Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes
#microbiology #metagenomes #bioinformatics
@natbiotech.nature.com
www.nature.com/articles/s41...

VIRE: A global data platform to better understand viruses Researchers have developed VIRE, a database that integrates approximately 1.7 million viral genomes derived from more than 100,000 metagenomes worldwide. Metagenomic data is obtained by…

A global data platform to better understand #viruses ...

| #genomes | #metagenomes | #sequencing | #DNA | By @embl.org via @sciencex.bsky.social

Using our #metagenomes, we also identified an extensive functional diversity, with genes linked to #carbon and #nitrogen cycling, organic matter degradation, and the uptake and transformation of contaminants 🧬

Benchmarking on mock #metagenomes showed that BEREN recovered 77% of NCLDV contigs and 100% of Preplasmiviricota genomes, outperforming other virus recovery tools in accuracy and completeness.

New tool alert! 🚀 MCAAT uses de Bruijn graphs to detect #CRISPR arrays in #metagenomes, capturing data lost in assemblies. A step forward in uncovering the hidden diversity of CRISPR-Cas systems. By Talibli & Voß
buff.ly/QMX9yIe

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences Viruses are integral to every biome on Earth, yet we still need a more comprehensive picture of their identity and global distribution. Global metagenomics sequencing efforts revealed the genomic content of tens of thousands of environmental samples, however identifying the viral sequences in these...

Jaeger uses #DeepLearning to rapidly detect bacteriophage sequences in #metagenomes with high accuracy and 20× speed gain over existing methods - extracting over five million #phage contigs from MGnify assemblies. #Bioinformatics 🦠⚡
📄 https://doi.org/10.1101/2024.09.24.612722
👤 EVBC: Lars Kaderali

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

A timely perspective urges restraint in calling viral #AMGs from #metagenomes and introduces “auxiliary viral genes (#AVGs)” with a framework for making robust biological inferences. #Viromics #Bioinformatics #ViralEcology 🦠🔬🧬
📄 https://doi.org/10.1038/s41564-025-02095-4
👤 EVBC members: Simon Roux

Our new paper just out in BMC Biology led by Johanna Winder: Environmental adaptations in #metagenomes revealed by deep learning. Artificial neural networks were used to classify ice-binding / substrate-binding proteins (DUF3494).

bmcbiol.biomedcentral.com/articles/10....

Targeted analysis of metagenomes: divide and conquer The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environm…

Targeted analysis of #metagenomes: divide and conquer

#SymbioSky #MicroSky #microbiomesky #Microbiology

www.sciencedirect.com/science/arti...

Gender differences in global antimicrobial resistance - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - Gender differences in global antimicrobial resistance

Antimicrobial resistance #AMR is a major #globalhealth threat. How does it vary between genders? We analyzed 14,641 open human gut #metagenomes from 32 countries to investigate gender differences in #antibioticResistance genes (ARGs). www.nature.com/articles/s41...

Super exciting talk on dark matter of metagenomes, proteins and viromes by Nikos Kyrpides from @jgi.doe.gov
#MicroSky #metagenomes

Venn diagram illustrating microbial diversity of bacteria and archaea captured by isolates, metagenome-assembled genomes (MAGs) from NCBI and IMG, and metagenomes from IMG. A large portion of microbial diversity, labeled as 'Microbial Dark Matter,' represents species not captured by isolates or MAGs. Image modified from https://www.science.org/doi/10.1126/sciadv.adq2166

Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes

...BUT: they still don't capture a lot of the 🦠 species that are out there

New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes - BMC Genomics Background Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically clustere...

With their fragmented assemblies, short reads struggle to recover complete BGCs, such as the long and repetitive NRPS and PKS. Recent advances in #longread sequencing, such as #PacBio HiFi, can retrieve both accurate and complete BGCs from #metagenomes.

bmcgenomics.biomedcentral.com/articles/10....

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes - BMC Genomics Background Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically clustere...

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes. #BiosyntheticGeneCluster #Metagenomes #HiFi @pacbio.bsky.social #BMCgenomics 🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

⚡️ Our latest preprint "Refined Enterotyping Reveals Dysbiosis in Global Fecal Metagenomes" led by @maelschermarisa.bsky.social is now available! We’ve revisited the concept of #enterotypes using a massive dataset of 16,772 human fecal #metagenomes from 38 countries! 🌍🧬 doi.org/10.1101/2024... 🧵

Solving genomic puzzles: computational methods for metagenomic binning Abstract. Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The fiel

Solving genomic puzzles: computational methods for metagenomic binning

Want to know more about finding #phage and #bacteria in #metagenomes?

💻🧬🦠#phagesky

academic.oup.com/bib/article/...

Discovery of Eremiobacterota with nifH homologues in tundra soil Here we describe Candidatus Lamibacter sapmiensis, a novel population of Eremiobacterota from tundra soil. Gene annotation and metabolic reconstruction suggest that Ca. Lamibacter sapmiensis is able ....

Happy to share our latest work on #tundra #metagenomes. We describe the genome of an Eremiobacterota population from tundra soil that suggests that N2 fixation might also be a part of the metabolic repertoire of this phylum.

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

New NIOO publication: Bacterial #genomes recovered from litter’s #metagenomes in Amazonian Dark Earths, by @FelipeZagatto and others. #AmazonRainforest #biodiversity #bacteria #environmentalDNA
https://doi.org/10.1128/mra.00422-24

MuDoGeR facilitates the recovery of prokaryotic, eukaryotic, and viral genomes from #metagenomes, with demonstrated applicability for both individual-isolated genomes and high-throughput #metagenomic datasets. doi.org/10.1111/1755...