DNA METABARCODING IN PASTURED POULTRY: DIET, MICROBIOME, AND MANAGEMENT

Author

Kantima Thongjued, Department of Entomology, University of KentuckyFollow

Author ORCID Identifier

https://orcid.org/0000-0003-1808-9800

Date Available

8-6-2027

Year of Publication

2025

Document Type

Doctoral Dissertation

Degree Name

Doctor of Philosophy (PhD)

College

Agriculture, Food and Environment

Department/School/Program

Entomology

Faculty

Julian Dupuis

Abstract

Chicken (Gallus gallus) is the most consumed meat globally, and demand for chicken meat has caused significant growing in poultry production. Unfortunately, more than 40 billion chickens each year are raised in conventional systems where the environment is controlled, and chickens suffer from overcrowding, stress, and metabolic-related health issues. In recent years, consumers have been prioritizing animal welfare and supporting alternative poultry productions (e.g., pasture-raised, free range, organic) where the birds are treated more humanely.

Integrating poultry into pasture and cropping systems is thought to have many ecological and economic benefits. This setting is an environment that makes the birds healthier and can produce higher quality meat and eggs compared to those raised in conventional systems. Farm profitability may also be increased through product diversification and decreased farm input (fertilizers). Additionally, poultry can potentially regulate pest populations, reduce weed seed banks, and manage crop residue that can be a shelter for pests in consecutive growing seasons. At the same time, poultry raised in these farms gain access to additional food such as vegetation, seeds, and insects. Taken together, it is clear that alternative poultry production systems represent an important part of the future of poultry production. However, diet composition of birds in such pastured settings has not been quantitatively studied.

Poultry production systems can be reservoirs of many infectious diseases that may be transmitted to humans and thus pose a risk to public health. Conventionally, bacterial pathogens have been controlled by antibiotics but these are generally prohibited in organic farming. Organic operations are growing in popularity among small-scaled farms across the United States, yet disease control practices or agents to substitute for antibiotics have not been well established. The gut microbial communities plays an important role in the health, production performance, and welfare of chickens. Prebiotic- or carbohydrate-enriched diets aided by beneficial bacteria in the gut have been used to modulate gut microbiota and boost immune systems in farmed animals. However, the influence of prebiotic under integrated poultry production system or pasture-raised system on the chicken gut microbiome is scarce.

This dissertation aim to use DNA metabarcoding as a tool to decipher diet composition and gut microbiome, and subsequently inform farm management to encourage pasture utilization by broiler chickens.

In chapter 2, I conducted a feeding trial experiment in backyard laying hens and collected their excreta to test the efficiency of multiple DNA extraction kits and primers for plants and arthropods in recovering known diet communities fed to the chickens. Additionally, I established customized databases and a bioinformatics workflow using QIIME2 to use for subsequent chapters. I found that DNA extraction kits incorporating bead homogenization significantly contributed to the success in recovering the diet communities. Additionally, use of multiple loci was generally required to have a fully complete picture of diet for mixed species communities.

In chapter 3, I used the validated workflow to determine the influence of farm management (stocking density, breed, sex, feed restriction) on diet richness and performance of pasture-raised broiler chickens across three years of study. I found that the birds from low stocking density group had significant higher diet richness than those from high stocking density group. Red ranger chickens tended to have higher diet richness than the Cornish cross chicken though this comparison did not account for different years. Feed restriction for four hours increased diet richness compared to unrestricted birds. However, diet richness was not significant different between male and female chicken.

In chapter 4, I used 16S rRNA sequencing to characterize gut microbial communities across the three-year study of pasture-raised broiler chickens. Three regions of the 16S rRNA gene, including V1-V3, V3-V4, V4-V5, were compared as well as two excreta types (fecal dropping, and cecal dropping). I found no significant difference between 16S rRNA regions and sample types at the community level. I then used the pooled sequences generated from the three regions and two sample types to evaluate the changes in gut microbial communities in broilers under different farm management. I compared alpha diversity indices, beta diversity, and relative abundance of bacteria in genera level between two chicken breed (Cornish Cross and Red Ranger), two stocking density and four berry prebiotic-supplemented feed. I found significant differences in relative abundance of 144, 4 and 3 bacteria genera across chicken breeds, stocking densities, and feed treatments, respectively. Notably, no significance differences in relative abundance of core microbiome was observed across all comparisons. However, relative abundance of opportunistic pathogens such as Pseudomonas, Escherichia were higher in Cornish Cross than Red Ranger broilers.

This dissertation will provide the first quantitative analysis of diet composition of pasture-raised broiler chickens using DNA-based techniques. This data will be used to characterize the ecology of poultry in such crop rotations, inform farm management strategies, and characterize the gut microbiome of pastured poultry.

Digital Object Identifier (DOI)

https://doi.org/10.13023/etd.2025.356

Recommended Citation

Thongjued, Kantima, "DNA METABARCODING IN PASTURED POULTRY: DIET, MICROBIOME, AND MANAGEMENT" (2025). Theses and Dissertations--Entomology. 92.
https://uknowledge.uky.edu/entomology_etds/92