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Nov 21, 2024 | 
biorxiv.org | Nishant Jha |Joshua Kravitz |Jacob West-Roberts |Antonio Pedro Camargo
AbstractProtein sequence similarity search is fundamental to genomics research, but current methods are typically not able to consider crucial genomic context information that can be indicative of protein function, especially in microbial systems. Here we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets.
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Oct 1, 2024 | 
biorxiv.org | Andre L Cornman |Jacob West-Roberts |Antonio Pedro Camargo |Simon Roux
AbstractBiological language model performance depends heavily on pretraining data quality, diversity, and size. While metagenomic datasets feature enormous biological diversity, their utilization as pretraining data has been limited due to challenges in data accessibility, quality filtering and deduplication.
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Sep 20, 2024 | 
nature.com | Antonio Pedro Camargo
Correction to: Nature Reviews Microbiology https://doi.org/10.1038/s41579-024-01093-3, published online 28 August 2024. In the version of this article initially published, the copyright line appeared incorrectly and has now been updated to “Lawrence Berkeley National Laboratory, under exclusive licence to Springer Nature Limited,” in the HTML and PDF versions of the article. About this articleCamargo, A.P. Publisher Correction: Unveiling plasmid diversity in nature. Nat Rev Microbiol (2024).
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Aug 28, 2024 | 
nature.com | Antonio Pedro Camargo
This Genome Watch highlights recent metagenomic surveys that have revealed the extensive prevalence and diversity of plasmids in the human gut microbiome and discusses the challenges in accurately reporting plasmid genomes identified from metagenomic data.
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Aug 17, 2024 | 
biorxiv.org | Andre L Cornman |Jacob West-Roberts |Antonio Pedro Camargo |Simon Roux
AbstractBiological language model performance depends heavily on pretraining data quality, diversity, and size. While metagenomic datasets feature enormous biological diversity, their utilization as pretraining data has been limited due to challenges in data accessibility, quality filtering and deduplication.
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Jun 19, 2024 | 
nature.com | Emily Graham |Antonio Pedro Camargo |Ruonan Wu |Russell Neches |Nikos Kyrpides |Jason McDermott | +1 more
AbstractHistorically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units.
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Dec 19, 2023 | 
biorxiv.org | Ryan Cook |Andrea Telatin |George Bouras |Antonio Pedro Camargo
AbstractThe majority of bacteriophage diversity remains uncharacterised, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and subsequent impacts on functional annotation.
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Oct 11, 2023 | 
nature.com | Fotis A. Baltoumas |Antonio Pedro Camargo |Stephen Nayfach |Natalia N. Ivanova |David Paez-Espino |Konstantinos T Konstantinidis | +7 more
AbstractMetagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes.
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Sep 21, 2023 | 
nature.com | Antonio Pedro Camargo |Frederik Schulz |Yan Xu |Stephen Nayfach
AbstractIdentifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses.
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Apr 21, 2023 | 
journals.plos.org | Simon Roux |Antonio Pedro Camargo |Felipe Coutinho
Estimating host diversity coverage by metagenome-derived virusesWe next evaluated these IMG/VR host predictions from the host perspective, specifically assessing which host taxa were most frequently associated with viruses, and how much of the bacterial and archaeal diversity remained without any known or predicted virus.
