Tanja Woyke

A genomic catalog of Earth's bacterial and archaeal symbionts

This study uses machine learning to predict symbiotic lifestyles in microbial genomes, identifying 15-23% of uncultivated microbes as potential symbionts and creating a new catalog of symbiont genomes.

Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem

This study uses a 20-year metagenomic time series to analyze the evolutionary dynamics of giant viruses in Lake Mendota, revealing gene duplication, horizontal transfer, and adaptive responses to environmental changes.

Protists as mediators of complex microbial and viral associations

This study investigates protist-associated microbiomes and viromes using single-cell isolation and metagenomics, revealing unique microbial and viral interactions and their ecological roles.

Genome-resolved expansion of Nucleocytoviricota and Mirusviricota reveals new diversity, functional potential, and biotechnological applications

The paper expands the database of giant virus genomes, identifies new viral taxa and functions, and highlights potential biotechnological applications.

Functional characterization of red-shifted rhodopsin channels from giant viruses explored by a machine-learning model for long-wavelength optogenetics

The paper uses a machine-learning model to predict red-shifted channelrhodopsin variants, identifying ChR024 with a maximum absorption wavelength of ~578 nm for optogenetics.

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes

The paper develops a tool to analyze tetranucleotide frequencies in metagenomes, revealing environmental-specific microbial community patterns and metabolic trends across 12,000 samples.

Global Environmental Genomics Reveals Vast Uncultivated Protist Diversity and Taxonomic Blind Spots

The paper analyzes global protist diversity using metagenomes and single-cell genomes, revealing extensive uncultivated and unclassified protist lineages and taxonomic blind spots.

A novel open-source cultivation system helps establish the first full cycle chemosynthetic symbiosis model system involving the giant ciliate Zoothamnium niveum

This paper introduces an open-source cultivation system for Zoothamnium niveum and its sulfur-oxidizing symbionts, enabling long-term, stable growth and detailed observation of symbiosis development.

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. nov.

This paper proposes a new genus and species, Patescibacterium danicum, to provide nomenclatural stability for the phylum Ca. Patescibacteria.

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

The paper analyzes time-series metagenomic data from Lake Mendota to study changes in protistan ecology, revealing shifts in community structure linked to invasive species and environmental factors.

scMicrobe PTA: Near Complete Genomes From Single Bacterial Cells

This study introduces PTA, a single-cell amplification technique that produces nearly complete bacterial genomes and improves viral and gene cluster recovery compared to standard methods.

A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome

Genome Constellation improves taxa assignment and discovers novel taxa in metagenomic datasets by clustering genomes based on k-mer similarities.

Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla

The paper identifies Solagigasbacteria as a newly named candidate phylum with large genomes and versatile metabolism, found in diverse terrestrial ecosystems.

Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria

The paper analyzes genome sequences of facultative endohyphal bacteria from diverse fungi, finding no genome reduction and no universal pathways for host interaction.