A prevalent huge phage clade in human and animal gut microbiomes https://t.co/FgbDy6Qhml #biorxiv_micrbio

We hope that HPGC and HPDB can serve as indispensable references for viral ecology and structural biology analyses and could make the study of huge phages easier in the future. Any comments or suggestions on the preprint are appreciated.

Additionally, 3% of the HPDB clusters were absent in other viral forms, including the plasmid-originated ArdC that could protect huge phages from the antiviral mechanisms of their hosts. HPDB contains thousands of other huge phages specific structures.

Complementing HPGC, we developed the Huge Phage Protein Structure Database (HPDB), which catalogs 15,594 structure clusters derived from 589,960 predicted proteomes. Notably, 40% of these clusters presented in huge phages only, exhibit specific protein folds.

Within HPGC, we identified an overlooked and prevalent clade, HP8026. This clade constitutes ~1.2% of human gut metagenomic reads, suggesting its potential in fecal contamination monitoring and as a promising modulator of gut microbiome dynamics.

We collected 10,690 potentially huge phage genomes and utilized vRep to screen for 7,295 non-redundant genomes that span 4,613 species-level groups. This curated Huge Phage Genome Collection (HPGC) represents the most comprehensive repository of huge phage genomes to date.

With vRep, we identified various types of misidentification of huge phage genomes within the publications, which may lead to misconclusions without identifying them, which include but are not limited to diversity, function, and evolution.

To create a comprehensive, huge phage genome collection (HPGC), we first developed vRep. This tool combines the strengths of Virsorter2, geNomad, and CheckV to predict viral sequences with high confidence from metagenomic assemblies.

Due to these advances, however, the study of huge phages has been hindered by challenges in genome identification and the lack of a comprehensive reference database. And that's why we conducted this work, details below.

The nucleus-like compartment in jumbo phages has been studied in detail, for example, https://t.co/z3lWZhpiEu, https://t.co/aDyxroR6WM, https://t.co/j5Yph9UQWr, https://t.co/BCCLe6AofI, to name a few.

These include genes involved in transcription and translation, CRISPR-Cas systems ( https://t.co/PcXEAcvLte), and aerobic methane oxidation ( https://t.co/CglZbHTmUb). Huge phages also encode a nucleus-like compartment to protect their DNA during replication.

Jumbo phages, or huge phages, are remarkable for their expansive genomes (≥200 kbp), global distribution, and intricate functional repertoires. In 2020, we reported the wide distribution of huge phages across Earth's ecosystems and identified their complex biological mechanisms.

📢 Preprint out. We are delighted to share our recent work regarding jumbo phages (or huge phages) from the Chen Lab at USTC, The hidden prevalence and unique protein folds of huge phages, which is available at bioRxiv,

Dive into our lab’s first peer-reviewed publication—co-led with our friends @ben_a_adler and Muntathar Al-Shimary from the Doudna lab! If you’ve already read the preprint, don’t miss the new updates: https://t.co/gNIbc6e3li @NatureMicrobiol

Happy to share our new work studying viral diversity, ecology, & evolution over long-time scales. We track 1.3 million viral genomes over 20 yrs to study viral interactions, ecological dynamics, & evolutionary trajectories.

happy to share this 'quick guide' the Candidate Phyla Radiation bacteria out today in @CurrentBiology its purpose is to be a plain language summary of all the great recent work in this space, with a few key papers for reference. https://t.co/kbFLmKLIXe

COBRA🐍 is finally out. Thank all the Banfielders @BanfieldLab for their help and especially Jill @BanfieldJill for all the huge supports. ❤️

Nearly 20 years ago, @BanfieldJill, Gene Tyson & team transformed #microbiology with their seminal paper on genome-resolved metagenomics. Their innovative approach in reconstructing microbial genomes opened new frontiers in understanding ecosystem dynamics! Read paper here:

This crazy rabbit hole of a project just came out! We started out with a new technology and a tonne of noisy data, and as we dug deeper and deeper unearthed a tonne of biology. @ItaiYanai @PeienJ @MagdaPodkowik A few big-picture take-homes:

Just shared at @KeystoneSymp a new @ArcInstitute discovery of the bridge RNA recombinase mechanism: a new class of natural RNA-guided systems that retains the key property of programmability from RNAi and CRISPR while enabling large-scale genome design beyond RNA and DNA cuts