UNIVERSITY PARK, PA. — For many years, antibiotics have been added to animal feed to help control harmful bacteria and improve growth. However, because of concerns about antibiotic resistance — when bacteria adapts to survive treatments that would normally kill them — the poultry producers are trying alternatives, including probiotics, which contain helpful bacteria, and essential oils, which come from plants and may have antimicrobial properties. Researchers at Penn State have now found that feeding broiler chickens an antibiotic, probiotic or essential oils did not significantly affect the overall diversity of antimicrobial resistance genes. Instead, the chickens’ age had a much stronger effect on the resistome — the collection of antimicrobial resistance genes — as the birds grew.

The researchers recently reported their findings, which indicate that the bacteria living in stomachs of chickens changes as the birds age rather than because of the presence of a specific additive, in Poultry Science.

“Antibiotic resistance is an important problem, and poultry producers are increasingly using products such as probiotics and essential oils instead of antibiotics, however, we don't fully know whether these products affect antibiotic-resistance genes in chickens,” said study senior author and team leader Erika Ganda, associate professor of food animal microbiomes in the Penn State College of Agricultural Sciences. “In this experiment, probiotics and essential oils did not produce substantial or sustained changes in the overall resistome, which supports further investigation of these products as antibiotic alternatives.”

In the study conducted at the Penn State Poultry Education and Research Center, the researchers fed 320 broiler chickens one of four diets: a normal diet with no additives, a diet containing an antibiotic, a diet containing essential oils and a diet containing a probiotic. They collected fecal samples when the birds were 1, 10 and 21 days old and used DNA sequencing to identify resistance genes. The DNA sequencing, called shotgun metagenomics, can detect resistance-gene sequences and allow scientists to assess their presence and relative abundance, but it does not determine whether the bacteria carrying those genes are resistant or whether the genes are actively expressed. In total, the researchers found 823 unique resistance genes.

Study first author Ana Fonseca, who graduated from Penn State with a dual-title doctorate in animal science and microbiome sciences and now is a poultry management educator with the Penn State Extension Poultry Team, said the research team was somewhat surprised that the antibiotic treatment did not produce a sustained change in the broiler chicken’s overall resistome. She said age was the much stronger factor for shaping the resistance-gene profiles.

“The resistome of a one-day-old chick looked quite different from that of a 10-day-old chick, and the resistome changed again by day 21,” she said. “As chickens grow, the community of bacteria living in their gut changes naturally. New bacteria arrive, some bacteria disappear and others become more abundant. We call this process microbial succession. Because different bacteria carry different resistance genes, natural changes in the microbial community also reshape the resistome.”

The study’s findings do not suggest that feed additives never affect antibiotic resistance in poultry, Fonseca explained. Rather, the results show that under the specific conditions of this experiment, the natural changes occurring in the chicken’s microbial community as the chickens grew appeared to have a bigger effect on the presence and types of genes related to antibiotic resistance than the dietary treatments.

“Understanding where resistance genes come from — and what causes them to change — can help us develop safer and more sustainable ways to raise poultry, while addressing the global problem of antimicrobial resistance.” Fonseca said.

The findings of this study, yielded by the huge amount of data generated by the shotgun metagenomics approach, were made possible by computing power provided by the high-performance Roar Collab cluster at the Penn State Institute for Computational and Data Sciences.

Contributing to the research were John Boney, Vernon E. Norris Faculty Fellow of Poultry Nutrition and associate professor of poultry science; Sophia Kenney, who graduated from the molecular, cellular and integrative biosciences doctorate program; and Stephanie Bierly, former research assistant in the Department of Animal Science.

This work was supported by the U.S. Department of Agriculture National Institute of Food and Agriculture and Hatch Appropriations under award numbers PEN04752 and PEN04731 accession numbers 1023328 and 1022444, as well as the Penn State College of Agricultural Sciences Strategic Networks and Initiatives Program. This content is solely the responsibility of the authors and does not necessarily reflect the views of the funders.