Days 4 and 5 of the meeting were a real mix of things including chemistry, evolution, and ‘omics.
Also Kevin Bonham took fairly detailed notes throughout the entire conference and put those all online here, worth checking out if you want more detail.
Started off the day with Mohamed S. Donia from Princeton University, “Small Molecule Mediated Interactions in the Human Microbiome”. After a warning about upcoming chemical structures he walked us through reviewing how bacteria make small molecules and discussing BGCs – biosynthetic gene clusters. Is looking for novel BGCs in metagenomic data. Talked about the application of their approach in Crohn’s Disease.
Next was Michi Taga from University of California, Berkeley “Decoding Nutritional Interactions in Microbial Communities”. Described different nutritional interactions – competition, syntrophy, and cross feeding. Focused on corrinoids (e.g. vitamin B-12). Created a large database of corrinoid pathways as part of a comparative genomics project.
Then Marc Strous from the University of Calgary, “An Omics Journey Through Microbial Ecophysiology”. Started with his end goal of bioenergy carbon capture and sequestration, a process by which they would remove CO2 from the air, use it to produce energy, and then bury the pure emissions afterwards. Discussed various reactor setups to maximize yield, but cross-feeding limits the system. Doing “genome-centric metagenomics” to study metabolic pathways in communities of interest. Tossed in some proteomics as well.
Jesse Shapiro from University of Montreal, “Ecological Drivers of Bacterial Speciation”. Discussing the “bacterial species problem” whereby bacteria recombine too little and too much to form new species. Looking at a variety of biotic and abiotic factors that can influence speciation. Tested their models on “wild” bacteria using the EMP dataset. Comparing two models… “ecological control” versus “diversity begets diversity”.
Next was Allison Hansen University of California Riverside, “Small RNAs Regulate Gene Expression in a Reduced Symbiont Genome”. Described mutalistic symbionts in aphids, in particular Buchnera. Many endosymbionts in this system have lot key genetic functionality, trying to figure out if small RNAs are compensating for some of this loss. Many sRNAs are conserved over long timeframes in these genomes.
Last of the morning talks was Anna Edlund J. Craig Venter Institute, “The Multi-Omics Promise of the Human Oral Microbiome”. Introduced the many potential impacts of oral conditions on general health. While we know the players involved in community succession, we don’t know what they’re doing. She described an in vitro biofilm model system and some deep sequencing of in vivo samples.
Started the afternoon with Neslihan Tas from Lawrence Berkeley National Laboratory, “Deep Look Into Deep Permafrost: Multi-omics Insights into Carbon Cycling upon Thaw”. Good introduction about permafrost, climate change, and GHG fluxes from the soil. Showed data that the permafrost is a complex microbial community, varies across areas, and looks very different from the active layer. Use LIDAR to understand the structure and age of the permafrost in order to optimally sample. Observed that freeze/thaw has big influence on the community.
Next was Christopher T. Brown from University of California, Berkeley, “Analysis of Genome Diversity Across the Bacterial Domain”. Introducing the various Banfield lab field sites (soil, acid mine drainage) from where they extract genomes. Talking about the CPR bugs that they work on… too small for the traditional .2um filters (small bugs and small genomes). Hundreds of novel genomes. Also got into the discussion about the GTDB taxonomy argument that all the CPR are a single phylum.
Last before dinner was Terence Crofts from Washington University St. Louis, “Mechanisms of antimicrobial bioconversion by environmental and host-associated bacteria”. Talking about bacterial catabolism of antibiotics as a carbon source. Used penicillin as the carbon source and genome sequencing to get at the mechanism. Then went back to the system with mutants and growth assays… some really nice curves showing which pathway components are required for which substrate.
Only two talks in the evening, starting with Irene G. Newton from Indiana University, “The Royal Treatment: How Honey Bee Microbes Contribute to Queen Physiology”. Nice video to start, showing bees licking the surfaces around them right after hatching. Talked about how queen honeybees have a unique microbiome and that there’s a genomic signature of historical association. The queen bee microbiome changes through development, and has more diverse and variable community compared to workers. Discussed evidence that these strains have signatures of association with bees (at least particularly due to HGT). Lastly showed that the queen been microbiome helps protect against fungi.
Last talk of the night was Janina Krumbeck from Zymo Research Corporation, “Resolving Challenges of Microbiome Analyses”. Going through the classic list of possible biases and problems in microbiome analysis… ranging from DNA extractions through choice of bioinformatic tools.
First talk of the morning was Nandita Garud from the University of California, San Francisco, “Adaptation of Commensal Gut Bacteria in the Human Microbiome”. Using shotgun sequencing to detect evolution in commensal bacteria. Talked about the various challenges in detecting evolutionary signals among the noise in the system. Presented data using these methods on human microbiome data.
Next was Pamela Yeh from University of California, Los Angeles, CA, “Higher-order interactions and emergent properties in drug combinations”. Talked at length about moving beyond pairwise interactions when understanding drug interactions. Described a variety of higher-order interactions, saw more antagonism than synergy.
Last talk of the conference was Justin Jia from Simon Fraser University “Revealing Antimicrobial resistance gene mobility trends using >15,000 replicons.” Trying to understand how antimicrobial resistance evolves as a proactive approach, instead of reactive approaches like limiting antimicrobial use. Found that disproportionate amount of AMR is on mobile elements. More specifically, AMR genes that are highly specialized are more likely to be mobile, possibly due to higher fitness cost.
Here’s all the tweets from Days 4 and 5. Another great conference!