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How can poor barn air quality affect the gut health of poultry?

Ammonia in the barn damages the intestinal lining of chickens — discover the warning signs and solutions.

Poor barn air quality can directly affect the gut health of poultry. Harmful gases such as ammonia not only damage the respiratory tract, but also disrupt the intestinal barrier, alter the composition of the gut microbiome, and increase susceptibility to infections. This applies to all poultry species, but broilers and laying hens in intensive housing are particularly vulnerable. In this article, we answer the most frequently asked questions about barn gases and gut health, from the first visible signs to concrete solutions.

Which harmful gases are released in a poultry house?

In a poultry house, four main groups of harmful gases are released: ammonia (NH3), hydrogen sulfide (H2S), carbon dioxide (CO2), and methane (CH4). Ammonia is by far the most problematic: it is produced during the breakdown of uric acid in manure and can quickly rise to harmful concentrations when ventilation is insufficient. Hydrogen sulfide is toxic even at low concentrations and has a recognizable rotten-egg odor.

The concentration of these gases depends on stocking density, litter quality, temperature, and ventilation. The wetter the litter, the faster bacteria convert uric acid into ammonia. At high stocking densities and insufficient air exchange, gases accumulate, causing animals to be continuously exposed to low but chronically harmful levels.

Ammonia (NH3): produced from manure, irritates mucous membranes and the intestinal wall
Hydrogen sulfide (H2S): toxic gas from anaerobic manure breakdown, harmful even at low concentrations
Carbon dioxide (CO2): high levels indicate insufficient ventilation and increase stress
Methane (CH4): less directly toxic, but an indicator of anaerobic fermentation in the litter

What many poultry farmers underestimate is that the harmful effects of barn air do not only occur through the respiratory tract. Chickens also absorb ammonia through the gastrointestinal tract, which has direct consequences for gut health.

How does ammonia damage the intestinal wall of chickens?

Ammonia damages the intestinal wall of chickens by damaging tight junctions, irritating epithelial cells (enterocytes), and causing oxidative stress. This increases the permeability of the intestinal barrier, allowing harmful substances and pathogens to more easily reach the bloodstream. With chronic exposure, villus height decreases and crypt depth increases, impairing nutrient absorption.

Tight junctions are the protein structures that connect intestinal cells to each other and form the barrier between the intestinal contents and the body. Proteins such as occludin and claudin-1 are sensitive to oxidative damage. Ammonia increases the production of free radicals in the intestinal wall, causing these proteins to be damaged and barrier function to decline.

The result is increased intestinal permeability, also known as “leaky gut.” This allows bacteria and their toxins from the gut to enter the bloodstream, triggering a systemic inflammatory response. This costs the animal energy that would otherwise go toward growth or egg production, while simultaneously increasing susceptibility to secondary infections such as coccidiosis or bacterial enteritis.

What are the visible signs of gut damage caused by barn air?

Visible signs of gut damage caused by poor barn air quality in poultry include: wet or watery droppings, reduced feed intake, uneven growth within a flock, pale mucous membranes, and poor feathering. At flock level, a deteriorating feed conversion ratio (FCR) and a lower average daily gain (ADG) are early indicators that gut health is under pressure.

Wet droppings are a particularly reliable signal. When the intestinal barrier is compromised, the gut loses its ability to absorb water efficiently, leading to watery feces. This wets the litter, which in turn further increases ammonia production. This creates a self-reinforcing cycle: poor air leads to gut damage, gut damage leads to wet droppings, wet droppings lead to more ammonia.

At necropsy or post-mortem examination, the abnormalities are more clearly visible: shortened intestinal villi, thickened intestinal mucosa, increased crypt depth, and sometimes petechial hemorrhages in the intestinal wall. These morphological changes confirm that the gut damage is structural and not merely temporary.

How does barn air affect the composition of the gut microbiome?

Poor barn air quality disrupts the gut microbiome of poultry by shifting the balance between beneficial and harmful bacteria. A healthy gut microbiome, also known as eubiosis, is characterized by a stable, diverse population dominated by Firmicutes and Bacteroidetes. With chronic exposure to ammonia and other barn gases, dysbiosis occurs: a decrease in microbiome diversity and an increase in pathogenic Proteobacteria.

