 Good afternoon. It's a good crowd so delighted to have you all here. I am Prem Paul. They have the pleasure of being Vice Chancellor for Research and Economic Development. We appreciate you joining us today for our spring Nebraska lecture, the first of the 2016 Chancellor's Distinguished Lecture Series. Today's lecture is being web streamed live so I want to welcome everyone who is joining us via the web. For those of you who use social media, the Twitter hashtag for today's lecture is Pound Neb Lecture and I've already tweeted using Neb Lecture. The Nebraska Lectures are an interdisciplinary lecture series designed to foster communication among students and faculty in different academic areas and among citizens of Lincoln and Nebraska. These lectures are sponsored by the UNL Research Council in cooperation with the Chancellor's Office and Vice Chancellor for Research, our office, as well as the OSHA Lifelong Learning Institute known as OLI. It's special welcome to any OLI members who joined us today. The Research Council is a very important council. You want to remember that especially if you're a faculty member. They are made up of faculty from many disciplines at UNL. They solicit nominations of faculty to be Nebraska lecturers based on major recent achievements and the lecturer's ability to explain his or her own work. Selection as a Nebraska lecturer is the highest recognition of the council can bestow on an individual faculty member. They also control a lot of money. They give out the seed grants competitively so you want to be nice to them. So if you see them, thank them. A few words about today's format. Following our lecture, Dr. Robert Powers, the chair of the Research Council and Professor of Chemistry will moderate a question and answer session. Then please join us for a reception in the Nick Banquet Hall right behind the auditorium. Now it is my pleasure to introduce Harvey Perlman, UNL Chancellor and fearless leader for the past 15 years. Actually 16 if you count his service as interim. Chancellor Perlman is stepping down in a couple of months. So this is the last time I get to introduce him at the Nebraska lecture, which we worked together to establish in 2003. Chancellor Perlman is a tireless champion and an exceptional partner for UNL research. During his tenure as Chancellor, our university has experienced tremendous and transformative growth with increased academic stature and research quality. Harvey on behalf of UNL research and the entire university, I want to thank you for all that you have done to enhance our university. Serving with you has been my personal great pleasure. So please join me welcoming Harvey. You know if you are longtime attenders at this lecture you start to believe that it's just a fraud and excuse so Prem can say nice things about me and I can say nice things about him but but thank you Prem. It's my pleasure to introduce today's speaker, Dr. Andrew Benson, the WW Marshall distinguished professor of microbiology in our Department of Food Science and Technology. Dr. Benson's work is a stellar example of UNL research far reaching potential to vastly improve food and human health. Dr. Benson is an accomplished microbiologist focused on gut micro flora which significantly influence our health and well-being. In his lecture today he will tell us what scientists are learning about gut bacteria and their impact on bodily functions. Throughout his UNL career he has studied gut health and bacteria including pathogenic microbes that invade the gut. Thanks to his expertise Dr. Benson is a highly sought expert in litigation cases involving foodborne illnesses outbreaks across the country. He also will share some of his experiences as a food detective and explain how studying gut pathogens laid the groundwork for establishing the UNL gut function initiative. That initiative's goal is to develop food-based strategies for balancing the gut ecosystem which will provide new ways to look at disease prevention and intervention. I want to note that it's especially fitting that we host his lecture at Nebraska Innovation Campus which is now the home to both his academic department Food Science and Technology and his startup company Metagenome Analytics LLC. He is managing partner in MGA which is the first faculty-based startup to move into this facility. The MGA team includes UNL faculty, graduate students and former students, the bioinformatics company's products target the food and public health sectors. Dr. Benson has been a UNL faculty member since 1996. He has a bachelor's degree in microbiology from Iowa State University and a doctorate in microbiology from the University of Texas. He was a post doctoral fellow at Princeton before joining us here in Lincoln. Please join me in welcoming Dr. Andrew Benson who will present Guts, Germs and Stainless Steel creating winners and losers in food. Andy? Thank you Chancellor Perlman. Thank you Vice Chancellor Prim Paul for the chance to to be here and thanks everyone for showing up today. We're going to get into the title for just a minute but Guts is going to be a resounding theme and I thought I would just show you that our administration has guts. This is a male. I didn't have to dig out too many emails to find one of these and this was a male from Prim Paul asking me to come and show up and give an after dinner presentation to the Science for Global Policy Conference. We wanted you to speak on the gut microbiome. So 20 years you finally asked me this time to give a talk when it's not after dinner or around a meal time. So we've learned how to give these talks without grossing too many people out. I have to say I thank the good Lord every day for this group of folks that's around me. They're sitting in the middle row. A lot of them are here today but my wife Renee who's who's been by my side since high school. There's us way back in 1984. Not too long ago the two of us there. My son Nathan who's here. There's girlfriends here as well. My daughter and son-in-law Sam. Wonderful grandchildren that we have and mother and father. A great supportive family here in town and we couldn't do I couldn't do any of the stuff that I do without having them