Evaluation of alternative protein sources on broiler performance and gut microbiota in commercial farms

Thesis Abstract

This study addresses the rising demand for sustainable poultry production by evaluating how alternative protein sources influence broiler performance and gut microbiota in commercial farming systems, with implications for growth efficiency, feed conversion, health status, and environmental sustainability. The aim is to quantify the effects of locally sourced, plant-based and insect-derived protein supplements on growth performance, carcass traits, nutrient utilization, and the structure and function of the caecal and ileal microbiota under commercial rearing conditions. Specific objectives are to determine (1) the impact of three alternative protein sources—soybean meal replacement with chickpea cotyledon meal, marigold seed meal, and Hermetia illucens (black soldier fly) meal—on body weight gain, feed intake, and feed conversion ratio across standard 42-day growth cycles; (2) changes in apparent nutrient digestibility and nitrogen balance; (3) alterations in gut microbial diversity, composition, and predicted functional capacity via 16S rRNA gene sequencing and shotgun metagenomics; (4) correlations between microbial profiles and growth or health indicators, including gizzard weight, intestinal morphology, and welfare indicators; and (5) economic and environmental implications assessed through partial budgeting and life cycle assessment to gauge net profitability and greenhouse gas emission footprints. A randomized complete block design will be employed in three commercial broiler production farms, each containing four dietary treatments with six replicate pens per treatment (n = 720 birds total; 30 birds per pen). The experimental period spans the entire 42-day grow-out cycle. Data will be collected on growth performance weekly (body weight, feed intake, feed conversion ratio), mortality, morbidity, and health scoring. Nutrient digestibility will be assessed using a total collection method for a subset of 96 birds (16 per treatment) over days 21–24, determining apparent ileal digestibility of crude protein, amino acids, fats, and minerals. Gut microbiota will be characterized by collecting ileal and caecal contents from 48 birds per treatment at day 42 for 16S rRNA gene sequencing (V3–V4 region) and metagenomic sequencing to profile microbial taxa and predicted functions; quantitative PCR will quantify key microbial groups (e.g., Lactobacillus, Bacteroides, Clostridium) and potential pathogens. Statistical analyses will include mixed-model ANOVA and generalized linear models to assess treatment effects on performance and digestibility, with farm as a random effect. Microbial diversity will be analyzed using alpha and beta diversity metrics (Shannon, Simpson, UniFrac distances), and differential abundance will be identified using DESeq2. Multivariate approaches, including redundancy analysis (RDA) and partial least squares regression (PLSR), will explore associations between diet, microbial features, and performance metrics. Regression models will test relationships between microbial community descriptors and production outcomes, while structural equation modeling (SEM) will evaluate direct and indirect pathways linking protein source, gut microbiota, and performance. Theories informing interpretation include the gut microbiota–host interaction framework and the ecological niche theory, with considerations for dietary niche shifts and microbial resilience. Expected findings anticipate that insect meal substitution will improve nitrogen retention, intestinal morphology, and broiler weight gain, with modestly improved feed efficiency; chickpea meal may serve as a viable plant-based alternative with variable effects depending on anti-nutritional factors; marigold seed meal could modestly influence growth but improve gut health through bioactive compounds. Shifts in microbial diversity are expected, with insect meal elevating beneficial taxa and enhancing microbial functional potential related to amino acid metabolism and short-chain fatty acid production, while plant-based alternatives may modulate carbohydrate-utilizing taxa. The study aims to contribute knowledge by linking specific protein sources to gut microbial ecology and production economics, providing a data-driven basis for feed formulation strategies that optimize performance while minimizing environmental impacts. The main conclusion is that alternative protein sources can sustain or improve broiler performance when precisely dosed and balanced for amino acid profiles, albeit with source-specific microbiota responses that influence health and efficiency. Recommendations include optimization of inclusion rates for each protein source, refinement of balancing protocols to address anti-nutritional factors, integration of microbial biomarkers into feeding strategies, and policy guidance for sustainable protein utilization in commercial poultry production.