The Human Gut Microbiota Part II

Written by ACA Contributor Andrew Chappell BSc (Hons), MSc, PhD, RNutr Sport

Prior to reading, this section it is worth stating that I would not expect the average reader to be able to memorise all the individual bacteria named or the interplay between them. I have included them to help the reader appreciate the complexity of the microbiota and emphasis the difficulty in making recommendations for human health.

The relationship between humans and the microorganisms that colonise the digestive track is a story of long and complex coevolution. This symbiotic relationship has led some to describe the two as a \”superorganism\”, greater than the sum of the parts. The human gut provides an energy abundant environment for microbes to thrive, while the host benefits from the additional energy provided via the fermentation of indigestible nutrients. There has been considerable interest in the gut microbiota from the health and fitness community and many associated microbes with conditions such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD) and Celiac disease. Conditions such as the metabolic syndrome (a term used
to describe the combination of obesity, type 2 diabetes mellitus (T2DM) high fasting triglycerides and blood pressure) have also been linked to good and bad gut bacteria with little for consideration the evidence to date. In this are the health and fitness field lacks experts and there is a limited understanding of the field of microbiology beyond food safety considerations. The interest in this area is obvious as practioner’s aim strive for improved quality of life for amongst their clients. However, causal links are yet to be drawn between the microbiota and the aforementioned conditions, save perhaps patients suffering from IBD. The role of the resident microbiota in health and disease is briefly summarised in Figure 5.

Figure 5. The Role of the Gut Microbiota in Health and Disease: Microbial products or activities presented in the centre column are actions of the whole community rather than single bacteria. Taken from Flint et al. 2012.

Collectively the microbes that coexist “within” or “on” the human body are referred to as the Human Microbiota, while the sum of the genes (DNA) associated with these microbes is referred to as the Microbiome. Be aware the term Microbiome is often used to refer to the microbiota. The microbes that make up the microbiota are largely bacteria, although a small amount of fungi, a vast community of viruses and another group of microbes called Archaea also call the human body home (figure 6). Little is known about these other groups of microbes and how they influence health and when researchers discuss the microbiota they are often only referring to the bacterial component of the microbiota which makes up over 95% of all microbial biomass of the gut.

Figure 6. Tree of life, Common ancestors of all life, Microbes that inhibit the gastrointestinal tract belong to the Prokaryote Bacteria, Achaea as well as Eukaryote Fungi. There is some debate as to whether viruses constitute a living division or a fourth domain. Note that within the bacterial division there are several potential categories called phylum that are as diverse as the Eukaryotic categories of plants and animals.

Microorganism are also not restricted to the colon; the mouth, scalp, hair, genitals, feet and arm pits all offer unique environments for microbes to thrive. These microbes are also included in the definition of the human microbiota and are subject to the same scrutiny by researchers for their role in health and disease as those that occupy the digestive tract. For example a disease such as eczema, may be characterised by its own a specific set of skin microbes. Likewise, researchers wishing to create a new anti-perspirant have to consider the role the arm pit microbiota during development.

The colon, is home to the largest microbial population in the human body, and believe it or not is one of the most densely populated microbial environment in the world. As many as 100 trillion (1014) microbial calls, or ten times the number of human cells call your colon home. Currently upwards of 1,150 different bacterial species have been identified from human samples, with that number increasing all the time thanks to programmes such as the Human Microbiome Project (HMP). An individual’s may harbour upwards of 150 different species, who’s composition and relative abundance is unique enough to create a microbial fingerprint influenced by; environment, diet, age and health status. The fact that any one individual may harbouring an almost infinite combination of species means there is considerable inter-individual variation. A common core of species may however constitute between 20 – 40 % of the bacteria that inhabit the colon. Despite having some shared species, the contribution these microbes may make to a person’s total bacterial biomass can also vary significantly.

The microbiota also varies significantly across the world, thus defined what constitutes a healthy microbiota is increasingly difficult. A healthy microbial community in one part of the world can be quite different from that in another part of the world. Indeed if there is a common core it appears apparent that those from western cultures have different microbiotas than those of the Hadza hunter gathers, Malawian tribes and Venezuelan farmers. This in part is likely to do with diet, but also environmental conditions, exposure to medicine and practices related to animal husbandry. This has led some to raise the hypothesis of the disappearing microbiota, whereby living in more primitive conditions results in a more diverse microbiota (figure 7). Here in lies one of the major problems facing microbial research, firstly establishing what microbes inhabit the gut, and thereafter what microbes inhabit a supposedly unhealthy or \”dysbiotic gut\”. When met with questions about dysbiosis and the healthy microbiota I often respond with my own set of questions. “Dysbiotic or unhealthy compared to what?” Indeed as I will go onto to discuss it is likely that the microbiota can exist in a number of configurations all of which are seemingly healthy for the individual. The addition of prebiotic or probiotic formulas in which case may do little if anything to improve health, while the suggests that there may be an optimal configurations seem almost puerile or at the very least based on a lack of understanding.

Figure 7. Differences in the gut microbiota between environments. Rampelli et al. 2015. Cell 25 (13) 1682-93.

