AG2PI Field Day #14 - December 15, 2021

Leveraging Microbiomes in Agriculture

December 15, 2021 @ 10:30 AM - 12:00 PM (US Central Time)
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December 15, 2021
10:30 AM - 12:00 PM
(US Central Time)


An exploration of how microbial research is being used to inform agricultural decisions and improve crops and livestock..


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The Challenges of Putting Microbes to Work for Human Benefit

Using our Genesis Platform, AgBiome discovers microbes and genes that solve important agricultural problems. This presentation will discuss our platform and some of the challenges associated with microbial isolation and the effective use of thousands of genomes.


Dr. Ben Holt

Dr. Ben Holt is a member of the Scientifc Leadership at AgBiome, Inc. (RTP, North Carolina), which partners with microbes to Feed the World, Responsibly. He leads the Core Technology Platform and Discovery Program, including AgBiome's microbial and genomics research platforms. Prior to joining AgBiome, he was a professor of plant biology at the University of Oklahoma and a program offcer at the National Science Foundation, where he led the Plant, Fungal, and Microbial Development Program.

Inter-Kingdom Communication in the Gut Bacteriome and Mycobiome of the Weanling Pig

The environmental changes and stress associated with the weaning transition in piglets can lead to poor growth performance and a predisposition to disease. Interactions between the gut bacteriome and mycobiome can alter host nutrition, development, and disease response, but these interactions remain poorly understood in swine. While the gut bacteriome displays a predictable pattern of colonization with increased diversity over time, the fungal populations are more effected by environmental effects such as feed. Our data confrmed sequence-based cross-kingdom inferred interactions through in vitro bioflm assays demonstrating the ability of gut bacteria to alter gut fungal behavior and bioflms. This data provides insights into microbial interactions in the piglet fecal ecosystem during weaning that can modify piglet performance.


Dr. Katie Lynn

Dr. Katie Lynn Summers is a research microbiologist at the USDA in the Animal Biosciences and Biotechnology Laboratory (ABBL) in Beltsville, MD. She specializes in understanding the role of the microbiome and antibiotic alternatives in piglet growth during the critical weaning transition.

Chat Questions

From the presentation, it sounds like AG Biome using these predictive approaches for more exploratory analyses (predicting which microbes will have neat genes, etc). Do you ever use approaches analogous to plant breeding/ genomic selection to drive genetic gain in these microbe species? For example, to improve or breed better microbes?
Dr. Ben Holt

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.

We have isolated 3 strains of endophytes from a halophyte naturally growing in coastal Bangladesh. This has phosphate and other solubilizing activities under salt. How much would it cost us to do a genomic characterization of these bacteria.
Dr. Ben Holt

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.

Is there public access to FindMyFriends?
Dr. Ben Holt

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.

How similar is FindMyFriends compared to Oxford Nanopore's WhatsInMyPot?
Dr. Ben Holt

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

What is the pipeline for the release of the active microbes; can these be used in organic production. Is Agbiome also looking for microbes with a unique set of genome-editing reagents using find my friends?
Dr. Ben Holt

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.

Gluten and peanut sensitivity are less prevalent in Asia and Africa, but when the immigrants from these areas are examined, they develop sensitivity later during life. But most interestingly, their children show a very high prevalence of these food sensitivities (even more than the western population). Do you think these food sensitivities could be managed by altering the gut microbiome?
Dr. Katie Lynn Summers

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.

How can you ensure the growth of a useful bacteria (and fungi) in different environments during practical application.
Dr. Katie Lynn Summers

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.

Your MiSeq project with the 16S and ITS2 regions is very informative. Have you considered using longer reads on either the PacBio or MinION platforms to detect native DNA and annotate cryptic fungal species (e.g., K. sloofiae)?
Dr. Katie Lynn Summers

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.

Are you investigat(ing) the mechanisms of enhancement effect of resistance in this fungi in animal and plant? how can this help animal?
Dr. Katie Lynn Summers

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.

Do you have a recommended DNA extraction protocol for fungal DNA in environmental samples?
Dr. Katie Lynn Summers

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.

In Ben's case, they use a lot of sequence data from lots of different microbes and Katie, you're starting to sequence some of these species, but a lot of the work is still at the level of understanding what's there rather than what they do. How do we get to where Ben is?
Dr. Katie Lynn Summers

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.