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Coccidiosis is a well-known poultry disease that causes the severe destruction of the intestinal tract, resulting in reduced growth performance and immunity, disrupted gut homeostasis and perturbed gut microbiota. Supplementation of probiotics were explored to play a key role in improving growth performance, enhancing innate and adaptive immunity, maintaining gut homeostasis and modulating gut microbiota during enteric infection. This study was therefore designed to investigate the chicken gut whole microbiota responses to <i>Bacillus subtilis</i> (<i>B. subtilis</i>) probiotic feeding in the presence as well as absence of <i>Eimeria</i> infection. For that purpose, 84 newly hatched chicks were assigned into four groups, including (1) non-treated non-challenged control group (CG − ET), (2) non-treated challenged control group (CG + ET), (3) <i>B. subtilis</i>-fed non-challenged group (BS − ET) and (4) <i>B. subtilis</i>-fed challenged group (BS + ET). CG + ET and BS + ET groups were challenged with <i>Eimeria tenella</i> (<i>E. tenella</i>) on 21 day of housing. Our results for Alpha diversity revealed that chickens in both infected groups (CG + ET and BS + ET) had lowest indexes of Ace, Chao 1 and Shannon, while highest indexes of Simpson were found in comparison to non-challenged groups (CG − ET and BS − ET). <i>Firmicutes</i> was the most affected phylum in all experimental groups following <i>Proteobacteria</i> and <i>Bacteroidota</i>, which showed increased abundance in both non-challenged groups, whereas <i>Proteobacteria</i> and <i>Bacteroidota</i> affected both challenged groups. The linear discriminant analysis effect size method (lEfSe) analysis revealed that compared to the CG + ET group, supplementation of probiotic in the presence of <i>Eimeria</i> infection increased the abundance of some commensal genera, included <i>Clostridium sensu stricto 1</i>, <i>Corynebacterium</i>, <i>Enterococcus</i>, <i>Romboutsia</i>, <i>Subdoligranulum</i>, <i>Bacillus</i>, <i>Turicibacter</i> and <i>Weissella</i>, with roles in butyrate production, anti-inflammation, metabolic reactions and the modulation of protective pathways against pathogens. Collectively, these findings evidenced that supplementation of <i>B. subtilis</i> probiotic was positively influenced with commensal genera, thereby alleviating the <i>Eimeria</i>-induced intestinal disruption.