Managing the Broiler Gut Microbiome

We have always been passionate about bird health, however, with the ongoing work to reduce antibiotic use and the increasing efficiency of our broiler chickens, we are increasingly looking at ‘farm health and microbiome management’.

Turnaround, disinfection and water quality are all essential areas of microbiome management. We focus here on how we can manage the gut microbiome of the broiler chick, how to set it up and manage it correctly, as well as consider the challenges to the stability of that gut flora throughout its life. 

The most important day in a bird’s life is the day of placement. A newly hatched chick’s gut is a blank canvas. The bacterial population of a bird’s gut is heavily dependent on what happens in the first few days of life; therefore, this time period provides us with the greatest opportunity to favourably influence the microbiome of the bird and therefore the shed (via its droppings).


The most common method of influencing the early gut bacterial population is using probiotics to take up the space in the gut leaving less room for harmful bacteria. These can be given either in the hatchery or on farm. There are two groups of probiotics (defined and undefined cultures). Undefined probiotics such as Aviguard are essentially made originally from the faeces of healthy chickens and contain hundreds of species of bacteria. Defined products such as Lactobacillus (Biacton) contain only one bacterial species.

Feed and Water

Some companies are looking at using probiotics being sprayed onto the eggs before hatching in the hatchery, so that immediately after hatching the chicks are exposed to ‘good bacteria’. When a chick is tipped, in addition to its gut being a blank canvas, its stomach doesn’t make protective acid until it feeds. It is essential that a chick gets feed and water as soon as possible after placement, the longer without feed and water, the longer a time frame there is for harmful bacteria to have an easy journey from the beak to the gut. Good chick crumb availability (at least 2 rows of chick paper per drinker line and 70-100g crumb/chick) and good drinker management (ensuring the drinker pressures are correct and that the drinker height is correct) are very important. It is essential that the water provided is clean, as are the drinker lines. If a bird’s gut is bombarded with harmful bacteria from the drinking water, then this can disrupt a healthy microbiome.

As an industry, we have typically measured the 24-hour crop fill but the difference in a bird that starts 2 hours after placement vs one that starts 24 hours after placement can equate to a huge window of opportunity for harmful bacteria to reach the gut and subsequently the bird’s blood stream. 22 hours is 92% of a day. At the end of the crop 92% of a day’s growth can equate to 92g in bodyweight. At £1/kg liveweight, across a site of say 300,000 birds, 92g can equate to a lot of weight and money. Furthermore, a delayed start can lead to increased unevenness and generally poor early gut development. A chick with poor gut development at 7 days will be much more susceptible to gut health challenges later in life. Chicks that are delayed in feeding will use up nutrients for maintenance rather than early gut development.

A day-old chick has a leaky gut wall (just like new-born mammals). Part of this is to allow antibodies from the yolk (which empties into the gut via the yolk sac stalk as the chick breathes) to enter the blood stream. Whilst a leaky gut wall allows antibodies to reach the blood, it can also allow bacteria from the gut to enter the chick’s blood stream too. If high numbers of E. coli reach the blood stream, we can get septicaemia (early mortality) and if Enterococcus reaches the blood stream, these bacteria can make their way into the joints to cause lameness later in the flock when the birds get heavier. Overheating and dehydration can increase the size of the spaces (tight junctions) between the cells lining the gut leading to increased leakage.

Bedding is another source of bacteria, and all bedding should be sourced from an approved supplier.

Seed Feed and Weed

Once the chick has started, the good bacteria (seed) can be encouraged to reproduce via the use of organic acids, such as ABC Start, and harmful bacteria can be discouraged through the use of yeast wall-based products which bind onto the surface of harmful bacteria and stop them attaching to the gut lining (weed). This is known as the seed, feed and weed concept.

Gut Flora Stability

Throughout the life of a modern broiler, there will be a number of challenges to the stability of that gut flora:

  • Diet changes: In a perfect world, a broiler’s diet would change daily as it gets older (lower protein), however, this is not practical, and most companies tend to have 3-5 different rations for the life of the broiler.
  • Vaccination: Any live vaccine involves giving a weakened (attenuated) strain of the disease to the bird. Despite being attenuated, the vaccine virus (usually gumboro or infectious bronchitis) still challenges the bird’s immune system. Additionally, the water withdrawal during in-water vaccination means the bird doesn’t eat and therefore challenges the stability of the gut bacteria.

