Genetics, environment shape broiler cecal microbiota

Consumer interest in poultry welfare has led to the expansion of unconventional poultry-rearing systems, such as silvopasture. But information on how different systems affect poultry and the cecal microbiota is limited.

To find answers, Justin Lowery, MS, and a team of researchers from North Carolina State University conducted a broiler research trial. The trial compared the impact of conventional and silvopasture production systems on the cecal microbiota of slow- and fast-growing broilers.

The results indicated that both genetics and environment shape the ceca of broilers.

“This means producers must carefully choose breeds that are most suited for specific environments,” Lowery said. “If you want a bird that performs very well in an outside environment, you need to pick that breed and vice versa for inside production.”

Lowery discussed his research at the 2025 Poultry Science Association annual meeting.

Measuring cecal content

“We hypothesized that we would see differences in the ceca between the slow-growing SASSO and fast-growing Ross 708 broilers and between floor-pen and silvopasture systems,” Lowery said.

The trial involved 500 SASSO broilers and 500 Ross 708 broilers placed separately in traditional floor-pen production and silvopasture environments. The silvopasture provided access to trees, grass and housing.

The Ross 708 birds were grown to 42 days of age, and the slower-growing SASSO birds grew to 56 days of age.

The cecal contents were aseptically collected at processing (after feather picking) from 10 birds per treatment, for a total of 40 birds. The ceca collections were stored in liquid hydrogen until microbiota analysis using 16S ribosomal RNA amplicon sequencing and other test methods.

The microbial analysis included determining alpha and beta diversity. Alpha diversity is the diversity of species within a sample, while beta diversity indicates how microbial communities differ between samples.

The researchers also examined evenness, which describes the distribution and relative abundance of species within a sample.

Microbiome diversity compared

“We saw higher overall evenness in cecal microbiota in the Sasso broilers than in the Ross birds,” said Lowery, adding, “There was also a trend toward higher microbiome evenness in floor pens than in silvopasture.

“We found a significant difference between microbial communities,” he continued. “What this shows is a more even distribution of microbes in the gut with a floor-pen system. Where there is a floor pen, birds don’t have outside access, so they aren’t getting many microbes into the gut. Additionally, SASSOs can maintain a more even distribution of microbes in the gut.”

Regarding beta diversity, the researchers observed that silvopasture birds exhibited more distinct microbial groups than birds on floor pens, regardless of broiler strain.

This was also true for breeds, with SASSO broilers displaying more microbial diversity than Ross 708 birds.

Match breed to rearing method

Altogether, trial results indicate that rearing slow-growing broilers in outdoor environments results in low microbial evenness and more distinct microbial groups than fast-growing broilers in floor pens.

“Silvopasture broilers have a more varied diet due to foraging outside and developing more dominant taxa in the gut from exposure to various microbes,” Lowery said.

“As trends continue toward alternative rearing environments, bird choice for each environment will become increasingly important,” he added. “Birds will need the ability to cope with a fluid environmental microbial load.

“If you want a bird to perform well in an outside environment, you need to pick a bird that can handle it,” Lowery concluded.

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