chapter 4: all disease begins in the gut
‘All disease begins in the gut.’
Hippocrates, c.460–370bc
Existing research shows that there is a significant amount of interaction between the body’s immune system and bacteria in the gut. Our many physiological systems in the body work in synergy together, and our gut microbiome and immune system are very much connected, especially when you consider the fact that approximately 70–80 per cent of your immune system is in your gut. Our microbiome and immunity are certainly not independent of each other, but appear to have an extremely close and important connection.
The microbiome
The human microbiome, which is now known as an organ in its own right and often referred to as the ‘second brain’, is composed of communities of bacteria, viruses and fungi, the majority of which live in our guts. An estimated 100 trillion microbes, weighing over four pounds, exist in the guts alone. When we define ‘microbiome’, we are referring to the microbes and their genetic material. Over millions of years, the microbes that comprise our microbiome have changed with us and live off the food we eat. Extraordinarily, the activities of the microbiome are involved in most, if not all, of the human biological processes. The microbes, to reward us for feeding them, provide lots of vital services to our bodies, such as extracting energy from our food, controlling the calories we absorb, providing enzymes, manufacturing vitamins, working with our nervous system, producing numerous hormones, and influencing our immunity.
MICROBES are types of microorganisms. The major groups of microorganisms are bacteria, archaea, fungi (yeasts and moulds), algae, protozoa and viruses.
MICROBIOTA refers to all the microbes in a community, such as bacteria, viruses and fungi. It was first defined by Lederberg and McCray34, who stressed the significance of microorganisms in the body and their role in human health.
MICROBIOME refers to the microorganisms AND their genes.
Over the last ten years, it has become evident that the gut microbiome plays an important role in shaping the immune system, as well as contributing to health and disease. Our understanding of the gut microbiome is also increasing quickly, due to the development and application of technological advances, particularly genomic approaches35. This is probably best demonstrated by large-scale studies, including the Human Microbiome Project, which was performed over ten years and in two phases. This was a United States NIH research initiative, to improve understanding of the microbiota involved in health and disease. Furthermore, the Human Microbiome Project helped establish the extensiveness of microbial variation and function across large populations, in addition to determining associations between microbiota alterations and disease states36.
The role of the microbiota in regulating metabolic activity has been demonstrated with increasing evidence, indicating an involvement in glucose regulation, weight management and also regulation of the hypothalamic-pituitaryadrenal (HPA) axis37. The autonomic nervous system, the HPA axis, and the nerves within the gastrointestinal tract connect the gut and the brain38. This allows the brain to affect gut activities, such as the activity of immune effector cells. If the HPA axis is disrupted, not only does this wreak havoc on our microbiota but also our immunity.
Our gut microbes play a crucial role in educating, training and modulating our immunity, lending it a helping hand to distinguish friend from foe. Furthermore, some researchers believe that the increase in autoimmune disease may be the result of a disruption in the relationship between our bodies and the microbes that we evolved with. Unlike other endocrine organs, the microbiota has significant plasticity and can change considerably and quickly in response to diet37.
PLASTICITY is the adaptability of an organism to changes in its environment or differences between its various habitats.
While our wonderful microbes clearly impact us, we can also influence them. In fact, what we eat and how we live has a massive effect on the type of microbes that make up our microbiomes, as we will discover.
Main functions of our microbes include:
Bacterial baptism
So, how do we get these marvellous microbes?
A recent large-scale study39, the largest ever study of neonatal microbiomes, provided further understanding about the development of the microbiome and whether the birth delivery method played a role in this. The study analysed 1,679 gut bacteria samples from almost 600 healthy babies and 175 mothers. Stool samples were performed on babies at four, seven or twenty-one days old, who had been delivered vaginally or by Caesarean section (C-section). The researchers employed DNA sequencing and genomics analysis to study which bacteria were in the babies’ guts. They reported a significant difference between the methods of delivery. Babies born by vaginal delivery had many more beneficial bacteria from their mothers than those that were delivered by C-section.
Previous limited studies had suggested that, while travelling down the birth canal, vaginal bacteria were swallowed by the baby, however this study reported that very few of the mother’s vaginal bacteria were present in the babies’ guts, with no difference observed between those delivered vaginally or by C-section. In fact, the researchers discovered it was the mother’s gut bacteria that comprised much of the microbiome in the babies born vaginally. On the other hand, babies born via C-section had significantly fewer of these bacteria and instead had more bacteria associated with hospital environments present in their guts. It should be noted that women who have a C-section are given antibiotics before the procedure to limit the risk of post-operative infections, which means that the baby also receives antibiotics via the placenta. This could perhaps, in part, explain some of the microbiome differences reported between the vaginal and C-section births.
