The fecal virome of domesticated animals

Mihalov-Kovács, Eszter; Fehér, Enikő; Martella, Vito; Bányai, Krisztiàn; Farkas, Szilvia L.

doi:10.1007/s13337-014-0192-1

Cited by 12 publications

(9 citation statements)

References 22 publications

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“…Culture-independent metagenomic approaches can aid in understanding the ecological role, phylogeny, and functionality of gut microbial communities in relation to host physiology 1 – 4 . Metagenomic shotgun sequencing investigations have been used to reveal specific features of the resistome 5 – 9 , mobilome 10 , 11 , virulome 12 and virome 13 . The increasing prevalence of antimicrobial resistance (AMR) in bacteria is one of the most important challenges facing public health.…”

Section: Introductionmentioning

confidence: 99%

Impact of sequencing depth on the characterization of the microbiome and resistome

Zaheer¹,

Noyes

Polo

et al. 2018

Sci Rep

167

144

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Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

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Section: Introductionmentioning

confidence: 99%

Impact of sequencing depth on the characterization of the microbiome and resistome

Zaheer¹,

Noyes

Polo

et al. 2018

Sci Rep

167

144

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“…Samples were subjected to random primed PCR and semiconductor sequencing using the Ion Torrent PGM platform. Library preparation, size selection of library DNA, emulsion PCR, templated Ion Sphere bead enrichment and sequencing, bioinformatics analysis was carried out as described in detail elsewhere (Mihalov-Kovács et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and recombination within bufaviruses: Detection of a novel strain in Hungarian bats

Kemenesi

Dallos

Görföl

et al. 2015

Infection, Genetics and Evolution

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Bats are important hosts of many viruses and in several cases they may serve as natural reservoirs even for viruses with zoonotic potential worldwide, including Europe. However, they also serve as natural reservoir for other virus groups with important evolutionary relevance and yet unknown zoonotic potential. We performed viral metagenomic analyses on Miniopterus schreibersii bat fecal samples. As a result, a novel parvovirus was detected for the first time in European bats. Although, bufavirus was recently discovered as a novel human infecting parvovirus, here we report sequence data of the first bufavirus from European bats related to human bufaviruses. Based on our sequence data a possible intragenic recombination event was detected within bufaviruses which may serves as an important milestone in their evolution.

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“…Other study reported in diarrheic dogs, the presence of canine parvovirus 2 (CPV2), canine enteric coronavirus (CcoV), rotavirus, insect and plant viruses, canine kobuviruses and sapoviruses (canine sapovirus 1 and 2). Finally, studies from bird feces (turkey and chicken with enteric disease) showed kobuviruses, calicivirus (Sapovirus and Lagovirus), avianastrovirus and avian reovirus [17].…”

Section: Metagenomics For Viral Diagnostics?mentioning

confidence: 99%

“…Percentage of sequences related to the main categories of existing viruses: vertebrate (blue), plant/fungal (green), invertebrate (brown), protozoan (yellow) viruses and bacteriophages (gray), and unassigned viral sequences (no data available concerning the taxonomic family, indicated in red). The total number of viral contigs is indicated below each pie chart (figure and legend were taken with permission from[17]). http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087194.…”

mentioning

confidence: 99%

Metagenomics and Diagnosis of Zoonotic Diseases

Cuervo-Soto¹,

López-Pazos²,

Batista-García³

2018

Farm Animals Diseases, Recent Omic Trends and New Strategies of Treatment

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Zoonotic diseases represent a public health problem worldwide, since approximately 60% of human pathogens have a zoonotic origin. A variety of methodologies have been developed to diagnose zoonosis, including culture-dependent and immunological-based methods, which allow the identification of a huge range of pathogens. However, some of them are not detected easily with these approaches. Additionally, molecular tests have been developed, and they are designed to identify a single pathogen or mixtures of them. In this context, metagenomics comes as an alternative to get genome sequences of different microorganisms, which comprise a microbial community. Metagenomics have been used to characterize microbiomes and viromes, which are not cultivable under laboratory conditions. This methodology could be a powerful tool in the diagnosis of zoonotic diseases because it allows not only identification of genus and species, but also detection of some proteins in specific conditions on specific tissues, through structural and functional metagenomics, respectively.

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The fecal virome of domesticated animals

Cited by 12 publications

References 22 publications

Impact of sequencing depth on the characterization of the microbiome and resistome

Impact of sequencing depth on the characterization of the microbiome and resistome

Genetic diversity and recombination within bufaviruses: Detection of a novel strain in Hungarian bats

Metagenomics and Diagnosis of Zoonotic Diseases

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