around. So thank you guys. And it lets me start off to where this story of gut germs and stainless steel really starts. And that's some 20 some years ago back in front of Kildee Hall and this is I think a newer picture prim of Kildee Hall but back it looked a little different when we were there but my wife Renee and I were there and I told her I think I really want to be a professor and she asked me or she said so what does that mean and she's learned what that's meant now the last 20 some odd years but it's been a fantastic journey that we've been on. So we're going to talk about guts germs and stainless steel. I'm going to reverse the order a little bit. We're going to talk about the germs first because that came first in the career but first let me tell you if you don't already know where that title comes from. I borrowed that from Jared Diamond's book. Jared Diamond's a professor of physiology at UCLA wrote a wonderful book Guns, Germs, and Stainless. See I'm already throwing stainless and guns germs and steel several years ago and it's a fantastic read if you're a big picture guy like I am because he took a very big picture of trying to explain trying to define the factors that explain success or failure of societies and when you look at those factors what it boils down to is that there were geographies where there were lots of species that were suitable for domestication and believe it or not there's not that many species out there that are suitable to domesticate along with species that could spread and that led to the early forms of agriculture. Domestication of plant and animal species that led to stores and surpluses of foods eventually led to large sedentary dense populations and with dense populations and people not having to hunt and find food all the time it allowed for specialization. Political organization and writing is one of those specializations and we can argue about whether or not that was a good specialization but it was useful at the time. That also led to many technological developments as well but having man in close proximity to dense populations of animals also led to the emergence of several different types of infectious diseases and epidemic diseases and so the wonderful book if you read through the book it's a fantastic read on that and so my talk today is a bit of a take on that but really as I said and thought about this the same things that made society successful a long time ago are probably the same things that are killing us today. Now think about that. We have sedentary populations with large surpluses of foods. We now have centralized production, globalized sourcing that definitely influences pathogen emergence and evolution and certainly contributes to food-borne illness. What's a bigger problem however is with types of things we've gone into our food production technologies. The way we're making our foods, the ingredients we're making them with, we're going to learn about a word today or a couple of words today called microbiome dysbiosis and the fact that that's contributing to a large increase in lifestyle diseases, complex diseases here in the United States. So it's kind of ironic that the same things that made us successful in a sense are also leading to our demise. Now I started my career here at the university at a very fortunate time and I thought it would be good to just throw a timeline up to throw in some of the major events for folks in the room that are familiar with biology to be aware of but right about when I got my bachelor's degree not long after that Francis Collins discovered the cystic fibrosis transmembrane receptor or CFTR gene that's the causative gene for cystic fibrosis and in 1995 right before I arrived here the first whole genome of a bacterium was sequenced and that was a pretty exciting time in the microbiology and in biological sciences and in general. Not long after I arrived in 2001 we had the draft of the human genome that was published and by 2005 next generation sequencing had been described and I'll say just a little bit about that later and by 2007 complex communities were already being sequenced so having started my career here at UNL in 1996 and been a postdoc prior to that graduate student prior to that this whole time this science of genomics DNA sequencing was evolving and so it was really fortunate to to be a part of that to be to be a part of educational process and academic process during that time when these things were coming online in 1997 there was a watershed event that happened after not a year after I'd arrived here at UNL and this sets the stage for the germs portion of the talk and in 1997 there was a recall event the Hudson recall event was the largest recall at the time 25 million pounds of ground beef that was contaminated with intro hemorrhagic E. Colam and introduce you to this organism here in just a minute but note what this recall caused because there was a remarkable amount of meat that was being processed at that plant here we said Burger King said 1600 restaurants were initially affected it was probably more than that a lot of the major stores Safeway Walmart Boston were simply out of ground beef for a period of time so it sort of put things in perspective especially for me as a young faculty member to appreciate the impact of that on our economy in the state and so that really turned my attention towards this organism and I had already been talking to Charlie Casper of the University of Wisconsin who was working on field epidemiology of this organism now let's talk just briefly about this bacterium this is an organism that has passed or as largely has its reservoir in bovine and it's passed from bovine into humans either through contaminated food most commonly it can get into land environments and contaminate food that way and directly it can directly contaminate individuals from direct contact as well and the organism is not like most E. Coli most E. Coli are harmless inhabitants of the GI tract this is a very pathogenic form it's a form that's acquired several sets of virulent genes that allows it to do some special things one is to attach to your colon another one is to produce toxins that cause massive inflammation