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Nayfach S, et al. (2021) A genomic catalog of Earth’s microbiomes. Nature Biotechnol . 39(4):499-509. Danko D. et … LB et al. (2017) A thermostable Cas9 with increased lifetime in human plasma.  Nat Commun . 8(1):1424. Sczyrba A, et … (2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.  Nature Commun. …

… which includes screening methods, genome mining in cave microbiomes, and using engineered biosynthetic pathways and … we could have gone on for a lot longer than we did, and I can say without reservation that Brian is one of the … off through these areas. And you can do– with a teaspoon of soil from outside, you maybe have to do a 10,000-fold …

Brad: You want to talk about those problems? No, I mean, can you imagine your parent is now… When we think of our … Not a big leap, but then we began looking at microbiomes associated with various invertebrate organisms, … on that and identified just a small subset of transcripts up-regulated during toxin-inducing …

Creek, California, to consolidate activities. The significant economies of scale achieved in doing so enabled the JGI … Understand the assembly, function, and the behavior of microbiomes and manipulate them to facilitate microbial … to contaminants such as heavy metals or radionuclides in soils, freshwater, coastal sediments (coastal here defined  …

… so I took a little break, but I’m hoping that from here I can get back to a regular schedule. I’m going to kick things … process descriptions that allowed us to at least firstly set up a baseline process. And then really dig deeper into … with a contract manufacturer to actually have them build a plant for production and fermentation and transfer that …

… them to users via the Integrated Microbial Genomes & Microbiomes (IMG/M) system. Research Team    … The … data. … The mission of the Integrated Microbial Genomes & Microbiomes (IMG/M) system is to support the annotation, … and distribution of microbial genome and microbiome datasets sequenced at the JGI. IMG/M is also open to scientists …

… link to it in the show notes. Which I’ll remind you, you can always find at naturalprodcast.com . You should know … of these environments? NADINE ZIEMERT: So we started with soil. But we also have, in collaboration with other people, lake sediments. We have microbiomes from different organisms, including the human …

… and cloned into a vector of choice; up to 210,000 variants can be made Pool of variant libraries; sample sequencing to … as a microcolony, microbial aggregate, or a specific subset of free-living cells. Extracted DNA may be amplified … contigs. Assembly, annotation ( IMG ) Depends on project Plant and Algal Standard Draft Whole genome shotgun …

… a new culture of a new bacteria that you pulled from the soil, maybe it’s, you know, we talked about sponges, go pull … problematic. And there’s a whole process to this, that can be really time consuming because you need to, you know, … doing things. ALISON: Right. Yeah. DAN: Alright, so a subset of proteins are enzymes. Enzymes are proteins that do …

… this is back in the 1970s. So, I thought to myself, maybe I can use my background in chemistry and start to do something … Dick Moore became a postdoc with him, and then ultimately settled there as well, as a faculty member. But we were all … are many others, including Streptomycetes, which are common soil bacteria. DAN UDWARY: Yeah, we talk about them a lot …

… … Adaptive strategies in a cosmopolitan and abundant soil bacterium: genetic microdiversity or core metabolic flexibility? … Microbial contributions to soil carbon storage during simulated range shifts of plant-fungal symbionts … Elucidation of the gene regulatory …

… analysis, visualization and interpretation using public datasets.  … The Integrated Microbial Genomes & Microbiomes system ( IMG/M ) supports the annotation, … of the denitrifying thermophile Geobacillus thermodenitrificans subsp. calidus DSM 22629T. M Snook, et. al.  2024 . …