Dietary Lees Supplementation Enhances Poultry Health Performance Through Gut Ecosystem Reprogramming

Abstract The search for sustainable alternatives to in-feed antibiotics has intensified with the global antimicrobial resistance crisis. While microbial by-products show potential, their mechanisms remain elusive. This study reveals that spent yeast lees, a fermentation by-product, profoundly reprograms the chicken gut ecosystem to enhance growth. We investigated the differential effects of live spent lees versus autoclaved spent lees from a molasses fermenter with Saccharomyces cerevisiae. In a 14-day controlled trial, 0-day-old poultry chicks (n=15) were assigned to a control diet (n=5), a live spent Lees-supplemented diet (n=5), or an autoclaved spent Lees-supplemented diet (n=5). Through the feeding trial with either live spent Lees or autoclaved spent Lees, we demonstrate significant enhancement of growth performance, with autoclaved spent Lees achieving the highest final body weight (573.4 ± 17.2 g). Using deep shotgun metagenomic sequencing of faecal samples, we demonstrate that both spent Lees forms induced a dramatic ecological shift, driving the gut microbiome to a state of monodominance by Bacteroides fragilis (reaching 74.83% with live spent Lees). This was accompanied by the near-complete eradication of enteropathogens like like Enterococcus faecium and Escherichia coli. Crucially, live spent Lees supplementation effectively countered a natural age-dependent expansion of the gut resistome, eliminating the high-risk oxazolidinone resistance gene o23S and restructuring the virulome away from offensive effector systems. However, this beneficial restructuring came at the cost of significantly reduced microbial diversity and suppression of beneficial commensals. A key finding was that autoclaved spent Lees, while inducing a less extreme microbial shift, yielded superior final body weight, suggesting its lysed cells provide enhanced nutritional availability. Our work establishes spent yeast Lees not as mere waste, but as a potent, multi-functional supplement that enhances growth through gut ecosystem engineering, yet necessitates a strategic choice between its live and autoclaved forms based on production priorities. Competing Interest Statement The authors have declared no competing interest.