in different parts of your body well Charlie Casper was studying this organism and he was looking at the genetic fingerprints and these are just to simply think of these as barcodes these are genetic fingerprints of the organism and what he noted was that even on a single farm one could identify several different subtypes of this organism and to me that led to a really remarkable question it made us think about and that is are all of these guys equally likely to cause disease so I've simplified those fingerprints and just by showing them to you as colors now and then the in the guts of these animals and are we seeing all of the same ones and animals show up in humans and we really didn't know the answer to that question and we didn't even have a method to answer that question at the point at that point in time the method I'm going to tell you and show you about in a minute simply couldn't let us predict the ancestry and you're going to understand what that means here in a second the methods that were based on short segments there wasn't enough resolution and whole genome sequencing was still way too expensive to do at the time there was no way we could do it certainly not do it here at this institution with with the capabilities that we had so that force is to be bold and innovative and develop the method that would let us answer the question now as I talk about this I want to walk you through this is going to help set the stage for things later on but I think it'll help you appreciate a little bit about genome biology so everybody to have a take home today maybe we'll have an exam on this afterwards but let's put it into perspective so first of all taxonomy we have talked about classifying organisms quickly and here's taxonomy and we can compare E. Coli to a book this makes life simple for us because you can everybody understands how to classify a book and I chose a book the wonderful Wizard of Oz and here's how one might classify that book and we can go down through different layers of the classification that relevant that reflect the taxonomic levels that we use to classify microorganisms the genome here is the word content of the book and there's the word content from a page wonderful Wizard of Oz and the genome here is a DNA sequence of E. Coli as you can see the two are not that different right there's just fewer characters there's only four different letters in the alphabet of a DNA sequence many more characters here in our alphabet that we use so these two are equivalent here think of them that way so we've got that part of the metaphor going and understand how genomes evolve let's look at how this book evolved into a lot of different forms of even different types of media from 1899 the original book all the way to 1930 probably didn't change too much there were a few different additions that were put out and we can think of these as in the normal forms of E. Coli there's a few little word changes here and there but not tremendous changes 1939 was the film version obviously the manuscript from that film version version was tremendously different than the original book and then from that launched a couple of different Broadway versions the Wiz theatrical version in 2011 and then Wicked of course in 2003 and these would represent the pathogenic E. Coli because he are quite divergent from the originally Coli strings now so now everybody would put that into perspective now if we were to take the way we were thinking of the genome and the way we're thinking of books and I said I want you to take these books without knowing when they were made and I want you to put them in the order in which they were produced put them in the chronological order in which these books were produced what you would not do is to look at the chapter links of the book right that's probably not how you would do it but that's essentially what the methodology at the time was doing the genome methodology that we had at the time that was used by CDC it's still used by CDC today it's very good at being able to differentiate the books but I would have a very hard time putting them in order just based on the length of their pages and so that was a problem to us and we started thinking about how are we going to get around this and Joe Neidfeld and I were at a conference in 1996 late 96 early 97 and we were starting to think about this and they were describing the genome of E. Coli hadn't quite been published yet and they were describing some characteristics of it and Fred Blatner from University of Wisconsin was talking about these frequently occurring words you can think of them as frequent words they're actually called skewed oligomers but let's think of them as words they're frequently occurring words they're tremendously over represented in that genome and so if I were to draw arrows around this circular genome where these words occurred you'd see they were all they'd be all over the place in this genome and what Joe and I thought of is that we could use these words to fragment this genome into very specific pieces and thousands of little pieces and it became a way for us to do comparative genomics and I have to stop here and mention that Joe Neidfeld has been with me for 20 years in my laboratory has been a laboratory manager and Joe is retiring at the end of this year in June so that's that's almost like losing a family member so he's been a tremendous resource to my laboratory and I want to make sure that that Joe can remember back to this day and we were at this conference and we came up where we hatched this plot I should say if we came up with this idea but Joe thank you for all of the the years of tremendous work that you've done in my group and for the whole department literally you've been a tremendous resource so now we have these over represented words and over represented words would be like and and the then this right those are words that are over represented in a book they're used frequently right and so I've done to show you what this little method that we developed us here's the segment of our book now and length between occurrences of and and there's the sentence right there and here in the genome now our words not hand we