UK Parliament to examine how to better support phage therapy research through funding and regulation
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Thousands of small, novel genes predicted in global phage genomes
https://pubmed.ncbi.nlm.nih.gov/35732113/
https://pubmed.ncbi.nlm.nih.gov/35732113/
Thousands of small, novel genes predicted in global phage genomes - PubMed
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more preval …
FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology
Tried submitting novel phage sequences to ENA. After two attempts to ask for new Taxon IDs which went completely ignored for 3 weeks, just about to give up and submit to JGI instead.
Combined proteomics and transcriptomics of T4 phage infection of E. coli
Integrated Omics Reveal Time-Resolved Insights into T4 Phage Infection of E. coli on Proteome and Transcriptome Levels
Integrated Omics Reveal Time-Resolved Insights into T4 Phage Infection of E. coli on Proteome and Transcriptome Levels
Bacteriophages are highly abundant viruses of bacteria. The major role of phages in shaping bacterial communities and their emerging medical potential as antibacterial agents has triggered a rebirth of phage research. To understand the molecular mechanisms by which phages hijack their host, omics technologies can provide novel insights into the organization of transcriptional and translational events occurring during the infection process. In this study, we apply transcriptomics and proteomics to characterize the temporal patterns of transcription and protein synthesis during the T4 phage infection of E. coli. We investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying the degradation of E. coli transcripts and the preservation of the host proteome. Moreover, the correlation between the phage transcriptome and proteome reveals specific T4 phage mRNAs and proteins that are temporally decoupled, suggesting post-transcriptional and translational regulation mechanisms. This study provides the first comprehensive insights into the molecular takeover of E. coli by bacteriophage T4. This data set represents a valuable resource for future studies seeking to study molecular and regulatory events during infection. We created a user-friendly online tool, POTATO4, which is available to the scientific community and allows access to gene expression patterns for E. coli and T4 genes.
Freya HarrisonDelighted to announce that our phase 1 safety trial of a natural product cocktail for topical antimicrobial applications is in print. Fab to work with Julie Bruce, Blessing Oyedemi and Nick Parsons via Warwick's Clinical Trials Unit https://nature.com/articles/s41598-022-22700-4 #ancientbiotics
Patrick ArthoferHello #ScienceMastodon
I am a PhD student in Matthias Horns lab in Vienna, Austria.
I work on giant viruses and symbiotic bacteria and how they interact with their hosts and each other. In general, I’m very much interested in viruses of microbes!
Cool paper on presence and distribution of viral auxilliary metabolic genes in environmental metaviromes and viral metatranscriptomes. Some interesting new putative metabolic genes in there that were not previously described in viral contigs
#phage #metavirome #metatranscriptome
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01384-y
Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts - Microbiome
Background Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts’ metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. Results Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. Conclusions Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract
Evelien AdriaenssensI'm excited to be able to share a new #publication in my first week on mstdn.science!
We investigated recent literature and speculated on the ecological and functional roles that #bacteriophages (#phages ) can play in different types of environments. We use 5 ecological models to describe the phage-host interactions and review the types of functional gene content contributions phages make to a microbiome.
https://www.sciencedirect.com/science/article/pii/S1369527422001138