The Human Gut Microbiota Part I

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

Foreword

Before writing these articles, I asked the ACA community if there were any particular subjects related to the gut microbiota they would like me to address. A diverse range of topics from chemotherapy to stress was mooted. It quickly became apparent the role the gut microbiota in human health is somewhat opaque and if you will forgive this author sometimes overstated. It is my belief that once a basic understanding is established a learner is able to answer many of their own questions, or seek the answers to those questions. The aim of these articles is therefore to provide the reader with an understanding so they may be able to form their own conclusions on topics related to the gut microbiota. Along with detail on microbes I’ve also included some basic concepts of physiology important in understanding the microbiota. The saying “the devil is in the detail”, is apt for the study of microorganism. There is perhaps no detail greater than peering into alien world at the end of a microscope. Simplified explanations although well intentioned, often they omit crucial detail or can be so simple they are wrong. Where possible I’ve simplify concepts and provided examples the reader might find useful. Concepts such as phylogeny I felt were relevant and provided the reader with additional understanding to help in dealing with issues like probiotics.

An important caveat when discussing the field of human health is that although nutrition and exercise are preventative measure against disease they are rarely panaceas. Nutrition and exercise interventions operate in the space between fullyfledged pathologies and the tipping points before disease. Mild vitamin deficiencies and pre-metabolic diseases maybe targeted with diet and exercise. However, once the tipping point is passed often pharmacological intervention is required to manage disease. Nutrition and exercise can of course help with management; however, practitioners should be sceptic of those proposing cures from curiosities like cinnamon, flaxseed or Acai berries. Conditions such as inflammatory bowel disease (IBD) – an umbrella term describing ulcerative colitis and Crohns disease- requires management by a multidisciplinary team of medical professionals including gastroenterologists and dieticians. Very often IBD patients are prescribed a cocktail of anti-inflammatory medications, may temporary or permanently live with a colostomy bag, or may undergoing surgery to have part of their lower bowel removed. Such conditions are not managed by fermented cabbage, low FODMAP diets and probiotics and should be left to professionals.

Microbiology Anatomy and Physiology of the Upper Gastrointestinal Tract

Prior understanding the role of the microbiota in health a grasp of the basic physiology of the gastrointestinal tract (GIT) is helpful. The following definition will also help in understanding of the microbiota:

The process of obtaining energy from food begins within the mouth. The mechanical process of chewing releases salivary amylases, which initiates the chemical digestion of long chain carbohydrates called polysaccharides. Once food is broken down into small enough portions (or not in some people’s case), it is propelled down the oesophagus to the stomach by the process of peristalsis. Once food passes from the oesophagus to the stomach it is called “Chyme”. The arrival of chyme in the stomach stretches it causing it to mix, knead, twist and compress. This stretching stimulates the stomach cells to release hydrochloric acid to aid with the digestion of food. The stomach environment as a result is extremely acidic. The pH within the stomach can drop below 2 and is relatively constant during digestion. For acid based diet or raw food enthusiasts such facts are worth remembering. The peristaltic movement of the stomach also stimulates the secretion of gastrin and the protease enzyme pepsin (responsible for the digestion of protein). A triacylglycerol lipase is secreted from glands within the stomach which aids in the digestion of fats (Mariebe & Hoehn 2007 and Frayn 2010). Once the chyme is suitably digested it passes through the pyloric sphincter into the first part of the small intestine called the duodenum (Figure 1). Bacteria that occupy the stomach have not been extensively characterised, although the bacteria belonging to five major phyla, which dominate the GIT: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria. The most common species detected in the stomach include H. pylori, Streptococcus spp. and Prevotella spp. (Bik et al. 2006). The extreme conditions of the stomach mean that the number of microbes which occupy the stomach are relatively low. However, an overgrowth of H.pylori can result in stomach ulcers, heartburn and other symptoms of irritable bowel syndrome (IBS). Patients may have to undergo treatment involving several courses of multiple antibiotics, and proton pump inhibitors to reduce stomach acid. A sauerkraut diet or exercise regime is unlikely to be effective in managing such conditions.

Figure 1. Anatomy of the Gastrointestinal Tract: Taken from Mariebe & Hoehn (2007).

