Gut microbiota dynamics in free-range layer hens during outbreaks of spotty liver disease and fowl cholera-a field study.

The livestock industry faces growing constraints due to antimicrobial resistance, particularly in poultry systems that have historically relied on antibiotic use. These challenges are exacerbated in free-range production, where restrictions on antimicrobial interventions coincide with heightened exposure to infectious diseases, leading to increased mortality and reduced productivity. On-farm disease outbreaks cannot be reproduced in high ethics standards approved animal houses, where they can be modeled to recognize some patterns of pathogen dynamics. While laboratory settings enable rigorous control and monitoring, they lack the environmental, management, production, pathogen pressures and complexity found on industrial farms and therefore cannot realistically recreate disease progression. Here, we present a field study in a layer flock that experienced three disease outbreaks of spotty liver disease (SLD) and fowl cholera (FC). The treatment group was supplemented with a precision biotic, a synthetic glycan product, while weekly performance measures and responses of microbial populations across major gut sections were observed. The precision biotic supplemented birds showed higher cumulative mortality but also higher egg output. However, as this was an unreplicated field study, these differences should be interpreted as descriptive associations. The intestinal microbial community responded differently to supplementation under concurrent environmental and disease pressures. This study provides large-scale field observations during concurrent outbreaks of SLD and FC, offering real-world insights that may inform future controlled studies of disease dynamics and performance management. KEY POINTS: • Free-range systems increase disease risk, reducing health and productivity in layer flocks. • Precision biotics were associated with higher egg output and higher cumulative mortality in hens. • Gut microbiota and liver congestion differed between precision biotic supplemented and control groups.