Is Intestinal Microbiota Fully Restored After Chickens Are Recovered from Coccidiosis

Intestinal microbiota is known to be altered by Eimeria-induced coccidiosis, but it remains un-clear whether the microbiota is fully restored to normal after recovery. To address this, 110 newly hatched Cobb male broiler chickens were challenged with 20000 sporulated oocysts of Eimeria maxima (EM) strain M6 or mock-infected with saline on day 10. Body weight and feed in-take were recorded. Additionally, 10 mock and 12 EM-infected birds were randomly selected to assess the small intestinal lesion, fecal oocyst shedding, and ileal and cecal microbiota composi-tion using 16S rRNA gene sequencing at 3, 5, 7, 14, and 21 days post-infection (dpi). EM infection significantly decreased (P < 0.001) body weight by 5 dpi, persisting through 21 dpi. The infection also reduced (P < 0.05) weight gain, feed intake, and feed efficiency in the first week; however, these parameters became comparable in the second and third weeks. At 7 dpi during the peak infection, lactic acid bacteria were largely enriched, while short chain fatty acid-producing bac-teria were mostly suppressed in both the ileum and cecum. Opportunistic pathogens such as Escherichia and Clostridium perfringens transiently bloomed at 7 dpi. By 14 dpi, differential bacte-rial enrichment subsided, and nearly all commensal bacteria returned to healthy levels by 21 dpi. Given comparable growth performance between healthy and EM-recovered chickens, we con-clude that the intestinal microbiota is largely restored to its original healthy state after recovery. Understanding microbiota responses to coccidiosis can inform probiotic-based mitigation strat-egies.