Microbial population analysis of broilers in different flock and embryonic ages from GI, yolk and egg wash via Illumina MiSeq and QIIME pipeline (abstract)

Authors: LEE, SANG IN - University Of Arkansas; PARK, SI HONG - University Of Arkansas; Hiett, Kelli; SELLERS, HOLLY - University Of Georgia; Rothrock, Michael; RICKE, STEVEN - University Of Arkansas

Submitted to: International Poultry Scientific Forum
Publication Type: Abstract Only
Publication Acceptance Date: 11/3/2016
Publication Date: 1/30/2017
Citation: Lee, S., Park, S., Hiett, K.L., Sellers, H., Rothrock Jr, M.J., Ricke, S. 2017. Microbial population analysis of broilers in different flock and embryonic ages from GI, yolk and egg wash via Illumina MiSeq and QIIME pipeline (abstract). International Poultry Scientific Forum, January 30-31, 2017, Atlanta, Georgia.

Interpretive Summary: There are several food-safety issues related to broiler egg production, including the introduction/proliferation of zoonotic pathogens during embryonic gastrointestinal (GI) tract development. Little is known about the overall GI bacterial communities, how they change over time, or how their composition could influence zoonotic pathogen survival/transmission. To determine the effects of embryonic age and broiler breeder flock age on developing GI and yolk bacterial communities the GI tracts and yolks were aseptically removed from commercial broiler eggs at 4 times (7-, 15-, 20-days post fertilization, and 1-day post-hatch) from broiler breeder flocks of three different ages (20, 35, and 60 weeks). Egg washes occurred only at the 20-day sampling point (Trial 1. As part of a second study, eggs from the 20-week-old flock were re-sampled at 35 and 60 weeks of age (Trial 2). For all samples. DNA was extracted and 16S microbiomic sequencing analysis (using QIIME) was performed using the Illumina MiSeq platform. In the hatchery trial 1, alpha diversity analysis revealed that younger embryonic age exhibits highest observed OTUs and decreased approaching hatch. Also, the younger breeder flock exhibited lower average observed OTUs in GI, yolk and egg wash samples and with the observed OTUs increasing as breeder flock age increased. The GI tract samples exhibited the highest observed OTUs, followed by the yolk and egg wash samples, respectively. In the beta diversity analysis, aside from clustering based on sample type (GI, yolk, egg wash), minor clustering was found based on embryonic age groups (7- and 14-day versus 20-day and 1-day post-hatch), but no clustering based on breeder flock age. In the hatchery trial 2, significantly higher observed OTUs were detected in egg wash compared to GI and yolk. Also, older flock age exhibited higher observed OTUs and group 3 of embryonic age exhibited significantly higher observed OTUs compared to other three groups. Beta diversity indicated almost complete clustering by flock age alone and combination of flock age and sample type.

Technical Abstract: There are several food-safety issues related to broiler egg production, including the introduction/proliferation of zoonotic pathogens during embryonic gastrointestinal (GI) tract development. Little is known about the overall GI bacterial communities, how they change over time, or how their composition could influence zoonotic pathogen survival/transmission. To determine the effects of embryonic age and broiler breeder flock age on developing GI and yolk bacterial communities the GI tracts and yolks were aseptically removed from commercial broiler eggs at 4 times (7-, 15-, 20-days post fertilization, and 1-day post-hatch) from broiler breeder flocks of three different ages (20, 35, and 60 weeks). Egg washes occurred only at the 20-day sampling point (Trial 1. As part of a second study, eggs from the 20-week-old flock were re-sampled at 35 and 60 weeks of age (Trial 2). For all samples. DNA was extracted and 16S microbiomic sequencing analysis (using QIIME) was performed using the Illumina MiSeq platform. In the hatchery trial 1, alpha diversity analysis revealed that younger embryonic age exhibits highest observed OTUs and decreased approaching hatch. Also, the younger breeder flock exhibited lower average observed OTUs in GI, yolk and egg wash samples and with the observed OTUs increasing as breeder flock age increased. The GI tract samples exhibited the highest observed OTUs, followed by the yolk and egg wash samples, respectively. In the beta diversity analysis, aside from clustering based on sample type (GI, yolk, egg wash), minor clustering was found based on embryonic age groups (7- and 14-day versus 20-day and 1-day post-hatch), but no clustering based on breeder flock age. In the hatchery trial 2, significantly higher observed OTUs were detected in egg wash compared to GI and yolk. Also, older flock age exhibited higher observed OTUs and group 3 of embryonic age exhibited significantly higher observed OTUs compared to other three groups. Beta diversity indicated almost complete clustering by flock age alone and combination of flock age and sample type.