Genomics of novel, yet-uncultured microbial lineages.
Our understanding of the phylogenetic diversity within the domains Archaea and Bacteria is currently undergoing an amazing transformation. Recent research efforts have clearly documented the occurrence of multiple novel yet-uncultured microbial phyla in a wide array of environments, and this expansion and discovery process is still actively ongoing. More importantly, the convergence of multiple methodological and bioinformatics advances is allowing an unprecedented access to the genomes of these novel lineages. Clearly, elucidation of the metabolic capabilities, physiological preferences, and ecological roles of these yet-uncultured bacterial phyla is one of the current grand challenges in microbial ecology.

Our laboratory contributes to this emerging field by analyzing the ecological distribution and genomes of multiple novel microbial lineages. Our “phylocentric” strategy targets specific lineages, and seek through comparative genomics to determine the global patterns of diversity and community structure, genomic architecture, metabolic capabilities, and adaptive features within genomes belonging to these target lineages.

Ecology, genomics, and biotechnological potential of the anaerobic gut fungi.
The anaerobic gut fungi represent a peculiar and fascinating group of organisms. They inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The anaerobic gut fungi represent a basal fungal lineage and have undergone multiple adaptations to survive and thrive within the prokaryotes-dominated strictly anaerobic conditions in the herbivorous gut. Further, members of this group of fungi are known to be an effective and versatile degrader of plant biomass.

We are interested in various aspects of the ecology, biochemistry, evolution, and genomics of anaerobic fungi. Of special interest is the use of anaerobic fungal isolates or enzymes for efficient sugar extraction and biofuel production from lignocellulosic biomass. Our current efforts span a wide range of approaches, ranging from the isolation and characterization of novel anaerobic fungal strains, taxonomic and evolutionary analysis of anaerobic gut fungi, development of anaerobic fungal enzyme cocktails for lignocellulosic biomass deconstruction, and development of new consolidated bioprocessing schemes for biofuel production from ligncoellulosic biomass using anaerobic fungi.

Additional research interests.
Ecology, genomics, and osmoadaptive strategies in halophilic archaea (Class Halobacteria).

Microbiology of shale gas formations.

Ecology and metabolic diversity within the phylum Planctomycetes.

Anaerobic degradation of aromatic and aliphatic hydrocarbons.