It's time for a new way of communication the swine industry one that you can get the latest updates while commuting or driving to Farms here. You have the brightest mind of the global swine industry in your pocket. Always take a look at the microbiome. See with the microbiome reveals. I would predict Marcia that in the future in 10 years from now microbiome is going to become PCR that means every lab in any Adversity or any lab in any company that you know make science or that you know makes feed stops or any other kind of feed additives going to have a microbiome station. Welcome to sign it podcast. My name is Martin Bohm Salvage your host for today's episode. This episode is brought to you by every Pig the truth is precision swine production is not the future it is the present every pig is the Jen Pig Health platform it is a simple yet powerful Pig health and production management tool request a free 20 minutes demonstration at www.arabinstruments.com. Co how everyone today we're going to talk about microbiome teasing out the bus from the reality today. We have dr. Andreas Gomez from the the city of Minnesota and undress. Thanks for joining us today. Thank you. Thanks for inviting me. It's a pleasure for me to be here appreciate that. So undress just to start things off. If you can walk us through how did you get involved in pig production and talk a little bit about your career until today true. So I'm basically a microbial ecologist. That's my training. That was my training during my Master's and PhD and my main interest is to investigate and explore the Position function of microbes in different system. So I started my career studying soil microbes or microbes living in soil at different depths interesting. Then I passed I moved on to looking at the microbiome. So while primates specifically gorilla populations in Africa and also human populations in in the Central African Republic just as As a way to understand the evolution of the human microbiome and and how diverse Lifestyles have altered the microbiome to the point. It's become a little bit different from what our ancestors were supposed to have. So that was a very important very important topic in my research is still is but now as a faculty member at the University of Minnesota. I'm interested in The microbiome of food animals and I have a very important research portfolio on the microbiome of swine and you know, basically exploring the swine microbiome and more importantly trying to look at strategies to manipulate it to improve health and performance and in big production systems, very nice. That's a very diverse background area from gorillas in Africa, too. Pigs in Minnesota, I love that. Yeah. Yeah, I mean that if you think about it, it's not that different. I mean if we can talk about it later in more detail, but but the system's themselves as far as the capacity to, you know to metabolize different substrates in diet is not very different from a gorilla comparing a gorilla to a big actually I can imagine that very nice. Well since we are at it Dr. Gomez, if you can't tell us what is the microbiome what the microbiome is basically defined as the collection of microorganisms that colonize or inhabit different surfaces, either within animals or environment. So all the collection of cells that are of the represent different microbes even bacteria fungi viruses. Viruses and protozoa is collectively known as the microbiome along with the functions, they incorporate so it's not just the cells of the microbes themselves, but also the functions that the metabolic capabilities that they have. So that's what we Define as the microbiomes. The microbiome is not just confined to the God. We have a micro biome also in the nasal surfaces in the skin in the reproductive tract and anywhere you look at your we're just surrounded by microbes this Microbial world that's that's why the area of microbiomes is so exciting today. Very nice. Well on that note, why is there a hype about gut microbes in different areas of science? Well, you know the high basically I would say so microbial ecology is a very old feel, you know, if you think about what an Tobin living who started doing with first trials Of the microscope and this little animal kills. He saw in the teeth scraping he was doing microbial ecology. It was basically looking at different different microorganisms in Teague surfaces. So those were the initial say the initial steps of microbial ecology Auntie what we know it as we know it today and I think we're revolutionized the microbial ecology or the microbiome field was the implementation of molecular tools. To study the microbiome, but at high resolution and in many many different subsample simultaneously, so with implementation of Next Generation sequencing, we realize that the diversity of the microbiome in different systems, especially in the god in the human or animal God is incredibly high. So we started applying those molecular techniques to study microbiomes in different systems. We realize further the microbiome is more diverse than we initially thought and second. That the functions that the microbiome performs or encodes are essential for Life as we know it, right. So so all the functions the microbiome performs as far as nutrient processing nutrients synthesis the a clearing between the microbiome and immune system are functions that guarantee Life as we know it and without the microbiome those functions would not be possible. So in other words, there is fun. She's performed by the microbiome that guarantee Life as we know it and without these functions we wouldn't be able to exist. So I think that's part of the reason that's the main reason actually there's such hype about the microbiome, you know, the we realize based on all these new molecular and sequencing techniques that we use to study microbes. We have realized that the functions that the micro bouncer form extend the physiologic capacities of of animals and humans in a way that will guarantee life and without those functions who wouldn't be able to exist interesting. Yeah. There's definitely has been an explosion in microbiome research in the last few years, right? Yeah. Yeah, and I think most of these high began with the work that Jeff Gordon University of Washington started doing with You know, if you know, this is a quintessential April microbial ecology about transferring the microbiome from an obese mice to amazed that it's lean and look in the how the phenotype of obesity is transferred along with the transfer of microbes. So that shows that there are some functions performed by microbes as for example energy harvest the can actually be transferred from one organism to another so that's that's pretty that's pretty amazing. So from those, you know trials and those experiments performed by Jeffrey Gordon, then you know, we realize that this the functions that the microbiomes form not only at the gut level but also, you know the gut brain access there's constant communication between microbes in your God and your brain and we believe that there is an association between certain behavioral traits and the function of the composition of my Groups in the gut so that's another area that is receiving increasing attention today. Also, you know the microbiome role in different diseases for instance in cancer. We know that there is a there is a connection between the presence and the function of certain microbes and the development developing of certain diseases as far as cancer diabetes autoimmune disease. So that's part of the big hype that we have about the microbiome today in the station the we can change things in the microbiome to alter phenotypes, which we haven't been able to to completely do but there's a lot of promise on that. So when you when you think about microbes and the genetic makeup that you have we're able to predict the probability of disease with higher confidence by looking at microbes compared to when we look at the nomic regions in our own genome, so, you know, so People are predisposed to certain diseases because they have a mutation. What they have is Nip in their genomes that are there is associated with that disease, but we realize that the predictive power of the genes of the genomic makeup is not as strong as a predictive power of the microbiome when it comes to predicting disease outcomes. Well, that's amazing. Yeah. Well, so on that note as well. What is the state and resolve? The gut microbiome research in pig production and what can we conclude so far? Well, there's there's been also an explosion of different work on analyze and exploring this why microbial the first work just intended to look at that microbial ecology specially along different segments of the GI, you know, when you compare the small intestine large intestine pieces, what is the microbial ecology on those specific segments? So so the first word really intended Look what what is the composition of the microbiome just to get a grasp of the of the microbial makeup and the functions they perform so apart from that then we've been moving from those that's a compositional surveys to specifically explore the function of those microbiomes, you know, what kind of functions those microbalance are performing and and and and then we'd be moving to actually exploring. Ation of those microbiomes to see the performance can be improved. So there is a lot of work being done on prebiotics and probiotics as well in different organic acids and other feed additives that we know have some influence from changing microbial composition, but the the manipulation of the microbiome as far as you know, you know feeding that's a prebiotics and probiotics and looking at that response in the animal is not always Reproducible which means we know there is a microbial ecology that is very specific along the GI of the pig. We know the by incorporating different additives in feed were able to get some changes in the microbiome, but we're not always able to get a response as far as the phenotype. We want to we want to reproduce and and and the reason is that the microbiome in pick systems is highly variable across different. Also different divisions have very different microbiomes even within the same species, you know, the basic commercial the white pig when you look at the different micro biomes in different in different subjects, we see that the micro amps highly variable. So that's one of the reasons why we haven't been able to replicate or to specifically manipulate microbes to improve specific phenotypes in pace. So I think that that's the state of the art of the pig microbiome work today. First of all, In a different looking at the composition in the function of the microbiome along different segments of the GI tract and then trying to manipulate those those microbial communities using different additives to see if we can improve performance and alter the phenotypes of those Peaks except that this this responses are not always consistent and reproducible highly variable interesting one thing that you and I talked in the past, I believe. It was the you know, a lot of litter tourism is inferring Association, right? And there is some recent work that that is doing more of a randomized type of approach even in that, you know, fecal transplantation all that kind of thing. So, can you give a comment to us and to our audience about you know the work done in microbiome on Association and you know versus causation and Or causality. And and where do you see that going? Is there a is there any type of trend there on the literature right now? I think most of the World produced right now. It's been based on Association. So we know that by feeding certain additives we see a change in the microbial but that doesn't really mean that we're actually targeting tracing the specific input that is causing that change in the microbiome. So this is what We call Association also Association is looking at the microbiome of different animals on their different disease conditions, you know, the deceased animals have a different microbiome compared to healthy animals. But again, this is a source. This is an association experiment to move to causation. There's different things that people have been doing in the field. So the area of when you took when talk about human microbiomes, there's a lot of hype in using free German mines, which Basically by the have been devoid of microbes so that way you can transfer those you can transfer different microbial Community committees to mice that are free jerk and see phenotypes can be reproduced of those mines that didn't have a microbiome previously. So so that's what we come a little bit closer to conversation rather than Association right in the in the peak. Microbiome World those words that relate to a conversation rather than Association is still in infancy. There's somewhere being done in fecal transplants in piglets and also in some other food animals for example in their assistance and what we see in this work related to fecal transplants to replicate or reproduce phenotypes, is that the microbiomes that's being transferred. Are difficult it's difficult for those microbes to settle in the new system that is for a new microbe to colonize a new system. It has to first of all compete with the microbes that are already there and established themselves so that you know, the communities can be settled there in that system since we don't have a lot of opportunities to work with fruit free germ pigs in in in you know, the pig production area those those works and those experience are very expensive the word that has been done as far as looking at fecal transplants are you know conventional picks and what we realize is that for that microbiome to be transferred to one that's a one thing that is high that is high in production to a pay that is low in production and see if the phenotype can be transferred. I think we're very far away from that yet because we Those microbes to be settle in the new system to be able to cause some sort of some sort of change. So for me, the high promise would be on on specific feed additives and looking at the effect of feed additives at the molecular level in pigs. So, so right now I think people are doing work on moving from this composition service on the micro of the microbiome to getting closer to the function. Reality of things and and the differences that the techniques to study the microbiome in both cases are different and of course there's costs involved. There's also a lot of promise with using organelles and this is something we're doing here the University of Minnesota. We're growing organelle specifically color noise and Androids in vitro and treating those color noise. So those in those androids with specific microbial communities. Also with specific additives and see if we can look at the changes in the organelle itself upon this stimuli with different microbes of different of different additives. That's a that's a better way to get close to do causation to get closer to the effect of specific additives or microbial communities in in a various related part of the system, but that's a start, you know looking at how How microbes and feed stops interact in organoids to see if there's some changes in gene expression or changes in God morphology that will help us get closer to probably what's happening enviable. Very interesting. Yeah, that's very cool research right there with us Enterprise. Dr. Gomez. What is the biggest misconception about the swine gut microbiome? I would say the biggest the biggest misconception. Okay. So I think people in the field are starting to learn more about microbes today. What are the misconceptions that we have in those studies whenever you know people in the industry approaches to conduct different studies or to you know to see whether specific additive they have would have an effect in the microbiome is that people sometimes are confused. Concept of composition versus function, right? So the typical let's say microbiome survey is based on answering the question who's there? So what kind of what kind of microbes make up the system so that basic microbiome survey does not really include the functions performed by those micro. So if we want to know what the functions are, we will have to look for other techniques that would allow us to look at the metagenomic makeup of those microbial communities. So that's that's one of the misconceptions people know that the typical microbiome survey would really reveal both composition and function but that's not the case to go to function there needs to be additional analysis to perform. Another misconception that people tend to have is that the microbes are easily or can be easily manipulated and that can be immediately translated to phenotype of Desire phenotype of Interest. That's a misconception because we're still far away from its say managing to to manipulate microbiome specifically to agree to to to have a phenotype of Interest. That's that's the still the still in infancy in the swan microbiome work. Those are probably one of the two misconceptions that I hear most when I interact. with people that are nervous in the era of microbiomes and want to have you know, what a perfect one to perform microbiome microbiome where another thing is a for, you know, designing an experiment or in the microbiome field as far as looking at the effect of different additives or or different it's a drugs or or any other compound that would have the promise to By health or phenotyping in pigs is number of samples. You know, we tend to look a very few number of samples in any given experiment and what we've demonstrated that more than let's say the depth at which look at them microbial system the number of samples that you use in a given experiment. The power is very important. So looking at any kind of effect on on any additives on Peak Performance as in the context of the microbiome is gun is not going to be attained using 10 or 9 pigs per treatment, you know, you need to look at you know, many more pics just to be able to get closer into that into into looking at what specific effect has your attitude into the microbial communities and see how that is be reproducing in the phenotype of the pig. Very nice, especially the high variation that you mentioned, right? So that large sample size will definitely help there. Right? Yeah. Yes. We saw with large sample sizes. We guarantee that we are able at least to counteract some of these some of that into individual variation. But but you know, as far as where we going with the pig microbiome world, I think we still need to do a lot of fishing Expeditions. We call it fishing Expeditions that I would say. Hypothesis generating work, you know, we still need to take a look at Peak systems right from the beginning. So right now we're doing a lot of work in my lap looking at the piglets microbiome before birth. So looking at what happened to the sow what happened to different feeding strategies in the south in gestation and how that contributes to sit in the microbiome in the picnic at the very beginning. I think those servings needs to be all those work, too. Experiments need to be done before you are able to devise any kind of feeding intervention or let's say additive intervention to be able to modify or to manipulate a specific phenotype in picks. We need to know what happens with the with the seating of the piglet microbiome right from the very beginning and this is something we're doing very intensely here in my lab right now. Very nice. Andrea is what information were benefits. Can we get from gut microbiome research in the swine nutrition health and production Fields. Was it the biggest benefits? So the microbiome is an interface that so is the one part of the Genome of the pig that we can modify immediately, you know, you can do genetic improvement with pigs and look, you know after certain generations to see if you have improve our phenotype of interests, but but the excitement About the microbiome is that is the is the one part of the Genome of the peak that we can modify to see if we can obtain, you know, a desired phenotype. So I would say that the microbiome is the is the interface for instance between feeding and the genome. So whatever kind of feeding strategy that you implement on your pigs is going to be directly influenced by microbes, so Is one of the one of the things that the people in the in the feeding industry can expect in defeating Pig industry can expect about about microbes anything any kind of feeding intervention needs to be or is intimately associated with what happens with the microbiome. So looking at you know, usually when you look at when you have any kind of, you know feeling trial in the swine nutrition field, you just feed the additive and you just see what happens with Organs, right you see if there was a way gain if the was fit and efficiency increased but I would say by not looking at what happens at the microbiome you lose in a piece of the picture because if you are able to trace what specific changes the microbiome experiences upon feeding certain, you know specific feed additives. You can formulate a more Or targeted approach especially if you know what specific microbes change your able to formulate a targeted approach to improve the efficiency of the animal systems. So in other words looking at changes in feed efficiency in weight gain upon finding certain additives and not looking at the microbiome becomes a black box, right? Because you want to know the microbiome is the is the engine transforming that feedstuff into into intro bio available material that the pig is going to take advantage of of course that depends on the nature of the of the feed additive but but I would say that's that's the most important piece of information that it's a pig nutritionist or swine nutrition is can get from microbiome work what specific communities and functions change in function of defeating additive that is being fed and by looking at that you're able to tweak to to adjust Let's say the formulation of your feet or the composition of your feet to either enhance or boost or even inhibit the growth or the functional certain microbes to make this grow faster and more efficient. I would say that in a nutshell. That's what I'm most excited about when it comes to swine microbiome work that by looking at this specific feeding strategies at the molecular level. We can know what specific members of the microbiome Increase or decrease and we can reformulate those feed additives in a way. They can perform the desired performance or the desired effect of phenotype can be streamlined or can be obtained faster. But without looking at the microbiome, you're not going to you know going to get that picture very very interesting Andres. That's sounds like a lot of work ahead of you. Yeah. Yeah. I mean I'll keep this is a very exciting time to work in microgravity. Biomes, I couldn't I couldn't pick a better topic, you know to run a lab the microbiomes right now because everybody wants to know everybody wants to have the secret, you know, what kind of specific manipulation can we can we what kind of specific strategy can we Implement to manipulate microbes and as a result improve health and performance in animal systems. However, we need to remember that the microbiome is only a piece of the puzzle. Right. So along with microbiome information with it. We also need information on functional genomics of the animal. We need information on nutrition. We need information information of the metabolites that are being produced by the microbiome upon feeding certain food additive. So by looking at these questions in an integrated manner, I think people that work in the nutrition and the swine. He'll feel could have a better assessment of whether they're additives or other. Order let's say products under over there. Any other kind of let's say product that is being formulated to improve health works right without if you don't look at these different components of the system microbes functional genomics metabolites feeding. I would say you're missing a very important part of the puzzle and I don't think you would be able to adjust and to into twig your formulation to make You know healthier and more productive that makes sense any final words our microbiome undress before we move to the three questions. We ask every guest. Well, I would say no my final work. I would say no the microbiome is a very exciting field of the animal and human health world right now. I would say that to to move forward with plans about new feed additives new. New Management strategies always take a look at the microbiome see with the microbiome reveals. I would predict Marshall that in the future in 10 years from now microbiome is going to become PCR that means every laugh in any University or any lab in any company that you know makes science or that, you know makes feed stops or any other kind of feed additives going to have a microbiome station just to Could hold microbiomes change for my help microbial communities change upon feeding certain, you know feeding additives. So so I would say my final word is is for especially for people that work in the swine industry, especially when it comes to pit stops and nutrition. You gotta take a look at the microbiome because you if you don't do that, you're missing a big piece of the puzzle. very nice celebrating its 25th anniversary just all manufacturers the original Wireless Standalone swine feeding system designed by pork producers for pork producers their simple reliable and provide peace of mind 24/7 365 days a year just all is not just manufactured by an equipment company, but by a family port production business with a slat level understanding Just talk always one step ahead and slide fitting. It is time to our famous and there's going to the three questions you ask you every guest every episode. What is your favorite swine related book? Oh, well my favorites wine-related book. Well, you know Marcy my background, even though is animal science. My background was never I was I was I was I wasn't It's a swine person in my early stages of of training. I my training was with non-human primates and that's how I got connected to the to the to the microbial ecology world or maybe good maybe another way to ask. Is that your favorite get related book? Oh God. Okay. That's a better question. So us Augustine tests on microbiology is a and of course, you know, it's written actually an edited by actually by my advisor for my PhD in the University Minnesota Bryan white and Rod Mackey. This is a this is the Bible of microbiomes is the Bible of microbial ecology when it comes to gut microbiomes. It was written in the 1990s. It has two volumes and it's called gastrointestinal microbiology. So these book was edited and written by the founding fathers of the microbial ecology world when it comes to God microbial. So anybody who's interested in microbial ecology anybody who's interested in microbiome work when it comes to monogastric soar ruminants needs to be aware of that books called gastrointestinal microbiology. So it's not a swine book, but there's also a lot of chapters and In sections dedicated to the swine gastrointestinal tract and it's microbial very interesting. Yeah. I was not aware of that. So what is your favorite book unrelated to swine besides the gut books of any topic any topic? Oh my God, that's that's I would say Malcolm X the autobiography of Malcolm X. I don't know. I don't think that has anything to do with microbiomes or Whatever meets been a very spiring book not only from a personal but also from a professional standpoint the autobiography of Malcolm X very nice. Very good in the last question arises what in your opinion sets apart successful professionals from those who are not. Well, I can talk I can talk from my experience and also from my experience advising students and what's made me? Well, I don't know if I'm a hundred percent successful. I would like to know I would like to know that I am but what's make me successful in this field I would say is opportunity. Experience science from different angles. So don't just focus on the specific narrow question. You have try to look at your question try to look at different angles of science to to get a better assessment of the the system that you're trying to understand. So for example in my career, I've been very fortunate of working with very say a wide range of seemingly very disparate. Eight people in different areas of Science of where we don't apologies. I work with psychology Psychiatry is people that work in the cancer field people that work in the ecology field Architects, you know, you name it very very different very different and diverse range of scientists have allow me to look at the problems that I deal with on an everyday basis. From very different perspectives. So I guess my I would say what separates a successful professional in my field to two other people is the willingness to listen to two different opinions and to diversify the science that you do in many different fields that different that those different assessments of Science and And to the problem you're addressing are going to help you deal and understand the questions that you have better. I would say that that that that for me it's what what's what's made me successful in the in the field that I'm dealing with and also this is what I try to tell my students all the time. You know, whenever you have a chance to look at different problems different questions in a general way. I would take advantage to that. Multidisciplinary approach. I love it. Very nice. Exactly. Exactly. Very cool. Does the word more multidisciplinary approach? Well, thanks a lot. Dr. Gomez. Your time is much appreciated and I'm sure you you shed a lot of light and the subject for me and for the audience as well. Oh Marshall, thanks so much, really enjoy the conversation and it was a very fun conversation. I hope my Sights on the microbiome world were of interest to the public and you know, I can be reached the University Minnesota animal science department in case you know, there is any other specific questions about microbes, which is what we love to do around here. Perfect. Thanks a lot under this. Have a good day. Thank you Marcy YouTube, bye-bye.
Today’s episode will cover the Microbiome: teasing out the buzz from reality. “The microbiome is the one part of the genome of the pigs that we can modify. In the future, microbiome analysis will be as common as PCR are today.” – Dr. Andres Gomez. Our guest is Dr. Andres Gomez, one of the bright minds of the Global Swine Industry. Dr. Gomez is Assistant Professor at University of Minnesota and his research interests focus on using molecular, bioinformatic and machine learning tools to study the composition and function of the microbiome associated to animals and humans, it's interaction with the host genomic landscape and it's influence on host nutrition, health, ecology and evolution. What you will learn:  - How he got involved in pig production and he walks us through his career until today; - What is the microbiome; - Why is there a hype about gut microbiomes in different areas of science; - The state of the gut microbiome research in pig production; - Association vs. Causation in gut microbiome research; - The biggest misconception about the swine gut microbiome; - The benefits can we get from gut microbiome research in the swine nutrition, health and production fields;  - What sets apart successful professionals from those who are not. - Andres’ favorite microbiome-related book: Gastrointestinal microbiology - Andres’ favorite book unrelated to microbiome: The autobiography of Malcolm X  Edited by Lauro Faccin 