Microbial traits from genomes and metagenomes | they/she 🏳️⚧️ | https://microbialgamut.com
JL Weissman
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This was the honors thesis of mGAMUT lab undergrad rockstar Jesse Natarajan who has now moved on to do her masters in comp bio
Hoping the soils folks will find this useful (we are trying to build out the utility of these tools across systems)
JL Weissman
JL Weissman
We initially developed this index for marine heterotrophs, so we're excited to see it predicting MAG trajectories in a totally different system! doi.org/10.1126/scie... (marine work with Emily Zakem and Jesse McNichol among others - our contribution really focused on the IoC bit)
The experiments were led by @joyobrien.bsky.social and supervised by Jessica Ernakovich (with help from other Ernakovich lab members) and sequencing support and sample sourcing came from Tom Douglas and Robyn Barbato
Another recent one from the group out in Elementa: "Assembly-free short-read metagenomic maximum growth rate prediction". You can now use gRodon's metagenomic maximum growth rate prediction directly on short reads (no assembly required)
doi.org/10.1525/elem...
JL Weissman
Now out in Soil Biology & Biochemistry: "Growth Optimization Predicts Microbial Success in a Permafrost Thaw Experiment". We use permafrost incubation experiments to benchmark a genomic index of copiotrophy that predicts growth trajectories during early thaw
authors.elsevier.com/a/1nCgL8g13j...
Functions to do this kind of analysis on your own data have now been implemented into gRodon, with a new tutorial as well: github.com/jlw-ecoevo/g...
Microbial maximum growth rates are key parameters in microbially explicit soil biogeochemical models that can also be estimated directly from genomes and metagenomes, therefore enabling model-data syn...
