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Microbiome management: What does it mean?

Richard Turner MA VetMB MRCVS

As a vet who started in clinical practice many years ago, the change in how I now approach unhealthy, or flocks with poor performance, has changed dramatically. Historically the approach was to examine the animal, carry out a range of tests on that animal, and possibly others in the flock, then to make a diagnosis of usually an infectious disease.

The effect of the microbiome, made up of micro-organisms such as bacteria, viruses, fungi and protozoa, on animal health was recognised where abnormalities in populations created clinical symptoms. However, the overall effect of the total microbiome was not really studied until very recently.

What various things can alter the microbiome for example age, genetics and diet
What can alter the microbiome?

Avian microbiome research

There is now a large volume of research into the avian microbiome to show how various bacteria make up specific eco systems in the gut, respiratory tract, skin and urogenital tracts. These bacteria work in a symbiotic way with the host bird and are now known to be transferred from the mother to the offspring even before hatching, with an embryo within the egg having a changing and developing microbiome as early as 4 days before hatching. How these bacteria get there is not clear but what is recognised is that an impaired gut microbiome in the hen can lead to a challenged chick. We now focus on the mother’s gut health, even if it is not causing obvious clinical issues as this will pay dividends in the health of the day-old chick.

As research develops, we will see even more reasons to support and help nurture these micro-organism populations.

Bacteria and bird behaviour

Some bacteria are even found to affect behaviour which is one of the reasons that specific fibre types in rations can change bird behaviours as it encourages changes in the bacterial populations in the gut. Specific bacteria in the intestine help with digestion, whilst others produce fatty acids which promote the gut immune system to improve coccidial immunity. Research in humans shows that the various cell types in the mother’s intestine actively collect specific bacteria from the lumen and transfer them to breast milk. Such an intricate interaction between the host and its bacterial population has evolved to allow for the newborn to have help developing a maternal like gut flora shows the detailed links that are now being recognised. Competitive exclusion as promoted 30 years ago is now seen to work naturally in humans and other species. The range of interactions is huge and still not fully understood.[JS1] 

What I know now as a vet is that rather than give a broad-spectrum antibiotic, which creates so much collateral damage to the target microbiome, I need to be more specific and careful how I treat and focus on recovery. In some cases, antibiotics are essential due to the clinical severity of the case, but our role is to also help the microbiome recover quickly.

Microbiomes throughout the production cycle

The young chick has already been in contact with a microbiome when inside the egg, both given to it by its mother as well as possible cross shell contamination. This is its first microbiome. It then hatches into an environment where there are already some pathogenic bacteria and may be next to a dead in shell chick with an anaerobic bacterial population or maybe a massive E.coli challenge. These new colonisers find niches in the developing microbiome of the chick (gut, mucus membranes, lungs etc) and might if pathogenic lead to disease or displace useful friendly bacteria.

From the hatcher to the lorry and onto the farm the chick is not living in a sterile environment, but hopefully maternal immunity and the level of challenge will allow it to survive and start developing its own beneficial microbiomes.

In the house there is the microbiome left from cleaning, the microbiome in the water lines and the microbiome of the litter. Whether these are significant populations of beneficial or pathogenic bacteria will depend on the attention to cleaning detail and the history of the previous flocks. We all now recognise that a house and a farm has its own developed microbiome which in some ways might be beneficial but in others can lead to challenges. Some types of antibiotic resistance can be linked to some detergent resistance, so not all house microbiomes are positive to the chick.

Linking microbiome management to performance

In the same way we link nutrition to health, we need to link all these microbiomes to the performance of the flock. It is here that the vet now must be more involved. We try to help the microbiome in the chick develop correctly and to do this we must also be certain that the microbiomes that impact the chick are also managed and where possible controlled.

Cleaning with the correct product to the correct level is essential, as we all know, as is water hygiene. Proper and detailed testing of the sites’ bacterial populations are essential to either support a hygiene plan or indicate where changes are needed. Each site should have a focused hygiene plan based on the health and performance history of the site which the farmer’s vet is involved in designing.

Adopting the seed, feed and weed approach

Once we have a degree of management of the farm’s microbiomes it is now very important that we help the immature chick microbiome develop by seeding it with beneficial bacteria, trying to coax these primary colonisers to develop and finally by trying to remove bad bacteria. When I first started working in poultry, we used vaccines to help develop the immune system but really only focused on antibiotics to kill bacteria, rather like throwing a weed killer on the garden. Now we see we should seed, feed and weed the garden, and do all we can to manage the microbiome wherever it is and however it impacts on our patients.

If you would like more information on microbiome management, please get in touch with your vet or call the team on 01392 872932.

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