Abstract:
The present study assessed the modulation of cecal microbiota and correlations with Campylobacter colonization
and animal welfare status. For these purposes, we conducted a cross sectional study of the cecal microbiota from
187 broilers reared in 13 batches from 10 poultry farms by performing 16S rRNA sequencing (regions V3–4). The
welfare of each batch was assessed using a simplified Welfare Quality® protocol, scoring higher in organic
batches, compared to both antibiotic-free and conventional batches. The bioinformatics analyses were conducted
in QIIME 2 and a linear discriminant analysis determined the association between microbiota and animals with
different Campylobacter carriage status and welfare levels. In the microbiota from the subjects negative for
Campylobacter or with high welfare scores, Bacteroidetes was the predominant phylum with the genus Megamonas
significantly increased in abundance. A greater abundance of Parabacteroides, Phascolarctobacterium, Helicobacter
in poultry negative for Campylobacter was also found at the genus level. Animals with the lowest welfare scores
showed an increased abundance of Proteobacteria. The results suggested a different microbial composition and
diversity in the analyzed groups.
