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Yan N, Yue H, Liu Q, Wang G, Tang C, Liao M. Isolation and Characteristics of a Novel Aichivirus D from Yak. Microbiol Spectr 2023; 11:e0009923. [PMID: 37097198 PMCID: PMC10269754 DOI: 10.1128/spectrum.00099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
Aichivirus D (AiV-D) is a newly emerging Kobuvirus detected in bovine and sheep, and information is limited regarding its biological significance and prevalence. This study aimed to explore both the prevalence and characteristics of AiV-D in yaks. From May to August 2021, 117 fecal samples were collected from yaks with diarrhea in three provinces of China's Qinghai-Tibet Plateau, 15 of which were selected and pooled for metagenomic analysis. A high abundance of AiV-D sequences was obtained. Of the 117 diarrhea samples, 29 (24.8%) tested AiV-D-positive, including 33.3% (14/42) from Sichuan, 21.1% (8/38) from Qinghai, and 18.9% (7/37) from Tibet, respectively, suggesting a wide geographical distribution of the AiV-D in yaks in the Qinghai-Tibet Plateau. Furthermore, three AiV-D strains were successfully isolated using Vero cells. Significantly, the AiV-D strain could cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, duodenum, colon, cecum, and rectum. Based on phylogenetic analysis of the genome and capsid protein P1 (VP0, VP3, and VP1 genes), the yak AiV-D strains likely represent a novel genotype of AiV-D. On the whole, this study identified a novel genotype of AiV-D from yaks, which was successfully isolated, and confirmed that this virus is a diarrhea pathogen in yaks and has a wide geographical distribution in the Qinghai-Tibet Plateau. Our results expand the host range of AiV-D and the pathogen spectrum of yaks and have significant implications for diagnosing and controlling diarrhea in yaks. IMPORTANCE In this study, we identified and successfully isolated a novel genotype of AiV-D from yaks. Animal infection confirmed that this virus can cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, cecum, duodenum, colon, and rectum. All of these results have significant implications for diagnosing and controlling diarrhea in yaks. These novel AiV-D strains have a wide geographical distribution in yaks from the Qinghai-Tibet Plateau in China. In addition to expanding the host range of AiV-D and the pathogen spectrum of yaks, these findings can increase knowledge of the prevalence and diversity of AiV-D.
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Affiliation(s)
- Nan Yan
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Hua Yue
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Quan Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Gang Wang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Guangzhou, China
- Field Observation and Experiment Station on Animal Blight of Guangdong Province, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Guangzhou, China
- Field Observation and Experiment Station on Animal Blight of Guangdong Province, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris). Viruses 2023; 15:v15030685. [PMID: 36992396 PMCID: PMC10058366 DOI: 10.3390/v15030685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.
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Vallenas-Sánchez YPA, Bautista-Valles MF, Llaque-Chávarri F, Mendoza-Coello ME. Bacteriophage cocktail as a substitute for antimicrobials in companion animal dermatology. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2022. [DOI: 10.36610/j.jsaas.2022.090200097x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Vallenas-Sánchez YPA, Bautista-Valles MF, Llaque-Chávarri F, Mendoza-Coello ME. Cóctel de bacteriófagos como sustituto de antimicrobianos en dermatología de animales de compañía. JOURNAL OF THE SELVA ANDINA ANIMAL SCIENCE 2022. [DOI: 10.36610/j.jsaas.2022.090200097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Yang S, He Y, Chen X, Kalim U, Wang Y, Yang S, Qi H, Cheng H, Lu X, Wang X, Shen Q, Zhang W. Viral Metagenomics Reveals Diverse Viruses in the Feces Samples of Raccoon Dogs. Front Vet Sci 2021; 8:693564. [PMID: 34322538 PMCID: PMC8311183 DOI: 10.3389/fvets.2021.693564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Raccoon dogs as an ancient species of Canidae are the host of many viruses, including rabies virus, canine distemper virus, severe acute respiratory syndrome coronavirus, and so on. With the development of raccoon dog breeding in recent years, some viruses which infected poultry or pigs were also detected from raccoon dogs. At present, the fecal virome of raccoon dogs has been rarely studied. Using an unbiased viral metagenomic approach, we investigated the fecal virome in raccoon dogs collected from one farm of Jilin Province, China. Many DNA or RNA viruses identified in those fecal samples were mainly from seven families, including Circoviridae, Smacoviridae, Genomoviridae, Parvoviridae, Picornaviridae, Astroviridae, and Hepeviridae. This study increased our understanding of the fecal virome in raccoon dog and provided valuable information for the monitoring, prevention, and treatment of viral diseases of these animals.
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Affiliation(s)
- Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yumin He
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xu Chen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ullah Kalim
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yan Wang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shuyu Yang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Haifeng Qi
- School of Medicine, Jiangsu University, Zhenjiang, China
| | | | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
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Jha AR, Shmalberg J, Tanprasertsuk J, Perry L, Massey D, Honaker RW. Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach. PLoS One 2020; 15:e0227289. [PMID: 32078625 PMCID: PMC7032713 DOI: 10.1371/journal.pone.0227289] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/16/2019] [Indexed: 01/13/2023] Open
Abstract
The role of gut microbiomes as important regulators of mammalian health is increasingly recognized, although feline and canine gut microbiomes remain poorly characterized. In this proof-of-concept study, we assessed the utility of a direct-to-consumer approach to executing pet microbiome studies. We characterized the gut microbiomes of 238 pets (46 cats and 192 dogs) by generating ~11 million merged reads that were mapped to the V4 region of 16S ribosomal RNA gene at a sequencing depth of 45,806 (±22,325) reads per sample. Analyses of these reads revealed that both feline and canine gut microbiomes are dominated by three major phyla, namely Firmicutes, Proteobacteria, and Bacteroides and that alpha diversity is higher in the feline gut. In addition to interspecies differences between the feline and canine gut, we also detected appreciable intraspecies bacterial variation within the canine population. While the dogs in this dataset could be assigned to three distinct clusters based on their gut microbiome, no clustering was observed within the feline population. Integration of additional data obtained from survey questionnaires revealed that geography and body weight may be associated with canine gut microbiome composition. Furthermore, we found that both the inter and intraspecies differences are more pronounced at finer taxonomic levels, indicating that strain-level investigations may be necessary in the future. This study demonstrates that the direct-to-consumer approach overcomes existing limitations in pet microbiome research, for example, it allows collection of large numbers of pet samples. The direct-to-consumer approach has proven successful in human genomics as well as human microbiomics and this study demonstrates that by building partnerships with an engaged general public this approach can also propel the field of pet microbiomics forward.
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Affiliation(s)
- Aashish R. Jha
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
- * E-mail:
| | - Justin Shmalberg
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
- Department of Comparative, Diagnostic & Population Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Jirayu Tanprasertsuk
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
| | - LeeAnn Perry
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
| | - Dan Massey
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
| | - Ryan W. Honaker
- Research & Development Division, NomNomNow, Inc., Oakland, California, United State of America
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