Luminal and mucosa-associated caecal microbiota of chickens after experimental infection in the absence of -specific phages of group II and III.

Campylobacteriosis is still the most commonly reported zoonosis in the European Union causing gastrointestinal disease in humans. One of the most common sources for these food-borne infections is broiler meat. Interactions between (.) and the intestinal microbiota might influence colonization in chickens. The aim of the present study was to gain further knowledge about exclusive interactions of the host microbiota with in -specific phage-free chickens under standardized conditions and special biosafety precautions.Therefore, 12 artificially infected ( inoculum with a challenge dose of 7.64 log c.f.u.) and 12 control chickens of the breed Ross 308 were kept under special biosafety measures in an animal facility. At day 42 of life, microbiota studies were performed on samples of caecal digesta and mucus. No -specific phages were detected by real-time PCR analysis of caecal digesta of control or artificially infected chickens. Amplification of the 16S rRNA gene was performed within the hypervariable region V4 and subsequently sequenced with Illumina MiSeq platform. R (version 4.0.2) was used to compare the microbiota between -negative and -positive chickens. The factor chickens' infection status contributed significantly to the differences in microbial composition of mucosal samples, explaining 10.6 % of the microbiota variation (=0.007) and in digesta samples, explaining 9.69 % of the microbiota variation (=0.015). The strongest difference between -non-infected and -infected birds was observed for the family whose presence in -infected birds could not be demonstrated. Further, several genera of the family appeared to be depressed in its abundance due to infection. A negative correlation was found between R-7 group and in -colonised chickens, both genera potentially competing for substrate. This makes R-7 group highly interesting for further studies that aim to find control options for infections and assess the relevance of this finding for chicken health and colonization.