9th International Conference on Microbial Genomes

October 28th-November 1st, 2001. Gatlinburg, TN

Rob Edwards, 11/06/01
 

The International Conference on Microbial Genomes was initially conceived as a meeting to discuss, promote, and analyze the E. coli genome. In subsequent years, the meeting has evolved to cover sequencing and assembly techniques and annotation of completed genomes. The conference has undeniably entered the post-genomic era, with the 9th meeting focusing on functional and comparative genomics.

The first session, as has become traditional at this meeting, was a summary of the funding opportunities from Federal Agencies. Unfortunately ill health prevented Peter Johnson, (USDA) from attending, however Dan Drell, (DOE) was an admirable stand in and provided information about all the government projects both planned and underway. The second session moved straight into the comparative genomics, diversity, and evolution with a slew of talks primarily from commercial companies. Perhaps indicative of the whole meeting, talks from Integrated Genomics were presented in both the second, and final, scientific sessions. The first presentation by Michael Fonstein, described their ERGO database that contains approximately 1 million open reading frames, 2,500 core functions (including replication, cell wall construction. and central metabolism). 73% of the biochemical pathways that have been characterized so far are found in all 3 domains of life. Michael moved on to describe the regulator database that looks for both potentially co-regulated genes that occur as operons, and DNA sequence patterns that may indicate promoters. Diversa, Protein Pathways, and the Institute for Systems Biology, were among other commercial interests represented at the meeting. The Diversa talk, presented by Martin Keller, centered around their 'Gel Maintained Diversity' system. They have isolated bacteria from different environments (such as different marine locations) and sorted them into semi-permeable gel matrices. The gel matrices are then separated into columns. The bacteria in suspensions can be fed a variety of nutrient resources to investigate growth effects. When fed rich nutrients the cultures are rapidly overgrown with marine Vibrio, however when fed sterilized sea water individual bacterial growth could be measured. This system will provide an interesting resource for the cultivation of otherwise "unculturable" bacteria. Jörg Hoheisel from Deutches Krebsforschungszentrum described several microarray techniques, including the advantages of adding betaine to the DNA prior to spotting (ref: Diehl et al Nucleic Acids Research, 2001) Owen White, from TIGR, presented details of the Comprehensive Microbial Resource, a data resource that allows comparisons of many genomes. This online system is available for individual researchers to download and install locally, as well as providing automated, remote, ORF calling and annotation techniques.

Several talks described proteomics techniques, cellular pathways, and regulatory networks, including proteomic chips, and the problems with annotations of multifunctional enzymes. A talk by Jeffrey Miller (UCLA) categorized DNA repair in E. coli and high temperature archea, noting that the latter group often lack many 'standard' mismatch repair systems found in bacteria. Miller described the mutation frequency of E. coli and Pyrobaculum. The GC->AT mutation rate is 0.5x10-9 mutations per generation in E. coli and 20x10-9 mutations per generation in Pyrobaculum. In contrast, the AT->GC mutation rate is 0.6x10-9 mutations per generation in E. coli and 100x10-9 mutations per generation in Pyrobaculum. Richard Smith, from the Pacific Northwest National Laboratory, described accurate mass tags to characterize proteins in Deinococcus, and comparing protein masses from MS and Fourier Transform Ion Cyclotron Resonance MS. They have also created a system for enhanced MS measurements calculated by removing the most abundant peaks and remeasuring the spectra.

An afternoon session on Bioremediation and Carbon Management focused on the using genetics and genomics to adapt bacteria to cleaning up human-created toxic wastes. A presentation by Frank Larimer, ORNL, on the C-fixing abilities of Prochlorococcus suggested that these versatile marine microbes fix about the same amount of carbon per year as the entire terrestrial ecosystems.

The fifth session of the meeting on the functional genomics of pathogenic organisms began with a comparison of different Listeria isolates being sequenced by a European consortia (incl. L. monocytogenes and L. innocua). This presentation by Claude Buchrieser, summarized the results of the comparison of these two Listeria that are about 90-95% identical at the DNA level and yet contain 10-15% of ORFs unique to each species. A talk by Vivek Kapur (U. Minnesota) described his analysis of Pasteurella multocida and said that about 14% of the coding sequences were unique to P. multocida.

Julian Parkhill, from the Sanger Center, compared the Salmonella genomes with E. coli, and then compared the Yersinia genome with both of these. Julian presented severl numbers: S. Typhi compared to E. coli: 32% of genome unique, 1505 genes in 290 groups; S. Typhi compared to S. Typhimurium 601 ORFs in 82 blocs (13% unique); S. Typhimurium compared to S. Typhi 479 ORFs in 80 blocs. The presentation also described the new Artemis genome comparison tool, available from the Sanger Center Website.

An excellent presentation by Ana Claudia Rasera de Silva from the University of Sao Paulo discussed their comparative analysis of a group of plant pathogens, including members of the Xylella and Xanthamonas families. This closely related family of plant pathogens cause different diseases in different plants (Xylella spp. display host-specific infectivity) or in different locations in the same plant (xylem restricted or systemic). George Weinstock (University of Texas) described the sequencing of Treponema pallidum, an obligate parasite that can not be grown outside of animals, and the closely related Treponema denticola, a dental pathogen that can be grown in vitro. This talk was complemented by a presentation from Timothy Palzkill on the proteomic analysis of T. pallidum using a surrogate host for gene expression that can be grown in vitro. Finally, Mark Schell provided insights into analysis performed at the Nestlé corporation on Bifidobacterium longum and clues from the genome about why this normally commensal organism is missing from young children fed formula milk.

The session on model organisms, biofilms, and extremophiles was led by the presentation from Fred Blattner on his comparison of E. coli and closely related organisms. By comparing the presence and absence of all possible 19-mers in the genomes they concluded that each genome is 10-15% unique, and that as they are adding more genomes they are not reducing this unique number, but they are finding different sequence that has never been seen before.

The final session on Applied Functional Genomics provided insights into novel drug discovery mechanisms, host-pathogen interactions, and a talk by Michael Ibba (Ohio State U.) on unusual and unique aminoacyl-tRNA synthetases. Although it was thought these enzymes were classified and understood, genome analysis has shown that there are large gaps in our knowledge, and that novel synthetases are being found all the time.

In addition to the 40 talks covering a variety of subjects, there were some 52 posters providing data from these and other genomics projects. The posters covered microarrays, cloning techniques, sequencing, and so on. The meeting was attended by approximately 175-200 people working in all aspects of microbial genomics, providing a stimulating and exciting environment for discussing genomics.