The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional prediction analysis. The alpha diversity analysis showed that Thoroughbred horses had a more abundant and diverse gut microbiota, while the diversity of gut microbiota in Hybrid horses was intermediate between Thoroughbred and Mongolian horses. Subsequent cluster analysis showed that Hybrid horses have a microbiota composition more similar to Mongolian horses. LEfSe analysis revealed that the bacterial biomarkers for Thoroughbred horses at the family level were Prevotellaceae, Rikenellaceae, Fibrobacteraceae, p_251_o5, Lactobacillaceae, and uncultured_bacterium_o_WCHB1_41; the bacterial biomarker for Mongolian horses was Planococcaceae; and the bacterial biomarkers for Hybrid horses were Moraxellaceae, Enterobacteriaceae, and Ruminococcaceae. The functional prediction results indicated that the metabolic pathways differ significantly between the breeds. Regarding metabolism, the Hybrid horses had the lowest proportion of the carbohydrate metabolic pathways, while the energy metabolic pathway had the highest proportion. The abundance ratios of the remaining eight metabolic pathways in Hybrid horses were between Thoroughbred and Mongolian horses. In conclusion, the results of this study showed an association between horse breeds and gut microbiota.

Background: Parasite infection and deworming treatment affect the host gut microbiota. Exploring the response mechanism of the gut microbiota in Rhinopithecus brelichi (R. brelichi) to albendazole deworming treatment is of great value for protecting this critically endangered species.Methods and results: This study used metataxonomics and metabolomics to explore the responses of the gut microbiota and metabolites of R. brelichi to albendazole deworming treatment. The results showed that deworming significantly reduced the eggs per gram of feces (EPG). The 16S rRNA gene sequencing results showed that the richness and diversity of the gut microbiota in R. brelichi after deworming were significantly increased. Meanwhile, deworming treatment also changed the composition of the gut microbiota. At the genus level, the Christensenellaceae R7 group, UCG 002, UCG 005, uncultured rumen bacterium, and Rikenellaceae RC9 gut group were significantly enriched in the pre-deworming samples. Unclassified Muribaculaceae, Prevotella 9, and Bacteroides were significantly enriched in the post-deworming samples. Metabolomics analysis revealed that the relative abundance of 382 out of 1,865 metabolites showed significant differences between the pre- and post-deworming samples. Among them, 103 metabolites were annotated based on the HMDB and mainly classified into Prenol lipids, Carboxylic acids and derivatives, and Organooxygen compounds, etc. The KEGG enrichment analysis result indicated that these metabolites were mainly involved in energy, amino acid, lipid, and purine metabolism. Correlation analysis showed that Bacteroides and unclassified Muribaculaceae, whose relative abundances were upregulated after deworming treatment, were positively correlated with Kaempferol, 5,7-Dihydroxy-3-methoxy-4′-prenyloxyflavone, Purpurin, and Rhein, which have anti-parasitic activities. The Christensenellaceae R7 group, with a downregulated relative abundance after deworming treatment, was not only negatively correlated with the above four metabolites, but also positively correlated with Retinyl beta-glucuronide, which is a storage form of vitamin A, and positively correlated with CDP-Choline, which increases the host’s susceptibility to Entamoeba histolytica and Plasmodium falciparum.Conclusion: This study emphasizes that deworming treatment has an impact on the gut microbiota and metabolic functions of R. brelichi. By exploiting the correlations between differential microbiota and metabolites, potential probiotics or prebiotics can be explored, thereby enhancing the efficiency of deworming and reducing its side effects.

The ruminant gut microbial community's importance has been widely acknowledged due to its positive roles in physiology, metabolism, and health maintenance. Diarrhea has been demonstrated to cause adverse effects on gastrointestinal health and intestinal microecosystem, but studies regarding diarrheal influence on gut microbiota in Giraffa camelopardalis have been insufficient to date. Here, this study was performed to investigate and compare gut microbial composition and variability between healthy and diarrheic G. camelopardalis. The results showed that the gut microbial community of diarrheal G. camelopardalis displayed a significant decrease in alpha diversity, accompanied by distinct alterations in taxonomic compositions. Bacterial taxonomic analysis indicated that the dominant bacterial phyla (Proteobacteria, Bacteroidetes, and Firmicutes) and genera (Escherichia Shigella and Acinetobacter) of both groups were the same but different in relative abundance. Specifically, the proportion of Proteobacteria in the diarrheal G. camelopardalis was increased as compared with healthy populations, whereas Bacteroidetes, Firmicutes, Tenericutes, and Spirochaetes were significantly decreased. Moreover, the relative abundance of one bacterial genus (Comamonas) dramatically increased in diarrheic G. camelopardalis, whereas the relative richness of 18 bacterial genera decreased compared with healthy populations. Among them, two bacterial genera (Ruminiclostridium_5 and Blautia) cannot be detected in the gut bacterial community of diarrheal G. camelopardalis. In summary, this study demonstrated that diarrhea could significantly change the gut microbial composition and diversity in G. camelopardalis by increasing the proportion of pathogenic to beneficial bacteria. Moreover, this study first characterized the distribution of gut microbial communities in G. camelopardalis with different health states. It contributed to providing a theoretical basis for establishing a prevention and treatment system for G. camelopardalis diarrhea.

The structure and composition of gut microbiota correlate with the occurrence and development of host health and disease. Diarrhea can cause alterations in gut microbiota in animals, and the changes in the gut microbial structure and composition may affect the development of diarrhea. However, there is a scarcity of information on the effects of diarrhea on gut fungal composition and structure, particularly in Baer's pochard (Aythya baeri). The current study was performed for high-throughput sequencing of the fungal-specific internal transcribed spacer 1 (ITS-1) to detect the differences of gut mycobiota in healthy and diarrheal Baer's pochard. Results showed that the gut mycobiota not only decreased significantly in diversity but also in structure and composition. Statistical analysis between two groups revealed a significant decrease in the abundance of phylum Rozellomycota, Zoopagomycota, Mortierellomycota, and Kickxellomycota in diarrheal Baer's pochard. At the genus levels, fungal relative abundance changed significantly in 95 genera, with 56 fungal genera, such as Wickerhamomyces, Alternaria, Penicillium, Cystofilobasidium, and Filobasidium, increasing significantly in the gut of the diarrheal Baer's pochard. In conclusion, the current study revealed the discrepancy in the gut fungal diversity and community composition between the healthy and diarrheal Baer's pochard, laying the basis for elucidating the relationship between diarrhea and the gut mycobiota in Baer's pochard.