Influence of Eimeria spp. infection on chicken jejunal microbiota and the efficacy of two alternative products against the infection

Eimeria spp. are important intestinal pathogens of chickens. Anticoccidial feed additives, including antibiotics, have traditionally been used to control Eimeria infections in broiler production. Thus, the trend to antibiotic-free and organic production requires new approaches to coccidiosis prevention. Two not mutually exclusive methods are the use of plant extracts with antiparasitic activity and the manipulation of the intestinal microbiota by pre- and probiotics. In the present study, we performed a combined challenge of broilers with E. acervulina, E. maxima and E. tenella. We profiled the jejunal microbiome at multiple time points post-infection to investigate the changes in jejunum microbiota to identify the time point of the maximum difference between infected and non-infected birds for future studies. In addition, we assessed the anticoccidial effects of two anecdotal treatment methods, green tea and apple cider vinegar as well as amprolium. Green tea and apple cider vinegar had no effect on oocyst shedding, but green tea reduced the mild unspecific lesions in coccidia infected birds. Jejunal contents were collected on the day of the infection and 1, 2, 4, 6, 10 and 14 dpi for investigation of the intestinal microbiota by 16S rDNA gene sequencing. Comparison of the untreated-uninfected and the untreated-infected groups showed the maximum community dissimilarity 10 dpi. From four days after the infection, Clostridiales were significantly enriched at the expense of Lactobacillales in infected compared to uninfected birds. Interestingly, treatment with green tea prevented proliferation of Clostridiales induced by the coccidia and increased the relative abundance of Melainabacteria.