Blog @ Illumina
Real scientists. Real commentary.

Pangenomes, outbreaks, and more- ASM Day 2

Amy Cullinan
| Jun 19, 2012

MiSeq ASM 061712One of the challenges of ASM is figuring out which sessions you can physically attend in the limited time. Don't get me started on finding time for the posters and following all the Twitter conversations, which actually caused #asm2012 to trend higher on than the usual celebrity news. Today, there were over 25 sections, or symposia, and more than 150 presentations. With my fellow 10,000 delegates, I hopped around to interrogating the genome, the ASM society president's forum on new technology, exploring the microbiome of nature's vampires, and discoveries with pangenomes. Here are some highlights:

In the Interrogating the Genome symposium, presenters talked about cutting edge genomic approaches to functional genomics and pathway construction. Christopher Lee, from the University of California Los Angeles and the Department of Energy Institute for Genomics and Proteomics discussed a next-gen sequencing approach to a common problem. If an organism strain with an interesting phenotype contains many mutations, say from a mutagenesis screen, it's a task to figure out which one causes a phenotype, and which are irrelevant. Using the statistics of independent selection events, one can quickly reveal the genes that cause a phenotype by sequencing. The actual sequence here is just means to an end- the key piece of data is the number of times each gene gets mutated. Critical to the success of the approach is sequencing many strains for proper separation of the target genes, and having a small number of potential target genes, such as those resulting from selection pressure rather than a heavy chemical mutagenesis. Dr. Lee gave an example of screening isobutanol-tolerant mutant strains using high throughput sequencing on the Illumina GA IIx. With just 90 million single reads, he reliably detected the genes responsible for the observed phenotype. He made a great case for the economy of this general method for reliably finding genes that contribute to phenotype, citing the more than 5-fold cost savings that next-gen sequencing delivers. He also emphasized that it is easy to get started and takes only 1-2 days from prepped libraries to data, analyzed with PhenoSeq, an open source software package for designing and analyzing these data.

The ASM president's forum on "A Brave New World of Technology: Informing Science and Health" featured two great speakers- Eric Schadt from Mount Sinai and John Mekalanos from Harvard Medical School. In addition to some stunning videos of dueling bacteria, Dr. Mekalanos highlighted new approaches to bacterial pathogenesis including deep sequencing applications for studying cholera pathogenesis and pandemic potential. Vibrio cholerae is an evolving human pathogen with several hotspots in the genome that contribute to pathogenesis. The most famous of which is ToxT that controls the virally encoded cholera toxin. Using an RNA-Seq based analysis of in vivo gene expression, they found highly induced pathogenicity gene expression in vivo compared to organisms cultured in vitro. In vivo, these horizontally acquired patho genes are turned on. Using ChIP-seq at enormous sequencing depth confidently identified four ToxT binding sites in the whole genome. Further experiments showed that ToxT regulates expression of a small RNA that in turn represses genes responsible for repressing a gene that enhances chemotaxis, or the movement of bacteria towards a chemical gradient. Thus, repressing the repressors in this pathway results in enhanced intestinal colonization leading to dramatic increases infectivity, explaining some of the transmission patterns noted in this pandemic strain.

Jumping to the "Microbiome of Nature's Vampires" session, I heard Jorge Graf of the University of Connecticut talk about using high-throughput RNA sequencing on the MiSeq system to investigate the microbiome of leeches used for certain therapies. I was fascinated to learn that leeches starve for months between feeding and after ingesting a blood meal, the microbiome rapidly proliferates. By sampling hungry and full leeches and their hosts and mapping an EST library show that one of the two dominant symbionts, Aeromonas veronii, utilizes nutrients in succession. I will spare you the awesome, gory medical leech picture.

Finally, in the Pangenomes symposium, Mark Eppinger from the Univeristy of Maryland Baltimore School of Medicine discussed outbreak dynamics and genomic plasticity in human pathogens using the 454 and HiSeq platforms and high-resolution phylogenomics. Citing data from the infamous Escherichia coli O157:H7 outbreak strain, its remarkable genomic heterogeneity in important genes like the Shiga toxin suggests that microbial populations rather than single sources should be studied during outbreaks. Since genomic variation is often represented by one or a few reference genomes, genome changes may be vastly underestimated. The global gene reservoir or pangenome of a species can now be evaluated with the massive amount of high-throughput sequencing data that a single run can produce, helping to define new markers, virulence factors, and evolutionary traits that can impact outbreak and human pathogen research.