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At ASM, Expert Highlights Potential and Challenges of 'Omics for Microbial Ecology

By Andrea Anderson

SAN DIEGO (GenomeWeb News) – Investigators need to recognize — and account for — the realities of genomic and metagenomic approaches if these methods are going to reach their full potential for studying microbial ecology, according to Kenneth Nealson, an environmental studies researcher affiliated with University of Southern California and the J. Craig Venter Institute.

"I was lured into this field because the promises were so doggone good," Nealson said during his D.C. White Research and Mentoring Award lecture at the American Society for Microbiology meeting here yesterday afternoon. "I think a lot of us have bought into this."

But while it's tantalizing to think that unraveling microbes' genome sequences will lead to information and predictions about organisms, their functions, and their environment, he added, genomic and metagenomic research are more complicated in practice than they seem from the outset.

In reality, Nealson said, genomics-based approaches have offered a host of clues about organisms, making it possible to develop testable models and hypotheses. But despite the success stories and genomes sequenced so far, he added, it's important to realize that interpreting genomic and metagenomic data is no simple task.

Using his team's experience with Shewanella bacteria as an example, Nealson noted that researchers still only understand a fraction of the genome — even for relatively well-characterized organisms.

For example, genes with very similar sequences can have different functions from one microbial species to the next, he said. On the other hand, Nealson noted, some bacterial species that are missing genes associated with specific functions can still perform those functions. Meanwhile, in other cases, known genes turn up in the genomes of bugs that can't perform functions typically attributed to those genes.

Coupled with the vast number of hypothetical genes and genes without known functions, he said, that means interpreting microbial genomic and metagenomic data hinges not only on defining genes but also exploring their role in the biological systems in which they function. Consequently, he argued, physiological and other experiments are needed to not only verify predictions coming from genomic data, but also to learn how to "read the genome."

Nealson also challenged the supposition that 16S RNA sequence and/or metagenomic data from environmental samples can provide straightforward information about organisms and their functions in that environment.

Given the tremendous variability between bacterial strains, he explained, it's clear that many bacteria have small core genomes and more extensive pan genomes, meaning genomes can vary a great deal even within the same species.

Still, Nealson was quick to point out the potential of genomic and metagenomic methods for tackling environmental questions.

By combining these sorts of data with information on reference strains and reference genomes and applying rigorous standards such as those endorsed by the Genomics Standards Consortium, he said, microbial and environmental sequences can yield a wealth of useful information.

For instance, Nealson, who is involved with JCVI's Global Ocean Survey, explained that 16S RNA and metagenomic sequence data from surface ocean samples is already offering a much clearer view of the core species found at ocean sites around the world.

"This is great science as long as we ask the right questions," Nealson said. "There are things that we have to worry about, but there are also very positive advances being made here."

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