Chyme passes from the stomach to the duodenum, the first part of the small intestine. The small intestine is around 6 – 7 m long adjacent to the colon (large intestine). The small intestine surface is covered in villi and microvilli known as the brush border membrane, which protrude like fingers from the epithelial surface increasing its surface area for absorption by as much as 600 times. Virtually all-human enzyme derived digestion takes place in the small intestine. This is also where the GIT organs, the pancreas, gall bladder and liver interconnect with the alimentary canal (mouth, oesophagus, stomach, small and large intestine) and the immune system interacts with the GIT. Specialists immune cells called Dendrite and Payers Patches sample microbes, nutrients, and other foreign bodies that find their way into the GIT at this point (Sansonetti 2004 and Bron et al. 2012). Indeed, one of the major roles of the gut microbiota is in the development and maintenance of the immune system via its constant interaction with these specialised immune cells. A thin mucus layer creates a barrier between the bacteria of the small intestinal and the cells that line the GIT (epithelial cells) preventing direct contact between the two. The presence of gut microbes stimulates these intestinal cells to continually secret mucus maintaining this barrier. The mucus itself is also full of antimicrobial compounds. The presence of microbes also forces intestinal cells to form tight junction barriers to prevent bacterial cells entering the blood stream (figure 2). Some have proposed that “Leaky Gut” (figure 3) -the infiltration of microbes into the blood stream via GIT- may be associated with IBS or IBD. However, this would essentially be a low or basal sepsis and more likely associated with a diseased rather than healthy individual, or IBS suffer for that matter. However, within IBD the lining of the GIT can become significantly damaged and in such a condition a Leaky Gut seems more probable. Under such circumstances a prebiotic, gluten free or FODMAP diet would clearly be in suffice to treats sepsis. Readers should be sceptic of those purporting healthy individuals may suffer from leaky gut or that “toxins”, poor diet or “bad” bacteria are the causes.

Figure 2. Components of the intestinal barrier Between the microbes that inhabit the gastro intestinal tract and the epithelial cells that line the small intestine there is a chemical barrier formed by mucus. The mucus layer contains antimicrobial compounds secreted by intestinal cells. Immune cells called dendrites interact with the small intestinal environment by extending dendrite arms into the mucin layer to sample microbes. (adapted from Hooper 2009. Nature Reviews Microbiology 7(5), 367-74.)

Figure 3. Proposed leaky gut syndrome and healthy/diseased intestinal tissue.

Left image, microbes infiltrate the body through gaps between intestinal cells. Right images, In inflammatory bowel disease the cell lining may be compromised. Image A, healthy intestinal lining, image B, C, and D progress damage to the intestinal wall in a IBD patient, may lead to infiltration.

As chyme passes into the small intestine from the stomach, the pancreas releases bicarbonate (an alkaline solution) to neutralise the acidic chyme. This release of bicarbonate influences pH of the small intestine and creating a gradient from pH 4 at the start to pH 5.5 as the small intestine reaches the colon. Pancreatic enzymes responsible for digesting macronutrients (amylases: carbohydrates, proteases: proteins and lipase: fatty acids) are secreted from the pancreatic duct, and act to reduce proteins to amino acids and digestible carbohydrates to individual sugars (monosaccharides) for absorption and transport to the liver. Bile salts from the gall bladder act as strong detergents to emulsifying fats allowing pancreatic lipase to digest the fats, which are then packaged (into chylomicrons) and transported to the liver through lymphatic system.

Constant peristaltic movement results in a fast transit time through the small intestine. This fast transit time keeps microbial numbers low as a result (only 10⁵ microbes per gram) compared to the densely populated large intestine (10¹² microbes per gram) (Breghouse et al. 1984, and Johansson et al. 2011). Microbes simply cannot grow fast enough before they are washed out of this region of the GIT. The small intestine is therefore not a major site of bacterial growth within the body. Microbes in the small intestine rarely exceeds 1 x 10⁵ per gram, except for disease conditions like small intestine bacterial overgrowth where microbial populations exceed 1 x 10⁶ per gram (DiBaise 2008). There are practical difficulties with sampling the small intestinal microbiota. Samples from patients undergoing surgery has identified several species of Lactobacillus spp., Candida albicans, Staphylococcus spp., Streptococcus spp., and Enterococcus spp. (Cregan & Hayward 1953). Subsequent trials in IBD patients where ileostomy effluent (collected from a bag similar to a colostomy bag positioned at the end of the small intestine) has been collected, have identified similar microbial species as well as Bacteroides spp. and Clostridium spp. (Breghouse et al. 1984). However, both circumstances may not be representative of the healthy human small intestinal microbiota. Conditions similar to the small intestine however can be replicated in the lab and generally show microbes capable of growing between pH 4 and 5 fare better. The more astute readers may have also concluded from this that different microbes thrive in different regions of the GIT. Microbes therefore unable to grow quickly and at pHs between 4 to 5.5 are unlikely to do very well in the small intestine, or be effective in combatting conditions like “leaky gut” or small intestinal bacterial overgrowth. This also begs the question could any microbe be an effective treatment for such a condition. Digestion and absorption in the small intestine is extremely efficient and any undigested nutrients, (mainly indigestible dietary fibre and resistant starch) pass into the large intestine where they can be fermented by the colonic gut microbiota.

