A genetically engineered probiotic showed positive results against a costly and difficult-to-detect condition in poultry, with new research published in the journal npj biofilms and microbiomes demonstrating it outperformed both antibiotics and conventional probiotics in broilers facing subclinical necrotic enteritis (SCNE).
Performance slowdown
Necrotic enteritis typically develops as a complication of other diseases, like coccidiosis, that impact intestinal function or cause immunosuppression. Intestinal damage allows C. perfringens, a normal inhabitant of the intestinal tract, to attach, proliferate and produce toxins.
Mortality associated with necrotic enteritis in broilers results in an estimated $6 billion in losses annually throughout the world. However, SCNE does not present with the dramatic mortality of clinical necrotic enteritis. Instead, it results in a performance slowdown — birds eat, they grow, but not as efficiently as they should.
"You don't see 50% of birds die and you don't see high signs of disease," Germán Plata, study co-author and senior director and lead scientist at BiomEdit, explained. "You just have kind of a reduced performance because there is this kind of low-level infection and inflammation.”
Promising results
The study tested an engineered strain of Limosilactobacillus reuteri designed to deliver nanobodies directly against the primary toxins produced by Clostridium perfringens in the poultry gut. Birds receiving the engineered probiotic showed improvements in feed conversion ratios and weight gain compared to birds receiving either antibiotic or the unmodified probiotic strain.
In addition, analysis of gene expression in the jejunum and liver revealed that the engineered probiotic effectively reversed the immune and oxidative stress responses triggered by the C. perfringens challenge — responses that appeared clearly in control birds between days 10 and 18 of the study. The same genes activated by the challenge were downregulated in birds receiving the engineered strain.
The mechanism behind the microbiome
Researchers also used microbial metatranscriptomics — which measures not just which microbes are present in the gut, but also which genes those microbes are actively expressing — to further validate the mechanism. The analysis confirmed that colonized birds were actively producing nanobodies in the gut, and revealed that the broader microbiome was also responding in ways consistent with reduced inflammation.
"We saw transcripts — genes expressed — that encode for the nanobodies," Plata explained. "We can tell these birds were colonized with the strains and they are producing the molecules in the gut. They're active."
The metatranscriptomic data also revealed upregulation of a pathway involved in synthesizing a molecule associated with improved resilience to inflammation, a finding Plata described as an unexpected bonus.
"That was pretty cool because it shows not only the intended mechanism, but this other response of the microbiome that's induced specifically by the treatment," he said.
The search for antibiotic alternatives
The findings address a growing industry need. Concerns about antimicrobial resistance have increased pressure on producers to reduce or eliminate antibiotic use, but effective antibiotic-free tools for managing SCNE have been limited.
Unlike traditional antibiotics that kill bacteria and potentially create resistance, this engineered probiotic neutralizes the disease-causing toxins while allowing the commensal bacteria to survive.
The probiotic is administered through a day-of-hatch spray application, with birds naturally ingesting the bacteria through pecking behavior. A booster dose delivered through drinking water around day 14 maintains colony levels through day 35 of a typical 43-day growth cycle, covering the critical period when necrotic enteritis typically occurs.
BiomEdit is currently conducting commercial safety trials, with a product launch targeted for Q4 2026. The company is open to additional trial partnerships as it moves toward commercialization.
