Targeted sequencing, a pivotal branch of next-generation sequencing (NGS), enables the selective enrichment of specific genomic regions and has demonstrated significant advantages in the detection of animal pathogens. This review systematically explores the underlying principles of targeted sequencing, various enrichment strategies—including PCR amplification, probe hybridization, and CRISPR-Cas systems—and their key applications in veterinary pathogen diagnostics. Due to its high throughput, sensitivity, and cost-effectiveness, targeted sequencing has been successfully applied in the multiplex detection of pathogens in economically significant livestock, such as cattle, as well as in the surveillance of antimicrobial resistance (AMR) genes, pathogen typing, and source tracing. It is particularly effective in identifying mixed infections and low-abundance pathogens. Nonetheless, wide application is restricted by some factors, like incomprehensive reference databases, cost-effectiveness, and limited application in primary-level laboratories. Further development directions are AI-based panel design, multimodal diagnostic platform integration, standard workflow construction, and introduction of a multi-omics method. Such progress focuses on enhancing the targeted sequencing scalability and precision consistent with the “One Health” initiative objective.

Dietary fiber plays a significant role in gastrointestinal health. In order to thoroughly comprehend the protective effect of dietary fiber on calf intestinal health, we conducted a randomized controlled trial with135 calves. We profiled the gut bacterial community in fecal samples from calves without diarrhea at five time points (0, 7, 14, 28, and 56 days of age) using both 16s amplicon sequencing and metagenomic sequencing. Our findings revealed significantly elevated abundance of Bifidobacterium and Prevotella in the intestine of calves fed with dietary fiber compared to the control group. Bifidobacterium and Prevotella may mitigate intestinal damage and protect intestinal health by modulating secondary bile acid metabolism and flavonoid metabolism pathways. Furthermore, CAZy differential analysis reveals that feeding different dietary fibers can induce increased abundance of CAZymes. We also found that changes in CAZymes abundance induced by feeding different dietary fibers are associated with distinct intestinal microbial communities. This suggests that feeding different dietary fibers stimulates the colonization of different bacterial species in the intestine, thereby increasing the activity of carbohydrate metabolism enzymes in the calf intestinal microbiota. This lays the foundation for health management in calves during transition period. Additionally, our research revealed that calves fed with psyllium husk powder at 56 days of age harbored intergeneric symbiotic clusters in their intestines consisting of Clostridium, Prevotella, Bacteriodes, and others. The symbiosis among these microbial species may collectively maintain intestinal micro-environment in calves. This study provides initial insights into the effect of dietary fiber on pre-weaning calf intestinal microbiota and lays theoretical groundwork for further research into this area.

This study comprised two related experiments. Experiment 1 evaluated the effects of low-temperature long-time pasteurization (LTLT, 63 °C for 30 min) on selected vitamins in bovine colostrum and mature milk. Experiment 2 independently evaluated the effects of dietary β-carotene supplementation on growth performance, fecal scores, oxidative status, cortisol concentrations, and fecal microbiota in preweaning calves. In Experiment 1, colostrum and mature milk were collected from four primiparous and four multiparous Holstein cows before and after LTLT. Concentrations of vitamin A, β-carotene, vitamin B1, vitamin B2, vitamin B9, and vitamin B12 were determined. In Experiment 2, 128 neonatal Holstein heifer calves were randomly assigned to a control group or a β-carotene-supplemented group (100 mg/day/calf) for 56 days. Growth performance, fecal scores, serum antioxidant indicators, cortisol concentrations, and fecal microbiota were evaluated. Colostrum contained substantially higher β-carotene concentrations than mature milk, particularly in primiparous cows (p < 0.001). LTLT reduced β-carotene concentrations by 30% in colostrum(p = 0.034) and significantly decreased vitamin B1 (p < 0.001), whereas the remaining vitamins were only minimally affected. Dietary β-carotene supplementation stabilized antioxidant enzyme activities, reduced serum malondialdehyde and cortisol concentrations (p < 0.001), decreased the occurrence of severe diarrhea (p = 0.046), increased the relative abundance of Blautia, and reduced Fusobacterium and Parabacteroides. Average daily gain did not differ between treatments (p = 0.154). Under the conditions evaluated in Experiment 1, β-carotene was the vitamin most affected by LTLT in colostrum. In the separate feeding experiment, dietary β-carotene supplementation affected several antioxidant indicators, reduced cortisol concentrations and the frequency of severe diarrhea scores, and altered fecal microbial composition, but did not affect average daily gain.