Caprine cryptosporidiosis mainly occurs in young goats, with morbidity rates of 80%–100% and mortality over 50% in goat kids. However, limited research has been conducted on the impact of Cryptosporidium parvum, a diarrhea-causing pathogen, on the intestinal microbiota of goat kids. In this study, 16S rRNA-based metataxonomic analysis was performed to compare the microbial diversity and abundance of the gut microbiota between C. parvum-infected and uninfected goat kids. In total, 12 goat fecal samples were collected, including seven naturally C. parvum-infected and five uninfected goats from Chungcheongbuk-do, Korea. After amplification of the V3–V4 hypervariable region of the bacterial 16S rRNA, high-throughput sequencing was performed. The results showed differences in the microbial composition between C. parvum-infected and uninfected groups based on beta diversity. Firmicutes and Bacteroidetes were the most dominant phyla in both groups. However, no significant difference was observed in the Bacteroidetes/Firmicutes ratio between the two groups. Compared with the uninfected group, the C. parvum-infected group showed significantly higher abundances of Tyzzerella nexillis, Lactobacillus johnsonii, Butyricicoccus pullicaecorum, Enterococcus raffinosus, Enterococcus faecalis, and Negativicoccus massiliensis, and significantly reduced abundances of Aerococcus vaginalis, Faecalicoccus pleomorphus, Oribacterium parvum, and Coprococcus comes. These findings indicate that C. parvum infection, which is associated with diarrhea in neonatal goats, induces alterations in the caprine gut microbiota.

INTRODUCTION
MATERIALS AND METHODS
    Sample collection
    DNA extraction and amplicon-based next-generation sequencing
    Sequence processing and amplicon sequence variant table construction
    Microbiota analysis with phyloseq
RESULTS
    Amplicon-based next-generation sequencing data
    Microbial diversity analysis
    Assessing microbial abundance and association at different taxonomic levels
DISCUSSION
References

• Subin Lee(College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea)
• Badriah Alkathiri(College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea)
• Ah-Young Kim(Graduate of Veterinary Biosecurity and Protection, Chungbuk National University, Cheongju 28644, Korea, Department of Animal Health, Agricultural Policy Bureau, Chungbuk Provincial Government, Cheongju 28515, Korea)
• Kyung-Hyo Do(College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea)
• Kwangwon Seo(College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea, Graduate of Veterinary Biosecurity and Protection, Chungbuk National University, Cheongju 28644, Korea)
• Soochong Kim(College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea, Graduate of Veterinary Biosecurity and Protection, Chungbuk National University, Cheongju 28644, Korea)
• Wan-Kyu Lee(College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea, Graduate of Veterinary Biosecurity and Protection, Chungbuk National University, Cheongju 28644, Korea)
• Dongmi Kwak(College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea)
• Seung-Hun Lee(College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea, Graduate of Veterinary Biosecurity and Protection, Chungbuk National University, Cheongju 28644, Korea) Corresponding author