To tackle the issue of trying to characterise the healthy gut researchers have come up with a range of solutions and ideas such as Entrotypes, community structures, and gene/species density have all been mooted to characterise the healthy gut. What is apparent is that a healthy gut microbiota likely has a significant number of permutations. As a result increasing consuming probiotic formulas (specialist microbial formulas that when consumed as part of the diet may confer a health benefit to the host), or comparing your gut microbiota to other fitness professionals with the aid of gut microbiota screening programmes (UBIOME for example) may have little if any consequence for gut health. Gut microbiota composition 1, 2, 3, 4, and 5 may likely be as good as composition 6, 7, 8, 9…1053, etc. The reason for this largely has to do with the genetic potential of the microbes themselves and their abilities to occupy a niche, or perform a function or role of another microbe. That’s not to say there are not keystone species, but rather microbes are tough little critters with many of them able to perform multiple roles, which allows for a degree of flexibility in the community composition. To use an example that many will be familiar with on a farm there a number of mammals that might be able to occupy a similar niche: voles, shrews, rats, and field mice might all be effective at keeping the insect population under control or stealing corn. These small mammals become a potential fuel source for birds of prey, and larger mammals such as cats, and foxes which go onto sustain the insect and plant population via their faeces (figure 8).

Figure 8. Ecosystems. The colonic environment has its own ecosystem where microbes inhabit different regions of the colon and thrive depending on the nutrients and conditions present. As with other ecosystems different microbes may be able to carry out similar roles or outcompete others to occupy the same niche.

The ecology of your own colon is no different and where one microbe may have a particular talent for breaking down a type of fibre which allows the community to flourish, several other species may also possess the same genes and given the chance could perform the same role. Like other ecosystem these environments are extremely competitive. Also worth considering is the
scale of our farm example comparison to our microbial environment. A farm ecosystem may span 3 to 4 square km, while the equivalent micro environment might contained as much life in 3 to 4 square mm. Environmental conditions are also important for microbes and Bacteroidetes and Proteobacteria grow better at pH conditions > 6.25, conversely Firmicutes and Actinobacteria tolerate lower pH conditions at pH 5.5 (Duncan et al. 2009). The ability of bacteria to degrade a number of substrates or act as specialist degraders is therefore important in determining if a bacterium is likely to be a transient or permanent member of the gut community. Within this environment, a microbe may have both aerobic and anaerobic regions and the opportunity to interact with different human cell types at the base of intestinal villi (figure 9). This is one of the reasons why the species and strain of a probiotic matters as it influences their genetic potential. A particular species may not have the same ability to degrade fibre as another, or even within a species a strain may be more or less adapt at living under certain pH conditions. Systematic reviews and meta-analysis therefore that cite the health promoting properties of probiotics attributed to multiple rather than single species therefore hold little weight when reviewed by the more astute microbiologist.

Figure 9 Microbial Microenvironments within the Large Intestine: 1 The inner mucin layer contains a limited number of bacteria in the healthy human; 2 The outer mucin layer is home to specialised mucin degraders such as Akkermansia muciniphila; 3 The gut lumen is home to a diverse array of bacteria; 4 undigested large particles can be home to specialised primary degraders like Ruminococcus spp. Taken from Flint et al. (2012a).

Basic Phylogeny

As stated previously there are upwards of a 1000 species within the gut and over 150 in any given individual. Despite a seemingly infinite number of variation in species composition, a relatively small number of phyla (categories of microbes of which there are between 12 to 30 in the tree of life) dominant the colonic gut microbiota including: Firmicutes, Bacteroidetes,
Actinobacteria and Proteobacteria. Beyond the phyla microbes can then be further sub divided into the family and genus level which I’ve detailed in the legend of Figure 10. After the genus level comes individual species and then strains of bacteria which contribute to the huge interindividual.

By comparison the process of categorisation is the same as the rest of the animal kingdom. Dog breeds for example can be categorised a similar way; a Yorkshire Terrier breed (strain) belongs to the common dog (species), part of the canine family, a subclass of placental mammals (phyla), part of a wider family of Eukaryotes to which plants and fungus are also members.

These descriptions of phyla, family and species are non-trivial and species and strain have distinct consequences for a microbes’ functional ability, which I alluded to earlier. To use another example, a Giant Panda and Vampire Bat are both Mammals part of the animal kingdom, however both have evolved separately and developed a distinct set of tools to cope with their environment. One is 160kg bear which eats primarily bamboo, the other a 200g flying real life Dracula whose diet consists of blood from other mammals. The same consideration need to be given to the study of microbes and even within a species differences between strains can have distinct consequences for human health. The well-known Proteobacteria, Escherichia coli, (E. coli) has at least 42 different strains, each containing its own compliment of genes suited to survival in its own unique environment. A small number of E. coli strains are pathogenic (harmful to your health). O157 for example can kill you, while others strains are benign and routeinly feature as part of probiotics being consistently found in the microbiotas of the Hadza hunter gathers. Such details is important when considering the role probiotics may play in human health. Not just any old combination of microbes will do, and even where you have formulas of 8 or more there\’s no guarantee any are capable of thriving in your colon.

