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
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...
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr
Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in t …
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Suguru Nishijima
Suguru Nishijima
Viruses are found in almost every ecosystem across the planet.
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
Suguru Nishijima
Our new paper „Variations in the latitudinal diversity gradients of the ocean microbiome“ was just published in @cp-cellhostmicrobe.bsky.social 🥳
We present a global analysis of prokaryotic #biodiversity in the surface and mesopelagic layers of the ocean 🦠🌊
www.cell.com/cell-host-mi...
Latitudinal diversity gradients (LDGs) are found across 🌱🐨🦠 but their underlying mechanisms remain unclear.
In this study, we highlight that LDGs are not universal in marine microbiomes but reflect lineage-specific ecological strategies and environmental responses.
doi.org/10.1101/2025...
Our work exploring host-microbial co-metabolism of bile acids in patients with alcohol-related liver disease (ALD) has been published in the JHEP Reports:
www.sciencedirect.com/science/arti...
🪐 A big thank you to everyone involved, to the GALAXY and MicrobLiver consortia who made this possible! 🙌
Daniel Podlesny
Eriksson et al. conduct a global marine microbiome diversity analysis and demonstrate
how the surface ocean latitudinal diversity gradient is disproportionately shaped
by a few species-rich taxa. Mask...
Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-relat…
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the oce...
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com :
www.nature.com/articles/s41...
See the linked threads for more details!
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social
www.biorxiv.org/content/10.1...
Cataloguing Earth's biodiversity remains one of the most formidable challenges in biology, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing cens...
