Comparison of gut viral communities in diarrhoea and healthy dairy calves

Abstract

Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.

Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India

“…Neonatal calf diarrhoea is most commonly caused by RVA, and its co-infection has been reported with BAstV in Korea ( Oem and An, 2014 ), China ( Alfred et al., 2015 ; Zhu et al., 2021 ), and Italy ( Martella et al., 2020 ). Although previous studies could not establish an association of AstV with diarrhoea, a recent metagenomics study found most of the BAstV reads in a diarrheic compared to the healthy Chinese calves ( Lu et al., 2021 ). Another study on Chinese calves established a positive correlation between the presence of only BAstV and co-infection in diarrhoea ( Zhu et al., 2022 ).…”

A survey of fecal virome and bacterial community of the diarrhea-affected cattle in northeast China reveals novel disease-associated ecological risk factors

“…The infection of pathogenic microorganisms and the change of intestinal flora and virome were the most important factors leading to the occurrence of bovine diarrhea. Previous research had mainly concentrated on the investigation of diarrhoea-causing microorganisms in the context of single disease-related ecological factors ( 8 , 15 , 18 ). The research population was generally limited in size, and there was an absence of systematic disease ecological factors such as pathogen-host-environment.…”

“…Five new CRESS-DNA viruses encoding replication-related proteins and three bovine parvoviruses have been identified in bovine plasma ( 26 ). In the macrogenomics sequencing study of cattle fecal samples, 26 viral families were identified and it was found that the reads of calicivirus and astrovirus in diarrhea calves were much higher than those in healthy calves ( 15 , 18 ). In this study, 39 virus families, 86 virus genera, and 110 virus species were identified in the fecal samples of cattle, which greatly enriched the virology study of cattle diarrhea fecal.…”

Phage as signatures of healthy microbiomes

“…The majority of the 39 studies that met our criterion for inclusion focused on human hosts (30 studies ( 29, 38-66 )), with the remaining studies using cow (1 study ( 67 )), pig (1 study ( 68 )), or mouse (7 studies ( 69-75 )) (Supplementary Table 2). These studies covered a diverse spectrum of dysbioses, spanning cancer to viral infections such as HIV and COVID-19, and varied conditions such as alcohol hepatitis, periodontal disease, spinal injury, bacterial vaginosis, cirrhosis, obesity, rheumatoid arthritis, inflammatory bowel disease.…”