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Nature research paper: Long-read metagenomics reveals phage dynamics in the human gut microbiome go.nature.com/44zgo1o
6mo
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–bacterial interactions in the human gut microbiome.
go.nature.com
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Our review on the Japanese gut microbiome is now published! By analyzing >30,000 gut metagenomes from 37 countries🧬, we re-evaluated the unique feature of the Japanese gut microbiome🦠 in a global context🌏. doi.org/10.2183/pjab...
4mo
Nature
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social. academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
6mo
doi.org
Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in t …
The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease
Suguru Nishijima
Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr
academic.oup.com
VIRE: a metagenome-derived, planetary-scale virome resource with environmental context
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
4mo
Suguru Nishijima
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
Multiple protein structure alignment at scale with FoldMason
Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...
Martin Steinegger 🇺🇦
1mo
Excited to share our review relating to the giant extrachromosomal elements (ECEs) We cover: why long-read metagenomics enables their discovery, genomic comparisons across recently characterized examples, and limitations of current classification tools. www.cell.com/trends/genet...
11d
Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field ha...
www.cell.com
Giants within: a new class of microbial mobile elements
Piotr Rozwalak
Yuya Kiguchi
Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6
13d
Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...
4mo
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N
9mo
github.com
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Jim Shaw
Jim Shaw
Jim Shaw
Sensitive long-read amplicon sequence variant recovery with savont https://www.biorxiv.org/content/10.64898/2026.05.26.727271v1