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Streptococcus equi subsp. equi (S. equi) is the pathogen causing strangles, a highly infectious disease that can affect equids including donkeys of all ages. It can persistently colonize the upper respiratory tract of animals asymptomatically for years, which serves as a source of infection. Several strangles outbreaks have been reported in the donkey industry in China in the last few years and pose a great threat to health, production, and the welfare of donkeys. Nasopharyngeal swab samples for culture and PCR are used widely in strangles diagnosis. Additionally, microbiomes within and on the body are essential to host homoeostasis and health. Therefore, the microbiome of the equid nasopharynx may provide insights into the health of the upper respiratory tract in animals. There has been no study investigating the nasopharyngeal microbiome in healthy donkeys, nor in donkeys shedding S. equi. This study aimed to compare nasopharyngeal microbiomes in healthy and carrier donkeys using 16S rRNA gene sequencing. Nasopharyngeal samples were obtained from 16 donkeys recovered from strangles (group S) and 14 healthy donkeys with no history of strangles exposure (group H). Of those sampled, 7 donkeys were determined to be carriers with positive PCR and culture results in group S. In group H, all 14 donkeys were considered free of strangles based on the history of negative exposure, negative results of PCR and culture. Samples from these 21 donkeys were used for microbial analysis. The nasopharyngeal microbiome composition was compared between the two groups. At the phylum level, relative abundance of Proteobacteria was predominantly higher in the S. equi carrier donkeys than in healthy donkeys (P < 0.01), while Firmicutes and Actinobacteria were significantly less abundant in the S. equi carrier donkeys than in healthy donkeys (P < 0.05). At the genus level, Nicoletella was detected in the upper respiratory tract of donkeys for the first time and dominated in carrier donkeys. It is suspected to suppress other normal flora of URT microbiota including Streptococcus spp., Staphylococcus spp., and Corynebacterium spp. We concluded that the nasopharyngeal microbiome in S. equi carrier donkeys still exhibited microbial dysbiosis, which might predispose them to other airway diseases.

Diet is an important factor affecting intestinal microbiota in horses. Fecal microbiota is commonly used as a substitute for studying hindgut microbiota when investigating the relationship between intestinal microbial changes and host health. So far, no study has compared the difference between the fecal microbiota found in horses that are fed pasture grass, silage, and hay. The present study aims to characterize the fecal microbiota in horses that were exclusively on one of the three forage diets, and to analyze the potential impact of these forages, especially silage, on horse intestinal health. There were 36 horses randomly assigned to each of the three groups; each group was fed only one type of forage for 8 weeks. High throughput sequencing was applied to analyze the bacterial taxa in fecal samples collected from the horses at the end of the feeding trial. The Lachnospiraceae family was statistically more abundant in horses fed with hay, while it was the least abundant in horses fed with silage. The Streptococcaceae spp., considered a core microbial component in equine intestinal microbiota, were present in significantly lower quantities in feces from horses that were fed pasture grass as compared to those from horses fed hay or silage. The novel data may help promote the balancing of horse intestinal microbiota and the maintenance of intestinal health in horses.

A 5-year-old Mongolian mare (Equus caballus Linnaeus, 1758) was observed to have corneal opacity and excessive ocular discharge. An ophthalmic examination revealed a moving thread-like cylindrical worm in the anterior chamber of the right eye. The parasite was successfully removed surgically. The worm was observed under light microscopy and confirmed as Setaria digitata by 12S rRNA gene amplification and sequencing. Phylogenetic analysis demonstrated similarity with Setaria digitata in the National Center for Biotechnology Information (NCBI) GenBank database isolated from other Asian countries. This report is the first confirmed case of equine ocular setariasis by molecular diagnosis in China, which may indicate its presence in livestock and promote research on its epidemiology.