Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses

Authors: ZWIRZITZ, BENJAMIN - University Of Natural Resources & Applied Life Sciences - Austria; Oladeinde, Adelumola - Ade; JOHNSON, JASMINE - University Of Georgia; ZOCK, GREGORY - University Of Georgia; MILFORT, MARIE - University Of Georgia; FULLER, LORRAINE - University Of Georgia; GHAREEB, AHMED - University Of Georgia; FOUTZ, JAMES - University Of Georgia; TERAN, JOSE - University Of Georgia; WOYDA, REED - Colorado State University; ABDOA, ZAID - Colorado State University; Looft, Torey; Plumblee Lawrence, Jodie; AGGREY, SAMUEL - University Of Georgia

Submitted to: Frontiers in Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/20/2023
Publication Date: 3/2/2023
Citation: Zwirzitz, B., Oladeinde, A.A., Johnson, J., Zock, G., Milfort, M.C., Fuller, L.A., Ghareeb, A., Foutz, J., Teran, J., Woyda, R., Abdoa, Z., Looft, T., Plumblee Lawrence, J.R., Aggrey, S.E. 2023. Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses. Frontiers in Physiology. https://doi.org/10.3389/fphys.2023.1083192.
DOI: https://doi.org/10.3389/fphys.2023.1083192

Interpretive Summary: Broiler house environment is one of the most important management factors that has been shown to significantly affect broiler performance, welfare, and health. However, there is limited data on how changes in house environmental factors affect the microbiome of broiler chickens. In this study, we showed that the environment inside a broiler house does not only affect broiler performance and health but also influences the bacterial community of chickens, and that these processes are interconnected and could influence antimicrobial resistance development. Therefore, it is crucial that animal studies pay close attention to environmental differences between houses/barns/cages as this can be a source of confounders and introduce variability in experimental outcomes.

Technical Abstract: In this study, we investigated the effect of broiler house environmental conditions on the microbiome of chickens from post-hatch through harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of E. coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily, and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and was influenced by the environmental parameters measured (P<0.05). Litter microbiome was affected by the five parameters measured while the cecal microbiome was influenced by house temperature only. We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (P< 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (P<0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (P< 0.05). These results show that broiler house environmental conditions play an integral role in shaping the microbiome of chickens.