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John McCulloch, September 20

Please join the department of Biology in welcoming Dr. John McCulloch, Staff Scientist of the Microbiome and Genetics Core – National Cancer Institute at the National Institute of Health, for his talk entitled, "JAMS – a comprehensive framework for advanced microbiome analysis." The talk will be held via Zoom on September 20, 2021 at 4pm EST. For access to the Zoom information, please contact Sarah Farris at

More on the talk:

The microbiome, which is the collection of microorganisms constantly present in the body of animals, has been shown to modulate host physiology in a number of ways. The composition of the microbiome varies more, from host to host, than intra-species host genetics. Not only that, the microbiome is also "plastic", in that its composition changes over time and due to certain events. With studies having consistently and unequivocally shown that the microbiome plays an important role in host disease outcomes, the potential for translational microbiome research to improve health outcomes is tangible. Yet, the burgeoning field of microbiome studies can still be regarded to be in its infancy due to the large complexity of the microbiome and the myriad of interactions which occur not only amongst the microbial species that comprise it, but also with the animal host. Although the cost of DNA sequencing has been decreasing exponentially, the de facto state of the art of genomic sequencing presents researchers with technical challenges which must be overcome when characterizing microbiome samples. Namely, technologies which yield sequencing reads in appropriate quantities for assessing the microbiome do so yielding reads which are very short in length, necessitating vast numbers of reads as a trade-off to comprehensively assess a single microbiome sample. Simpler 16S rDNA sequencing, which targets only 0.01% of a bacterial genome can only yield taxonomic information and is fast being supplanted by unbiased whole (meta)genomic "shotgun" sequencing, as the relative price of sequencing per sample using the latter is now competitive. Shotgun sequencing yields not only taxonomic information, but crucially, functional information, as genes composing the microbiome can be directly gauged. Translating the tens or hundreds of gigabytes of data generated for a typical cohort of samples involves advanced computer processing of the raw data using a panoply of different software and parametric decisions which is somewhat baffling to the non-bioinformatician research scientist, who usually has a microbiome component only as part of a more encompassing project. In order to facilitate and standardize advanced shotgun microbiome analysis, Dr. McCulloch and collaborators have developed a unitary, open-source software package, Just a Microbiology System (JAMS) which automates, or at least massively facilitates, the generation of comparative statistics and high-quality plots of microbiome samples using only raw sequencing data and metadata as input. This framework has been used in several projects to show differences in the microbiota of humans and mice which affect health outcomes. Highlights are the use of JAMS for showing that Fecal Microbiota Transplantation (FMT) can improve response to cancer immunotherapy; that the microbiome of wild mice confer resistance to diet-induced obesity; and that previous infections with pathogenic bacteria confer changes to the microbiome making the host more resistant to subsequent infections.

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