50 Result(s)

Article

Phylogenomics and genetic analysis of solvent-producing Clostridium species

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose break...

Rasmus O. Jensen, Frederik Schulz, Simon Roux, Dawn M. Klingeman… in Scientific Data (2024)

Article

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distr...

Clement Coclet, Patrick O. Sorensen, Ulas Karaoz, Shi Wang, Eoin L. Brodie… in Microbiome (2023)

Article

Unraveling the functional dark matter through global metagenomics

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities^1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference...

Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi… in Nature (2023)

Article

Identification of mobile genetic elements with geNomad

Identifying 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 g...

Antonio Pedro Camargo, Simon Roux, Frederik Schulz, Michal Babinski… in Nature Biotechnology (2023)

Article

Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Evelien M. Adriaenssens, Simon Roux, J. Rodney Brister… in Nature Biotechnology (2023)

Article

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems,...

Dean Vik, Benjamin Bolduc, Simon Roux, Christine L. Sun… in ISME Communications (2023)

Article

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have b...

Cassandra L. Ettinger, Morgan Saunders, Laura Selbmann… in Microbiome (2023)

Article

Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats

Many microbes in nature reside in dense, metabolically interdependent communities. We investigated the nature and extent of microbe-virus interactions in relation to microbial density and syntrophy by examinin...

Yunha Hwang, Simon Roux, Clément Coclet, Sebastian J. E. Krause… in Nature Microbiology (2023)

Article

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in c...

Hoon Je Seong, Simon Roux, Chung Yeon Hwang, Woo Jun Sul in Microbiome (2022)

Article

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans

Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale m...

Anthony Duncan, Kerrie Barry, Chris Daum, Emiley Eloe-Fadrosh, Simon Roux… in Microbiome (2022)

Article

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To c...

Benjamin Bolduc, Olivier Zablocki, Jiarong Guo, Ahmed A. Zayed… in ISME Communications (2021)

Article

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although dif...

Kara Martin, Katrin Schmidt, Andrew Toseland, Chris A. Boulton… in Nature Communications (2021)

Article

Glacier ice archives nearly 15,000-year-old microbes and phages

Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approache...

Zhi-** Zhong, Funing Tian, Simon Roux, M. Consuelo Gazitúa… in Microbiome (2021)

Article

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metaboli...

Kristopher Kieft, Zhichao Zhou, Rika E. Anderson, Alison Buchan… in Nature Communications (2021)

Article

Ecology and molecular targets of hypermutation in the global microbiome

Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversi...

Simon Roux, Blair G. Paul, Sarah C. Bagby, Stephen Nayfach… in Nature Communications (2021)

Article

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58...

Silvia G. Acinas, Pablo Sánchez, Guillem Salazar… in Communications Biology (2021)

Article

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying close...

Stephen Nayfach, Antonio Pedro Camargo, Frederik Schulz… in Nature Biotechnology (2021)