Microbial Metabolomics
Microbes are essential to our existence; nearly every aspect of our lives is integrally tied to microbes. Utah State University researchers are exploring the genetics and physiology of microbes to define the ways microbes impact the quality of life.
Why this research is important
Although ?bad bugs? usually get public attention, beneficial microbes—the ?good bugs?—are everywhere. Microbes affect the flavors of our food, they drive the ecosystems on which we rely, they keep the environment clean, they protect animal and crop health, and they influence the way our bodies function.
Researchers at Utah State University are part of a growing worldwide effort to fully understand the genetics of good microbes. USU scientists are defining every gene in an organism and how together they influence cellular processes, rather than just looking at individual genes in isolation. This ambitious combining of physiology with genetics is an approach that leads to better strategies for cleaning up the environment, improving the food supply, and protecting plant and human health.
Chemical waste sites can be cleaned by adding bacteria to the soil that naturally decompose toxins and restore soil vitality. Adding microbes during food processing creates a safer food supply and promotes better health. Understanding the interaction between genetics and physiology allows the implementation of new, novel approaches to promoting human health and safety.
What is metabolomics?
Metabolomics is the study of physiology using the entire set of genes in an organism—also known as genomics. A genome is the complete set of ?instructions? or sequence of genes that determines how every form of life grows, develops, functions, and ages. The goal of metabolomics at USU is to engineer good organisms to have broader uses towards improving the quality of life.
Scientific Perspective
Investigators at Utah State University are involved in individual and multidisciplinary efforts to the study genetics, proteomes, and metabolism of many different microbes. These efforts range from description of metabolism and the cellular products to molecular genetic techniques for individual genes with gene expression in complex populations. The studies cover broad areas in environmental systems, food processing, soil ecology, enzyme structure & function, and commensalism between microbes and plants. The underlying theme is to discover of how microbes impact humans and the environment—society as a whole.
Topical Overview
Lactic acid bacteria
A core group of USU investigators are part of a larger collective consortium to sequence the genomes of 11 bacteria associated with fermented food. In fact, one of the co-founders of the Lactic Acid Bacteria Genome Consortium is one of USU's faculty members. The genome sequencing effort is being followed by genome finishing and investigations of the physiology of these organisms to fundamentally understand their inner workings related to stress and production of food.
Flavor & fragrance
USU investigators are involved in discovering how bacteria use substrates (like amino acids and fat) to produce commercially valuable compounds involved in flavors and fragrances. Additionally, investigators are working to define how carbohydrate starvation and other stress conditions regulate the genes and enzymes needed to produce these valuable products. Applications in dairy and meat science are particularly interesting. Pathway analysis is being done to determine how these compounds can be produced. This is done by combining gene expression analysis and proteomics for a number of compounds, including volatile sulfur compounds, fatty acids, organic acids, and aromatic hydrocarbons. The metabolism of lactococci, lactobacilli, brevibacteria, and yeast are under investigation in these projects.
Characterization of bacterial enzymes capable of ethylene,propylene or butylene catabolism
Other investigators are examining the microbial pathways of short-chain hydrocarbon oxidation and the biochemical, mechanistic, and spectroscopic properties of the enzymes involved in these pathways. The metabolism of aliphatic hydrocarbons by aerobic bacteria involves their activation to alcohols or epoxides. This research has led to the identification of new microbial transformations and enzymes of significant biotechnological and environmental interest. These studies examine two soil bacteria, Xanthobacter strain Py2 and Rhodococcus rhodochrous, each of which can grow using ethylene, propylene, or butylene as their carbon and energy source.
Characterization of bacterial enzymes capable of acetone degradation
The focus of another project is to determine how bacteria break down acetone. Acetone is a toxic molecule that is synthesized industrially and formed biologically during bacterial fermentation and mammalian starvation. A number of bacteria are able to grow with acetone as a source of carbon and energy.
Characterization of nitrogenase enzymes that convert nitrogen into ammonia
This research program studies the mechanism of action of the nitrogenase enzyme that is responsible for the conversion of nitrogen into ammonia. The nitrogenase enzyme is a metalloproteinase that is critical for the global nitrogen cycle. This metabolic cycle is important due to the role of many organisms as commensual organisms in root nodule formation that allows plants to become independent of nitrogen fertilization. The genome of Nitrosomonas has been sequenced to aid in this effort.
Sulfur metabolism
An interesting set of projects that define the sulfur metabolism of various organisms is underway. Sulfur is a key element that holds a special and specific spot in bacterial metabolism. In some organisms, sulfur can be used as the ultimate electron acceptor to create a unique metabolism and niche in life. In other organisms, this element can be fixed and used to produce cellular energy, modulate the oxidation/ reduction conditions, and become incorporated into volatile compounds that are important in food and environmental applications.
Antimicrobial discovery
The prevalence of antibiotic resistance is increasing at an alarming rate. A group of USU investigators are working to discover new compounds that can be used to inhibit a broad set of organisms ranging from fungal species to food-borne pathogens to viral inhibitors. Efforts include synthetic approaches, wide-scale screening for natural antimicrobials (including strain isolation for those organisms that produce an effect), and screening commercial products for novel activities. Larger collaborative efforts are underway for this group of investigators.