Landscapes of Enteric Virome Signatures in Early-Weaned Piglets

Tao, Shiyu; Zou, Huicong; Li, Jingjing; Wei, Hong

doi:10.1128/spectrum.01698-22

Cited by 10 publications

(13 citation statements)

References 45 publications

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“…A recent study on the human gut microbiome constructed reference databases of DNA viruses by using an assembly metagenomic approach, and more than 75% of the genomes represented double-stranded DNA phages that infect members of the classes Bacteroidia and Clostridia ( 25 ). At present, most studies on swine enteric viruses have focused mainly on disease models ( 26 , 27 ). In fact, as the main component of the gut microbiome, enteric viruses play an important role in maintaining intestinal homeostasis and physiological functions ( 28 ).…”

Section: Discussionmentioning

confidence: 99%

Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs

Zhang

Shi

et al. 2023

Microbiol Spectr

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Section: Discussionmentioning

confidence: 99%

Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs

Zhang

Shi

et al. 2023

Microbiol Spectr

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“…Our laboratory has previously profiled the gut virome landscape of healthy and diarrheal weaning piglets using bulk metagenomics and meta-transcriptomics [ 19 ]. To the best of our knowledge, this is the first study to investigate the relationship between diarrhea and gut virome in pigs using a culture-independent method.…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Sequencing Identified Specific Bacteriophage Signature Discriminating between Healthy and Diarrheal Neonatal Piglets

Wang

et al. 2023

Nutrients

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Neonatal diarrhea is one of the most severe diseases in human beings and pigs, leading to high mortality and growth faltering. Gut microbiome-related studies mostly focus on the relationship between bacteria and neonatal diarrhea onset, and no research study has investigated the role of the gut virome in neonatal diarrhea. Here, using metagenomic sequencing, we characterized the fecal viral community of diarrheal and healthy neonatal piglets. We found that the viral community of diarrheal piglets showed higher individual heterogeneity and elevated abundance of Myoviridae. By predicting the bacterial host of the identified viral genomes, phages infecting Proteobacteria, especially E. coli, were the dominant taxa in neonatal diarrheal piglets. Consistent with this, the antibiotic resistance gene of E. coli origin was also enriched in neonatal diarrheal piglets. Finally, we established a random forest model to accurately discriminate between neonatal diarrheal piglets and healthy controls and identified genus E. coli- and genus listeria-infecting bacteriophages, including psa and C5 viruses, as key biomarkers. In conclusion, we provide the first glance of viral community and function characteristics in diarrheal and healthy neonatal piglets. These findings expand our understanding of the relationship among phages, bacteria and diarrhea, and may facilitate the development of therapeutics for the prevention and treatment of neonatal diarrhea.

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“…Viral sequences were identified based on VirSorter2's SOP with (Guo et al, 2021b) and P>=0.95 using DeepVriFinder. We collected metagenomics data from various sources, including SRP188615/PRJNA526405 (Gaio et al, 2022;Gaio et al, 2021), CNP0000824 (Chen et al, 2021b), PRJEB11755 (Xiao et al, 2016), PRJNA788462 (Gaire et al, 2022), PRJNA775062 (Tao et al, 2022), PRJEB22062 (Luiken et al, 2020), PRJCA009609 (Wu et al, 2022a), PRJEB44118 (Zhang et al, 2022), and 70 samples collected in our lab. In total, 4,650 samples were used in our study to extract the viral contigs.…”

Section: Data Assembly and Viral Identificationmentioning

confidence: 99%

“…Several databases, such as GOV2 (Gregory et al, 2019), IMG/VR4 (Camargo et al, 2023a), GVD (Gregory et al, 2020), MGV (Nayfach et al, 2021b), and GPD (Camarillo-Guerrero et al, 2021), have been established to facilitate the analysis of virome from various environments using metagenomic data. Since the establishment of these databases, the number of publicly available pig gut microbiota datasets has rapidly increased (Chen et al, 2021b;Gaio et al, 2022;Gaio et al, 2021;Gaire et al, 2022;Luiken et al, 2020;Tao et al, 2022;Wu et al, 2022a;Xiao et al, 2016;Zhang et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Massive expansion of the pig gut virome based on global metagenomic mining

Jing

et al. 2023

Preprint

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The pig gut virome plays a crucial role in the gut microbial ecosystem of pigs, yet a comprehensive reference database is still lacking. To address this gap, we established the Pig Virome Database (PVD) of the gut that comprises 5,566,804 viral contig sequences from 4,650 publicly available gut metagenomic samples using a pipeline named metav developed in this study. The majority of viral operational taxonomic units (vOTUs) were identified as Caudoviricetes (65.36%). By clustering sequences, we identified 48,299 vOTU genomes, of which 92.83% were not found in existing major databases. The PVD database contains a total of 18,161,503 protein-coding genes that can be used to explore the functional potential of the pig gut virome. Our study showed that the PVD can improve the detection of viruses that carry antibiotic/metal resistance genes, mobile genetic elements, virulence factor genes, and quorum sensing systems. These findings highlight the extensive diversity of viruses in the pig gut and provide detailed insight into host-virus interactions.

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Landscapes of Enteric Virome Signatures in Early-Weaned Piglets

Cited by 10 publications

References 45 publications

Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs

Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs

Metagenomic Sequencing Identified Specific Bacteriophage Signature Discriminating between Healthy and Diarrheal Neonatal Piglets

Massive expansion of the pig gut virome based on global metagenomic mining

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