Microbial Program

The Microbial Program focuses on using advanced sequencing technologies to explore microbial diversity — with an emphasis on bacteria and archaea, and including those associated with microeukaryotes. The program also studies giant viruses. Key research areas include terrestrial biogeochemical cycling and inter-organismal interactions, which are critical for advancing sustainable solutions in agriculture, energy and ecosystem management.

The program aims to generate high-quality genomic datasets, particularly for uncultivated microorganisms, by sequencing large populations of bacteria and archaea in their natural environments using single cell approaches. This includes linking strain-level genetic variation to ecological niche adaptations.  Single cell sequencing approaches are also used for micro-eukaryotes, in particular to study inter-organismal interactions. Novel approaches are being explored to predict microbial lifestyles using AI-driven analysis of such datasets.

The program also collaborates with isolate collections to complete large-scale sequencing projects, including 10,000 Actinomycetota strains and 10,000 type strains. These efforts will provide valuable data for further microbial research and applications. One key program goal is focused on establishing data driven prioritization lists for laboratory isolation and genome sequencing of underexplored bacterial and archaeal lineages that are important for bioeconomy applications.

By expanding our knowledge of microbial functions and interactions, the Microbial Program supports innovations in sustainable agriculture, carbon sequestration and biotechnology.

• Diversification of the microbial product catalog: Beyond minimal draft and improved draft microbial genomes the program offers single-cell sequencing, resequencing, RNA sequencing and epigenomics.
• Expansion of sequence space: The JGI generates reference genomes from diverse bacterial and archaeal lineages to improve phylogenetic analysis, metagenomic annotations, and function distribution. These are derived from isolates and single cells. This effort uncovers novel genes, protein families, and pathways, enhancing our understanding of evolutionary diversification and microbial diversity. Learn more about this work and further details on our Genomic Encyclopedia of Bacteria and Archaea.
• Exploration of inter-organismal interactions: In an effort to gain insights into the interactions between microbial organisms and how these interactions might influence their environment, we utilize single-cell sequencing of micro-eukaryotes directly isolated from environmental samples.