Simon Roux
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Articles by Simon Roux
Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems
Abstract Interactions between microorganisms and their mobile genetic elements (MGEs), including viruses and plasmids, impact microbiome dynamics. CRISPR–Cas systems are important regulators of these host–MGE interactions, but a global understanding of the diversity, activity and roles of CRISPR spacers across Earth’s biomes is still lacking.
Overcoming circularity bias reveals a hidden linear DNA and RNA virosphere
Abstract Metagenomic sequencing has transformed our view of the global viral diversity, yet a fundamental bias limits our understanding of the diversity of complete viral genomes. Current quality assessment tools rely on identifying circular contigs, systematically underestimating the completeness of linear DNA and RNA viruses, thus leaving a large fraction of the virosphere uncharacterized.
Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids
Abstract The HK97-fold is an ancient, conserved protein structure that assembles protein shells, forming the capsids of Duplodnaviria viruses and prokaryotic biochemical compartments called encapsulsins. It has been proposed that encapsulins evolved from HK97-fold viruses. But the higher complexity of viral capsids represents a biophysical paradox in the evolution of HK97-fold protein shells.
The biogeography of giant viruses and interactions with Eukaryotes across European lakes
Abstract Advances in genomics have revealed a diversity of nucleocytoplasmic large DNA viruses (phylum Nucleocytoviricota) that infect eukaryotes, but their ecology beyond the oceans remains poorly understood. We recover 208 Nucleocytoviricota genomes, including 205 putative new species and 33 novel virus-host linkages by sampling 87 lakes spanning 30° of latitude from southern Italy to northern Norway.
Composition of plant-associated RNA virus communities in two Brazilian regions with different levels of human intervention
Abstract Recent high-throughput sequencing (HTS)-based studies of transcriptomes and metatranscriptomes have expanded our understanding of the global RNA virome with a vast number of novel RNA viruses revealed in diverse host organisms. Nevertheless, ecosystem-level understanding of plant virus dynamics is hampered by the paucity of information from wild communities, as most plant viral dynamics monitoring has been performed on cropping systems.
Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils
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Abstract Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited.
By Jiarong Guo, Samuel Aroney, Guillermo Dominguez-Huerta, Derek Smith, Dean Vik, Carlos Owusu-Ansah, Akbar Adjie Pratama, Sergei Solonenko, Funing Tian, Cristina Howard-Varona, Zhi-Ping Zhong, Aminata Fofana, Garrett Smith, Suzanne B. Hodgkins, Dylan R. Cronin, EMERGE Coordinators, Ben J. Woodcroft, Gene Tyson, Virginia Rich, Matthew Sullivan, Simon Roux, Sarah Bagby
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Nature
Verified
Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient - Nature Communications
Abstract Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization.
STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies - Nature Microbiology
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Abstract The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research.
By Julia M. Kelliher, Sarah R Bordenstein, Christina A. Kellogg, Petr Baldrian, Vlastimil Novak, Gregory Bonito, Joanne Emerson, Ahmed Moustafa, Trent Northen, Nonia Pariente Verified, Jennifer Pett-Ridge, Anna-Louise Reysenbach, Virginia Rich, Simon Roux, Lynn M Schriml, Maria A Sierra, Matthew Sullivan, Punithavathi Sundaramurthy, Luke Thompson, Alexis Palucki, Katherine M. Thibault
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Nature
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A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology
Abstract Virus-encoded auxiliary metabolic genes (AMGs) are non-essential genes that increase viral fitness by maintaining or manipulating host metabolism during infection. AMGs are intriguing from an evolutionary perspective, as most viral genomes are highly compact and have limited coding capacity for accessory genes. Advances in viral (meta)genomics have expanded the detection of putative AMGs from viruses in diverse environments.
Viromics approaches for the study of viral diversity and ecology in microbiomes - Nature Reviews Genetics
Abstract Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems.
