Margie Lee wears many hats at the Virginia-Maryland College of Veterinary Medicine, serving as the associate dean for research and graduate studies and the interim director of the Animal Cancer Care and Research Center - but she also holds another title.

“I’m the queen of chicken poop,” she joked.

A paper published this spring in Frontiers in Microbiology is the culmination of decades of research for Lee that has uncovered the secrets of the chicken’s microbiome and changed the way the poultry industry tackles salmonella. 


Source: Photo by Andrew Mann for Virginia Tech.

Margie Lee.

The research advanced understanding of the ways that competing bacteria in chicken intestines fight against salmonella. The findings carry implications not only for combatting salmonella in chicken populations, but potentially for increasing understanding of the human gut biome, which trails what is known about the poultry gut biome by decades.

Foodborne illness

If foodborne illness had a leaderboard, salmonella would be the champion. It’s the No. 1 cause of foodborne illness worldwide. Eating undercooked, contaminated chicken is a major cause of illness. According to Centers of Disease Control, one out of every 25 packages of chicken is contaminated with salmonella. 

Antibiotics have proven to be subpar in ridding chickens of salmonella, but for the sake of food safety and bird health, the poultry industry needs to eliminate the bacteria from its flocks. 

The solution lies in a diverse, flourishing community that just so happens to exist between a chicken’s small and large intestine: the gut microbiome. 

Lee’s research into how the chicken gut microbiome fights off salmonella has the potential to go beyond chicken health and aid in the development of better probiotics for humans as well. 

Chicken probiotics

After completing a postdoctoral fellowship at Washington University in St. Louis, Lee was working at the University of Georgia on salmonella in newly hatched chicks when she found something peculiar: Day-of-hatch chicks with a high bacterial load of salmonella often died, but chicks that were at least a day old always lived, even with enough salmonella in their systems to make a human ill. Something happens over the course of a single day in a chick’s life that stops salmonella from packing such a punch.

“I was fascinated by that concept — it was clear that it was a microbiome thing, but what is the microbiome telling salmonella that the salmonella says, ‘OK, I’ll behave’?”

That question has driven Lee to author 25 papers on chicken microbiome in a quest to understand how it affects pathogens like salmonella. The results of her research have made quite a splash.

Poultry health

“Poultry companies started using this information almost immediately. It changed how we looked at how we were managing poultry health and what we would expect,” said Lee.

In her early research, Lee borrowed techniques used by soil microbiologists and marine biologists to learn more about poultry gut microbiomes, salmonella, and competitive exclusion products. 

Competitive exclusion is a process in which other bacteria exclude pathogens from taking hold in the intestines. Basically, competitive exclusion products for poultry are derived from the poop of adult, salmonella-free chickens. When chicks come into contact with these products, helpful bacteria enters their bodies, and the chicks develop a more robust gut microbiome. 

Scientists have known for decades that competitive exclusion products work wonders, Lee and her collaborators shed light on the hows and whys behind competitive exclusion.

Two-pronged approach

In Frontiers in Microbiology, the researchers took a two-pronged approach. First, they looked at how salmonella responded to Aviguard, a commercially available competitive exclusion product, versus a microbial community from chicken cecum that contained salmonella.

Second, they examined the response of the cecal communities to salmonella in birds with high and low amounts of salmonella colonization. To do this, her collaborator created a “reporter strain” using fluorescence to monitor salmonella growth and to track SPI-1, which codes for a protein secretion responsible for virulence.

The research hasn’t been without its hurdles, however. For years, Lee’s research ambitions have been one step — or sometimes several steps — ahead of technology. 

Massive data set

“We were one of the early labs that could take the microbes out, take all their RNA, and sequence it before a lot of the sequencing technologies could do it,” said Lee. “We had this massive data set that we had no software to analyze — and I’m talking massive. We had 29 transcriptions with billions of sequences, but we could only say who was there, not what they were doing.” 

With the help of a lab tech skilled in bioinformatics, Lee conducted a network analysis and gleaned new insights from the data. 

Still, the team ran up against the limitations of technology — Lee’s husband and collaborator John J. Maurer, professor of microbiology in the university’s School of Animal Science, had to analyze data and sketch figures out by hand because the software to generate them doesn’t exist.  

The holy grail

The researchers found that the chicken’s microbiome engages in a combination of competition — as in competing for limited resources — with attenuation, or weakening salmonella’s virulence, and antagonism, or generating antimicrobials to fight salmonella. 

Even though the process is called competitive exclusion, they found that antagonism was actually the biggest part of the puzzle — the organisms within the gut produce their own antibiotics to combat salmonella. 

Through these mechanisms, the gut bacteria introduced by the competitive exclusion product regulate their new community.

“It’s about basic principles of behavior within a community — what is allowable? We’ve never really thought about how bacteria may practice the same thing that a pack of dogs would practice or a herd of deer or horses would practice,” said Lee. 

Implications for everything

A greater understanding of the function and mechanism of competitive exclusion products means that these products can be developed and tested more accurately — and this goes far beyond the poultry industry. 

One of the major hurdles to developing new, more effective probiotics is simply that we don’t fully understand probiotics’ mechanisms, and as it stands, our understanding of the human gut microbiome is some 20 years behind that of poultry. This research can provide insight on human and companion animal microbiomes in addition to that of chickens, guiding the development of better probiotics. 

“This has been the holy grail of gut health and respiratory health. When we’re talking about pathogen control, this has implications for everything,” said Lee.