ASM General Meeting 2015

Tom and Chris both delivered excellent presentations at American Society for Microbiology general meeting in New Orleans. Chris presented a poster entitled "Zebrafish as a Model for the Interactions Between Hosts, Microbiomes, and the Environment" and Tom presented his work on shotMAP in an oral presentation titled "Accurate and High-throughput Metagenome Annotation Reveals Differences in Enteric Microbiome Function that Associate with Inflammatory Bowel Disease". Both presentations were well received and generated lots of interesting discussion. The abstracts for both presentations follow below.

Website Launch

With the website about to launch I wanted to take a moment to express my gratitude for all the hard work that Holman Jue put into getting Drupal up and running, designing the website, and managing the user accounts. Although getting the website running took longer than we anticipated, it was a great experience working with Holman and we will be sad to see him leave when he graduates in June. Thanks again Holman for all your hard work.


New Publication: An Introduction to the Analysis of Shotgun Metagenomic Data

I was recently invited to submit a review on the analysis of metagenomic sequence data. The manuscript, entitled "An Introduction to the Analysis of Shotgun Metagenomic Data" has been published as part of a special topics edition of Frontiers in Plant Science. I've not done much work in plant systems in the past, though I'm hopeful that this publication may help inspire some collaborations in this area.

The abstract follows.

New Publication: Quantification of the Hunter-Gatherer Oral Microbiome through Analysis of Exome Sequences

Teaching a new course (Microbial Genomics and Bioinformatics) has kept me pretty busy this quarter, so I’m a bit behind on announcing lab developments. With the bulk of teaching behind me, I’m now going to play a little catch-up with the next few posts.

First up, we published a paper in BMC Genomics entitled “Exome capture from saliva produces high quality genomic and metagenomic data” in collaboration with several other research groups, most notably the labs of Brenna Henn (Stony Brook) and Jeff Kidd (U Michigan).

We collected saliva samples from several Khoesan individuals, including several that live traditional hunter-gatherer lifestyles, and subjected DNA extracted from these samples to human exome capture and sequencing. This targeted sequencing approach facilitated population genetic analysis of human coding sequences. But, a fraction of the sequences didn’t show any discernible similarity to the human genome. We compared this fraction of sequences to genomes of known oral microbiota and determined that we can use this data to quantify the diversity of the oral microbiome . We then used this data to characterize, for the first time, the Khoesan oral microbiome and how it differs from the healthy American oral microbiome.

We are excited about this work because it (1) clarifies how microbiome composition scales across diverse human populations and (2) indicates that exome-capture sequencing of saliva DNA, which is increasingly used to study human populations, provides the added feature of resolving oral microbiome structure and diversity. Our hope is that we will be able to use this platform to study how microbiome composition covaries with human genomic variation.

The abstract for the manuscript follows.

New Publication: Gut Microbiome and Obesity

In collaboration with Katherine Pollard‘s lab at the Gladstone Institutes, we published a paper in PLoS ONE yesterday entitled “A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter.”

We analyzed  the taxonomic diversity of human gut microbiome samples collected from several distinct clinical studies for which each patient’s body-mass index (BMI) was measured. While some independent studies find an association between taxonomic diversity and obesity (as measured by high BMI), we do not observe any taxonomic signature that is consistent across high-BMI patient populations. This suggests that there is no simple signature of obesity in  human gut microbiome structure and that cryptic variables may contribute to the signatures identified in some independent studies. The abstract follows:

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