Metagenome Program

The Metagenome Program focuses on the high-throughput sequencing of microbial communities to uncover the complex interactions and functions that shape ecosystems. By decoding the microbial DNA in natural environments, the Program provides a snapshot of microbial diversity and their metabolic functional potential. This research enables us to better understand how microbial communities contribute to critical processes such as carbon cycling, nutrient cycling, and energy flow.

One of the key goals of the Program is to develop a deeper understanding of microbial community assembly and microbial interactions, including microbe-microbe and virus-microbe interactions, over ecological and evolutionary time scales.The Metagenome Program combines large-scale, time-series metagenomic data with detailed characterization of model systems to explore the dynamics of microbial ecosystems and their evolution. The Program focuses on developing computational tools and visualization resources that support user analysis of biogeochemically-relevant pathways, enabling modeling of microbiomes based on functional traits. These advancements provide new insights into microbial ecosystems. 

The Program also aims to build a global-scale catalog of viral, microbial, and microeukaryote genomes and mobile genetic elements, linked to custom interfaces and visualization tools for user analysis. Additionally, the Program works to link community-scale microbial activity measurements, such as quantitative stable isotope probing (qSIP)-metagenomics and metatranscriptomics, to metagenomics and metabolomics data, shedding light on microbial metabolism and activity in natural environments. Integrating metatranscriptomes and metagenomes can, for instance, deepens our understanding of microbial and viral activity, transcription regulation, and noncoding RNAs in microbiomes. The insights from this work have the potential to drive innovations in energy, environmental sustainability, microbiome manipulation, and other fields, offering new approaches to address some of the world’s most pressing challenges.

• Exploration of phylogenomic novelty: Advances in metagenomic sequencing, assembly and binning have enabled reconstruction of complete or near-complete population genomes directly from the environment. These advances have led to groundbreaking discoveries in diversity and novel functions identified in unexpected microbial clades. We leverage genome-resolved metagenomics and targeted gene searches to expand representation of uncultivated microbial lineages.
• Charting viral ‘dark matter’:  Viruses are abundant in the biosphere and influence microbial dynamics, evolution, and ecosystems. Sequencing technologies have expanded viral diversity knowledge, enabling global exploration. We develop computational tools for analyzing viral fragments via IMG/VR and methods to capture environmental viral populations.
• Enabling microbiome data science: The JGI supports microbiome data science by enabling comparative genomics and metagenomics analysis through the IMG/M platform. Further, the JGI partners with the National Microbiome Data Collaborative (NMDC) to enable the research community to perform large-scale multi-omics analyses on new and existing microbiome data.