Monday, May 24
4:00 p.m.
On Zoom
Drilling deeper into microbiomes’ status and future
By Professor James M. Tiedje, Center for microbial ecology and Departments of plant, soil and microbial sciences and of microbiology and molecular genetics, Michigan State University
Abstract
Metagenomics and its derivative, the microbiome, has become a core of new age microbial ecology. Metagenomics has advanced rapidly and taken many directions – those determined by the various methods employed, the complexity of the different communities, the resources available and of course the compelling questions. I will illustrate how a new computational tool, MiGA, provides more insight into the microbial world by using genomes, not 16S rRNA, to more accurately characterize the cultured and uncultured microbial world. I will then show how we use ecofunctional genes, i.e. those genes that directly control important ecological functions, to directly probe community functions with two examples: one of nitrogen cycle genes in soil and its rhizosphere, and the other of understanding the ecology of antibiotic resistance genes, one of the new environmental pollutants. For these we use a gene–targeted assembler Xander, to more reliably identify, classify and quantify these genes. For antibiotic resistance we also use highly parallel qPCR, with over 300 primer pairs for antibiotic resistances and mobile genetic elements, and long read sequencing, to assess quantity, type, potential mobility and fate of natural and human-selected resistomes.
Metagenomics and microbiome science is a field with big opportunities since there are many habitats, directions and needs, especially for creative ways to interrogate data to uncover new knowledge. I will also speculate a bit into the future of what microbiome science may look like and contribute too. It is a great opportunity area for students.
About the speaker
Dr. Tiedje is University distinguished Professor Emeritus of microbiology and molecular genetics and of plant, soil and microbial sciences at Michigan State University, and was director of the Center for microbial ecology for 30 years. His contributions have been on microbial ecology, physiology and diversity, especially regarding the nitrogen cycle, biodegradation of pollutants and on the use of genomics and metagenomics to understand speciation, community structure and functions.
He served as editor-in-chief of Applied and Environmental Microbiology and editor of Microbial and Molecular Biology Reviews and mBio. He served on the board on Life Sciences of the National Research Council, EPA’s Science advisory panel and on DOE’s Biological and Environmental Research Advisory Committee. He was president of the American Society for Microbiology (ASM) and the International Society of Microbial Ecology (ISME). He is Fellow of the AAAS, the American Academy of Microbiology, the Ecological Society of America, the Soil Science Society of America, and a member of the U.S. National Academy of Sciences. He was raised on an Iowa farm, BS from Iowa State University and Ph.D from Cornell University.
His publications can be viewed here.
