Diversity and potential function of pig gut DNA viruses

Qin, Junjun; Ji, Bingzhen; Ma, Yijia; Liu, Xin; Liu, Guiming; Li, Bugao; Wang, Guoliang; Gao, Pengfei

doi:10.1016/j.heliyon.2023.e14020

Cited by 7 publications

(13 citation statements)

References 99 publications

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“…In a separate study in Hubei Province (Duroc x Landrace x Yorkshire), Podoviridae was found to be the most dominant viral community, followed by Siphoviridae ( Caudoviricetes ), and then Myoviridae [ 15 ]. In a study from Shanxi, the characterization results varied across different regions, with Siphoviridae , Podoviridae , and Microviridae being the primary communities, respectively, in the domestic pig gut [ 44 ]. Meanwhile, Podoviridae and Caudoviricetes ranked lower in Tibetan pigs compared to domestic pigs.…”

Section: Discussionmentioning

confidence: 99%

“…Environmental factors, such as dietary patterns and living conditions, significantly influence the gut microbiome relative to the host’s genetic background [ 54 ]. Despite the debate over whether geography impacts the composition of viral communities in the pig gut [ 44 , 55 ], Microviridae were not the predominant community in lower-altitude areas [ 15 , 53 ]. Our findings in Tibetan pigs revealed that Microviridae were consistently the predominant viral community at all the stages of development in Linzhi, Xizang, PR China (altitude ≈ 3000 m) ( Figure 1 B).…”

Section: Discussionmentioning

confidence: 99%

“…Those without gene IDs or gene descriptions were also discarded, and annotation matches for KEGG were present for all retained vAMGs. Following the previous reports [ 44 , 45 , 46 ], we manually removed specific metabolic pathways that would be expected in viruses, including nucleotide metabolism, glycosyl transferases, and ribosomal proteins.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Luo,

Guan,

et al. 2024

Viruses

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Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai–Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Luo,

Guan,

et al. 2024

Viruses

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“…It may alter biogeochemical processes in other environments like water and soil [ 60 ]. In addition, studies have shown that cysH may serve as a fitness modulator during sulfur-limiting periods in Burkholderia -phage infection and help pig gut viruses adapt to the complex gut environment and homeostasis [ 71 , 72 , 73 ]. Nutrient availability, including other factors, influences the distribution of dcm and cysH in different ecosystems [ 68 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models

Ishola,

Kublik,

Durai Raj

et al. 2024

Microorganisms

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Gnotobiotic murine models are important to understand microbiota–host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host’s environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome “dark matter” and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.

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“…coli strains isolated from pig feces was also observed . Besides, environmental viral metagenomic studies have been carried out for the detection of phage-carried ARGs; only a few ARGs were found in soil, pig feces, chicken feces, and human gut virome. − However, the category and diversity of ARGs presented in AD virome have not been reported yet, despite the fact that the direct disposal of AD sludge to the receiving environment may cause severe environmental risks. More than this, an assessment of the overall contribution of phages to the prevalence and dissemination of ARGs was carried out.…”

Section: Introductionmentioning

confidence: 99%

Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant

Liu,

Xu,

et al. 2024

Environ. Sci. Technol.

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Anaerobic digestion (AD) is an important biological resource recovery process, where microorganisms play key roles for material transformation. There has been some knowledge about the prokaryotic community and antibiotic resistance genes (ARGs) in AD, but there has been very limited knowledge of phages. In this study, samples from a full-scale AD plant were collected over 13 months, sequenced, and analyzed for viral and prokaryotic metagenomes. Totally, 3015 viral operational taxonomic units (vOTUs) were detected, mostly assigned to Caudoviricetes. The phage community had faster temporal variation than the prokaryotic community. Warm seasons harbored a higher abundance of both temperate phages and broad host-range phages. Seven ARGs of 6 subtypes were carried by 20 vOTUs, a representative ermT gene was synthesized and expressed, and the resistance activity in the host was examined, confirming the real activity of virus-carried ARGs in the AD process. Some of the ARGs were horizontally transferred between the phage and prokaryotic genomes. However, phage infection was not found to contribute to ARG transfer. This study provided an insight into the ecological patterns of the phage community, confirmed the antibiotic resistance activity of virus-carried ARGs, evaluated the contribution of phages on the ARG prevalence, and laid the foundation for the control strategies of the community and antibiotic resistance in the AD process.

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Diversity and potential function of pig gut DNA viruses

Cited by 7 publications

References 99 publications

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models

Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant

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