PHAGE, Journal Year: 2021, Volume and Issue: 2(4), P. 170 - 182
Published: Dec. 1, 2021
All sequencing projects of bacteriophages (phages) should seek to report an accurate and comprehensive annotation their genomes. This article defines 14 questions for those new phage genomics that be addressed before submitting a genome sequence the International Nucleotide Sequence Database Collaboration or writing publication.
Language: Английский
Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 24, 2025
Language: Английский
Citations
3
Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: unknown
Published: Feb. 9, 2021
Bacteriophages (phages) evolve rapidly by acquiring genes from other phages. This results in mosaic genomes. Here, we identify numerous genetic transfers between distantly related phages and aim at understanding their frequency, consequences, the conditions favoring them. Gene flow tends to occur that are enriched for recombinases, transposases, nonhomologous end joining, suggesting both homologous illegitimate recombination contribute gene flow. Phage family host phyla strong barriers exchange, but phage lifestyle is not. Even if observe four times more recent temperate than pairs, there extensive virulent phages, latter. These predominantly involve with large genomes previously classed as low flux, lead preferential transfer of encoding functions involved cell energetics, nucleotide metabolism, DNA packaging injection, virion assembly. Such exchanges may observed twice larger We used transfers, which upon coinfection a host, compare range. found have broader ranges can mediate narrow range infecting distant bacterial hosts, thus contributing well drastically expands repertoires available evolution, including functional innovations across taxa.
Language: Английский
Citations
83
Frontiers in Cellular and Infection Microbiology, Journal Year: 2022, Volume and Issue: 11
Published: Jan. 4, 2022
Phages, short for bacteriophages, are viruses that specifically infect bacteria and the most abundant biological entities on earth found in every explored environment, from deep sea to Sahara Desert. Phages within human biome gaining increasing recognition as potential modulators of gut ecosystem. For example, they have been connected gastrointestinal diseases treatment efficacy Fecal Microbiota Transplant. The ability phages modulate microbiome has attributed predation or promotion bacterial survival by transfer genes enhance fitness upon infection. In addition, shown interact with immune system variable outcomes. Despite evidence supporting importance ecosystem, extent their influence shape ecosystem is yet be fully understood. Here, we discuss phage modulation microbiome, postulating pivotal contributors dynamics. We therefore propose novel research questions further elucidate role(s) its impact our health well-being.
Language: Английский
Citations
60
Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)
Published: Sept. 6, 2022
Indigenous bacteriophage communities (virome) in the human gut have a huge impact on structure and function of bacterial (bacteriome), but virome variation at population scale is not fully investigated yet. Here, we analyse dsDNA Japanese 4D cohort 4198 deeply phenotyped individuals. By assembling metagenomic reads, discover thousands high-quality phage genomes including previously uncharacterised clades with different hosts than known major ones. The distribution host bacteria strong determinant for phages gut, diversity highly correlated anti-viral defence mechanisms bacteriome, such as CRISPR-Cas restriction-modification systems. We identify 97 various intrinsic/extrinsic factors that significantly affect structure, age, sex, lifestyle, diet, most which showed consistent associations both their predicted hosts. Among metadata categories, disease medication strongest effects structure. Overall, these results present basis to understand symbiotic viruses will facilitate medical industrial applications indigenous viruses.
Language: Английский
Citations
59
Microbiome, Journal Year: 2022, Volume and Issue: 10(1)
Published: July 8, 2022
Abstract Background Inflammatory bowel diseases (IBDs) including Crohn’s disease (CD) and ulcerative colitis (UC) are characterized by chronic debilitating gut inflammation. Altered bacterial communities of the intestine strongly associated with IBD initiation progression. The virome, which is primarily composed viruses (bacteriophages, phages), thought to be an important factor regulating shaping microbial in gut. While alterations virome have been observed patients, contribution these community heightened inflammatory responses patients remains largely unknown. Results Here, we performed vivo cross-infection experiments follow effects fecal virus-like particles (VLPs) isolated from UC healthy controls on diversity severity experimental human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred HMA mice, resulting treatment-specific virome. VLPs also shifted effect was amplified during colitis. specifically altered relative abundance taxa previously implicated Additionally, VLP administration as indicated shortened colon length increased pro-inflammatory cytokine production. Importantly, this dependent intact VLPs. Conclusions Our findings build recent literature indicating dynamic regulators implicate intestinal modulating inflammation disease.
Language: Английский
Citations
56
Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(8), P. 1301 - 1311
Published: Aug. 2, 2022
Language: Английский
Citations
45
iScience, Journal Year: 2023, Volume and Issue: 26(2), P. 106007 - 106007
Published: Jan. 18, 2023
Bacteriophages, viruses specific to bacteria, coexist with their bacterial hosts limited diversity fluctuations in the guts of healthy individuals where they replicate mostly via lysogenic replication. This favors 'piggy-back-the-winner' over 'kill-the-winner' dynamics which are driven by lytic bacteriophage Revisiting deep-viral sequencing data a individual sampled 2.4 years, we explore how these occur. Prophages found assembled metagenomes were also extra-cellularly, as induced phage particles (iPPs), likely derived from prophage activation. These iPPs diverse and continually present low abundance, relative highly abundant but less population. The continuous detection levels suggests that spontaneous induction regularly occurs this individual, possibly allowing prophages maintain ability avoiding degradation loss gut microbiota.
Language: Английский
Citations
35
Neural Regeneration Research, Journal Year: 2023, Volume and Issue: 19(4), P. 833 - 845
Published: Aug. 14, 2023
A growing body of evidence suggests that the gut microbiota contributes to development neurodegenerative diseases via microbiota-gut-brain axis. As a contributing factor, dysbiosis always occurs in pathological changes diseases, such as Alzheimer's disease, Parkinson's and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped reveal bidirectional communication between central nervous system enteric is facilitated by microbiota's diverse microorganisms, for both neuroimmune neuroendocrine systems. Here, we summarize bioinformatics analysis wet-biology validation metagenomics with an emphasis on multi-omics studies virome. The pathogen-associated signaling biomarkers identifying brain disorders potential therapeutic targets are also elucidated. Finally, discuss role diet, prebiotics, probiotics, postbiotics exercise interventions remodeling microbiome reducing symptoms diseases.
Language: Английский
Citations
29
Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(4), P. 651 - 662
Published: May 25, 2023
Language: Английский
Citations
28
Microbiome, Journal Year: 2023, Volume and Issue: 11(1)
Published: Oct. 27, 2023
Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral have been identified, with a global distribution seemingly driven by multiple biotic abiotic factors, especially soil temperature moisture. However, our current understanding of the stability across time response to strong seasonal changes in environmental parameters remains limited. Here, we investigated diversity activity DNA RNA viruses, focusing bacteriophages, dynamics' snow-dominated mountainous watershed examining paired metagenomes metatranscriptomes.
Language: Английский
Citations
26