woodlands or the desert. Each of these destinations are ecosystems. An ecosystem can be defined as: ‘A community of biological organisms that interact with one another and their physical environment’. We can see in a coral reef for example, how the aquatic organisms such as fish, turtles, corals all play an important role with one another but also in maintaining a healthy reef.

This is the same as the microbiome. The microbiome is a microscopic eco system made up of bacteria, yeasts and viruses that live on and inside us. That’s right! We are covered in microbes! But do not panic! Most of these microbes are friendly and offer benefits to us, as their host. We just have to keep the harmful ones in low numbers. We have evolved with these microbes over the millennia and have formed a symbiotic relationship with them. We pass them on in our generations- you likely have similar microbes to what your grandparents and great grandparents had. But ultimately your microbiome is completely unique to you.

We have microbes in our mouths, stomach, small intestine, large intestine, uro genital tract, skin, feet, tummy button and lung. The colon (the large intestine) contains the most microbes. Scientists estimate there are approximately 40 trillion microbes in the small and large intestine (the gut1) - that’s 5000x more bacteria in your gut than people on the planet!

Not only does the amount differ, but the types of bacteria vary in each location. This is due to the different environments. For example microbes on the skin can tolerate oxygen well where as microbes in the colon have adapted to live without oxygen.

It was always thought by scientists that there were more bacterial cells than human cells i.e. we are more bacteria than human! However, due to advances in technology, it is now considered more equal (although this is still debated). What’s interesting, is that although our own cells (and DNA) is ‘fixed’ – we cannot change our makeup. But we can control our second genome - our microbial genome. The DNA belonging to our microbes can be influenced through numerous factors.

The human microbiome | Probiotics Learning Lab
The human microbiome

The gut microbiome (i.e. all the microbes in our gut) has received lots of attention in recent years as scientists discover more and more ways in which it benefits various aspects of human health.

More often than not, when people talk about ‘the microbiome’, they are referring to the gut microbiome, as this huge population of microbes is the most researched, and arguably has the most profound influence over our health.

The role of the microbiome

We completely rely on our microbiome. It estimated our microbes have 150 times more genes than we do. They carry out essential tasks for us, and our health and wellbeing would be non-existent without them. The list of known functions is long and growing all the time as more and more research is carried out into the microbiome.

Let’s take a look at a healthy gut and the role gut microbes can play. Many microbes live on the gut lining where they contribute to our digestion and defence systems. You may also like to read: Gut Health - All you need to know

healthy villi in gut

  • Digestion: The microbes living in the intestines produce different enzymes (a type of protein) that help us to digest and break down our food. They can help break down lactose and gluten amongst other food sources. When friendly bacteria break down some specialised fibres known as prebiotics, they produce beneficial substances that support a healthy gut environment. 
  • First line defence: You can see from the diagram above that our friendly microbes form our first barrier. Imagine it as a line of soldiers, shoulder to shoulder with their swords and shields out ready to defend - they stop invaders getting through. In this case, the bacterial barrier limits harmful bacteria or toxins getting through to the gut cells and immune system. The gut cells are responsible for the absorption of our nutrients from our food. An overwhelmed immune system can lead to many health issues. So, this initial defence system is very important.
  • Energy levels: Certain strains of bacteria are capable of making B-vitamins, which are known to help with our energy. Also, by ensuring good digestion of food and healthy gut cells, this will help us absorb the nutrients well.
  • Immunity: From the diagram, can you see how close the immune system and gut microbiome are? In fact, 70% of our immune system is located in the gut, allowing for direct interaction between the microbiota and our immune cells. They go hand in hand- what affects one, affects the others. Essentially the microbiome helps modulate immune responses. Healthcare professionals can read more about the gut and immunity on the Probiotic Professionals site.
  • Skin health: Friendly bacteria produce beneficial substances in the body, as opposed to the toxins produced by pathogenic (bad) bacteria which can contribute to poor skin. Therefore, an unhealthy gut can be reflected in our face. Learn more by reading: Probiotics for skin health
  • Mental health: An emerging area of research is the ‘gut brain axis’. That’s right, our gut and brain communicate with each other. Many hormones are produced and modulated in the gut, including our happy hormone Serotonin. Find out more information on the gut brain axis.

The vaginal microbiome is unique, it’s a completely different environment to the gut. The microbes here have one major job- reduce the risk of vaginal infections. They create an environment in which friendly bacteria thrive whilst also inhibiting the growth of harmful ones. Have a read for more info on the vaginal microbiome.

Dysbiosis: When things go wrong

What is the key for a flourishing ecosystem? Balance.

