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Pigeons, as the only altricial birds in poultry, are the primary  Trichomonas gallinae  ( T. gallinae ) host. To study the effects of  T. gallinae  infection on gut microbiota, we compared the microbiota diversity and composition in gastrointestinal (GI) tracts of pigeons at the age of 14 and 21 day with different degrees of  T. gallinae  infection. Thirty-six nestling pigeons were divided into three groups: the healthy group, low-grade and high-grade trichomonosis group. Then, the crop, small intestine and rectum contents were obtained for sequencing of the 16S rRNA gene V3–V4 hypervariable region. The results showed that the microbiota diversity was higher in crop than in small intestine and rectum, and the abundance of  Lactobacillus  genus was dominant in small intestine and rectum of healthy pigeons at 21 days.  T. gallinae  infection decreased the microbiota richness in crop at 14 days. The abundance of the  Firmicutes  phylum and  Lactobacillus  genus in small intestine of birds at 21 days were decreased by infection, however the abundances of  Proteobacteria  phylum and  Enterococcus, Atopobium, Roseburia, Aeriscardovia  and  Peptostreptococcus  genus increased. The above results indicated that crop had the highest microbiota diversity among GI tract of pigeons, and the gut microbiota diversity and composition of pigeon squabs were altered by  T. gallinae  infection.

Changes in the diversity and composition of gut microbiota in pigeon squabs infected with Trichomonas gallinae