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Microbiology

Image of Akkermansia cells, in red fluorescence, bound to human CACO-2 cells (in blue fluorescence from nuclear DNA staining with DAPI)

The Microbiology Area in the Department of Biology at CSUN is a vibrant, collaborative group of faculty and students performing research that addresses some of society’s most pressing issues including antibiotic resistance, the human microbiome, and climate change. Faculty in this area train undergraduate and graduate students in cutting-edge microbiology, molecular biology, and multi-omic techniques to study microbial processes and systematics at a molecular to planetary scale. In the classroom, a diversity of upper-division CURE-style and field-based courses are offered that provide students opportunities to acquire marketable skills leading to successful careers in clinical microbiology, biotechnology, public health, medicine, and academia.

 

Professor
Ph.D. Boston University
Email: david.bermudes@csun.edu
Phone: (818) 677-6062
Fax: (818) 677-2034
Office: Magnolia Hall 4216

Certain pathogenic bacteria such as Salmonella typhimurium have the innate ability to target and selectively replicate within solid tumors in a number of different animal species, including humans. Pathogenic bacteria can be genetically modified in order to eliminate debilitating aspects of their pathogenesis while retaining their ability to traverse the body and target tumors.  My laboratory is exploring a variety of mutations in Salmonella that decrease pathogenesis and/or increase their ability to colonize solid tumors in order to identify strains that have the potential to serve as anticancer agents in humans. In these studies, and in attempts to understand the fundamental nature of the bacterial physiology relating to tumor-targeting, we have identified spontaneous and genetically engineered mutations that have compensatory functions relating to their ability to exist under mammalian physiological conditions and may have the ability to enhance their antitumor effects.

Associate Professor
Ph.D. Portland State University
Email: gilberto.flores@csun.edu
Phone: (818) 677-4276
Fax: (818) 677-2034
Office: Eucalyptus Hall 2208
Website


The recognition of the importance of the ‘microbiome,’ whether associated with plants, animals, or ecosystems, has dramatically transformed our understanding of biology. No longer can we understand the biology of an organism or ecosystem without also considering the identity and activity of any associated microorganisms. This paradigm shift has been driven primarily by advances in DNA sequencing technologies that allow us to peer into the vastness of the microbial world without needing to grow organisms in the lab. However, as illuminating as these approaches are, many microorganisms remain ‘uncultured’ and thus, a fundamental understanding of their basic biology is unknown. Furthermore, for those that can be cultured in the lab, detailed physiological experimentation coupled with multi-omic (i.e., genomics, transcriptomics, metabolomics, and proteomics) approaches are needed to understand how they influence ecosystem or host health. It is the blending of these approaches that will yield our most significant advances in microbiome research. To that end, my research program uses a combination of cutting-edge molecular biology (e.g., high-throughput sequencing, genomics, metagenomics) and bioinformatics tools, coupled with more traditional microbiological techniques (e.g., cultivation, microscopy, systematics) to address fundamental questions about the ecology and evolution of microorganisms associated with the human gut.

Professor
Ph.D. University of Washington
Email: rachel.mackelprang@csun.edu
Phone: (818) 677-4589
Fax: (818) 677-2034
Office: Eucalyptus Hall 2207
Website

I am a genomicist focused on environmental metagenomics. Microbes are the engines that power fundamental biogeochemical cycles. Large-scale anthropogenic alterations in the environment are predicted to greatly affect microbial life, altering the balance of these cycles in the biosphere. While most microbes in the environment are recalcitrant to culturing, metagenomics provides access to the genomes of "inaccessible" organisms by isolating and sequencing all DNA from a particular environment. I am interested in leveraging ultra high-throughput sequencing, bioinformatic analysis, and microbiology-based approaches to study microbial community response to human-caused environmental perturbations and determine the impact of microbes on biogeochemical cycles. Current study systems include the thawing permafrost, the Gulf of Mexico Deepwater Horizon oil spill, and the great prairie of the Midwestern United States.

Professor
Ph.D. Yale University, 2003
Email: sean.murray@csun.edu
Website

The dimorphic bacterium Caulobacter crescentus is a model organism for studying the bacterial cell cycle. Its asymmetric cell division results in one swarmer and one stalked cell progeny. Motile swarmer cells can not undergo DNA replication until they differentiate into stationary stalked cells. If sufficient nutrients are available, swarmer cells eject their polar flagellum and build a stalk (with adhesive at its end; for attaching to a surface near nutrients) at the same pole formerly occupied by the flagellum. Stalked cells are competent for DNA replication and cell division. During cell division, a flagellum is placed at the pole opposite that of the stalk. Caulobacter's obligate cell cycle is controlled by oscillating master regulators that control different genetic modules in space and time. As a result of this carefully orchestrated process, a flagellum is synthesized only when needed (just prior to cell division) and is placed at the pole opposite that of the stalk. Likewise, a new stalk is synthesized only at the pole previously occupied by a flagellum. Our lab studies the roles of lipid biosynthesis in this process, using pharmacological, genetic, and molecular approaches. Only by further elucidating the control mechanisms of bacterial cell division can we advance the development of new antimicrobial compounds. Lipid biosynthesis is essential for cell viability and bacterial fatty acid synthetic enzymes have been suggested as antibiotic targets. In fact, compounds specific to bacterial fatty acid biosynthetic compounds have been generated. Most previous studies on bacterial lipid metabolism have focused on E. coli, a gamma-proteobacteria. Caulobacter in contrast, as an alpha-proteobacteria, is closely related to human pathogenic bacteria, such as Brucella and Rickettsia.

Associate Professor
Ph.D. University of Barcelona
Email: cristian.ruiz-rueda@csun.edu
Phone: (818) 677-6217 (Office) ; (818) 677-7874 (Lab)
Fax: (818) 677-2034
Office: Chaparral Hall 5211
Lab: Chaparral Hall 5205
Website

The Ruiz Rueda’s lab ultimate goal is to develop novel ways of preventing and treating infectious diseases caused by bacteria resistant to multiple antibiotics. These bacteria are major threat to public health worldwide, and in many cases, have become completely untreatable.  My laboratory uses a multidisciplinary approach to: (1) Study the molecular mechanisms of multidrug resistance in order to develop new antimicrobials; (2) Study the role of multidrug efflux pumps and their regulators in metabolism and cell physiology; and (3) Study the distribution of antibiotic-resistant bacteria and identify novel antibiotic resistance genes. Please visit our website for additional information.

Assistant Professor
Email: melissa.takahashi@csun.edu
Phone: (818) 677-4336 (Office); (818) 677-4336 (Lab)
Fax: (818) 677-2034
Office: Eucalyptus Hall 2226D
Lab: Eucalyptus Hall 2209C
Website

RNA gene regulation is ubiquitous in bacteria. There are well documented RNA mechanisms that regulate nearly all aspects of gene expression including transcription, translation, and mRNA degradation. These mechanisms regulate genes involved in essential processes such as amino acid biosynthesis, bacterial motility, and metabolism. Moreover, RNAs are known to regulate the expression of key virulence factors and antibiotic resistance genes in pathogenic bacteria. My overall research goal is to uncover the biological principles behind RNA gene regulation in bacteria to create new tools for engineering bacteria and develop new strategies for antimicrobial therapies. My laboratory uses synthetic biology tools such as cell-free transcription-translation systems to: (1) Investigate sRNA regulatory responses to environmental changes; (2) Develop transcription attenuation mechanisms to engineer bacteria; and (3) Discover novel antimicrobial agents that target sRNA regulated antibiotic resistance mechanisms.

Cheryl Hogue

Vergine Madelian

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