Poultry Litter Microbiome Shifts in Commercial Broiler Houses Following a Biotic-Based Litter Treatment

Abstract

Litter management plays a critical role in broiler production, affecting bird health, performance, and environmental impact. This preliminary study evaluated the effects of IndigoLT, a biological amendment, in combination with a 40% sodium bisulfate (NaHSO) regimen on litter microbiome composition, compared to a standard NaHSO-only treatment. Litter samples (n = 18) were collected from three commercial broiler houses following flock removal: one control (NaHSO-only), one treated with IndigoLT for a single flock, and one treated for two consecutive flocks. The V4 region of the 16S rRNA gene was sequenced to assess prokaryotic community composition. Alpha diversity metrics (Faith's phylogenetic diversity, observed ASVs, Pielou's evenness, Shannon diversity) did not differ significantly across treatments (ANOVA, p > 0.05). In contrast, PERMANOVA analyses of Bray-Curtis, Jaccard, Weighted and Unweighted UniFrac distances revealed significant shifts in {beta} diversity between IndigoLT-amended and control groups (q < 0.05), with no significant differences between the one- and two-flock IndigoLT treatments. Core microbiome and differential abundance analyses suggested that IndigoLT, when paired with reduced NaHSO input, may accelerate organic matter decomposition, promote nitrogen retention, and suppress potentially pathogenic taxa. Although limited by the absence of baseline sampling and biological replication, these findings suggest that IndigoLT influences litter microbial succession. Future work should aim to optimize inclusion rates most complementary between NaHSO and IndigoLT to enhance litter quality, reduce NH volatilization, and support bird health.