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Genomic Analyses Could Lead to “Field Guide to Microbes”

 

The swell of enthusiasm for analyzing microbial genomes continues, with keen interest in doing more and more genomes in smaller analytic formats at lower costs. Even while greater numbers of microbiologists jump into this fray, some continue to fret over what to make of these expanding findings, sharing thoughts and insights during several sessions, including the symposium "Microbial Single-Cell Genomics" and the colloquium "The $1 Bacterial Genome," convened during the 109th ASM General Meeting, held last May in Philadelphia, Pa.

"Single-cell genomics is a reality," says symposium participant Paul Blainey of Stanford University in Stanford, Calif. He described an approach that depends on microfluidic devices and other comparably scaled manipulative procedures for plucking single bacterial cells, including from human anatomic sites such as the skin and oral cavity, for genomic analysis. "You need 1 pg or less of DNA to carry out a sequencing run, even though manufacturers recommend samples containing 1,000 times more material," he says.

Microbial genomic sequencing is not merely driving miniaturization and other innovative technologydevelopment projects. It is also leading some experts in the field to ponder new means for collating and analyzing the volumes of sequencing data being produced, and also to identify which segments of the microbial world are underanalyzed and thus still poorly appreciated in the new genomicscentric scheme, according to colloquium participant Jonathan Eisen of the University of California, Davis, Genome Center.

For instance, a genomic encyclopedia project sponsored by the Department of Energy lays out which phyla include species whose genomic sequences are already analyzed, which are not, and which ones are "sparsely populated," Eisen points out. Such collections can provide a valuable "scaffold" for sorting genomic data and also for "annotating predicted functions," he says, suggesting such efforts could lead to a "field guide to microbiology."

Audio interview with Jonathan Eisen


"A massive amount of diversity is untouched by genomic sequencing," Eisen continues. On the microbial side, viral and eukaryotic microorganisms are both "poorly sampled." Moreover, he says, "We need to fill in the tree of life in terms of experiments, not just sequencing . . . ‘Metadata rocks' when it's about the microorganism and its known physiology. I didn't realize at first how fundamentally important this would be." Amid enthusiasm for genomic sequencing, including at the single-cell level, and other analytic approaches to enrich and extend sequencing come some startling predictions, including that sequencing will bring about the downfall of microarray analyses, according to another colloquium participant, Julian Parkhill of the Sanger Institute in Cambridge, United Kingdom. "Highly dynamic and accurate" sequence-based analyses of singlestranded RNA molecules "eventually will replace microarrays" to measure gene expression, he asserts. "They'll be gone . . . and we'll be doing phenotyping at the rate we do genotyping in the very near future."

Moreover, Parkhill says, sequencing can be used as an "assay" to track the geographic spread of specific bacterial strains responsible for hospital and community outbreaks, including those involving methicillin-resistant Staphylococcus aureus (MRSA). With that approach, a particular MRSA outbreak in England was "traced back to a nurse from Thailand. This is really exciting stuff."

Others working in this field also anticipate genome-based analyses being harnessed for similarly pragmatic purposes. For instance, sentinel genomic analysis might be used to "track epidemics, like a weather map," says colloquium participant George Church of Harvard University Medical School in Boston, Mass. "You could study the microorganisms [pathogens] themselves, or host immune responses to them."

"Genomic analysis could be helpful for following foodborne disease outbreaks," adds Paul Keim of Northern Arizona University in Flagstaff. He draws that conclusion from a study that entailed applying genomic analysis to determine how Bacillus anthracis strains, which associate with bison and cattle herds, came to be distributed throughout regions of North America. B. anthracis apparently "went from Canada south, and from bison to cattle, instead of from south to north," he says. "It's just the opposite of what we'd believed before."

Meanwhile, some microbiologists are touting the advantages of applying genomic analyses to single bacterial cells. "Why do single-cell analysis on something you can culture?" asks symposium participant Roger Lasken of the J. Craig Venter Institute in San Diego, Calif. One reason is that "culturing modifies genetics, and virulence factors can be lost," he says. Plus, he adds, "It's an exciting way to study pathogens. You can look at wounds [and recover] single cells."

Single-cell analyses require scrupulous care in preparing reagents and maintaining quality controls at several different levels, Lasken continues. For one thing, DNA contaminants are everywhere. Another challenge is finding appropriate methods and conditions to lyse particular bacterial cells to ensure that they release their DNA molecules. Single-cell analysis can prove useful in searching for new species as part of a microbiome project, he points out. "One way to get rid of human DNA is to [analyze] a single cell instead of using a skin swab."

Microfluidic devices also help to overcome the challenge of extraneous DNA contaminants when doing single-cell genomic analyses, adds Blainey of Stanford University. "Inside the device, there's no pipetting," he says. Another advantage is its "precise control, eliminating sample-borne contaminants by reducing the volumes used [and] by bringing thoroughly washed cells into the reaction chamber."

Expanding such plans and uses of genomic analysis is expected to accelerate as costs come down, according to Church of Harvard Medical School. "I think we can do better than $1 per genome, and maybe get down to $0.01," he says. "We've gone 4 logs in 4 years, and I predict we'll go another 2 logs in the next 2 years." Which of several technologies will prove key in realizing those log-order cost savings is uncertain, but nanopore- based and electron microscopybased contenders are both "making progress," he notes. Moreover, at least 15 companies are in the running with these technologies, providing improvements of one sort or another in terms of advances, cost and time savings, portability, or other useful features.

Jeffrey L. Fox
Jeffrey L. Fox is the Microbe Current Topics and Features Editor.

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