ArticleMicrobiome2022
Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 36 citations in OpenAlex.
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- Substrate-driven phage community structure and phage-host dynamics in anaerobic digesters.Environmental microbiome · 2026Article
- Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.Nature communications · 2026Article
- Hydrogen excess drives metabolic reprogramming and viral dynamics in syngas-converting microbiomes.Environmental science and ecotechnology · 2025Article
- Characterization and Genome Comparison of Bacteriophage KKU62-1 Infecting Hypervirulent Streptococcus agalactiae ST283.Current microbiology · 2025Article
- Characterization of a novelMicrobiology spectrum · 2025Article
- Article
- Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics.Environmental science & technology · 2024Article
- A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes.Environmental microbiome · 2024Article
- Detection, isolation and characterization of phage-host complexes using BONCAT and click chemistry.Frontiers in microbiology · 2024Article
- Presence and role of viruses in anaerobic digestion of food waste under environmental variability.Microbiome · 2023Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle.
resultsThe sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale.
conclusionsViruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.
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