Research in the Youssef Lab
Currently, research in the Youssef lab is actively involved with four research fronts: 1) Single-cell genomics of yet-uncultured bacterial, and archaeal phyla, 2) Investigating the phylogenetic and evolutionary position of the anaerobic fungal phylum Neocallimastigomycota, 3) Purification and characterization of novel lignocellulolytic enzymes from the anaerobic fungus Orpinomyces C1A, and 4) Studying the change in microbial community composition and structure with respect to algal blooms. The lab is located in the Venture I Building at the Oklahoma Research and Technology Park.
Single cell genomics is one of the emerging techniques to study yet-uncultured phyla. Small subunit ribosomal RNA studies have shown that the absolute majority of bacterial and archaeal phyla are not yet cultured. In fact, more than 85% of all microbial isolates belong to four bacterial phyla. While the advances in culturing technologies and methods promise an increase in the number of phyla with cultured representatives, a lot can be learned from studying the genomes of the yet-uncultured phyla. Single cell genomics, the amplification and sequencing of DNA from single cells obtained directly from environmental samples, is a promising approach for targeted recovery genomes.
Recently, using this technique, 201 such genomes were obtained (Rinke et al., 2013. Nature 499:431-437). The Youssef lab is currently analyzing genomes of some candidate bacterial and archaeal phyla obtained in this study. Examples include bacterial candidate divisions WWE1 and WS3, as well as the newly proposed archaeal candidate phylum Diapherotrites. Genomic analysis of such phyla provides insights into their lifestyle, modes of metabolism, evolution, and may also suggest substrates and cofactors for their enrichment or isolation.
Neocallimastigomycota evolutionary history
Anaerobic gut fungi (AGF) belong to a distinct phylum (Neocallimastigomycota), play an important role in plant biomass degradation in many herbivores, and represent the only strictly anaerobic fungal group. Overall research progress on AGF has been hampered by their anaerobic and eukaryotic nature. Mycologists usually display little interest in working with strict anaerobes, and similarly, bacteriologists display little interest in working with eukaryotes.
Left in the proverbial no man's land, very few research laboratories in the world are currently researching various aspects of the biology of AGF. Our laboratory has been active in investigating the ecology, metabolic capabilities, and genomics of the Neocallimastigomycota. Our culture-independent diversity surveys of AGF in herbivores identified multiple lineages that are yet to be obtained in pure cultures, and revealed patterns of distribution of AGF genera in various animal hosts (Liggenstoffer et al, 2010. ISME J 4:1225-1235). Our more recent efforts produced the first published genome draft of an AGF isolate (Orpinomyces sp. strain C1A) (Youssef et al. 2013. Appl. Environ. Microbiol. 79:4620-4634), and identified multiple unique genomic features and adaptations to their anaerobic gut habitats.
Currently the research in the Youssef lab is building on these efforts by conducting a pan genomic survey of all 6 known AGF genera, in addition to isolation efforts of AGF strains belonging to novel genera, and utilizing the data for an extensive phylogenomic analysis of this phylum, especially for resolving the evolutionary history of Neocallimastigomycota within the fungal tree of life, and correlate the timing of its diversification to the evolution of its mammalian and reptilian hosts.
Other research on AGF in our lab includes investigating the use of lignocellulolytic enzyme cocktails from Orpinomyces C1A for degradation of plant biomass. We successfully cloned and expressed and are currently characterizing several ligocellulolytic enzymes from C1A.
We also are interested in the utility of the incomplete focal adhesion machinery in C1A. Focal adhesion, an attachment strategy employed by Metazoa and higher eukaryotes, is known to be absent in Dikarya Fungi. Orpinomyces C1A genome encodes partial focal adhesion machinery. Previous research on ciliated and flagellated eukaryotes suggests that partial focal adhesion machineries might be employed in basal body assembly. We are currently conducting transcriptional studies to investigate the role of focal adhesion in zoospore flagellar assembly in Orpinomyces C1A.
Microbial community in anaerobic sediments and stratified water bodies and its role in anaerobic degradation of algal detritus
Currently, most research on algal detritus degradation in soil, sediments, and water bodies is focused on the aerobic processes. Single cell genomics analysis of representatives of the WS3 bacterial phylum suggests that some members of this yet-uncultured phylum could possibly degrade algal detritus under anaerobic conditions. We are interested in studying the change in microbial community composition and structure with respect to algal blooms and subsequent water bodies stratification, as well as enriching for the algal cell wall degrading community under anaerobic conditions.