Reduced antibiotic use in poultry production increases the need for maintaining a healthy and functioning gut. A key component of this is a balanced microbiota. This article will cover the sometimes-overlooked aspects of the microbiota as it relates to everyday production:

The vertical transfer of good and bad microbes

Today, most producers are laser-focused on the bird in front of them, especially when it comes to their health if they’re raising them for meat. When we think about the microbes inside a chicken or turkey, such as bacteria and fungi, we don’t always contemplate where they originated. We’ve known for a very long time some of these things can be transferred through the egg, which is what we refer to as vertical transfer. Salmonella is one of the negative microbes that can be transmitted and is a major concern when it comes to food safety. However, more and more studies are indicating it’s not just bad bacteria being passed along. It’s a lot of good bacteria too. These are the first microbes already colonizing the egg when it’s hatched. When it comes to establishing a healthy microbiota for living organisms, we must think about nature vs. human interaction. In nature, an egg is laid, exposed to a natural environment, and microbes colonize on the surface. Commercially, humans’ clean eggs, disinfect, and remove those natural microbes in the process.

So, what’s the biggest dilemma? Because we eliminate their competition through clean processes in a hatchery, it can take more time to control harmful bacteria such as E. coli and Salmonella when problems arise. When we try to manipulate the young bird’s microbiome, we shouldn’t think of just the bird. It needs to be a more holistic view, going back up to the breeder source.

Can we be too clean?

We live in an age of cleanliness. Most of our household cleaners promise to kill 99.9% of bacteria. Hand sanitizer is being bought in bulk. But science is also telling us being too clean is not always a good thing.

Evidence shows people who grew up on farms have fewer allergies and asthma compared to people from suburban areas or houses that tend to be cleaner. When we’re born, we encounter many different microbes. It’s up to our immune system to decide which ones are good and which ones are bad. As we become cleaner and cleaner, we eliminate healthy bacteria which overall changes our microbiota. This can play a game on our immune system, causing it to develop immunotolerance to the good bacteria. So, what does this mean? The immune system can develop differently in humans exposed to “clean” environments, compared to environments where we aren’t using as many disinfectants.

In chickens and turkeys that are being raised for consumption, it’s a lot of the same idea. Typically, barns at the highest risk for disease are ones where there are young birds. Often, those barns are cleaned extremely well between flocks. In turkey production, the brood barn supports turkey poults raised until about 4 weeks of age. Then turkeys get moved to the grow-out barn where they are raised for the rest of their lives. Brood barns typically do extensive cleanouts in between flocks. There’s good reason for this, to keep bad viruses and bacteria at a low level or keep them out completely. However, in doing so, it’s mimicking the hygiene hypothesis from the perspective of the microbiome. We can reduce disease but we’re sacrificing the normal establishment of a healthy gut.


How do we choose the best practice? We must find a balance between clean and supporting a natural microbiota. This means not cleaning too much but keeping the pathogen level and load down. Another idea is to incorporate commercial products to supplement the microbiome, such as probiotics, prebiotics, or a yeast fermentation product in feed. These could potentially help build the gut early, even if it doesn’t have a rich source of bacteria to draw from.

How will reduction of antibiotic use impact the microbiome? 

Dr. Martin Blaser, the author of Missing Microbes, has been looking at microbes in humans for many years as it relates to antibiotic use. In his book, his evidence shows that as we’ve used antibiotics repeatedly over time, certain bacteria have disappeared from the human population, never to come back. They’ve proven this by comparing westernized societies, such as ourselves, to tribal nations that are untouched by civilization. Research studies have discovered there are distinct populations of bacteria that were present in westernized humans 40 to 50 years ago that we cannot find in humans today. This is his idea of the missing microbe. As we use antibiotics over time, we’re having a permanent impact on an animal’s life. It is very likely that the sustained use of antibiotics in animal agriculture has had a similar impact in that it’s had a long-lasting change on the bird’s microbiome.

If we look at a wild turkey vs. a commercial turkey, there are drastic microbiome differences between the two that would indicate what we’re doing in commercial production has long-term impact on the microbiome. Some of these differences are undoubtedly attributable to the long-term use of antibiotics in commercial turkey production, which has resulted in long-lasting impact on their microbiomes. Even though the animal itself is short-lived, it’s about the big picture of the poultry production pyramid, where genetic stocks of these birds are used to grow millions and millions of them. How will reductions in use impact that? One would hope all the changes taking place in the U.S. and around the world recently, which include initiatives to reduce using antibiotics at high frequency in animals, is going to eventually start to restore the microbiome. But it might not happen by itself. It’s up to us to facilitate, perhaps through supplementation, to get those microbes back into animals. Perhaps over time, without having a prolonged use of antibiotics, those microbes will have a lasting impact going from parent to progeny.

As it relates to resistance, it’s a similar story. Antibiotic use in animal agriculture over the last 50 years has resulted in a fair amount of antibiotic resistant bacteria. Creating it can happen quickly. Getting rid of it can take longer. As we now slow the use of antibiotics in food animals, we’re going to see changes in the levels of resistance. Resistance will eventually go down, but it will never disappear. The problem is that while we would like this to happen quickly, it will probably take a long period. However, it creates an opportunity. If we’re already committed to reducing antibiotic use, this opens the door to try and target resistance and lower it. There’s a lot of technologies out there, one of them being the CRISPR technology, aka gene editing in humans, which originated from bacteria. Bacteria have developed CRISPR systems as natural “immune systems” that are geared up to kill other microbes. To do this, they survey and collect pieces of DNA, which recognize other microorganisms. They can then produce substances that chop up the DNA of that foreign microbe. There has been work done that shows you can do the same thing in the lab to create strains of bacteria that can target antibiotic resistance. If you could deliver this to a poultry barn, or even the bird, it can target those drug bacteria and either inactivate the resistance or kill the bacteria overall. Technologies like this have opened the door for us to start trying to reduce resistance at a faster clip rather than waiting for it to happen naturally.

A balancing act

In the end, these thoughts come back to the idea of sustaining a healthy gut. The bird’s microbiome plays a key role in health, and we can impact this through management and products, all while trying to keep birds healthy and free from disease. Remember, it’s a balancing act. It’s also important to acknowledge, on the antibiotic side, what we’ve done in the past, and what we’re doing today are two different things. Historically, we had high usage. Now, with all the new technology and developed products, we’re better geared to produce birds in an antibiotic-free environment while not negatively impacting human or animal health.