Day 3 of the meeting was virus day! Viruses have often gotten short shrift at these kinds of meeting, especially once 16S rRNA sequencing took over the microbial world. But the balance is shifting back, largely because of metagenomics.
First up was Andrew J. Hryckowian from Stanford University “Bacteriodes thetaiotaomicron as a Chassis for Understanding Gut Resident Bacteriophages”. Talked about the importance of studying bacteriophages. Studied wastewater treatment as a source pool of thousands of gut microbiomes. Generated a whole collection of capsid mutants to use as bait in their phage assays. Also some comparative genome sequencing of the phages.
Next was Robert A. Edwards from San Diego State University “Global and Local Evolution of the Ubiquitous Human Gut Phage crAssphage”. Started off talking about metagenome-assembled genomes. Really engaging talk about crAssphage, which they have collected from around the world. Those global samples are very location-specific, can identify location from phage. But in San Diego, it’s temporal… they see a seasonally dominate variant. Looked in individuals, some have 1 genotype and some have hundreds. Trying to understand what this phage might do… appears benign.
Then Shannon Bennett from the California Academy of Sciences, “Evolutionary and Ecological Drivers in the Transmission of Viral Diseases from Animals to Humans”. Good background on the spread of emerging diseases and mosquitoes as vectors. Interested in mosquito microbiome-viral interactions, looking also at host interactions across an urbanization gradient. Made the arguement that biodiversity may mitigate against viral disease emergence.
After the break we started with David Pride from UC San Diego “Role of Viruses in the Human Microbiome”. Talking about our shifting understanding of where microbes are in the human body… many sites previously believed to be sterile are not. Asking a lot of question about the location and distribution of viruses between body sites and hosts. Find them to be ubiquitous and persistent, contrary to the assumptions of the medical literature… even in places like cerebral spinal fluid. Cool data showing that viral communities are both individuals-specific and household-specific… can identify which individuals come from which household.
Next was Ashlee Earl from The Broad Institute Cambridge, MA talked about “Making of a (enterococcal) Pathogen”. Started off explaining why Enterococci are important, and the transition from living with people to causing multi-drug resistant infections. Tried to figure out why two distantly related and low abundance species became the problematic ones. Looked at evolutionary history, comparative genomics, etc. Proposed that host evolution and dietary changes then drives speciation in the microbiome. Really amazing data with a molecular clock showing that there’s a relationship between Enterococci speciation and terrestrial events (the big extinctions).
Last of the morning talks was Samuel Diaz-Munoz from the University of California, Davis “Uncovering How Virus-Virus Interactions Shape Viral Genomes”. Started off questioning the classic diagram of a single virion infecting a cell… he is interested in co-infection and viral-viral interactions. Social interactions are under-appreciated with viruses. Showed interesting work on re-assortment in influenza.
Started off the evening with Michael Baym from Harvard University, “Antibiotic Resistance: Experimental Evolution to Diagnostics”. Really fascinating talk about an experimental setup for observing the evolution of antibiotic resistance. They made a giant plate (2′ by 4′) with a gradient of antibiotics and allowed bacteria to grow into the gradient and evolve resistance. Amazing videos. E.coli is capable of evolving high levels of resistance to everything they tested.
Next was Stephanie Porter from Washington State University “Mosaics of Environmental Adaptation in Coevolving Symbionts and Their Hosts”. Spent time introducing various models of evolutionary adaptation in symbioses incl. “tradeoff model”, smartphone app model, and others. Studies these questions in serpentine soils, focusing on nickel. Collected a bunch of genomes to use for GWAS to look for genes involved in nickel resistance.
Last talk of the evening was Ivan Liachko from Phase Genomics “From Contigs to Chromosomes: Culture Free Metagenome Deconvolution using Hi-C”. Gave an overview of the Hi-C technology as implemented at Phase Genomics… especially focused on metagenomic applications. Went through a number of examples from various systems… people are doing some pretty cool projects with Hi-C these days.
Here’s all the tweets from Day 3: