Response of chicken litter microbiota to the invasion of Salmonella Infantis throughout the Broiler Production Cycle

Description

The microbiota of chicken manure is complex and dynamic and has a direct effect on the welfare and development of diseases in poultry. Leaf litter is composed of fungi, protozoa, archaea and bacteria. Communities can vary depending on the stage of the production cycle and the use of antimicrobial growth promoters. Our hypothesis was that the litter microbiota changed according to the age of the birds and that the addition of microorganisms altered the litter microbiota and the interaction of the microbial communities.

Steps to reproduce

The quality of the raw sequences was checked in FastQC and subsequently optimized in the QIIME2 pipeline, for which the sequences were imported, visualized and filtered by quality, and taxa identified as chloroplasts or mitochondria were removed using the DADA2 algorithm. From a table of amplicon sequence variants (ASVs), a table of relative abundances was constructed and used to determine abundance per taxon at the different taxonomic levels, phylum, family and genus per sample, using the SILVA v138 database. The microbial community data were analyzed and visualized in the R program, exporting the abundance table with taxonomic assignment in the phyloseq package of R, focused on processing microbiome information to generate various graphs with ggplot2 of genus and family.

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