Figure 10. Phylum and Genus Level Analysis of the Gut Microbiota of 27 Hadza Hunter Gathers Compared to 11 Italians.

Panel A, Phylum analysis of the gut microbiota, note the most dominant species belong to the Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. Spirochaetos and Proteobacteria are largely only found in the Hadza Cohort. Panel B, Genus analysis of the same cohort where individual differences become more apparent. Bacteroides, Roseburia, Ruminococcus and predominate. Note the difference between the two populations and the fact that the Bifidobacterium genus to which Probiotic Bifidobacteria belongs is only present in the Italian cohort. The Bacilli or Lactobacillaceae family to which the probiotic bacteria Lactobacillus is a member is undetected or not present in any of the 38 individuals sampled. Beyond the Genus level induvial species diversity can then be sampled.

Energy Production by the Microbiota

The host benefits from bacterial metabolism of indigestible nutrients from the upper GIT, as well as salvaging energy from host mucus, and other proteins. So, as well as indigestible dietary fibre, resistant starch, excess protein and fats which reaches the large intestine are also fermented. The human body possesses a limited number of different digestive enzymes capable of chemically breaking down macronutrients to there individual components, sugars, amino acids and lipids. By comparisons the gut microbiota possesses hundreds of different enzymes to breakdown the indigestible food that reaches the colon. It\’s not just food that microbes degrade, the mucus layer which lines the small intestine, any enzymes or bile salts not reabsorbed and shed intestinal cells (which are consistently shed and being replaced) are also fermented by the gut microbiota. Bacteria generate energy and multiply by the process of fermentation, which means they generating energy in the absence of oxygen. Humans combine O₂ with the nutrients in food to generate energy creating CO₂ as a by-product. Microbes on the other hand ferment nutrients without O₂, and create a variety of by-products including short chain fatty acids, hydrogen sulphide H₂S, Methane CH₄, CO₂, and branch chain fatty acids. It is even possible to broadly classify people into two distinct groups of either methane or hydrogen producers dependent on their gut microbiota composition. Methanogen producers make up roughly 30 to 50% of the population and can be assessed by using a simple breath hydrogen testing. Such tests can also be used to help in the diagnosis of conditions such as IBD. Interestingly many of the fermentation products produced by the gut microbiota can be further metabolised by other species within the large intestine, in the same way insects or plants might be able to grow from the faeces of other larger mammals in the example above. These reactions are described as cross feeding. overall this bacterial fermentation produces SCFA that provide up to 3 to 7 % of an animal’s metabolic needs (Cummings & Englyst 1991, Cummings & Macfarlane 1991, and Flint 2011).

Immune system development

The resident microbes that populate the GIT play an important role in the development and priming the immune system as the host’s primary objective is to protect itself from infection (Sansonetti 2004). Perturbations to this complex relationship between host immune system and microbes may result in the development of disease and some have suggested a causal link with the “hygiene hypothesis” and autoimmune disorders (Bach 2002) as seen in figure 11. It is worth pointing out that the same mechanisms may in part be related to the development of food intolerances. i.e the long term abstinence from certain foods may reduce the tolerance from the immune system for certain bio-active molecules associated with foods.

Figure 11. The Hygiene Hypothesis: As infectious diseases have been reduced over the last 60 years the incidence of autoimmune conditions has increased. Some have suggested a lack of exposure to microbes and an overly clean environment may be a contributing factor.

The hygiene hypothesis suggests the decline in infectious diseases in Western society may play a role in the rise of autoimmune diseases, because of a lack of immune system priming. Thus it is important to establish the composition of a healthy gut microbiota, its functional capacity, what the keystone species may be, why certain species may be more competitive than others, how microbial metabolites may be beneficial or deleterious to health and how we may be able to modulate the microbiota (Duncan et al. 2007, MacFarlane et al. 2008, Russell et al. 2011, Walker et al. 2011, Ritchie & Romanuk 2012, David et al. 2014a, Scott et al. 2013, and Sonnenburg & Sonnenburg 2014).

Written by ACA Contributor Andrew Chappell BSc (Hons), MSc, PhD, RNutr Sport

Andrew is a professional natural bodybuilder and has been involved in the health and fitness industry for over 10 years as an instructor, coach, nutritionist, researcher and lecturer. Andrew has an undergraduate degree in sport and exercise science from Herriot Watt University, a post-graduate degree in human nutrition and metabolism from Aberdeen University and PhD in human nutrition from the Rowett Research Institute. During his PhD Andrew studied the effects of dietary fibre on human health, specialising in; the environmental and genetic factors influencing the nutrient composition of cereals, and the effect of dietary fibre on the colonic gut microbiota. Andrew lectures in sports nutrition at Sheffield Hallam University with a current research focus on, the dietary strategies of natural bodybuilding populations and ergogenic aids in resistance training. As a course tutor with ACA he’ll be delivering content with a specific focus on gut health and disease.