Managing the Microbiome
Managing the Microbiome



So what is the Microbiome? Recent work now suggests that of all the cells in the body of a mammal, at least 90% are bacteria. On top of that, there are at least one hundred times as many viruses as bacteria. Once this statement is understood, it becomes clear that helping the correct bacterial population to develop will lead to better health.

The bacteria interact closely with the host animal. There is evidence that they block receptor sites for other pathogenic bacteria, help develop the gut immune system by stimulating certain types of intestinal cell, produce products called bacterins which will interfere or kill other “non-friendly” bacteria and even help with digestion.

Where does a neonate collect its bacterial Microbiome? It is now recognised that there are bacteria transferred before birth/hatching and the embryo has some of the mother’s bacteria developing in the intestine. The birth canal is found to change in bacterial flora to lactobacillus type, which then are the early colonisers via the mouth in mammals. In birds, the embryo in the egg has bacteria within the intestine from the mother. Recent research has shown that in humans, a type of immune cell collects bacteria from the intestine and transfers them to the breast, ensuring transfer to the breast feeding baby. There is no reason to assume this system works in other mammals. So there is a range of ways normal bacteria cross to the neonate and start the development of a healthy normal microbiome.

So what goes wrong? The developing intestinal tract is open to many bacteria as early on, some of the natural barriers, such as the acid levels of the intestine and the normal mature immune system, are not fully developed. Unfriendly bacteria such as E. coli gain access from the environment and therefore water cleanliness and general environmental contamination is very important. If the mother’s canals have an abnormal intestinal flora due to stress, feed restrictions, or the actual type of feed this will also lead to the transfer of abnormal bacteria.

With this information, it is clear that the solution is to provide as many normal bacteria as early as possible to the neonate so as to encourage the quicker development of a normal gut flora and environment. Some bacteria will occupy sites in the intestine and others will be able to produce anti-bacterial products. Most importantly, we aim to help develop the natural intestinal environment by speeding up the acidification of the upper gut.

The seeding process is particularly important in poultry where often there is separation of the day old animal from the mother’s environment and there is less chance for it to develop a normal gut flora from seeding from the environment. However, in pigs, calves and lambs, it is important to ensure that the initial seeding is correct. Otherwise, an abnormal microflora can develop. 

The Poultry Case:


There are a range of bacterial colonies we can use. The ultimate solution in poultry is the use of a complete bacterial adult population (or as close as this can be made) which should be given as soon as the chick hatches. This product is called Aviguard and is known as a competitive exclusion product.

The alternative approach is to supply a probiotic, often a single source of bacteria which will have a specific function. We recommend a single bacteria called Lactobacillus farciminis. This produces a very high level of lactic acid and can be used in a range of species such as birds, pigs and calves. The product is given for the first week of life where normally the intestine has high lactobacillus and needs to be acidified. The lactic acid feeds other bacteria which then produce butyrates which have a positive effect on the intestinal cellular integrity and the development of the immune system. This product is called Biacton and can be given in feed or in water.

Whether it is a competitive exclusion product or a probiotic we need to deliver it correctly to the animal. We have developed gels, water treatments and in-feed products and systems to apply them to the farm, hatchery or neonatal unit. 

As well as simple bacterial cultures, it is possible to add killed bacteria which will specifically develop the immune system and, together with mucopolysaccharides, will lock up the surface of the intestine to prevent or reduce unfriendly bacterial binding and creating damage. We use a product called Zoolac either as a paste for piglets or in feed to achieve this aim.

Some bacteria focus on production of anti-bacterial products called bacterins. These often do not colonise the intestine for long and are sometimes not true commensals. The classic product is based on a patented bacteria called Bacillus subtilis trademarked CLOSTAT®.   The bacteria is produced in a feed supplement called Intestinal Essential and focuses on killing Clostridia perfringens bacteria which cause enteritis and toxins which damage the intestine. The use of an in-feed product rather than water has problems but we have sourced feed additive machines which will add this licensed product to feed at the required low rate. 

Finally we have added useful bacteria to electrolytes and other probiotics (products which will support the developing bacteria) and produced a water additive called Enterocid Duo which contains two bacteria as well as minerals. 

ABC’s aim with developing the microbiome is to support the good bacteria and help speed up the normal changes in the intestinal environment. It is clear that each farm will have other factors in the environment competing with these interventions. As well as adding bacteria we have to look to remove or reduce abnormal bacteria and so a core protocol in ABC is to review the site and parental bacterial populations. If the neonate already is infected before “friendly” bacteria are added then the outcome will be considerably worse. So as well as Seed we have to Weed.



ABC’s aim with developing the microbiome is to support the good bacteria and help speed up the normal changes in the intestinal environment. It is clear that each farm will have other factors in the environment competing with these interventions. As well as adding bacteria we have to look to remove or reduce abnormal bacteria and so a core protocol in ABC is to review the site and parental bacterial populations. If the neonate already is infected before “friendly” bacteria are added then the outcome will be considerably worse. So as well as Seed we have to Weed.