When a bird eats its stomach makes acid which then enters the gut with the broken-down food. This acidifies the gut helping ‘good bacteria’ which are acid loving and discourages the growth of ‘bad bacteria’ which prefer alkaline conditions. The further down the birds gut the more alkaline the ph. There tends to be more harmful bacteria the further down the gut we look, with the caecae having the most harmful bacteria. These ’harmful bacteria’ do not affect gut health if they remain in the lower gut as food absorption takes place in the upper gut.   Prolonged periods without feed can cause the upper gut to become more alkaline allowing harmful bacteria which normally live in the lower gut (without harming the bird) to move up into the small intestine where they can produce toxins and create inflammation reducing the absorption of nutrients. This causes two issues; firstly, the nutrients aren’t absorbed leading to a poorer FCR and secondly when the undigested nutrients reach the lower gut, they feed the harmful bacteria allowing them to creep up the gut.

Note feed outages, thinning and heat stress (which reduces appetite) can cause similar issues.

  •  Coccidiosis: Coccidiosis is the biggest endemic disease of broilers. The parasite is very difficult to control and is therefore found in virtually all broiler sheds. The mainstay of our coccidiosis control is using in-feed coccidiostats. Whilst these products are effective in stopping clinical coccidiosis and associated mortality, sub-clinical coccidiosis, is rather common. Coccidia infect the cells lining the small intestine reducing the absorption of nutrients, compromising FCR and feeding harmful bacteria in the lower gut. Furthermore, the damage caused by coccidiosis causes the gut to make excessive mucus which acts as a food source for harmful bacteria such as clostridia which further inflame the gut!

From an evolutionary point of view, birds have a short gut in relation to their body size compared to mammals. This allows birds to be light enough to fly. To get away with having a short gut, yet being able to absorb enough energy to fly, in a bird’s intestine feed doesn’t move one way as it does in mammals, instead feed moves back and forth up and down the gut and between the gut and stomach to maximise absorption. This is known as retro-peristalsis. Unfortunately, this process is vulnerable to stress (in the wild if a bird was stressed it would empty its gut to be light enough to fly away from say a predator). In modern broilers, stressors such as those listed above interfere with peristalsis causing a reduced number of times feed passes along the absorptive part of the gut negatively affecting FCR and again allowing undigested nutrients to reach the lower gut undigested therefore feeding ‘harmful bacteria’.

In order to counteract the above stressors, there are a number of interventions we can make. Whilst obviously reducing stress is key, many of the above stressors cannot be prevented, but we can manage them.


In water, acidification is the most useful of them all, this helps the bird counteract the effects of reduced feed intake (from say thinning, vaccination, heat stress etc) or from a challenge to the bacterial population from ration changes and should be given after the event in the case of thinning or vaccination or a few days either side of ration changes. Ultimate Acid is an effective and cost-effective way of acidifying the gut. The benefits of organic acids can be bolstered through the strategic use of probiotics (for older birds, undefined probiotics tend to be too expensive but defined probiotics such as Biacton+ are cost effective). Some probiotic products such as Galliprofit produce compounds in the gut that help to destroy harmful bacteria. Other probiotics help produce large amounts of acids in the gut having a similar effect to in-water acidification.  

Essential Oils

As discussed above, coccidiosis represents the greatest challenge to gut health. There are a number of nutraceuticals designed to help your flock through their coccidiosis challenge. Necox and Coccillin V Plus are two essential oil-based products which have been successfully used across a number of farms to mitigate the intestinal effects of coccidiosis. Coccidiosis is incredibly difficult to control at turnaround and a disinfectant specifically approved to control coccidiosis should be used. Timing of such products is key and only through routine gut health checks on farm can we determine when the peak gut health challenge is likely to be. This differs between farms.

Salmonella Control

Exotic salmonella species can be controlled through the use of probiotics (such as Aviguard) to competitively exclude Salmonella and through the use of buffered organic acids (such as Ultimate Acid in water or Formaxol in feed) which discourage the harmful salmonella bacteria. Intercid disinfectant bacteria is one of the best products on the market to control Salmonella.


It is important that systemic viral diseases such as gumboro (which damages the immune system) and IB are controlled and monitored. Regular PCR testing can often pick up an issue before they become clinically evident.

Give us a call today if you would like more information on anything discussed in this article.