Comparison of Gut Microbiome Profile of Chickens Infected with Three Eimeria Species Reveals New Insights on Pathogenicity of Avian Coccidia

Avian coccidiosis is an intestinal disease caused by <i>Eimeria</i> spp. infection. A deeper understanding of the interaction between host gut microbiota and the <i>Eimeria</i> parasite is crucial for developing alternative therapies to control avian coccidiosis. Here, we used full-length sequencing of 16S ribosomal RNA amplicons to compare changes in the gut microbiota of chickens infected with <i>Eimeria tenella</i>, <i>Eimeria maxima</i>, and <i>Eimeria necatrix</i>, aiming to identify both species-specific and common alterations in gut microbiota at 4 and 10 days post-infection. The result revealed that infection with all three <i>Eimeria</i> species led to a decrease in the abundance of the microbial genera <i>Limosilactobacillus</i>, <i>Streptococcus</i>, <i>Alistipes</i>, <i>Lactobacillus</i> and <i>Phocaeicola</i>, while the abundance of <i>Bacteroides</i>, <i>Escherichia</i> and <i>Ligilactobacillus</i> increased. <i>Escherichia</i> and <i>Enterococcus</i> were most abundant in the jejunum of the <i>E. necatrix</i>-infected group and in the cecum of the <i>E. tenella</i>-infected group, whereas <i>Megamonas</i> abundance was highest in the <i>E. maxima</i>-infected group. LEfSe analysis showed that infection with all three <i>Eimeria</i> species significantly reduced the abundance of 13 bacterial species, including <i>Acetilactobacillus jinshanensis</i>, <i>Bacteroides ndongoniae</i>, <i>Barnesiella viscericola</i>, <i>Christensenella minuta</i>, <i>Enterocloster clostridioformis, Gemella haemolysans</i>_A, <i>Granulicatella adiacens</i>, <i>Lawsonibacter</i> sp000177015, <i>Limosilactobacillus reuteri</i>, <i>Limosilactobacillus reuteri</i>_D, <i>Limosilactobacillus vaginalis</i>_A, <i>Limosilactobacillus caviae</i>, <i>Limosilactobacillus vaginalis</i>. Infection with <i>E. tenella</i> significantly increased the abundance of five bacterial species, including <i>Bacteroides fragilis</i>, <i>Enterococcus cecorum</i>, <i>Helicobacter pylori</i>, <i>Methylovirgula ligni</i>, and <i>Phocaeicola</i> sp900066445. Infection with <i>E. maxima</i> significantly increased the abundance of seven bacterial species, including <i>Clostridioides difficile</i>, <i>Faecalibacterium prausnitzii</i>, <i>Mediterraneibacter torques</i>, <i>Muribaculum intestinale</i>, <i>Mediterraneibacter massiliensis</i>, <i>Phascolarctobacterium faecium</i>, and <i>Phocaeicola plebeius</i>. Infection with <i>E. necatrix</i> significantly increased the abundance of seven bacterial species, including <i>Alistipes</i> sp900290115, <i>Anaerotignum faecicola</i>, <i>Bacteroides fragilis</i>_A, <i>Escherichia coli</i>, <i>Harryflintia acetispora</i>, <i>Pseudoclostridium thermosuccinogenes</i>, and <i>Tidjanibacter inops</i>_A. The results showed that <i>Eimeria</i> infection causes significant species- and time-dependent changes in the gut microbiota of chickens. These findings enhance our understanding of coccidiosis pathogenesis and offer potential targets for developing probiotics.