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A Conversation on “Omics” with Professor Laura Hug

How has environmental microbiology research changed since you started working in the field?

Laura Hug: The field has changed dramatically and rapidly. Metagenomes, where the total DNA of a microbial community is routinely sequenced, allows identification of which organisms are present, as well as the functional potential of the community. The first metagenomes were conducted in 2004, while I was an undergraduate, and the technique has since become a common and powerful tool in environmental microbiology research.

We hear a lot these days about “omics”. What exactly do all these omics mean and what do they offer remediation practitioners? Do you have a favorite “omics”?

Laura Hug: “Omics” is a suffix to mean “field of study” and it gets applied to just about everything these days! I saw a housewares store named “Kitchenomics”. That one might be my favorite. With metagenomics (total DNA), you can identify which organisms and functions are present, but metatranscriptomics (all RNA) or proteomics (all proteins) can confirm a predicted activity is actually occurring at a site. Lipidomics (all fats) and metabolomics (all of the small molecules a cell generates) can also help identify organisms and activities.

In terms of our current understanding of microbial ecology how would you characterize where we are at this point in time?

Laura Hug: We are at a really interesting inflection point. With the increase in sequencing, and the refinement of metagenomic assays, we have identified hundreds of new lineages of microbes, including large branches on the tree of life that were previously unknown because the organisms could not be cultured in the lab. This explosion of genome sequences and metabolic information for previously unknown organisms has come with a torrent of identified genes for which there are no predicted functions. Many labs are working to identify the functions of some of these “known-unknowns”. My group is looking to identify the genes involved in some of the contaminant transformations that are observed at contaminated sites, but which are not yet characterized. This will allow us to identify biomarkers for these activities, to assess
the degradation potential at a site.

What do you see as the major challenge in realizing the full potential of the molecular biological tools in bioremediation?

Laura Hug: The dataset sizes are huge, and can take a lot of person hours to interpret. There are ways to automate specific analyses, but it still takes more time than a simpler assay. A limit to any molecular tool is that if the molecular mechanism isn’t known, it can’t be looked for. If an activity of interest is taking place in an environment, identifying what organism is responsible and/or which genes are required can be years of work.

What do you like to do in your spare time when you are not unravelling the mysteries of microbiology?

Laura Hug: I am an avid traveler, and love to explore new locations, cultures, and foods. I am mildly obsessed with ultimate Frisbee, and have played at a competitive level for many years. I also read for fun quite a bit, a mix of nonfiction, sci-fi/fantasy, and endless board books with my one
year old.

Jamie Raper

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