C51217: The inside story of the human microbiota

The common-knowledge perception of malnutrition is that it is a disease of deprivation leading to starvation and illness. In 2015 there were 793 million undernourished people in the world, a reduction of 216 million since 1990. 1 However, increasing affluence and easier access to food, particularly in highly refined forms, has led to malnutrition of excess usually manifested as obesity and its associated pathologies, many of which have ocular repercussions. With an estimated 600 million sufferers worldwide,2 and a quarter of the adult population in the UK being obese 3 it is now the leading preventable cause of death.4 Obesity is an increasing strain on health service resources 5 because it causes chronic inflammation which has repercussions on many conditions requiring treatment such as insulin intolerance, type 2 diabetes, hypertension and cardiovascular disease.

Primary care practitioners such as optometrists and dentists see people for regular checks while they are still healthy, and carry a responsibility for early identification of illness. They are in an ideal position to provide or refer for preventative care and counselling and for this role will need to have an understanding of nutrition. Closely linked to nutrition, the human microbiota (body microbe population) and microbiome (the genome of this population) are the subject of extensive study which is leading to a growing body of knowledge based on their considerable influence on health and disease.6-8,9

The human microbiota and microbiome

We each have about 1012 body cells, which sounds impressive until you know that we have as many as ten times this number  of microbes living in and on us. We have tended to think of them as passengers or commensals that do little else than use us as a home, but a growing body of research tells us that they are instrumental in our development and our health, both physical and mental. There is a growing belief that, rather than thinking we are a single organism, we should consider ourselves as a superorganism with an interdependent ecology between our microbes and us.

Microbes fall into three main categories. Archaea are the oldest, single-celled organisms that specialise in living in difficult environments with extremes of heat, cold or toxic substances. Many derive their energy from non-carbon sources such as sulphur or iron, and in our guts they specialise in the production of methane. Bacteria have different cell membrane compositions although they resemble Archaea in that they have no nuclear membrane. Eukaria are bigger, multi-celled organisms that include fungi, plant and animal forms.

Identification of bacteria by traditional means involves separating them out on special growth media and growing them into colonies of individual organisms so that we can run tests on them. This is relatively easy with organisms from accessible places such as skin, mouth and rectum, but much more difficult for organisms which live deep inside the intestines. They are difficult to access under normal conditions – we can get samples by putting tubes into the gut from either end, but they will be contaminated by the populations on the way to and from the sampling point. Samples can be obtained from people who have had parts of the intestine excised because of cancer and other ailments, but these do not represent normal conditions. Many gut organisms are strict anaerobes, so that exposure to oxygen kills them and makes it difficult to collect live specimens to run tests.

An alternative approach, and the subject of a very large worldwide study,10 is to identify the organisms from their RNA and DNA sequencing, which does not need them to be alive. This is a hugely complex task – to put it into perspective, the human genome contains about 20’000 genes while our microbiota have a collective genome of between two and twenty million. The person on earth who is the most different from you still shares 99% of your genes. Compared to this, the microbiome of someone in your family has only a 10% overlap with yours – theoretically, this means that it is far easier to identify someone from their microbiome than from their own genome. Sequencing involves splitting genes into shorter strips and then using the overlaps between them to piece together a picture of the whole. A much simpler task would be to cut all the words out of the biggest newspaper that you know, throw them into a bucket, and then re-assemble them correctly. These new metagenomic techniques are revealing a much wider spectrum of organisms than we have been able to identify using culture techniques.11

Development

Figure 1 shows a map of adult microbiota from the human microbiome project. Each sphere represents a distinct population of microbes, and they are concentrated in the mouth, skin, vagina and faecal areas.

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The womb is a sterile environment, and a baby’s first exposure to microbes comes during birth when it collects both vaginal (mostly lactobacilli) and faecal (many kinds, mostly bacteriodes) bacteria, at the top, right-hand corner of the diagram. In contrast, a baby that is born by caesarian section collects mostly skin bacteria such as staphylococci and firmicutes. During breast feeding the baby will ingest a variety of other organisms with a predominance of bifidobacteria, whereas formula-fed babies are more prone to collecting intestinal bacteria such as E. coli and Clostridium difficile. Babies go on to encounter a wide range of organisms through exposure to their parents, animals and their environment, all of which influence the final microbiota that they will carry as adults. In many cultures, mothers wean their babies by first chewing food for them, providing an effective transfer of their biota to the baby from the top-left part of Figure 1. Differences in early exposure have an enormous impact on subsequently developing microbial populations, and the balance between them strongly influences our health.9,13

The gut

By far the largest population of microbes that we carry is in our gut,14 about the same mass as our brain. Figure 2 diagrams the various structures of the intestine. By far the largest population of microbes that we carry is about 1.5kg in our gut, about the same mass as our brain.