The Colonic Gut Microbiota

The large intestine, or colon at one time was only thought to be important in the reabsorption of water and the transit of waste materials from the body. This view has changed dramatically, and the colon is now recognised for the important role the microbiota plays in fermentation of non-digestible dietary and host derived components.

The large intestine has a greater diameter than the small intestine (around 7 cm) but is considerably shorter (around 150 cm) and has a smaller surface area (around 1300 cm²). Nutrients enter the large intestine via the Ileocecal valve into the Cecum before traveling up the ascending/proximal colon, across the transverse colon, down the descending/distal colon before reaching the sigmoid colon where undigested/unfermented nutrients and bacterial biomass are excreted via the rectum as faeces (figure 4).

Figure 4. Anatomy of the colon.

Peristaltic movements are limited within the colon to the descending and sigmoidal regions to around one every 30 minutes which results in longer transit times compared to the small intestine (60 h compared to a few hours in the small intestine) (Mariebe & Hoehn 2007 and Ghoshal et al. 2012). There is however, considerable inter individual variation in the transit time, which has consequences for diagnosing conditions such as IBS. Defining the symptoms associated with IBS such as transit time can therefore be challenging, as what may be considered a healthy number of bowel movements in one patient may be excessive for another.

This difference in transit time influences bacterial fermentation and the absorption of short chain fatty acids (SCFA) produce as by product from fermentation. Nutrients pass quicker through the initial regions of the colon and fermentation is greater in this region as more nutrients are readily available. The generation of these SCFAs is one of the major roles of the gut microbiota and the proportion and quantity of SCFA produced seems to have major consequences for gut health. The SCFA are important in both the maintenance and development of the GIT, immune system as well as being an energy source for the body\’s cells. The SCFAs are also anticancer properties associated with them. The three main SCFAs produced by the microbiota are acetate, propionate and butyrate. All three are absorbed by the colonic cells (colonocytes), acetete can be utilised as an energy source by the cells around the body, propionate is primarily an energy source utilised by the liver and butyrate is the main energy source for colonoctyes as well as having potential anti-cancer properties. Such is the importance of these three SCFAs the presence of high amounts of the SCFA lactate at the expense of other SCFAs is often a marker of ill health.

Because of the nutrient availability in the initial regions of the colon the microbes that inhabit this region are equipped with the ability to degrade an assortment of soluble carbohydrates. This results in greater fermentation and therefore a pH gradient between the regions of the colon from an initial 5.5 in the proximal to 6.5 in the distal colon. As well as a pH gradient there is a mucus gradient whereby the mucin lining becomes progressively thicker from the proximal to the distal colon (Johansson et al. 2011). This mucin layer in the colon is considerably thicker than in the small intestine and consists of two separate layers. There is a dense inner layer with a limited number of bacteria and a more defused outer layer populated by bacteria. The mucin layer itself is full of antimicrobial peptides, secreted by colonocytes and goblet cells which limits the number of bacteria that may interact directly with the cells the line the large intestine (Sansonetti 2004, Bron et al. 2012 and Johansson et al. 2011). The pH, transit time, mucin layer, antimicrobial compounds, cross feeding interactions and sampling immune cells all influence the bacteria which are capable of occupying the different regions of the GIT and thus the ability of microbes to influence human health (Duncan et al. 2009). These are therefore important considerations for the probiotic scientist.

Differences in pH and transit time between regions are non-trivial, particularly since most diseases of the lower bowel occur in the transverse and sigmoidal regions. One of the reasons for this may be because of the increased contact time between potentially harmful carcinogenic compounds and the intestinal cell lining. Harmful microbes or carcinogens pass quickly from the start of the GIT until they reach the end of the colon. As a result, they have little time to interact with cells the line the GIT until they reach the descending colon. Likewise, pathogenic bacteria (disease creating microbes) don’t tend to fair very well at lower pH conditions, and thus tend to do better at the higher pHs of the transverse and sigmoidal colon where they can be more competitive and are able to grow at a slower rate. Therefore, one of the major challenges for researchers working in this area is how they might be able to increase SCFA production in this region of the colon thereby reducing the likelihood of disease.

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.