use different words in the genome and here's the segment that's occurring between TCTTGC and there's the length of the piece right there so this is how we were able to fragment the genome and I won't bore you with the details of exactly how the fragmentation was done but I'll let you know we fragmented the genomes on these and we separated these on these live core on these machines from like where they were automated DNA sequences at the time fantastic machines and it would develop these wonderful images like this and these are the fragmentation patterns each little line here is a different strain of E. Coli that we're looking at so you can see we could look at lots of strains at one point at one time and we could compare thousands of different segments of the genome one to another extremely high resolution and we had to do this by hand because at the time there was no image analysis software that could handle this data you know these machines were capable of producing fantastic data and so Jayhom Kim and I would sit in my office and we always did this at the end of the day we'd start about two o'clock in the afternoon because after doing this for three hours you couldn't take it anymore using me to be one person would read up the image calling ones and zeros for binaries and the other person would be typing it into a spreadsheet so we did that for hours and hours and days and days upon end but we could see already the pattern that was emerging so let's go back to the question now remember the question was are there the same populations in bovine are all of them still showing up in humans and the answer to that question we could already see as we were analyzing these images was well yes and no in fact what we found was that there were two very distinct subpopulations of the organism and one was clearly overrepresented in the bovine population was underrepresented among isolates from humans and you can look at the length of the bases this is the amount of the genome that we were comparing was a tremendous amount of the genome we were comparing at exquisitely high resolution at the time now we went on just quickly to show a couple of different things first of all that this divergence event was ancestral meaning that it happened a long time ago and we knew that because we could detect these descendants of this event on on different parts of the planet specifically we looked down on Australia looked in UK we looked in the United States we had representation across different locations lost across different geographies so it was an ancestral event that happened some time ago and secondarily the thing we found was that the diversity that it was causing was creating diversity in the in the expression of genes that this organism uses to attach to the colon which was a remarkable find to us so the diversity that was happening because of this because of the genetic differences between these strains was causing differences in their ability to form these specialized attachment structures and this is important because those structures are used not only to attach to your colon to help cause disease they're also used by that organism to attach to the colon of the animals that they reside in in their reservoir and so literally what the organism is doing is it's identified ways that it can evolve and it can manipulate gene expression patterns to optimize its ability to attach in the bovine environment and that somehow has an impact on the humans as well so to us this was remarkable to be able to find this over a period of several different years across these different studies that we had done we played this game in multiple organisms at the time several different pathogens I don't want to bore you with this but in about 2005 something happened that just leveled the playing field in DNA sequencing and it completely changed what we thought about what I thought about in terms of food science and that was a publication that came out describing the first of the next generation sequencers and this is that actual publication here and this next generation sequencing parallelized the DNA sequencing process that's all you really need to understand about it but it made it so that it was literally available to the common man which was us and once that happened it definitely leveled the playing field in terms of the types of science that we could do and the things that we could approach here's what it allowed us to do rather than looking at fragmentation patterns in my office going crazy in the afternoons three hours at a time just to compare maybe one genome we could sequence the genomes that would have essentially represent entire libraries we could sequence entire communities and define the content of that library I'm going to switch from books now to a little better visual and that is colored gumballs because that's a little easier to think of when we're thinking of communities so we could use DNA sequencing as an analytical tool now and we could define the populations of organisms in these complex communities and to us that was just a tremendous capability and let me tell you to describe what it was like the first time to look at that kind of data was mind-blowing it was real it was it was so exciting because you almost had to pinch yourself to tell yourself this was real people have dreamed of this kind of thing for 200 years and now you have the opportunity actually look at that kind of data and as we sat and thought about this in a food science department Bob Hutkins and I started thinking that wow this meant that we could systematically look at these entire microbial populations and ecosystems one of them being in the GI tract and it would let us explore this whole black box known as the gut microbiome and when we think about we think about nutrition we think about health we think about food a lot with a fair amount was known about the host factors that were involved and a fair amount was known about diet and some of the environmental factors but the composition of the microbiome was a black box people had no way to study this complex community for a long time so to us this was pretty exciting and this next slide represents a remarkable