So now we have a developing microbiome and if we are lucky or have planned it properly, we have more friendly bacteria than ‘enemies.’ But with the numbers involved and the natural environment, whatever we do will have enemy “incursions.” Therefore, we need to supply solutions which will encourage the friendly to survive and multiply and slow down the development of the bad bacteria.

In general, the bacteria we want to survive are the acid loving bacteria and in particular, the ones that use short chain fatty acids (SCFA) to survive. These products have to be supplied to the correct part of the intestine. Our problem: bacteria inhabit the lower intestine where the pH is alkaline. The bad bacteria cannot survive in an acid environment and as the SCFA move passively across the bacterial cell wall, they enter the bacterial cytoplasm where the pH is alkaline. Once inside the bacterial cell, and as long as they are still a complete molecule, there is loss of their hydrogen ions and they acidify the bacteria.

The alkaline loving bacteria include E coli, Salmonella and Campylobacter species. The effect of hydrogen ions appearing in the bacterial cytoplasm is to create an energy drain on the bacteria as they attempt to remove these H+ ions. This energy loss either leads to bacterial death or a reduction in viability. The term is often used to acidify the intestine. We want to acidify the alkaline bacteria which is a different concept.


Delivering the SCFA to the lower intestine as a complete molecule is difficult as these are weak acids and normally give up their hydrogen ions in the face of a weak alkaline environment. We therefore either use a buffered SCFA mixture or a bespoke mixture with other strong acids which we supply via the water.

Kanters produce an excellent buffered acid called Ultimate Acid which we have used on many farms with great success. The complete approach is to use the LMS acid system which also adds chlorine to ensure a biofilm does not develop. The LMS system uses bespoke mixes which are designed to suit the water on the farm and are supplied by automated dosing pumps.

Water is often the easiest route of administration, especially where there is already a need to make sure the water is bacteriologically clean. However, in some situations it makes sense to also look at acids in the feed. Due to the buffering effects of feed, and the above described requirement to deliver the acid complete to the lower gut, we need to protect the acid. There are many techniques and after looking at all options we believe the system used by Kemin in their product Butipearl to be the best you can use. We have developed a range of in-feed protected acids based on this product and have a product called Intestinal Support to help prevent intestinal disturbance and Intestinal Recovery to aim to actively treat a disputed microbiome.

Once the basic concept is understood, we then need to look at specific acids to fit with specific age bands. The young animal (first week of life) has a Microbiome in nature based around Lactobacillus bacteria which produce lactic acid. These acids then help other bacteria produce butyrates. With the addition of chelated minerals and probiotics we would advise the use of a Kanters product called Intesti-Flora in the young animal. This can be used as well as the LMS system with suitable adjustments or as a primary dose before using Ultimate Acid. The best solution is to supply bacteria which produce lactic acids and supply the raw lactic acid in Intesti-Flora to help support the bacterial development

We need to feed the good bacteria in the same way as we would use a specific fertiliser in the garden to improve the soil. It is not as simple as acidifying the gut and needs correct application of the correct product at the right time. The good news is this approach is not expensive other than in management input.


We have set up the gut flora with bacteria which either colonise the intestine or produce products which encourage the development of the immature Microbiome. The early colonisers which we want to help have been fed with the correct mixture of short chain fatty acids and hopefully those unfriendly bacteria have been outmanoeuvred and are at a low level in the lower intestine. The challenge is to maintain this. In the case of the intestine, this is the stage where we try to stop E. coli of various sorts from finding a place to grow and multiply. E. coli have surface proteins called Fimbriae which are used to attach to the intestinal wall. There are specific sites on the intestinal cells which have matching proteins allowing the E. coli to attach and gain closer access to the intestinal cell. Once attached, the bacteria can multiply and, depending on the actual type of bacteria, might even produce chemicals which either create a water loss into the gut lumen or invade into the body.

Weeding out these bacteria is an essential component in looking after the garden. The most recognised method of weeding is the use of a fimbriae blocker which is usually added to the feed. These products will attach to the fimbriae and in effect stop them attaching to the receptors on the intestinal wall. We have designed with Alltech a product called Powertrac which not only contains fimbriae blockers but also has added protected minerals and importantly mycotoxin binders.

In birds, the gizzard is an important part of the control of the intestinal flow. If food fails to move in the correct manner throughout the intestine the outcome can be to allow some bacteria to populate areas of the intestine where they shouldn't be, or to attach to cells and even produce toxins leading to gut damage. Many believe that mycotoxins which are more prevalent will in some cases cause gizzard damage and this then leads to a disrupted gut flow. So Powertrac is a combined in-feed product which will form a major component of the weeding programme.

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