ArticleMicrobiome2020
Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil.
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 100 citations in OpenAlex.
- Isolation of Bacteriophage: An Antibiotic Alternative for the Control of Salmonella Infections.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts.mSystems · 2026Article
- Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities.Nature communications · 2026Article
- High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.bioRxiv : the preprint server for biology · 2026Article
- A Novel Lytic Podovirus AP-20-A InfectingInternational journal of molecular sciences · 2026Article
- DNA Viral Size Fraction Metagenomics for Human Stool Samples.Journal of visualized experiments : JoVE · 2026Article
- Large-genome phage vB_Eco_ZCEC15 targets gastrointestinal MDR E. coli: evidence from in vitro and Caco-2 cell models.BMC microbiology · 2026Article
- Diverse Temperate Coliphages of the Urinary Tract.Viruses · 2026Article
- HtPIP: High-throughput phage isolation platform increases diversity and reduces isolation time using multiple bacteria.Frontiers in microbiology · 2026Article
- Discovery and Genomic Characterization of a Novel Phage P284 with Potential Lytic Ability AgainstPlants (Basel, Switzerland) · 2025Article
- Recovering new viruses from New Mexico soils.Microbiology resource announcements · 2025Article
- The Global Challenge of Antimicrobial Resistance: Mechanisms, Case Studies, and Mitigation Approaches.Health science reports · 2025Article
- Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.Microbiome · 2025Article
- Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes.PeerJ · 2025Article
- Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.Microbiome · 2024Article
- Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.Applied and environmental microbiology · 2024Article
- Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments.Nature communications · 2024Article
- Genomic analysis of seven mycobacteriophages identifies three novel species with differing phenotypic stabilities.Heliyon · 2024Article
- Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.The ISME journal · 2023Article
- Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils.Nature ecology & evolution · 2023Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBacteriophages (phages) are the most numerous biological entities on Earth and play a crucial role in shaping microbial communities. Investigating the bacteriophage community from soil will shed light not only on the yet largely unknown phage diversity, but may also result in novel insights towards their functioning in the global biogeochemical nutrient cycle and their significance in earthbound ecosystems. Unfortunately, information about soil viromes is rather scarce compared to aquatic environments, due to the heterogeneous soil matrix, which rises major technical difficulties in the extraction process. Resolving these technical challenges and establishing a standardized extraction protocol is, therefore, a fundamental prerequisite for replicable results and comparative virome studies.
resultsWe here report the optimization of protocols for the extraction of phage DNA from agricultural soil preceding metagenomic analysis such that the protocol can equally be harnessed for phage isolation. As an optimization strategy, soil samples were spiked with Listeria phage A511 (Myovirus), Staphylococcus phage 2638AΔLCR (Siphovirus) and Escherichia phage T7 (Podovirus) (each 10
conclusionWe have shown a considerably enhanced extraction of the soil phage community by protocol optimization that has proven robust in both culture-dependent as well as through viromic analyses. Our huge data set of manually curated soil viral contigs substantially increases the amount of currently available soil virome data, and provides insights into the yet largely undescribed soil viral sequence space.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.