"Let food be thy medicine and medicine be thy food." That directive, credited to Hippocrates, is not only based on observing the positive results of good nutrition but has also inspired subsequent generations to seek out natural and beneficial foods and ingredients to both heal and maintain good health. So, how might this philosophy translate to raising healthier flocks of chickens?
Clemson researcher Dr. Vishal Manjunatha, under the supervision of Clemson professor of food microbiology Dr. Xiuping Jiang and a team of collaborating scientists*, seems to have found important, natural alternatives to using antibiotics in the poultry industry, one of South Carolina’s largest agricultural businesses.
There’s a common gut disease among chickens that poultry farmers contend with called “necrotic enteritis,” or “NE.” Manjunatha explains that the gastrointestinal disease is marked by scarring lesions, ruffled feathers, diarrhea, reduced performance, and mortality. And it’s contagious, spread through droppings.
Although antibiotics can be used by poultry farmers to treat diseases like NE, doing so can not only contribute to antibiotic resistance in chickens but also humans via the food chain, direct contact, or environmental routes. For these reasons, the U.S. Food and Drug Administration implemented a ban on the use of antibiotics for growth promotion in livestock and poultry in 2017.
“The goal of this project was to find natural alternatives to replace antibiotics in disease prevention or mitigation.” Manjunatha explained that his study investigated the use of three natural products: black cumin, also known as Nigella sativa; kefir, which is a probiotic; and bacteriophages, which are viruses that infect and replicate only in bacterial cells, and in this case, Clostridium perfringens, the bacteria that cause NE.

“Black cumin has been used for more than 2,000 years in folk medicine and specifically in the Middle East. It's used as a spice. It has various antimicrobial properties, anti-inflammatory, anti-parasitic, and antiviral properties.” Manjunatha notes that an additional benefit of black cumin is that it’s been shown to promote growth performance in chickens when there is no disease in general.
The kefir used in the study is not like the kind sold in the refrigerated section of grocery stores. Manjunatha explains that store-bought kefir in the U.S. is typically made from a defined blend of lactic acid bacteria. In contrast, traditional or authentic kefir is produced using kefir grains—a symbiotic culture of lactic acid bacteria, acetic acid bacteria, and yeasts embedded in a polysaccharide matrix called kefiran. This complex microbial community gives traditional kefir its distinct probiotic profile and potential health benefits. Kefir grains are native to the Caucasus region, including parts of Eastern Europe and the Middle East, and are passed down through generations, much like a sourdough starter or mother dough.
As for bacteriophages, Manjunatha explains that they’ve been used to target bacterial infections and have been approved for use against Listeria monocytogenes in food safety applications, including in the dairy industry. Unlike antibiotics, which are often broad-spectrum and can disrupt beneficial gut bacteria, bacteriophages are highly specific and act only against their target pathogen.
The conclusion from Manjunatha’s study was, “We found that the combination of these treatments functions better, and it was equivalent to that of the antibiotics, reducing the mortality as well as reducing the intestinal scarring in the chickens. It helped promote the gut microflora, which is not seen in antibiotics.”

So, how might the results of this study benefit South Carolina’s poultry industry? Manjunatha says the project was funded by the state’s ACRE program, an initiative by the South Carolina Department of Agriculture that helps our state’s farmers and agribusinesses. Through its partnership with Clemson, the knowledge from this particular study is provided to poultry farmers.
What’s the next natural ingredient the university will be studying? “Clemson is actively exploring various natural products for use in poultry to help combat infections. One promising candidate is sorghum—some researchers at Clemson have already observed potential benefits, and given that sorghum is widely grown in the U.S., it could have a significant impact,” said Manjunatha.
*Other contributing scientists for the study include Dr. Xiuping Jiang (advisor), Annel K. Greene, Greg F. Mathis, Brett S. Lumpkins, Zeynep B. Güzel-Seydim, Atif C. Seydim, and Julian E. Nixon.