time for us at UNL in 2007 to 2009 and a community of the university community really rallied around this idea of studying the gut microbiome and we hired we were able to hire two researchers out of some of the top gut laboratories in the world because we were very early in this game of thinking about studying the gut microbiome Jens Walther and Dan Peterson and what was remarkable about those recruitment processes was that first of all we had a department head who had just walked in the door so he literally walked into the door and has to see oh my gosh I've got guys wanting to study guts here and he was our department head was a food engineer so we have to appreciate the fact that he he surrounded he put his arms around this and was able to support this we had folks from the you from the Center for Plant Science and Innovation which was actually called the plant science initiative at the time that were involved in helping us recruit I can still remember Sally Mackenzie who was a director at that time coming and coming to the seminars and meeting with these guys we had folks from the Center for Biotechnology that were involved in the recruiting process and we've had folks from here in the community and I had to show Dr. Doug Dahlke's picture up here Doug was a gastroenterologist here in town he was my gastroenterologist and I'm betting that there's more than one of us in this room that has seen Dr. Dahlke over there over their period of their life and Dr. Dahlke was killed tragically in a car accident two years ago and that was a great loss to this community but he was there he was at the seminars of these guys and it was it's remarkable that somebody with and who's an MD who's out in our community would take the time to come meet with these individuals and would take the time to be involved in this recruiting process so I want to make sure to give tribute to him because that that was very much appreciated well by 2008's we actually had an initiative and it started to get scary because we called this the gut function initiative and all of a sudden everybody was talking about it and that's kind of scary because it's got a life of its own all the sudden it's not just you trying to to sell it and we even had some some concepts that we were wrapping our heads around first of all we're science driven we're focused on the three main factors the host factors the microbial factors and the dietary factors that allow this ecosystem to function and we're also translation focused we want to turn this knowledge into something we're focused on developing novel probicrobials or antimicrobials novel prebiotics as well as potential animal breeding markers and we're even on the we're on the cover of the Lincoln Journal star and this is a photo of us here and I'll have to say this is one of multiple wardrobe malfunctions that all of us had because and looking at that photo it's just like wow that was on the cover of LJS but one of many wardrobe malfunctions to come but it was it was an interesting time when that group came together it wasn't just us we had some remarkable resources that we were endowed with here in the university by 2008 we had one of these next generation sequencers it was up in one of the food science department was still in Philly Hall it was number 100 in the world believe it or not that was the 100th machine in the world that we had here that's how far ahead of the game we were with this initiative we had a germ-free mouse facility that allows us to propagate mice germ-free and allows us to introduce organisms into them in ways that allow us to test hypotheses we had a wonderful bioinformatics and supercutimating community that we're able to interface with to get all of our bioinformatics work done that we needed to do we had a food processing center that allowed us to develop foods that could be used in some of the human studies that have been done by some of my colleagues and we also have the Center for Biotechnology which has some of the core facilities that are used as well by this group so we had this remarkable set of of infrastructure swirling around us so let's get started with some gut microbiome basics before we dive into the good stuff so first of all many of you might know this already because it's such a popular topic there's certainly lots of organisms that lots of organisms that are there indeed there's tens to hundreds of trillions of bacteria there they outnumber ourselves by 10 to 100 fold their genomic content is a hundred times or so what we have in our own genomes in fact we think of them as an entire metabolic organ they have complete metabolic pathways that we don't have and they help our bodies do things that our bodies cannot do so things that are not encoded within our genome there's about 500 to around 2,000 different species and any one individual if I went and looked and we could and they're present at different proportions just like the gumballs that I showed you I wanted to get that visual in your mind and the species composition of every individual in this room is unique it's as unique as your fingerprint is alright so you have this own little ecosystem that's present in your GI tract and it's doing a lot of different things some of which we're just learning but one thing we do know for sure is that balance in this ecosystem is really important and balance as a mean everybody's present at the same proportions it just means that the ecosystem is functioning as a balanced ecosystem and when it's doing that it's important or it's contributing to development of the the immune system it's contributing to development of actual gut tissue the gut tissue won't develop properly without a microbiome it's contributing to nutrient acquisition to function of your gut motility electrolyte balance resistance to infectious diseases detoxification of things that we we might ingest as well as contributing to host metabolism all these things the microbiome is doing and in fact animals that lack the microbiome these germ free animals they're weird they are not normal animals you'll find that there are defects in all these different circles in an animal that lacks a microbiome so it's playing a very very