Some babies up to 12 months old were also followed up, and the researchers found the differences in gut bacteria between the babies delivered vaginally and those born by C-section had essentially evened out. The researchers confirmed that their findings demonstrated that as the babies age and ‘ingest’ bacteria from the food they eat and from their environment, the vaginally born and C-section-delivered babies’ microbiomes become more alike. This is an exciting area of research. However, large followup studies are required to determine if the initial differences do influence health outcomes.
As a mother, I know that vaginal birth is not always possible. Both of my children were delivered by C-section due to the presence of fibroids. In many cases, a C-section is a lifesaving procedure, and can be the best option for a woman and her baby. Experts from the Royal College of Obstetricians and Gynaecologists confirmed that these findings should not deter women from having a C-section birth. Also, if you do end up having a C-section birth, you are still able to encourage a healthy and balanced biome for your baby.
One of the best ways of doing this is by breastfeeding. Breast milk consists of carbohydrates, fat and protein, as well as sugars called oligosaccharides. While the baby can’t digest these complex sugars, they do feed the ‘good’ bacteria in the baby’s gut and promote accurate development of its immunity. As baby grows up, his or her food choices broaden, which in turn influences the microbiome. When baby reaches toddlerhood, around the age of three, their microbiome will be more or less established. However, it can still be altered by nutrition, diet changes, antibiotic use and infections acquired.
In conclusion, although we can’t do anything about how we were born, or whether we were breast- or bottle-fed, we do have the power to choose what we subsequently eat and thereby feed our gut microbiomes.
The missing microbes
Our microbiota plays a fundamental role in the education, training and function of our immunity. Learning to recognize a threat – and what is not a threat – is key. It is believed that a rich and diverse microbiome allows the gut immune system to remain ‘stimulated and in a constant state of readiness, so there will be no over-reaction to strange proteins’.40
We certainly don’t want our immune system attacking our ‘good’ gut microbes, which are crucial to our health and well being. However, due to a highly processed and often nutrient-deficient diet, in addition to antibiotic use, many of the gut microbes that have evolved with us over millions of years are either no longer present or exist in much smaller quantities. This loss of these microbes impacts our immunity, so it doesn’t perform and behave as well as it should. Fortunately, through our nutrition and lifestyle choices, we have the power to cultivate and re-establish these missing microbes, in order to successfully fight infection, bring an over-active immune system back into balance and decrease our risk of allergies.
The epigenetic link
It is generally acknowledged that factors such as diet, lifestyle and genetics have the greatest influence on shaping the gut microbiome. While we can’t change our genes, we can influence the composition of the different species of bacteria in our guts through diet and lifestyle choices. Furthermore, researchers have found that ‘good’ gut bacteria can control genes in our cells. They demonstrated that chemical messages from the gut bacteria can alter chemical markers through the entire human genome41. This interaction suggests that gut bacteria could potentially play an infection-fighting role.
Working alongside our genome, we have the epigenome, which is a set of chemical switches and markers that influence gene activity and expression. The epigenome is influenced by environmental factors, such as diet, physical activity, stress and sleep.
Referred to as ‘epigenetic modifications’, when these chemicals are placed on parts of the DNA or associated proteins, they influence their role and function. A direct consequence of these modifications is that genes can be switched on or off. Recent studies have shown that short-chain fatty acids (SCFAs), such as butyrate, which are produced when our gut microbes digest fibre-rich fruit and vegetables, can in fact influence these modifications.
In a study, researchers found that feeding mice with a diet that was rich in sugar and fat, but deficient in fibre, led to significant changes. The researchers observed that the mice had significantly reduced levels of Bacteroidetes and a greater amount of Firmicutes (two common types of bacteria) compared to mice fed a fibre-rich diet. As we will learn shortly, this isn’t a good thing, as having high levels of Firmicutes has been associated with a greater risk of obesity, while reduced levels of Bacteroidetes is associated with higher levels of inflammation in the gut. These findings emphasize the importance of diet on the composition of our gut bacteria.
Further recent studies have established a link between the gut microbiota, epigenetics and the occurrence of conditions such as immune disorders, inflammatory bowel diseases and even cancer.
A shout-out for butyrate
Butyrate is a very special SCFA. It has significant anti-inflammatory powers that promote the mucus we need in order to protect our gut lining. This is paramount, as without a healthy gut lining our immunity, skin and mental health can suffer. A damaged gut lining can also result in ‘leaky gut’. Unlike most other cells in your body, which use glucose as their main energy source, the cells of the lining of your gut mainly use butyrate. Without it, these cells can’t perform their functions adequately. It also keeps inflammation at bay, our gut cells healthy and our ‘good’ gut bacteria species, such as Bacteroidetes, thriving.
LEAKY GUT is when toxins or particles of undigested food escape into the bloodstream, which can lead to impaired immunity, IBS, mood issues, skin problems and allergy-type symptoms.
