Serres Lab


Gretta Serres
Associate Research Scientist
p: 508 289 7388
f: 508 457 4727


Dr. Margrethe (Gretta) H. Serres is currently an Adjunct Associate Scientist in the Josephine Bay Paul Center at the Marine Biological Laboratory. She has been working at the Center since 1999 when she arrived as a Postdoctoral Scientist. Dr. Serres is also a lecturer of Microbiology at the Cape Cod Community College in Barnstable, MA.

Dr. Serres is a microbiologist by training and is broadly interested in microbial physiology and the functional diversity of microbes in relation to their evolutionary history and the environment they inhabit. Her research is computational in nature. She curates pathway genome databases and predicts metabolic pathways and cellular roles for gene products based on genome sequences and on available experimental datasets. Her work has included functional analyses of model organisms, sets of sequence related species, and microbial communities.

The functional potential of microbes, the most abundant life form, still remains largely unknown. A complex relationship exists between the gene content (genotype) and observable characteristics (phenotype) of organisms, and a significan fraction of genomes remain without functional attribution. In addition microbes produce metabolites that are essential for the stability of their consortia and that can be exploited for human health and instrustrial processes. By analyzing genomes for their functional composition in a metabolic framework making use of genome clues (i.e protein families) and related experimental data (transcriptome, proteome, metabolome), Dr. Serres is seeking to improve our understanding of the relatioship between functional diversity and survival in select environments.

Dr. Serres has collaborated for several years to research efforts at the Pacific Northwest National Lab (Shewanella Federation, Biological Systems Interaction FSFA). She has received her funding from Department of Energy.

PCC7002ov1Genome annotation and analysis.

My research includes curating and predicting functions encoded by microbial genomes. Functions are predicted from sequence similarity, protein domain content, protein family membership, and genome context. We also make use of omics based data for our predictions (i.e. gene and protein expression data, mutant analysis, promoter predictions). We use Pathway Genome Databases of the BioCyc type to capture our annotations and predictions. These databases are further used as frameworks to analyze the functional compositions of organisms, to interpret omics-type datasets, and to do cross genome comparisons. My group has worked on the annotation of Shewanella oneidensis MR-1 and members of the Shewanella genus, microbes with unique respiratory capabilities that are important to biogeochemical cycles. We are also curating cyanobacterial genomes of the genus Synechococcus.

Ecophysiological adaptations and speciation of Shewanella.PNAS

Members of the Shewanella genus occupy a variety of ecological niches including lakes, rivers, oceans, sediments, and terrestrial sub-surfaces. This suggests a high degree of diversity in environmental response and metabolic capability, and in the existence of several ecotypes. We are using cross genome comparisons to link functional diversity to habitat and environmental factors. We area also interested in the link between genotypes and phenotypes displayed by members of this genus.

InteractionSlideBiological Interactions.

We are using our annotation efforts and genome analyses to better understand how organisms interact with one another and with their environment. In collaboration with microbiologists at the Biological Division of the Pacific Northwest National Lab we are studying interactions between photoautotrophs and heterotrophs grown in co-cultures or found in natural environments. Using transcriptome and metabolome data we are predicting metabolic pathways that are active under axenic growth or co-culturing of Synechococcus sp. PCC7002 (photoautotroph) and Shewanella putrefaciens W3-18-1 (heterotroph).

Protein family studies.

My research interests also involve protein families; how they can be used to improve functional assignments and how their family memberships vary between related microbial genomes. The protein families provide insight into diversity of functions, metabolic capabilities, and evolutionary histories of the organisms they are found in.  We are using genome wide protein family memberships to shed light on functional capacity and adaptation of related microbes.



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