After the successful animation film involving clown fish, clown fish became a popular choice of fish for children. Lots of clown fish were taken from their natural environments, which affected anemone health and more. By reducing the levels of one key player this impacted other species and potentially the environment.  The other example is the ‘Wolves of Yellowstone Park’. The park had high numbers of deer, who had eaten most of the vegetation, leaving little food for other animals. When scientists introduced wolves to the park, they reduced the number of deer and wildlife flooded back- from rabbits, beavers, hawks, bears and fish. The physical environment even changed, the river beds got stronger from lack of deer grazing and so the river changed shape.

It’s exactly the same for the microbiome. When an imbalance between friendly microbes and harmful ones arise, this is associated with numerous health conditions. All microbes have a role to play in the gut, but opportunistic microbes- i.e. those that could cause disease, need to be kept in check. A reduced number of friendly bacteria can result in a weakened barrier, this exposes the gut cells and immune system to potential attack.

Many different lifestyle factors have been shown to have a negative impact on our guts. This means maintaining a healthy balance of microbes in the gut can be a bit of a challenge at times.

The name given to an imbalance of gut bacteria is dysbiosis, and the following are all factors that can contribute to this:

  • Taking antibiotics
  • A high-sugar diet
  • Processed foods
  • A low-fibre diet
  • Stress
  • Travel
  • Certain medications, including NSAIDs, steroids and HRT
woman lying on her side
Certain lifestyle factors can lead to a decrease in friendly bacteria, causing dysbiosis

Although not truly a lifestyle factor, age can have an impact on the microbiome. As the microbiome develops in the early years we see significant changes. It then starts to stabilise and changes significantly again through pregnancy, menopause and as we enter old age. Read more about the microbiome in childhood years.

Correcting dysbiosis

Given that the microbes living in our gut are fragile and susceptible to damage, it is important that we know how to actively encourage their growth and proliferation, as well as simply preventing their losses. In addition to avoiding the factors listed above where possible, it is also a good idea to consume a number of different sources of prebiotic fibre and consider topping up with researched friendly bacteria, also known as probiotics. For more information, read: What are probiotics?

Prebiotics are the preferred ‘food source’ for our probiotic colonies, allowing them to flourish, and are found in many different fruits and vegetables, including: bananas, artichokes, onions and garlic. You may also like to read: What are prebiotics?

The future of the microbiome

Much research is being done into the microbiome that will hopefully enable scientists to know exactly how to manipulate the microbes in the gut to elicit positive changes in our health. Centres of excellence that are leading the way in to this research include Reading University, Cork University and Stanford University.

Our microbiome has been shown to impact on many areas of our health. Links have been made between dysbiosis in the gut and numerous different diseases and health symptoms. These health conditions might be fairly obvious in some cases, but others you may find surprising.

  • IBS 
  • Colic 
  • Mental health disorders
  • Allergies
  • Inflammatory bowel disease- Ulcerative Colitis and Crohn’s disease
  • Poor immunity
  • Obesity
  • Skin disorders- eczema, psoriasis, acne
  • Heart health
  • Food intolerances
  • Intimate health
  • Autism
  • Liver disease
  • Metabolic syndrome
  • Diabetes
  • Parkinson’s

What’s really exciting, is research is going one further for a few of these health conditions. Differences in microbial composition can be seen between ‘healthy’ and ‘disease’ state, as such researchers are looking to develop a ‘microbial algorithm’. The aim of these algorithms is to act as a diagnostic tool and save invasive procedures. This work is in its early days but is promising for the future.

This actually touches on one of the biggest research questions- what came first?

  • Dysbiosis and then disease
  • Or the disease and then dysbiosis

Either way it opens up an opportunity to intervene either by reducing the risk of the disease or managing symptoms.

As Hippocrates states ‘All disease begins in the gut.’

The Microbiome Project

In 2008 eminent scientists from four different medical centres in the U.S established the Human Microbiome Project, which set out to ‘further our understanding of how the microbiome impacts human health and disease’. The ultimate goal of this project is to establish whether there is a core healthy microbiome seen in the guts of well individuals. It is already known that the exact composition of the intestinal microbiome differs hugely between individuals, and that our gut microbiome is said to be as unique to us as our fingerprint.

However, scientists now believe that one third of the total number of species of bacteria may be common to most people, opening up the possibility for ‘mapping’ this percentage of the microbial population, and looking for anomalies present in different diseases and health conditions.

So, it's clear to see that our microbiome plays an enormous role in overall health, so we hope this article has helped you to understand this fascinating system a little bit better.

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Sender R et al., “Revised Estimates for the Number of Human and Bacteria Cells in the Body,” PLoS ONE, p. 14(8): e1002533., 2016