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Food is mixed into chyme in the stomach from where it passes through the pyloric sphincter into the small intestine, which is about three centimetres wide and over three metres long. The liver adds bile early in this passage to emulsify fats for easier digestion. Next the contents pass through the large intestine, about 6.5cm wide and 1.5 metres long, ending in the colon and the rectum. The microbes encountered in this more than five-metre passage have many functions,15 and their composition can have a significant effect on health and disease.16

Energy metabolism

Much of our understanding of bacterial contributions to energy metabolism has come from working with mice, which has several advantages. They eat much the same food as we do, and their high metabolic rates and short lifespan provide results much more quickly. Furthermore, they are coprophages, and will eat their own and other mice’s faeces, making it easy to transfer microbial populations between them. We can raise mice in a sterile environment (called germ-free or GF mice) without any microbiota, giving us a comparator with normal bacteria-carrying mice. GF mice fed on the same diet as normals grow to smaller body weights and need more food to achieve the same weight. The microbiota help to digest food and derive energy from it.

Additional energy is made available by bacteria in the colon that convert large indigestible carbohydrate molecules such as soluble fibre into digestible short-chain fatty acids (SCFA), boosting our energy uptake by about 10-15%. They also influence the physical make-up of the intestine – GF mice have smaller microvilli in the intestinal wall than normals, exposing a smaller surface area for food absorbtion.

Mice fed on a low-fibre, high-fat diet become obese in the same way that people do, and their microbiota profiles are changed.17 If microbiota are transferred from obese mice to normals, the normals become obese, and vice-versa. Furthermore, the transfer of bacteria from an obese person to a normal mouse will also result in its weight gain - the mouse model relates to the human one. Gut microbiota shifts have been linked to increases in obesity, which in turn triggers inflammation, insulin resistance and type-2 diabetes.18

Exposure to cold results in a shift in gut microbiota to increase insulin sensitivity and the ability to derive energy from food to keep warm.19 Gut microvilli length increases adding surface area to help absorbtion. White fat is converted to brown, which, unlike the inactive white fat, burns energy in a similar way to muscle to generate heat.

Digestive/bioactive conversion

In addition to secreting bile to help with fat emulsification and digestion, the liver adds sugar molecules to active substances, a process called ‘conjugation’ that renders the substances inactive. For instance, cholesterol is removed from the bloodstream and conjugated before being released with bile into the small intestine. At the far end of the digestive tract, colonic microbes deconjugate the inactive molecule, appropriating the sugar for their own use and releasing the cholesterol to be re-absorbed and re-circulated in the bloodstream. If we eat food containing phenolics, such as apple skins or cloves, they prevent cholesterol deconjugation so that it is egested with the faeces.20 This has the net effect of reducing cholesterol levels as the liver will now take fresh, rather than recycled, cholesterol from the blood.

Digoxin, used to steady the heartbeat, is neutralised by conjugation in the liver. About 10% of the population have colonic microbes that deconjugate it again, resulting in a potentiated and prolonged effect. GF mice are more susceptible to liver damage from alcohol ingestion than normals, suggesting that some of our microbiota play a protective role in protecting the liver from damage.21 However, alcohol exposure causes some populations resident in the mucosal reservoir to proliferate, resulting in increased gut wall permeability and allowing microbes access to the liver through the bloodstream, where they are attacked by T-cells, causing inflammation and scarring.22

Immune system regulation

Peyer’s patches are elongated lymphoid structures, about 30 in number, nestling in the epithelium of the ileum, the last part of the small intestine (Figure 3). They carry a population of white blood cells, macrophages and lymphocytes that are the heavy artillery of the immune system engulfing and destroying potential pathogens, and clearing the site of dead tissue.

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Behind the epithelium are dendritic cells, which have protuberances, dendrites, that reach between the epithelia and into the lumen. The dendrites contain T-killer cells, which initiate attacks against pathogens, T-regulatory (T-reg) cells, which damp down the immune response for substances which are either ‘friendly’ or ‘self’, and T-helper cells which help both of the other two do their work.

The dendrites maintain constant contact with lumen-borne organisms, enabling them to evaluate what is harmful, triggering the release of T-killer cells, or harmless, activating the T-reg cells to damp down the potential immune system response against them. The activated T-killer cells release chemical messengers, cytokines, to bring in the white blood cells. The negotiation between the dendritic cells and the gut microbiota governs the status of the immune system, and alterations to gut populations can modify behaviour leading to sensitivity, allergies and other distortions of the normally operating system. Figure 4 shows the gut in section.