important role in our bodies and when it gets out of balance it can get out of balance in a couple of different types of forms in one form it causes sort of local defects and those local defects translate into inflammatory bowel diseases chronic C. diff infection gastrointestinal cancers necrotizing under colitis these are examples of things that happen in the locally and in the GI tract when the gut microbiome is out of balance and it can also have effects at distal sites and these tend to be metabolic defects so it's involved in coronary artery disease or coronary heart disease obesity metabolic diseases and both type 1 and type 2 diabetes so defects in the microbiome are associated with all of these different types of diseases now the causality is still not quite well understood because that's really difficult to determine whether the messed up microbiome is what's causing the disease or whether it's an effect of the disease but in certain cases we know that it's certainly a cause so that made us start to ask the question well what factors actually govern assembly of this thing how does this microbiome actually come together in an individual and what happens that causes this dysbiosis or what happens when things go awry and you can put those factors again into those three different balls the host factors microbial factors and the diet environment and ecological factors and if you talk to and look at individuals that are with part of the gut microbiome group or the gut function group you'll find that they are in one of these balls working and sometimes crossing over multiple balls I'm going to tell you a little quick story or couple of quick stories about some of the balls we did I want to tell you about one of things that led us to think about that a few years ago this got us started down looking at the host genetic contribution to that we were working with Merlin Nielsen over in animal science Merlin had a population of mice that he had selectively bred from multiple generations to study caloric utilization and feed intake and Jens Walter and I were starting to look at the microbiome of those animals and this was before we had the sequencing in place and so each little line here represents a different organism each strip is a different mouse and we were comparing the outbred populations that he had used here in his selection processes to some of the inbred populations that he had here and this was a day because I can still remember looking at this image as we walked back from the animal science department and this tells you something about how different people view the outcome of an experiment because Jens was focused on the experiment at hand and and his expression was for dot which I think that's how you pronounce it which is a German expression you can look that one up and see what it means but darn it would be a good translation there's too much variability in these animals here we won't be it won't be easy to do the experiment in these animals and I looked at it and I thought wow if you compare the inbreds to the outbreds that tells me that genetics must be a real big factor here and that's something we ought to go after so diversity I say this often diversity is a currency of creativity and it truly is so diversity in thought and diversity the way we may look at outcomes is important so how do you study that how do you get at that how are you going to study whether host genetics is a contributing factor how do you get at these complex genetic effects well first of all let's understand what a complex trait actually is complex traits arise from variation in genetic factors and environmental factors and variation in the genetic and environmental factors come together in populations of individuals to bring about a distribution of traits and I've got a couple of extremes of distribution in terms of height and height is a very good example of a complex trait and it's funny when I show these to students in classes they have no earthly idea who these people are when you point that out that's Willie Shoemaker will chamberlain and Willie Shoemaker there but they would be on the extremes of this distribution curve across our population and height is definitely a complex trait there are hundreds of genes that contribute to height as well as many different environmental factors as well so it's the convergence of those two that bring about that trait in an individual and bring about the population of traits across individuals and so I called up our friend Daniel Pomp who at the time was working on obesity and exercise characteristics in mice and I told him we were interested in studying getting at whether or not genetics has a contribution makes a measurable contribution to the microbiome and Daniel was very excited because he'd been thinking about this too and Daniel actually used to be here in in the animal science department many years ago and he's out in North Carolina right now but Daniel also had the perfect experiment underway in which we could test this hypothesis and so it was a remarkable time almost a marriage made in heaven when when I called him and the study is this he has two different mouse lines that he had crossed and we're just going to represent them by two chromosomes from each to keep things simple the yellow which is the C57 black six line and the blue which was HR and that stands for high running this was a line that was been selected for its running characteristics and Lisa literally marathon runners of mice and now you can think about the progeny of these animals that are coming out and instead of looking at height or weight of these animals we're looking at different organisms in their guts and we're measuring their abundances and you can see that we have a distribution this is the number of animals and this is the relative abundance down here we have a distribution just like we would get if we were looking at height or any other complex trait and so these microorganisms and their abundances became the traits and we studied them as traits and the only thing I'll tell you more about the analysis is just to know that it's a statistical association between the abundance of these traits and the