Physiology and Ecology of the Intestinal Tract

Áine Condon, Jacob Hinds, Uilliam O' ’Regan

Introduction

The intestinal tract harbours a vast array of microbiota which play a vital role in numerous physiological processes, including digestion and the development and maintenance of intestinal immunity. These microbiota inhabit the intestinal tract from birth, and will eventually outnumber the host’s own cell count by a factor of 10 (in the human this equates to about 400g).

How Do They Get There? Colonisation of the intestinal tract

Throughout foetal development in the womb the intestinal tract is sterile. It is during birth that the new-born collects its first dose of microorganisms from the vagina and the surrounding area of the mother’s genitalia. Other microorganisms are gathered once the infant is exposed to environmental sources, e.g. bacteria on the teats of the mother (Savage, 1977).  These bacteria will be unconsciously ingested. This all happens within the first 24 hours of neonatal life (Li et al., 2012).

The majority of these microorganisms however are unsuitable, will not survive in the intestinal tract and will disappear. Some however will go on to form the beginnings of the young animal’s intestinal microbiota.

Current understanding of the sequence of bacteria uptake is poor however it is widely accepted that the first bacteria are lactobacillus taken from the mother’s milk. They inhabit all of the intestinal tract (Savage, 1977). Closely following are facultative anaerobes (e.g. Streptococcus faecialis), bacteria that are normally aerobic but can switch to anaerobism if there is not enough oxygen. Due to the lack of other bacteria these can achieve high populations within a short space of time and will gain a majority by the second day (Li et al., 2012).

The useful bacteria do not start to colonise the gut until the animal begins to eat solid food. This is when the animal can ingest anaerobic microbiota that throughout its adult life will help to digest food. At the same time due to competition for space initial bacteria (facultative anaerobes) will experience a drop in population consistent with the anaerobic bacteria’s rise. Finally after the animal is weaned yeasts inhabit the small intestine (Savage, 1977) and the animal has all the micro fauna it will need for the rest of its life.

The Role of the Microbiota in Digestion

Cellulose Digestion:

The main functions of the microbiota in the IT are to digest substances that could not otherwise be digested e.g. fibre and the anaerobic breaking down of peptides to recover nitrogen for the host (Nicholson et al., 2005).

The key purpose of digestive bacteria in the gut is the breaking down and digestion of cellulose. This is carried out with great success in the forestomachs of all ruminants; however monogastric animals also have to digest cellulose through fermentation (especially important in herbivores). To this end the fermentation process is moved into the IT.

The degree of fermentation is found by measuring the number of short chain fatty acids (SCFA) in the area you suspect fermentation to be taking place. This works because the cellulose fermenting bacteria rather than excreting water and carbon dioxide at the end of respiration excrete SCFA.

In the small intestine low levels of SCFA are found in most species except for the red bellied turtle and the emu which both show signs of fermentation on a similar scale to a cow’s rumen. Several fish, mainly tropical, show a moderately high level of SCFA in their midgut. This is thought to be in reaction to the amount of cellulose and laminarin (food reserve for brown algae) in their diet (Stevens et al., 1998).

The majority of fermentation takes place in the colon. It is here that starch and endogenous carbohydrates (e.g. mucous) are broken down in carnivores and omnivores and where cellulose is broken down in the herbivore, 70% of the natural detergent fibre (fibre found naturally in food) is digested in the colon of ponies.

Some species have specific microbiota that allows them to better digest their diet, for example there are bacteria in the IT of the minke whale which allow it to break down the tough exoskeleton of krill (made of chitin), the minke whale’'s main diet. The colon of the koala has bacteria specifically to digest the tannin complexes that are plentiful in their sole food, eucalyptus leaves (Stevens et al., 1998).

Nitrogen Recycling:

Microbiota of the IT also plays a part in nitrogen recycling in monogastric animals, especially animals with a low protein diet. The majority of nitrogen is found in the mucous (endogenous nitrogen) and in urea which is secreted at points into the lumen. Most of this nitrogen is synthesised to ammonia by the bacteria which use it as a food source. The host will then digest the bacteria as a source of protein. The rest of the nitrogen is returned to the liver. This process is especially necessary in herbivores. Donkeys that were switched from alfalfa (protein rich) to wheat, showed an increase in nitrogen recycling from 50 to 90% (Stevens et al., 1998).

The main bulk of avian microbiota is given towards the degradation of uric acid into amino acids which in turn can be absorbed by the gut (Kohl, 2012). This is especially important in birds that have a low protein diet e.g. hummingbirds. Interestingly hummingbirds have quite a hostile environment for microbiota due to the fast transit of food (Stevens et al., 1998).

Assisting normal digestive function:

Initially it was presumed that the microbiota were solely for providing a means to break down tough food sources e.g. cellulose. It is now known that they also play a part in the normal digestive function. When examined, the avian intestines show substantial numbers of saccharolytic bacteria (sugar utilizers) rather than the high amount of cellulolytic bacteria that are found in mammals. This shows that even though a bird can digest sugars itself there are still bacteria to do it. The crop of most avian species also contains bacteria which produce amylase to compensate for the bird’s poor production of the enzyme (Kohl, 2012).

Microbes can also help nutrient transfer. Gnotobiotic mice (mice given specific microbiota) were tested for sodium-glucose transporters and compared to mice with no intestinal ecology. Mice with an intestinal ecology had 2.6 times more sodium glucose transporters than those without (Kohl, 2012).

The Microbiome and Immunity:

It is well known that the presence of the intestinal microbiome confers an immunological advantage to the host. A healthy microbiome protects the animal against pathological infection and its presence continually stimulates the immune system.

Promoting Tolerance:

A tolerance of the immune system to IT microbial inhabitants must exist otherwise excessive immune reactions occur at the intestinal mucosa, resulting in pathogenic inflammation. Tolerance can be achieved in a number of ways; modification of the immune cells themselves, modification of the portions of the microbes eliciting an immune response or a physical separation of the host’s own cells from the microbial inhabitants.

Resident dendritic cells (DCs) of the intestinal mucosa are distinct from DCs found elsewhere. They preferentially differentiate T cells into Th2 and Treg cells, encouraging a more tolerant environment in the intestinal tract (Iwasaki et al., 2009). This modification of DCs is dependant on the TSLP secretion of intestinal epithelial cells. This secretion is induced by various microbiota such as Lacttobacillus ssp and various Escherichia coli (Zeuthen et al., 2008).

Modification of the microbes themselves can be accomplished by intestinal alkaline phosphatases. These dephosphorylate LPS (lipopolysaccharide) endotoxin complexes found on the surface of Gram-negative bacteria, rendering them less toxic to the host (Bates et al., 2007).

The third method is to physically separate the host cells from the microbes. The mucosa of the colon is divided into two layers, the top layer being resident to the diversity of the microbiome, while the bottom layer is impermeable to bacteria, thus it is free from bacteria altogether (Johannson et al., 2011).

The Germ-free Murine:

An interesting way to examine the benefits of the microbiome to immunity is to study the germ free animal; that is a rat or mouse whose IT is completely free of autochthonous microbes including bacteria, parasites, fungi and viruses. Germ free animals show significant abnormalities in immune function including developmental defects in lymphoid structures (spleen, lymph nodes and Peyer’s patches) and reduced levels of immunoglobulin secretion (IgA and IgG) (Sekirov et al., 2010). The reduced level of IgA production is significant since it plays an important role in intestinal mucosal immunity.

Macrophage functions such as lysosomal enzyme activities and their chemotactic response were reduced or absent in GF (germ free) mice, suggesting that the presence of microbiota is required for full macrophage activation (Yi et al., 2012).

The microvilli of GF mice were shown to be shortened or absent and their susceptibility and mortality as a result of intestinal pathogenic infection was increased (Yi et al., 2012). This shows that the presence of the microbiota play a critical role in maintaining proper development and function of the immune system. CD4+ cells were shown to be absent in GF mice. However this was completely reversed by the introduction of Bacteroides fragilis to the intestinal tract (Mazmanian et al., 2005).

How the microbes benefit immunity:

The intestinal mucosa is the first line of defence against invading pathogens in the gut and also the site of the microbial habitat. The host and the microbial community thus have a mutual interest in maintaining its integrity. Loss of this integrity due to infection or injury can lead to an increase in intestinal permeability, resulting in pathogenic inflammation. Several Lactobacillus strains are known to contribute barrier integrity by maintaining tight junctions in the intestinal epithelium (Lutgendorff et al., 2008)

Another barrier to colonization of pathogenic bacteria in the intestine is the sheer number of bacteria already present. These autochthonous bacteria provide competition for space and nutrients to transient bacteria, inhibiting their occupation. After colonization the microbiome reaches a so-called "“climax community”" where the population and composition of the microbiome become stable. Autochthonous bacteria find their place within the IT habitat and occupy a so-called niche. Transient bacteria may take up residence within the intestinal tract only when a niche becomes vacated by its indigenous occupant. This may occur as a result of some disturbance in the balance of the intestinal environment. Once the balance is re-set, the indigenous bacteria return to occupy their niche, evicting the invading bacteria in the process (Savage et al., 1977). Inflammation in response to an invading pathogen however, may inadvertently affect the indigenous bacteria as well, leaving vacated niches free for pathological colonization (Sekirov et al., 2009).

