The Association between Broiler Litter Microbiota and the Supplementation of Bacillus Probiotics in a Leaky Gut Model

The last decade of intensive research on the role and importance of intestinal microbial communities has brought abundant novel information and a high appreciation of microbiome contribution to medical and veterinary research that stretches beyond probiotic and pathogenic effects. We can now investigate the complex microbial community inhabiting major host cavities and colonising organs. In poultry research, it is common to collect cloacal swabs or faecal droppings for non-invasive sample collection or caecum and other intestinal origins to investigate their specific microbial communities. Litter samples are less frequently collected for microbial community investigation despite them being in close contact with birds and playing a significant role in microbiota colonisation, development, and maturation. Here, we explored the microbiota of litter and compared them with selected gut sections and bird health status. Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the litter microbial community and litter parameters. The probiotic product was a mix of three Bacillus amyloliquefaciens strains. The litter microbiota were compared to the microbial communities from other gut sections. The litter samples had higher microbial diversity compared to the caecum, gizzard, jejunum, and jejunal mucosa. The high similarity between the litter phylum-level microbiota and gizzard microbiota detected in our study could be a consequence of ingested feed and litter passing through the gizzard. Moreover, the litter microbial community is fundamentally distinct from the intestinal microbiota, as evidenced by the number of genera present in the litter but absent from all the intestinal sections and vice versa. Furthermore, LEfSe analysis identified distinct microbial taxa across different groups, with specific genera associated with different treatments. In terms of litter quality, the birds in the DEX groups had a significantly higher moisture content, indicating successful leaky gut challenge, while probiotic supplementation did not significantly affect the moisture levels. These findings provide comprehensive insights into the distinct microbiota characteristics of litter.