movement of different segments of the chromosomes from these parents and the progeny of the animals and sure enough we found that indeed there were several different positions in the mouse chromosome where we could identify variation in those animals that was contributing to that variation in the gut microbiome and each different line here these are the mouse chromosome shown around the outside each different line here represents a different place in the chromosome that affected that and the different organisms that they're infecting are rep is represented by this filogram and they're colored here color-coded according to the organism that's being controlled and this publication where this bit of data was published in the proceeds National Academy of Science and this figure has actually become iconic because it was a way of representing at the time and a host organism controlling a set of microorganisms within it so it was kind of a neat representation that's about as artistic as you'll see the gut group get remember we're challenged in terms of even dressing ourselves so but this was a widely recognized discovery this was pointed out in nature reviews microbiology and there were several discoveries coming out of the group this wasn't the only one there was three big discoveries that came out of the group at this time within that to within about a two or three year span this was just one of them Jens Walter had another one in Dan Peterson did as well so there were remarkable things coming out of this group we did a subsequent study where we introduced a dietary challenge into the end of the animals and so we split the animals the progeny half of them put on high-fat diets half of them put on 20 and the only I'll say quickly about this is that we found three different positions where the genetics was showing an interaction effect with diet and what that means what's the take-home is from that is a diet can potentially use to overcome genetic defects that caused this biosis and that's good news because that means if we can understand how that process works we can potentially develop diets and dietary molecules that could be used to perturb the microbiome or reconfigure it back into a form that would be beneficial for the host not detrimental I want to show you one quick study we're going to zoom through some cool slides and I had to show these next few just for the wow factor because this is where we are right now in these studies so this is a very complex population of mice that we're working on the ones I was talking about previously don't really reflect the genetics of a human population and we wanted something that reflects the genetics of human population and so they've gone to another model here this is called the diversity outbred and it begins with eight different progenitor lines so this is a multi-parent cross that's done and these eight lines have as much genetic diversity between them as you can get so almost think of as eight different races or eight different nationalities of humans if you will they've been bred together and randomized totally and this is what their chromosomes look like if we color code each of these animals with a color this is what their chromosomes it's a patchwork just like our chromosomes would look like if we looked at the ancestry of our chromosomes and in fact these are two different litters that are coming up this is one litter right here this is another litter I mean if you can imagine look at the diversity that showing up in there in terms of color the sizes of those animals tremendous diversity represented in this population of animals so it starts to reflect what a human population actually looks like and so the study in this population that we've been looking at here the last couple of years 300 animals on a purified diet after six weeks they've been split into two populations half of half of those animals were on a high fat plus colic acid diet that's an atherogenic or a diet that will generate atherosclerosis in those animals and the other half was put onto a high protein diet and these animals were sampled at three different time points for lots of different things including the microbiome now we're going to represent the microbiome a different way and again this is for the wow factor you don't have to understand this but follow the balls that's all you have to do if you follow the ball should be okay what these are these are network diagrams that represent the co-occurrences of these organisms so all the organisms that you see each of these is a different species and these guys co-occur together across that population of animals it means if you see one you see all the rest of them okay and if one of them increases in an abundance the other ones do too okay so they they a co-occur together and we could split them into four different groups of core we call core groups core group one core group two three and four and don't worry about the guys sort of the other colors at this point this is what the situation looks like initially before we switch the diet on them and as we switch the diet that situation changes so here's our our reference set right there the green ones and after you switch the diet on the high fat it shifts like this you'll see this ring when gets disrupted and at 24 weeks it shifts back again and if we do it on high protein it looks a little bit different I'm just gonna sit here and flip back and forth between this because that lets you really start to see what's going on right you can see what's happening here when you start to flip that the diet or the microbiome is shifting dramatically in response to the diet and you can see this core group here splits into two and sort of resolves again here at 24 weeks and then a high protein situation it's quite a bit different so we can track these organisms just by putting them into these core groups based on their behavior and that's important because we could categorize them being able to categorize them was was critical to be able to understand or do the analysis and here's another slide again I show just for the wow factor but it's the genetic map now of all the places on the chromosomes of these animals that we