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The wall of the gut is lined with epithelial cells and goblet cells, the latter of which secrete copious amounts of mucus. The epithelial cells actively remove moisture from the layer of mucus adjacent to the gut wall, making it very thick in consistency, and impenetrable to the microbes in the lumen.

Over this lies a gradient of less dehydrated and very sticky mucus that holds a representative sample of the bacteria passing through. It acts as a reservoir protecting the microbes from purging events such as fasting, diarrhoea and antibiotics, and then releasing them after the event is over to re-populate the lumen.

Infection prevention

Within the gut microbiota population are small populations of pathogens. They never manage to grow into threatening numbers because, simply by weight of numbers, the surrounding friendly bacteria in the gut competitively deny them access to enough nutrients to do so. This balance can be upset by a course of broad-spectrum antibiotics, which depletes many of the resident populations.

The ones that survive, both friendly and pathogenic, are resistant to the antibiotic, and the depleted population of friendly microbes allows surviving resistant pathogen strains access to nutrients so that they can bloom. To fortify their position, many of these microbes produce their own antibiotics to kill surrounding nutrient competitors. This is a mechanism by which pathogens such as Clostridium difficile can become established, causing a debilitating and painful infection.

Babies born by caesarian section are more prone to infections in the first two years of life, particularly ear infections, and this is thought to be related to their microbiota profile. The situation is aggravated by the use of broad-spectrum antibiotics to treat the infections, which further modifies the resident population and leaves footholds for potential pathogens.23

Host behaviour modification

One of the more unexpected areas relating to the microbiota is that they can influence brain function and behaviour. The self-same microbes that increase our energy uptake by converting insoluble fibre to SCFA, are also able to digest mucin. If there is insufficient fibre to satisfy their needs they will turn their attention to the mucus lining of the gut, allowing microbes to access and colonise the gut wall and resulting in increased permeability. From this, cells and toxins can leak through the gut wall and into the bloodstream behind it. This is also an associated mechanism in the development of inflammatory and irritable bowel conditions, Cohn’s disease and colorectal cancer.23, 24

Babies born by caesarian section and those who have received antibiotic treatment in the first two postnatal years are more prone in later life to autism, anxiety conditions and schizophrenia. This is now thought to be connected at least partially to modification of their microbiota by these events.25 People with these psychological conditions are more prone to gastro-intestinal problems associated with different microbiota profiles.24 This can be aggravated by a low-fibre diet and the resulting cell and toxin leakage though a leaky gut wall. As this structure has similar elements in its chemistry to the blood-brain barrier, leakage through one increases the probability of leakage through the other, causing oxidative and inflammatory stress which have a bearing on the psychological state.25

Modification of the microbiota

Our gut microbe populations vary according to our diet, which can have considerable influence on health.26 Microbes that can derive nutrients from what we eat will bloom and those that cannot will decline. Having said this, we have historically based micro-populations of microbes, passed on from our families, to help us digest diets that have changed over time. Should we switch back to eating that type of diet, these populations would bloom. This diversity of our microbe populations is important, and linked to good health.

Apart from radical interventions such as the use of antibiotics, we can modify our microbiota profiles by the use of probiotic, prebiotic or symbiotic foods.27,28,29 Probiotics are live microbes that we can eat to adjust our internal fauna – think yoghurt of either the Lactobacillus or Bifidobacteria types. Prebiotics are foods that provide nutrients for desireable bacteria and can cause them to bloom, and synbiotics are a combination of the two. We know that this can work in mice25 because giving them dietary Bifidobacterium infantis ameliorates stress symptoms, and giving them E. coli aggravates them. It must be said that the strains that achieve this are often very specific, and that not every strain of Bifidobacterium would do the same.

A person’s microbe population can also be modified by a relatively new technique, faecal microbiota transplant, with sometimes remarkable results. As previously mentioned, Clostridium difficile infections cause severe stomach ache and diarrhoea which can be resistant to antibiotic treatment and can persist for years. Recent interventions in which microbiota were transferred from healthy individuals to long-term, antibiotic resistant sufferers have resulted in a better than 80% success rate in permanently curing the condition.30,31,32 As we learn what other health conditions are affected by imbalances in the microbiota, we can expect the unfolding of new and effective remedies.

Conclusions

Much still needs to be learned. But there is a steadily growing body of knowledge that shows that the human microbiota have much wider-ranging influences than we have previously thought, and the implications are that the use of this in science and medicine will lead to therapies. Over time, we can expect treatments to move from the domain of therapeutic medicine to preventative measures. If and when this happens, primary care practitioners will have a key role in identifying potential conditions early, and referring appropriately for corrective action, for which an understanding of our microbiota and their influences will be important.

Ross Grant is an optometrist and co-founder of Toolbox Training and Consultancy

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