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As the information about the effect of pectin prebiotics on chicken gut microbiota is scarce, by using high throughput metagenomic sequencing with Illumina Miseq we examined the cloaca bacteriobiome of male and female chickens receiving antibiotic- or pectin-containing drinking water. The bacteriobiome was dominated by two phyla (Firmicutes and Proteobacteria) and three classes (Clostridia, Bacilli and Gammaproteobacteria), with the difference displayed by the relative abundance of 42 OTUs. At the level of the major dominant OTUs, prebiotic supplementation drastically increased Enterococcus abundance (from 0 to 11% and 23% in males and females, respectively). The better feed use efficiency and growth performance of the pectin-receiving chickens implied their better health and corroborated putative beneficial role of the altered bacteriobiome, although its ecophysiological and/or pathogenic importance could not be readily inferred. Notably, the gut microbiota response to antibiotics showed more sex-related differential OTUs as compared to the pectin prebiotic (19 vs. 4), suggesting different mechanisms of the studied supplementations in shaping the gut bacteriobiome in different sexes. Therefore, we recommend targeting sex as a separate factor in interventional studies to account for sex-specific peculiarities in the microbiome response and taking into account the male/female ratio of industrial flocks prior to choosing a production technology. The studied prebiotic (pectin) can be used in developing new pre/symbiotic preparations and supplementation regimes as alternatives to antibiotics for stimulating broiler chicken production.

No-Antibiotic-Pectin-Based Treatment Differently Modified Cloaca Bacteriobiome of Male and Female Broiler Chickens