Dataset Information

Calf respiratory microbiome

ABSTRACT: Effects of tilmicosin treatment on the nasopharyngeal microbiota of feedlot cattle with respiratory disease

PROVIDER: PRJNA508519 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8440610_1.fastq.gz	Fastqsanger.gz
	SRR8440610_2.fastq.gz	Fastqsanger.gz
	SRR8440620_1.fastq.gz	Fastqsanger.gz
	SRR8440620_2.fastq.gz	Fastqsanger.gz
	SRR8440700_1.fastq.gz	Fastqsanger.gz

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Project description:BACKGROUND: Long-distance transportation, a frequent practice in the cattle industry, stresses calves and results in morbidity, mortality and growth suppression, leading to welfare concerns and economic losses. Alkaline mineral water (AMW) is an electrolyte additive containing multiple mineral elements and shows stress-mitigating effects on humans and bovines.RESULTS: Here, we monitored the respiratory health status and growth performance of 60 Simmental calves subjected to 30 hours of road transportation using a clinical scoring system. Within the three days of commingling before the transportation and 30 days after the transportation, calves in the AMW group (n = 30) were supplied with AMW, while calves in the Control group (n = 29) were not. On three specific days, namely the day before transportation (day -3), the 30th day (day 30) and the 60th day (day 60) after transportation, sets of venous blood, serum and nasopharyngeal swab samples were collected from ten calves for routine blood testing, serology detection, whole blood transcriptomic sequencing, serum untargeted metabolic sequencing and 16S rDNA sequencing. The field data showed that calves in the AMW group displayed lower rectal temperatures (38.967 vs 39.022 °C; p < 0.001), respiratory scores (0.079 vs 0.144; p < 0.001), appetite scores (0.024 vs 0.055; p < 0.001), ocular and ear scores (0.185 vs 0.338; p < 0.001), nasal discharge scores (0.143 vs 0.241; p < 0.001) and higher body weight gains (30.87 vs 7.552 kg; p < 0.001). The outcomes of laboratory and high throughput sequencing data revealed that the calves in the AMW group demonstrated higher cellular and humoral immunities, antioxidant capacities, intestinal absorption and lipogenesis abilities, and lower inflammatory levels on days -3 and 60. The nasopharynx 16S rDNA microbiome results revealed the different composition and structure of the nasopharyngeal microflora in the two groups of calves on day 30. Joint analysis of multi-omics revealed that on days -3 and 30, bile secretion was a shared pathway enriched by differentially expressed genes and metabolites, and there were strong correlations between the differentially expressed metabolites and the main genera in the nasopharynx.CONCLUSIONS: These results suggest that AMW supplementation enhances peripheral immunity, nutrition absorption and metabolic processes, subsequently affecting the nasopharyngeal microbiota and improving the respiratory health and growth performance of transported calves. This investigation provided a practical approach to mitigate transportation stress and explored its underlying mechanisms, which are beneficial for the development of the livestock industry.

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Calf respiratory microbiome

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