Ammonia alters the pH in the gut and creates an environment that is less favorable for beneficial bacteria. At the same time, the compromised intestinal barrier weakens the local immune system, making it easier for pathogens such as Clostridium perfringens and Salmonella to gain a foothold. This increases the risk of necrotic enteritis, one of the most costly intestinal diseases in the poultry sector.

A disrupted microbiome also has indirect consequences: reduced production of short-chain fatty acids such as butyrate, which normally nourish intestinal cells and support barrier function. In this way, barn air and dysbiosis reinforce each other mutually, resulting in increasingly poor technical performance.

Which barn management measures improve air quality most quickly?

The barn management measures that improve air quality most quickly are focused on keeping the litter dry, optimizing ventilation, and limiting manure fermentation. Concrete adjustments can be implemented quickly and have a direct effect on ammonia concentration in the barn.

The following measures deliver the fastest results:

Optimize ventilation: Ensure sufficient air exchange tailored to the season and stocking density. Avoid cold draft spots that moisten the litter.
Monitor litter quality: Remove wet or caked litter promptly. Dry litter strongly inhibits the bacterial conversion of uric acid to ammonia.
Address water leaks: Dripping nipple drinkers are one of the most important causes of wet litter. Regular inspection is essential.
Monitor stocking density: Excessive stocking density increases both manure production and the heat and moisture load in the barn.
Consider litter treatment: Adding litter improvers based on organic acids can lower the pH and thereby inhibit ammonia formation.

Ventilation and litter management are the two levers with the most direct impact. Even a small improvement in litter dryness can measurably reduce ammonia concentration in the barn within a few days.

Can feed and drinking water products strengthen gut resilience in poor air conditions?

Yes, feed and drinking water products can demonstrably strengthen the gut resilience of poultry in poor barn air conditions. Specific additives such as betaine, organic acids, butyrate, and medium-chain fatty acids (MCFA) support the barrier function of the gut, reduce oxidative stress, and promote a healthy gut microbiome. They are a valuable complement to barn management, not a replacement for it.

Betaine plays a special role here. As an osmolyte, it protects enterocytes against stress by maintaining the osmotic balance in the intestinal cell. At the same time, it strengthens the expression of tight junction proteins such as occludin and claudin-1, making the intestinal barrier more robust. Scientific research shows that betaine also increases villus height and reduces crypt depth, leading to a larger absorptive surface and better nutrient utilization.

Drinking water is an attractive delivery vehicle in this regard. During stress or illness, feed intake in chickens drops sooner than water intake, making drinking water additives more reliably absorbed. The dosage is fully flexible and controllable by the farmer, allowing rapid adjustment when problems arise. More information about available drinking water and feed additives for poultry can be found on our product page.

How Jodoco helps with gut health under pressure from barn air

We at Jodoco develop feed and drinking water products specifically designed to support the gut health of poultry, even under challenging barn conditions. Our approach combines multiple mechanisms of action in one formula, so that the gut is protected and strengthened from multiple angles.

Our products offer concrete benefits for poultry farmers dealing with poor barn air quality:

Betaine (Jodobet): strengthens tight junctions, protects enterocytes against oxidative stress, and supports the osmotic balance in the intestinal cell. Read more about the action of betaine as a gut-supporting ingredient.
Grovax: combines organic acids, slow-release butyrate, MCFA, and essential oils for broad gut support. Butyrate feeds the intestinal cells directly, while MCFA work antimicrobially against gram-negative and gram-positive pathogens. View the complete Grovax product profile for more details.
Yeast cell walls (beta-glucans and MOS): support the local immune system and promote eubiosis in the microbiome.
Flexible administration via drinking water: also applicable when feed intake drops due to stress or illness.

Our products fit within a “No Antibiotic Ever” (NAE) strategy and are scientifically supported through trials in collaboration with institutes such as ILVO Gent. Whether you are dealing with chronically wet droppings, a deteriorating FCR, or increased mortality, we are happy to think along with you about the right approach. Contact us and discover which solution best fits your situation.