We need lots of variety when it comes to gut bacteria, so it is important to make sure our guts have as many different bacteria species as possible. This can be achieved by eating a variety of different foods, rich in different species of bacteria – all of which promote a healthy gut lining and balanced microbiome, in addition to healthy and balanced immunity.
Beneficial gut bacteria species have been demonstrated to impact both the innate and acquired immune systems. They have also been shown to shorten the duration of having a common cold, and decrease the severity of the symptoms. However, if you have ever had antibiotics, chances are a lot of your ‘good’ bacteria have been wiped out. Certain antibiotics can induce long-term changes to the gut microbiota. In fact, just one antibiotic treatment may lead to adverse changes in the composition and diversity of the microbiota42. In comparison with our ancestors, who survived without antibiotics, we only have a tiny proportion of the diversity of gut bacteria species they had.
Our microbes educate and ‘train’ our immunity from the day we are born, and this may explain the ‘hygiene hypothesis’, which maintains that being too clean, especially in infancy, results in less exposure to different microbes and a subsequent reduction in microbiota diversity. This can also mean that the diversity in the development and education of the immune system is decreased as well, and may be one reason why autoimmune disease and allergies are increasing to critical levels.
When the microbiome malfunctions
Two of the main potential problems that may result when our gut health goes awry are ‘dysbiosis’ and impaired intestinal permeability, a.k.a. ‘leaky gut’. These can lead to impaired immunity, painful gut symptoms and illness.
Dysbiosis
When our gut microbiota and microbiome is imbalanced this is known as ‘dysbiosis’. This is mainly due to the increasing presence of harmful bacteria. It has also been reported that dysbiosis may be influencing how well messages are being sent via the gut-brain axis, by promoting inflammation and triggering our gut lining to become more permeable43. This means more foods may be entering the intestine undigested, resulting in ‘leaky gut’ (see below), and painful consequences such as gas, diarrhoea, constipation and bloating44. Not chewing our food properly may also result in undigested particles of food reaching the large intestine, where the harmful microbes may feed on it and then multiply. Furthermore, dysbiosis can also lead to systemic inflammation, which has been associated with autoimmune disease.
Leaky gut
Leaky gut occurs when the tight junctions of your intestinal wall loosen, which may then allow harmful bacteria, toxins or particles of undigested food to escape into the bloodstream. This can lead to impaired immunity, pain, fatigue, IBS, mood issues, skin problems and allergy-type symptoms. There are numerous reasons why leaky gut can occur, including after antibiotic treatment, a gut infection, or as a result of a nutrient-deficient diet. Our gut barrier is meant to keep ‘invaders’ out, but when the tight junctions loosen, the ‘invaders’ can enter and wreak havoc. This highlights the importance of ensuring we have sufficient amounts of our ‘good’ gut bacteria and also diversity, since these beneficial bacteria help to strengthen our gut barrier. Without a strong gut barrier, our immune system may begin to mount an immune response if these toxins and undigested particles of food enter the blood stream.
A healthy gut microbiome has been demonstrated to help prevent leaky gut syndrome and even reverse the condition if you do find yourself suffering from it. By embarking on the gut repair programme in the next chapter (see chapter 5), gut irritants will be removed, thus allowing your gut to begin to repair.
How healthy is your gut and immune system?
The following questionnaire, which looks at various symptoms and lifestyle factors, will give you a good idea as to how healthy your gut is and how balanced your immunity is at present.
Score 1 point for each time you answer ‘yes’.
Part 1 – General health
Part 2 – Daily diet
Part 3 – Lifestyle
Once you have answered this questionnaire, please add up all your ‘yes’ answers and refer to the points system below.
20+
If you want to achieve a strong and healthy gut and immune system, you should make substantial modifications to your lifestyle and diet. This book will guide you on how to embrace and implement these changes, but in addition you may want to see a dietician or registered nutritionist who can help you further.
10+
Your gut and immune system is likely to be performing satisfactorily, but not at its optimum. Focus on working on the areas where you have answered ‘yes’ to support your gut and immune system. This book will guide you on how to embrace and implement these changes.
9 and below
Well done – it sounds as though you have good gut health and a healthy and efficient immune system. To support your gut health and immune system even further, check where you answered ‘yes’ and focus on making changes to these areas. This book will guide you on how to embrace and implement these changes.
Our gut microbiome plays a key role in our immunity, and the interaction between our gut microbiome and immune system is ultimately what maintains our health. Moreover, the foods we choose to consume influence not only our gut bacteria, but also our immunity. Strengthening our immune system is vital to fight infection, reduce our risk of autoimmune disease and allergies, as well as preventing chronic disease.
It is very clear that one of the most important factors for a healthy immune system is good gut health, and the next chapter will guide you on this journey. You will learn how to repair and transform the health of your gut, which in turn will help promote strong and balanced immunity.