AG2PI Field Day #14 - December 15, 2021

It hasn't been a heavy area of emphasis. We have mostly focused on finding microbes where the activities are sufficient in their naturally occurring form. But things like driving evolution in the lab to more purposeful engineering efforts are in the plans, they just haven't been our top priority to-date.

You can get a pretty good genome sequence done for a few hundred dollars. You can get a high quality, relatively closed genome sequence that you can explore, but I don't know the extent of data science support you would have for annotating and exploring that genome. So, it's a little tricky for me to give a specific dollar amount.

It is not publicly available, but we have partnered with academic institutions for particular experimental approaches or have used in-house algorithms and approaches in those relationships.

I am not familiar with Whats In My Pot, but I'll be looking into it.

Regarding the first question: we have full development and commercial wings in addition to our research wings here that that will, in a phased approach, take an active and move it through the stages of development into commercial. We currently have one product in the market and a second that should be released this year. The first product is called Howler. It is fermented at-scale and sold as an antifungal. It is OMRI-listed, so it can be used both in conventional and in organic agriculture.

As to the second question: We are we doing that and we have we built out a subsidiary called Life Edit that was completely designed around identifying CRISPR enzymes and other DNA-modifying enzymes in the collection. That subsidiary was recently purchased by Elevate Bio and AgBiome still has a stake in the overall Elevate Bio company. Their focus is on human pharmaceuticals or human diseases. And we have retained the rights here at AgBiome for CRISPR work coming from the collection in the agricultural indications, and we are developing some ideas there as well.

Potentially. The idea is the more antibiotics you're exposed to younger in life, the more likely you are to develop allergies and asthma down the road. Because when you take an antibiotic it actually alters your mucosal immune response not just in your gut, but in your lungs, your reproductive tract and all of that. So these changes in your gut, bacteria and fungi, are changing the immune response for the whole person in that case, or pigs in our case. While I do not know the mechanism behind that and we would love to know how antibiotics do that, I think it does point to the fact that we can manipulate allergies and asthma-type responses, those TH-2 immune responses, through some gut manipulation. Now regarding the immigrants, I don't know any of their medical data, but we also have different food types here, too. What we eat here is not the same as Africa, so that's also altering the gut. All these signs point to yes, potentially those sensitivities will be managed down the road.

You can't. That's that's the goal of our lab. When you think about the microbial network in the gut, just one organ at one time point. You have millions of bacteria, many fungi, viruses and the host, and the epithelium as well. All of these are close together, they're interacting. All these molecules are being produced and certain microbes can recognize them and some can't. It's this busy, very crowded area, where there's lots of communication. What happens if you knock out microbe A? Does that eliminate the food source for microbe B and D? Like you, these networks are very complex. Many studies are needed to ensure that the useful bacteria are being amplified and not the bad ones. A lot of this comes back to some very basic microbiology that needs to be done.

The draft genome we did of Kazachstania slooffiae was a combination of Illumina and PacBio reads. We have not used MinION. Metagenome studies have not been useful because of the inherent rare biosphere that the fungi are, so when we do metagenome we miss the fungi all together, so that's an option we can't do.

This fungi that I showed today, Kazachstania, does not demonstrate any anti-fungal resistance, so that's good. It seems to be high in amino acids like lysine and nitrogen and helps produce more short chain fatty acids like butyrate that are considered beneficial in the gut. We also see beneficial interactions with like Lactobacillus acidophilus, so by promoting a healthier gut environment we might be preventing infectious disease and we might be promoting growth. I do not have a mechanism yet. We're not there yet but we're trying to get there.

Yes and no. Qiagen has created a line of DNA isolation kits that are called the Pro Kits. There's a DNeasy Pro Kit and I believe they have two of them now, maybe more. The Pro Kits take into account some fungal species, so those can be a useful, good starting point to go with. Not every environmental sample is the same but I know the DNeasy Pro Kit worked very well in pig, chicken, and other environmental samples. So may be a good place to start.

Ben: Bacteria and the genomes are considerably smaller and much simpler than what Katie's dealing with, so we at AgBiome also do fungal genomes. But as Katie said and the reason why they're doing some combination work with Illumina and PacBio is to solve part of that problem. It's a much trickier thing to close a fungal genome.

Katie: And, unfortunately, they can be polyploid. Based on your sequence, you don't know necessarily if it's a diploid or a polyploid or whatever, when you get those big datasets back. Those are difficult and the fungal studies have all lagged behind because they are harder. The primers aren't as good, the databases aren't as good. DNA is harder to isolate without damaging it. It lags behind the bacteriome at least a decade. But we've got to do those preliminary studies.