Comparison of gut viral communities in diarrhoea and healthy dairy calves

Lu, Xiang; Hua, Xiuguo; Zhang, Dong; Jiang, Shengyao; Yang, Shixing; Wang, Xiaochun; Shen, Qing; Zhou, Tianji; Wang, Qisheng; Zhang, Wen; Cui, Li

doi:10.1099/jgv.0.001663

Cited by 6 publications

(7 citation statements)

References 62 publications

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…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.…”

Section: Discussionmentioning

confidence: 99%

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

Zhu,

Qi,

Guo

et al. 2024

mSystems

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Limited information on the virome and bacterial community hampers our ability to discern systemic ecological risk factors that cause cattle diarrhea, which has become a pressing issue in the control of disease. A total of 110 viruses, 1,011 bacterial genera, and 322 complete viral genomes were identified from 70 sequencing samples mixed with 1,120 fecal samples from 58 farms in northeast China. For the diarrheic samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, and geographic distribution in relation to different disease-associated ecological factors; the abundance of identified viruses and bacteria was significantly correlated with the host factors of clinical status, cattle type, and age, and with environmental factors such as aquaculture model and geographical location ( P < 0.05); a significant interaction occurred between viruses and viruses, bacteria and bacteria, as well as between bacteria and viruses ( P < 0.05). The abundance of SMB53 , Butyrivibrio , Facklamia , Trichococcus , and Turicibacter was significantly correlated with the health status of cattle ( P < 0.05). The proportion of BRV, BCoV, BKV, BToV, BoNoV, BoNeV, BoAstV, BEV, BoPV, and BVDV in 1,120 fecal samples varied from 1.61% to 12.05%. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. A genome-based phylogenetic analysis revealed high variability of 10 bovine enteric viruses. The bovine hungarovirus was initially identified in both dairy and beef cattle in China. This study elucidates the fecal virome and bacterial community signatures of cattle affected by diarrhea, and reveals novel disease-associated ecological risk factors, including cattle type, cattle age, aquaculture model, and geographical location. IMPORTANCE The lack of data on the virome and bacterial community restricts our capability to recognize ecological risk factors for bovine diarrhea disease, thereby hindering our overall comprehension of the disease’s cause. In this study, we found that, for the diarrheal samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, configuration, and geographic distribution in relation to different disease-associated ecological factors. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. Our study aims to uncover novel ecological risk factors of bovine diarrheal disease by examining the pathogenic microorganism-host-environment disease ecology, thereby providing a new perspective on the control of bovine diarrheal diseases.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Zhu,

Qi,

Guo

et al. 2024

mSystems

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“… 23 Lu et al identified a significantly lower alpha diversity of the gut virome in diarrheal dairy calves. 24 The study by the team of Becerra revealed the dissimilarity of the gut virome of diarrheal children. 25 The human virome has a more complex gut viral community than experimental mice and dairy calves and a better capacity of resisting disturbance.…”

Section: Discussionmentioning

confidence: 99%

Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection

Bao

Wang

et al. 2023

Gut Microbes

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Diarrhea is a leading cause of morbidity and mortality in children worldwide and represents a major dysbiosis event. Rotavirus has been recognized as a global leading pathogen of diarrhea. This study is aimed at investigating differences in the gut virome between diarrheal children and healthy controls. In 2018, 76 diarrheal fecal samples and 27 healthy fecal samples in Shanghai and 40 diarrheal fecal samples and 19 healthy fecal samples in Taizhou were collected to investigate the composition of the gut virome. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, and the beta diversity had a significant difference between diarrheal and healthy children. The diarrheal virome was mainly dominated by the families Adenoviridae , Astroviridae , Caliciviridae , and Picornaviridae . Meanwhile, the healthy virome also contains phages, including Microviridae and Caudovirales . The high prevalence of diverse enteric viruses in all samples and the little abundance of Microviridae and Caudovirales in diarrheal groups were identified. The study introduced a general overview of the gut virome in diarrheal children, revealed the compositional differences in the gut viral community compared to healthy controls, and provided a reference for efficient treatments and prevention of virus-infectious diarrhea in children.

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“…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.…”

Section: Methodsmentioning

confidence: 99%

Phage as signatures of healthy microbiomes

Wheatley,

Holtappels,

Koskella

2024

Preprint

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Parasites are foundational to ecosystem health both as indicator species of community productivity but also as drivers of diversity. In bacterial communities, bacteriophage viruses can play such a role as they track the dynamic composition of bacterial hosts, and in the case of lytic phages, confer a growth advantage to lower abundance bacteria while adapting to more common ones. We set out to test whether viromes can be used as signatures of microbiome health using previously published results across systems. By comparing observed phage and bacterial diversity between microbiomes characterized by disturbance (so-called dysbiosis) and those considered control populations, we were able to identify some key commonalities. While just under half of studies report significant changes in viral species richness in dysbiosis, just under two thirds of studies find the viral composition to shift in dysbiosis, with specific viral taxa enrichment acting as a common signature of dysbiosis. Our analyses also suggest that the positive relationship between bacteriome and virome alpha diversity observed in health breaks down under microbiome disturbance. Overall, while specific viral signatures of dysbiosis are likely to be highly disease- and condition-specific, existing ecological theory shows clear promise in predicting and explaining microbiome health. Future data on bacteria-phage diversity relationships may provide us with much needed opportunity to diagnose, treat, and better understand the causes of dysbiosis.

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Comparison of gut viral communities in diarrhoea and healthy dairy calves

Cited by 6 publications

References 62 publications

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

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

Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection

Phage as signatures of healthy microbiomes

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