Aside from forming a physical barrier against invaders, certain bacterial strains actively aid in the immune response. Members of the Lactobacillus spp produce lactic acid, disrupting the outer membrane of bacteria and aiding the host cell’s lysosomal activity (Alakomi et al., 2000). Lactobacillus has also been shown to produce antimicrobial substances which are active against invading bacteria (Liévin-Le et al., 2007)

The microbiome and disease: upsetting the balance

Harmony within the intestinal tract is maintained by the stable population of its microbiome. This population is vital for metabolic, digestive and immune processes. An imbalance within the microbiome due to a change in composition or population can lead to a diseased state.

In humans a well known example is IBD and Crohn'’s disease, where an abnormal composition of bacteria has been noted compared to normal subjects (Seksik, 2010). Pathogenic inflammation is characteristic of this disease.

Metabolic disorders due to microbial imbalance can also occur, for example fat and lipid-soluble vitamins may not be absorbed due to the deconjugation of bile acids by microbial bacteria (Hooda et al., 2012).

Disorder and sudden change causing disease is a common problem in post weaning piglets who develop diarrhoea. The problem is believed to be caused by a combination of stress and the profound alterations in the microbiotic composition brought about by the sudden change in diet. The addition of prebiotics (carbohydrates) to the post weaning diet can significantly improve intestinal health in weaned piglets (Lallés et al., 2007).

Factors affecting microbial population

Food intake and diet:

It seems obvious that composition and population would be significantly influenced by the diet of the host, given the close connection between microbial population and digestive processes. Although imbalance in the composition of the microbiome can lead to disease, it is also flexible and can adapt to dietary changes of the host. This has been demonstrated in numerous studies on several species. Pigs fed an unconventional diet containing cooked rice supplement showed a change in the composition of their microbiome compared to those fed a conventional diet. This suggests that the microbiome changed to adapt to this new digestive task (Isaacson et al., 2009, Leser et al., 2000).

GI host health is measured by the composition of bacteria in the faeces. An increase in beneficial bacteria such as bifidobacteria and lactobacilli are considered to be a good indicator of intestinal health (Hooda et al., 2012). Prebiotics (non-digestible components added to the diet which stimulate the growth of beneficial bacteria in the gut) and probiotics (the administration of live beneficial micro organisms to the host) have been shown to alter the microbiome in a positive way.

The addition of carbohydrate to pet food for example can alter the microbiome and improve the IT health of dogs and promote the growth of beneficial bacteria, as well as improving laxation and stool quality (Hooda et al., 2012). Middelbos et al. (2009) demonstrated that dogs fed blends of fermentable carbohydrates showed an increase in faecal bifidobacteria compared to controls. Similarly, in cats with chronic diarrhoea the addition of prebiotics lessened its frequency and duration (Minamoto et al., 2012).

Temperature:

This can most obviously be seen in a comparison between birds and mammals. The mammalian IT exhibits more species of bacteria due to the more hospitable temperature of their bodies. However avian specific Borrelia garinii, a Lyme’s disease agent, has adapted to thrive at higher temperatures than its mammalian counterparts (Kohl, 2012).

Habitat:

The Baas-Becking hypothesis proposes that

“"All microbial life is distributed worldwide but that the local environment selects upon, and is therefore in part responsible for, the variation in microbial biodiversity between different environments."” (Camp et al., 2009)

As an example an animal in a habitat with less protein rich food would have a less wasteful nitrogen recycling process.

pH:

In a study carried out on pigs it was found that a lower pH had little effect on any beneficial microbiota in the lumen but had a negative effect on E. coli. and therefore a positive benefit on the pigs. (Mikkelsen et al., 2007)

Location within the GI tract:

The population of the micro biota differs in different regions of the GI tract. Population in regions where digesta passes relatively quickly is possible only by species that can attach themselves to the epithelial surface, for example in the small intestine. Thus populations of bacteria are much greater in more stable regions, such as the cecum and colon (Savage et al., 1977).

Other factors:

These include age and digestive throughput and have been dealt with in colonization and digestion respectively.

Conclusion

The animals microbiome also has serious implications for human health. An imbalance in the microbiome of intensively farmed can cause an increase in bacteria which could travel down the food chain and ultimately cause disease in humans (Dunkley et al., 2009).

The microbiome clearly has a huge impact on the health and wellbeing of the host. More research is needed to properly understand fully its role and potentially utilise it to treat intestinal disease, enhance wellbeing and increase productivity.

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