Micro Mornings

Genome scale metabolic modeling of gut microbial communities

Tahmineh Khazaei, Ismagilov Lab

The human gut harbors a remarkably diverse community of microbial species, which play a

critical role in human health. Bloom of pathogenic bacteria disrupt the composition of the

microbiota and are associated with diseases such as Inflammatory Bowel Disease (IBD), colon

cancer, diabetes, obesity, and other metabolic and autoimmune disorders. In this work, we use

the ModelSEED pipeline to develop high quality genome scale models of representative

bacteria of the gut in the healthy (Bacteroides thetaiotaomicron and Coprococcus comes) and

disease states (Klebsiella pneumonia) in order to gain insight into the microbial interactions of

the gut and the metabolic shift that occurs with the introduction of a pathogenic community

member. This presentation will focus mainly on the theory behind the computational

methodologies for developing highly curated genome scale metabolic models.

A Heart of Carbon: Using X-ray Crystallography to Identify the Elusive

Light Atom at the Center of the Nitrogenase Active Site

Christine Morrison, Rees Lab

Nitrogenase catalyzes the reduction of dinitrogen to its bioavailable form, ammonia. This is

accomplished by the transfer of electrons through the iron-sulfur clusters of two proteins, called

the molybdenum-iron and iron proteins. A buildup of electrons and protons at the active site,

[7Fe:Mo:9S:C:R-homocitrate], allows for dinitrogen reduction. At the heart of this iron-sulfur

cluster is a light atom whose identity was unknown until 2011. A combination of spectroscopic

techniques as well as electron density calculations from a 1.0-Å resolution X-ray crystal

structure indicated that the light atom is carbon. By obtaining a 1.08-Å X-ray structure of the

same protein from a different bacterium, we were able to use similar calculations to show that

the identity of the light atom is conserved across bacterial species that express nitrogenase