An interview with Tim Johnson, PhD, University of Minnesota
The poultry gut is more than just a digestive organ — it’s a dynamic ecosystem that plays a critical role in bird health, disease resistance and overall performance. As the industry continues moving beyond blanket antibiotic use, producers and researchers alike are zooming in on the gut microbiome and how to manage it more effectively.
Tim Johnson, PhD, professor and poultry microbiologist at the University of Minnesota, is helping to lead that charge, with some of his latest work focused on the surprising benefits of vaccination on the microbiome. In the following Q&A, Dr. Johnson shares what producers need to know about the evolving science of gut health and how vaccination can be a powerful tool in the quest for stronger, more resilient flocks.
How has our understanding of the poultry microbiome evolved in recent years, and what are the implications for managing bird health?
The industry’s understanding of the microbiome has grown dramatically in the last 15 years. That’s largely because it’s now much easier and more cost-effective to sequence and profile the full microbial community in the gut. We’ve learned to define what a normal, healthy gut looks like and how it changes as birds age.
One of the key findings is that the first three weeks of life are a period of rapid, predictable microbiome development that’s critical for both gut health and productivity. Early on, the gut is populated by opportunistic pathogens — bacteria that don’t always cause disease but can under stress. Over time, the gut environment becomes more anaerobic, and more permanent, beneficial microbes take hold. By tracking the presence of certain bacterial markers, we can now assess how well the gut is maturing and whether it’s on the expected trajectory.
From a practical standpoint, how closely is microbial stability linked to key performance metrics like feed conversion and livability?
Very closely. While microbiome research is often descriptive — meaning we can say what’s present, but not always why — it’s clear that subtle changes in microbial populations can influence performance. For example, certain feed additives like prebiotics have been shown to cause shifts in the microbiome that correlate with improved feed conversion, although we don’t always know which microbial players are driving that change.
We also see immune-related microbial markers that appear consistently in well-performing birds. When the gut is off-track — a condition known as dysbiosis — those markers show up later, which likely reflects a delay in immune system development. So while the changes might be subtle, they can have significant downstream effects on both immunity and production.
Are there certain points in the production cycle when the microbiome is especially vulnerable?
The first few weeks are critical, but we also see disruptions around times of stress, like moving birds between facilities, environmental challenges or heat stress. Vaccination can also impact the microbiome, depending on the type and timing.
In some cases, we’ve seen a rapid shift toward dysbiosis following certain vaccines, particularly when there’s a degree of immunosuppression. But it’s important to note that not all vaccines have this effect. In fact, some, especially enteric vaccines, can contribute to microbiome stability and help protect the gut during vulnerable periods. That’s something we’ve seen in our recent work with Eimeria vaccination.
Can you expand on that? What does your research show about how Eimeria vaccination influences the microbiome, beyond just controlling the pathogen itself?
That’s been a key focus of our recent work with Boehringer Ingelheim. When you vaccinate against a gut pathogen like Eimeria, you’re not just preventing physical damage to the intestinal lining — you’re also helping preserve the microbial balance within the gut.
In our challenge studies, unvaccinated birds exposed to Eimeria showed clear signs of dysbiosis, including increased levels of undesirable bacteria like Clostridium. Vaccinated birds, by contrast, maintained a more stable microbiome and were better protected against those shifts. What was especially interesting is that even before the challenge, we saw increases in beneficial bacteria like Lactobacillus in the vaccinated group. That suggests the vaccine may help prime the immune system and promote a more resilient gut environment, even in the absence of active disease pressure.
Given these findings, do you see vaccines as part of a broader gut health strategy?
Absolutely. Vaccines — especially Eimeria vaccines — can be more than just a tool for disease prevention. They can help stabilize the gut microbiome during those vulnerable early stages, which has ripple effects for performance and resistance to secondary pathogens. So yes, I think vaccination should be considered a core component of any gut health program.
What’s the best way to integrate vaccines with other microbiome-supportive tools?
It really needs to be a systems-level approach. There’s no silver bullet. We’ve been looking at how combinations of products — like probiotics, prebiotics and phytogenics — interact, and the results aren’t always predictable. Sometimes, combining two effective products actually results in a performance decline. So, it’s important not to make assumptions and to test combinations before adopting them widely.
What’s next for microbiome research and gut health management?
We’re shifting from asking ‘who’s in the gut?’ to ‘what are they doing?’. Functional profiling — tracking microbial metabolites — will be key. On-farm microbiome testing is also advancing; soon, service representatives may use portable tools to analyze gut health in real-time and recommend tailored solutions. Customized products, like prebiotics designed for specific probiotics, could further optimize outcomes.
As we consider these advances, what should producers prioritize when building their gut health programs for the coming years?
The big takeaway is that gut health is multifaceted. No single solution exists, but integrating vaccines, microbial management and stress reduction can create a more resilient flock. Producers should validate tools in their systems and stay open to emerging technologies that personalize gut health strategies.
Editor’s note: Content on Modern Poultry’s Industry Insights pages is provided and/or commissioned by our sponsors, who assume full responsibility for its accuracy and compliance.
