Report and Storify from Lake Arrowhead: Day 3

The last full day of the Lake Arrowhead meeting was as awesome as the first two. It must have been incredible to watch microbial genomics evolve over the last 20 years that the meeting has existed… a time span that just covers the first ever bacterial genome to the 100’s or 1000’s of genomes that a single project might now entail (not to mention metagenomics and increased throughoutput of 16S surveys).   Thanks again to Surya Saha (@SahaSurya) for compiling the Storify of all the tweets from day 3.   A few of my random thoughts below, but the real meat is in the Storify.  The sessions on this day were “Pathogens; Systems Biology, Synthetic Biology” and “New Model Systems”.


Brucella is very widespread, and provides a good system for understanding the phylogenetic relationships between hosts and pathogen. Human transmission from soil is possible.

One host can be colonized with multiple strains of a pathogen and can transmit different strains to different people at various time. Complicates tracking and understanding of outbreaks.

Sequencing can’t solve all problems.  Saw great example of an outbreak case where sequencing was difficult but couldn’t have effectively informed public policy and practice regardless.

There are ways to use resistance-profiling and genome sequencing to better inform drug regimes for difficult diseases (e.g. drug-resistant TB)

Hearing over and over again about the resilience of the human gut microbiome to perturbations.  Sure antibiotics mess it up, sometimes for a fairly long time, but in the end most people return to some sort of stable state.   Although the lower level of taxonomic resolution used, the less this is true it seems.

Gene inactivation can lead to increased virulence… I had usually thought of gene acquisition as being the major driver.

I heard some more calls for a move back to complete genomes, but even more calls for the importance of culturing.  A few speakers showing data from freshly isolated (often novel) species.

A few speakers mentioned the importance of doing mock communities when sequencing, I think we’re going to have to start doing this.

Fecal transplants are even more effective and awesome than I thought.  However, a lot of people are trying them for diseases where efficacy and safety has not been tested.

Cheese is a great model system to understand interactions between members of a microbial community in a tractable way.

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David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter