Lake Arrowhead Microbial Genomes #LAMG16: Day 3

First up today was Rachel Dutton talking about “Horizontal gene transfer in Cheese”.  She began by talking about cheese as a great model system for understanding the principles behind microbial community formation.  Many replicates, controlled conditions, manipulable etc.  After doing initial 16S/ITS survey they cultured representatives of all the dominant genera in the cheeses and used those for in vitro succession experiments.  Remainder of the talk was on Horizontal Gene Transfer… the why, how, and what genes in cheese-associated microbes.  Showed some cool pictures from imaging mass spec which was a new technique to me.

Next was Elizabeth Henaff, “The Microbiome of the Gowanus Canal, Brooklyn’s Hippiest SuperFund”.  Gave a depressing intro on SuperFund sites, including the difficulty and failures of cleanup.  Collected samples in Hazmat suits, did the DNA extractions with a DIY Bio lab, then metagenomics in the lab.  Very cool citizen science involvement… also put data online for people to interact with.  Found a lot of bioremediation pathways in the existing communities.  Also talked about using Nanopore in the context of citizen science which is a topic that I think has a lot of future potential.  She described two different approaches to bioremediation… either modifying  the bacteria themselves or changing their environment to select for bioremediation pathways.

Roxana Hickey “Microbial Interactions Between Humans and the Built Environment”.  She gave a detailed overview of the BioBE Center at Oregon and all the cool research they’ve done over the last 6 years or so.  Also talked about the various ongoing projects there including effect of light on dust microbiome viability, weatherization and microbes, multi-person microbial clouds, microbial transmission in the BE, and antimicrobials in the BE.  In particular she talked a lot about the multi-person microbial cloud project which sounds really neat.

Next was my own talk… I talked about microBEnet, our Space Microbes project, and Gut Check: The Microbiome Game.  The focus of the talk was on communication and outreach.

Gautam Dantas talked about “Antibiotic Resistance Reservoirs”.  Talked about the complex interaction networks that lead to resistance… the “resistome network”.  Started with early life, for example 99% of early pre-term births get antibiotics.  Showed data that NICU infants have many of the most worrisome bacterial species present, many are drug resistant.  Made an impassioned call for more culturing study and experiments.  As an example they plan to humanize germ-free mice with NICU microbiota. Talked about antibiotic resistance in soil, it’s ancient, most (all?) antibiotics made by soil bacteria, and levels in soil are increasing over time.  Currently also looking for antibiotic resistance genes in less developed and more rural locations.  Finished with potential ways to “invert selection” to combat resistance.

Alyssa Kent presented on “Increased Biofilm Formation During Evolution to High Temperature in the Widespread Marine Roeobacter“.  Started by introducing the oceans, climate change, and the fact that microbes not often part of the discussion.  Showed that her Roebacter isolates formed unexpected biofilms in a 500-generation evolution.  Sequenced some genomes and got at the probable mechanism (oxygen limitation).

After lunch Chris Waters talked about “Elucidating and Targeting Cyclic di-GMP Signaling”  Warned the crowd that he wasn’t into genomics but was heading in that direction.  Talked about cyclic di-nucleotides as molecules that are sensed by the host.  Described the signaling pathways of cyclic di-GMP in Vibrio cholera.

Then Ilano Britto discussed “Transmission of Mobile Elements and Microbes in the Human Genome”.  Gave a really interesting talk about her FijiCOMP project, started on a shoestring budget, ended up with 92 lanes of metagenomic sequencing.   Developed a tool called “latent strain analysis” to deal with the fact that the human microbiome reference samples aren’t great for non-American populations.  Looked at what bacteria match with social/familial patterns in the village.  Showed some cool graphs where Prevotella strains are more similar in a household than between family members in different households.  Described a novel single-cell sequencing method that’s much cheaper than traditional approach.

Mary Anne Moran talked about “Cryptic Interactions in the Ocean Microbiome”.  She described a cool in vitro bacteria-phytoplankton model system where T. pseudonana (B12) and R. pomeroyi (C & N) are co-dependent for nutrients.  Put this relationship in the context of the ocean carbon cycle.  Was thought for a long time that the bacteria were just loosely dispersed scavengers, presented evidence of co-localization with phytoplankton.

The evening session began with Pradeep Singh “Population Genomics of Pseudomonas”.  Talking about Pseudomonas in cystic fibrosis patients.  Started off with 1000 (!) isolates from one patient, looking for phenotypic variation.  Also did a biogeography of isolates, several lungs, several sites, hundreds of isolates.  Sequenced 100 of the genomes.  Used all this to tell a story of compartmentalized evolution… different strains are arising in different locations, and this drives population diversity.  The result of all this is that traits like motility and antibiotic resistance vary widely within the lung.

The last talk of the day was Elodie Ghedin “The virome in the respiratory tract”.  Glad to see some viruses!  Giving a good introduction to influenza, talking about the huge number of variants in a person even though we talk about “a strain” in a person.  Talked about ways they attempt to measure the effective population size.  Also discussed ferret studies where they test viral isolates from different decades for virulence/protection.  Finished by talking about the Lung HIV Microbiome Project (focus on COPD cases).  Problems of getting enough pure material.


Leave a Reply

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