Planetary-scale metagenomic search reveals new patterns of CRISPR targeting
The authors have declared no competing interest. Data availability Raw data used for this study are available at https://portal.nersc.gov/dna/microbial/prokpubs/spacer_database_resources/, and from NCBI SRA using accession numbers listed in the file “ Supplementary_Data_File_2_samples.tsv”. Access to the spacer database including spacer information and spacer hits against IMG/VR and IMG/PR is documented at https://spacers.jgi.doe.gov.
Tracking Persistence and Dynamics of Active Soil Viruses with SIP-Viromics
Abstract We integrated 18O-stable isotope probing and viromics (SIP-viromics) to investigate soil viral activity after rewetting. Among 354 detected viral populations, only 22% incorporated 18O, indicating most virions persisted through this induction event without replicating, forming a genetic reservoir of viral diversity. Actinomycetota were dominant predicted hosts of lytic infections, supporting Cull-the-Winner dynamics.
Quantifying the impact of workshops promoting microbiome data standards and data stewardship - Scientific Reports
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Abstract The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used to interrogate diverse microbiome samples. However, due to lagging awareness and implementation of standards and data stewardship, many datasets are produced that are not comparable, reproducible, or reusable.
By Julia M. Kelliher, Francisca Rodriguez, Leah Johnson, Simon Roux, Montana Smith, Ishi Keenum, Heng-An Lin, Reid Longley, Ryan McDonald, Thomas M Pitot, Josué A. Rodríguez-Ramos, Jiaxian Shen, Daniel Sprockett, Joel F Swift, Archana Yadav, Alicia Clum, Wendi Lynch, Candace Hope Bias, Sarai S. Finks, E. Anders Kiledal
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Nature
Verified
Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome-specificity
Abstract Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase.
The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling
Abstract Biological 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.
The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling
Abstract Biological 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.
Solvent-Producing Clostridia Revisited
1. Introduction The review includes both a historical perspective and the current status of the solvent-producing clostridia. This encompasses the comparative genomic and phylogenetic analysis of clostridial species and a survey of prophages and R-type tailocins. In order to provide a general background context to the review, an updated historical account has been included.
Counting dots or counting reads? Complementary approaches to estimate virus-to-microbe ratios - The ISME Journal
“How many viruses are there in the environment, compared to cells ?”. This deceptively simple question remains challenging to address today, yet because it relates to fundamental processes and characteristics of viral communities, even the imperfect approximations available have been critical for the field of viral ecology.
Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales
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Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient
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iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
Estimating host diversity coverage by metagenome-derived viruses We 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.
You can move, but you can't hide: identification of mobile genetic elements with geNomad
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Long-term CRISPR array dynamics and stable host-virus co-existence in subsurface fractured shales
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Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs
Putative distinct viroid-like cccRNAs We briefly describe the 5 largest distinct ANI90 clusters (denoted 1 to 5, in the descending order of the cluster size) derived from the metatranscriptomic data to exemplify the type of findings obtained in this work. All these clusters included members with symmetric, matched ribozymes. The cccRNAs in four of these clusters contained matched HHR3s, whereas those in the fifth cluster contained twister-P1 ribozymes.
Updated Virophage Taxonomy and Distinction from Polinton-Like Viruses
Abstract : Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of “hyperparasitism” in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes.
Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes
For whole genome comparisons, isolate or MAG genomes were carefully selected from the IMG database using available metadata fields pertaining to isolation source or manually curated when possible. Comparisons of gene counts for individual Pfams, Tigrfams or KO terms between members of each set or group of isolates were performed.
From motor protein to toxin: Mutations in the zonula occludens toxin (Zot) of Vibrio cholerae phage CTXϕ suggest a loss of phage assembly function
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Diversity in the soil virosphere: to infinity and beyond?
Glossary Dormant soil viruses viruses temporarily inactive but able to resume their replication cycle in favorable conditions. Operationally, these encompass integrated prophages, pseudolysogenized viral genomes stalled in mid-infection inside host cells, and free virions that have been in their respective states (i.e., that have not undergone a complete lytic replication cycle) for at least a week, often longer.
Glacier ice archives nearly 15,000-year-old microbes and phages - Microbiome
Zhi-Ping Zhong ORCID: orcid.org/0000-0002-4275-04031,2,3, Funing Tian2,3, Simon Roux4, M. Consuelo Gazitúa2, Natalie E. Solonenko2,3, Yueh-Fen Li2,3, Mary E. Davis1, James L. Van Etten5, 1,3,6, Virginia I. Rich1,2,3, Matthew B. Sullivan1,2,3,7 & Lonnie G.
Extreme dimensions - how big (or small) can tailed phages be?
This month’s Genome Watch highlights the search for unusually large (or small) tailed phages driven by metagenomics. References 1. Iyer, L. M., Anantharaman, V., Krishnan, A., Burroughs, A. M. & Aravind, L. Jumbo phages: a comparative genomic overview of core functions and adaptions for biological conflicts. Viruses 13, 1–42 (2021). Article Google Scholar 2. Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020). CAS Article Google Scholar 3. Pausch, P. et al.
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
Abstract The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts.
Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal
Genome Sequences Ranjit Sah, Alfonso J. Rodriguez-Morales, Runa Jha, Daniel K. W. Chu, Haogao Gu, Malik Peiris, Anup Bastola, Bibek Kumar Lal, Hemant Chanda Ojha, Ali A. Rabaan, Lysien I. Zambrano, Anthony Costello, Kouichi Morita, Basu Dev Pandey, Leo L. M.
Giant virus diversity and host interactions through global metagenomics
Abstract Current knowledge about the nucleocytoplasmic large DNA viruses (NCLDV) is largely derived from viral isolates co-cultivated with protists and algae. Building on the rapidly increasing wealth of publicly available metagenome data, we reconstructed 2,074 NCLDV genomes from sampling sites spanning the globe. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity.
Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust
Research Article | Host-Microbe Biology Marc W. Van Goethem, Tami L. Swenson, Gareth Trubl, Simon Roux, Trent R. Northen Jennifer B. H. Martiny, Editor DOI: 10.1128/mBio.02287-19 ABSTRACT Biological soil crusts (biocrusts) are photosynthetic “hot spots” in deserts and cover ∼12% of the Earth’s terrestrial surface, and yet they face an uncertain future given expected shifts in rainfall events.
Expanding inovirus diversity: the rise of the small and inconspicuous
## Read the full paper at: https://rdcu.be/bLije ## One may first ask: why even look for inoviruses ? The short answer is that inoviruses are bacteriophages with two fascinating properties: (i) their short (~5-15kb) single-stranded DNA genome is enclosed in an unusual filamentous particle, and (ii) they replicate through a unique “chronic” cycle by which they can produce new infectious virions without killing their host cell (1).
A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”
Special Issue Perspective | Ecological and Evolutionary Science DOI: 10.1128/mSystems.00111-19 ABSTRACT Microbes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection.
Numerous cultivated and uncultivated viruses encode ribosomal proteins
Abstract Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses.
Minimum Information about an Uncultivated Virus Genome (MIUViG)
1. Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N.A. Phage puppet masters of the marine microbial realm. Nat. Microbiol. 3, 754–766 (2018). 2. Youle, M., Haynes, M. & Rohwer, F. in Viruses: Essential Agents of Life (ed. Witzany, G.) 61–81 (Springer Netherlands, 2012). 3. Brum, J.R. & Sullivan, M.B. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat. Rev. Microbiol. 13, 147–159 (2015). 4. Páez-Espino, D. et al. Uncovering Earth's virome. Nature 536, 425–430 (2016). 5. Shi, M.
Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing
1. Suttle, C. A. Viruses in the sea. Nature 437, 356–361 (2005). 2. Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998). 3. De Smet, J. et al. High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection. ISME J. 10, 1823–1835 (2016). 4. Wommack, K. E. & Colwell, R. R. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64, 69–114 (2000). 5.
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