saw affecting these particular core groups and all you really need to follow is the red and the green so this is our diet before the shift or this is the animals before the shift and this is after the shift and these are our five different core groups in the different rings the different chromosomes are shown around here in the circle don't worry about the color the chromosomes all you need to know is red is when there's a genetic effect in its significant and green is meanings it's going away so there's the heat map right there from high to low and what you'll notice if you look around here is that in most cases diet completely abolishes the genetic effect after we shift the diet we can no longer see that genetic effect and again remember I said there's a diet gene by diet interaction that's actually a good thing because it tells us that we may be able to overcome genetic effects with diet but there's one case over here right here in particular where diet actually unmask the genetic effect so it can do two different things in some instances it'll abolish the genetic effect in other cases it'll actually reveal the genetic impact so two different things that the diet can do now in addition to just the microbiome that same position that we were looking at that I was pointing to on chromosome 13 it affects the green balls the green cord group it also controls fat content and body mass those same traits map to that same position and it tells you that the same genes are said the genes that are underlying this are contributing to both the microbiome composition as well as fat mass and body content that's interesting and we can sort of draw this down here and and in the chromosome representation now and think of this as three very different types of traits a microbiome trait a host metabolic trait and disease predisposition traits and if I do that what you'll see is that this starts to look very much like what's known as pleotropy it starts to look very much like the anatomy of complex diseases that we see in humans this is a figure from inflammatory bowel disease and the multiple loci that are involved in predisposition to inflammatory bowel disease many of those loci are contributing to host metabolic and immune dysfunction in these individuals they also predispose them to dysbiosis and the microbiome as well and all together these cause are predisposed these individuals to disease so this really starts to look a lot like what a complex disease really translates into into humans now remember with dietary modulation we have hope because that will allow us to or could potentially allow us to overcome disease predisposition and now we can think about doing it in multiple ways and this is an entirely different way of thinking about treating disease we're not talking about treating a disease with a medicine we're talking about treating a disease with a dietary modulation that can impact the microbiome and can also impact potentially or overcome the effects of genetic predisposition but we still have a lot to learn in order to be able to do that so what we know for sure dietary modulation can have significant health outcomes this was an experiment done with Jens Walter and by Devin Rose one of the newer members of the gut group and this was just simply a whole grain diet looking at different types of whole grain diets and now doing detailed studies on the microbiome of these individuals as well as measuring health characteristics and them and showing that there are very specific changes going on in the microbiome and that there are also very specific changes going on in in terms of the host health and the inflammatory tone and you can start to connect changes in the microbiome with those changes in the inflammatory tone so it gives you the idea that we could very systematically begin to modulate the microbiome through dietary changes other studies from Bob Hutkin's group from Jens Walter's group both showing that you could use things called prebiotics these are non digestible fibers that could be introduced into the diets of humans and that those would cause very specific changes in the microbiome very specific organisms could be changed in their abundances and could be modulated up and down with these particular dietary changes and one of the things that was seen in both of those studies is this phenomenon of responders and non responders there's always populations of the people that will respond to that diet but there's always a percentage of the individuals that don't respond to that challenge as well and we don't quite know what that means so part of the road ahead of us lies in understanding what's the difference between a responder and a non-responder and one last little thing I'll show here quickly from again one of the one of the newer gut group members of Dr. Amanda Raymurtate and this is the fact that some of these compounds that we thought required or had to be digested by the microbiome to have an effect on health that in fact there are microbiome dependent and independent pathways through which these things can impact our health and all you need to do is follow the colors here again that a resistant starch can have an impact on appetite and glucose homeostasis both through the microbiome but it can also do it independently of the microbiome and part of that depends on genetics depends on which animal line you do the experiment in so these are three different big picture things that have come out of that group in the last few years to tell us about how this dietary modulation works and what we've got to learn to do this now that gets us back to stainless steel and one of my collaborators is asking me what the stainless steel represent in the title it means the food stainless steel is used in food production so that represents the food in the title and one of the things that's happened over the last several thousand years and this was put out last year by Justin Sonnenberg's group is that as our diet has changed it's reduced it's been reduced in terms of its diversity dramatically over a period of time and especially if you look at four hundred years ago with the introduction of industrialized food and now processed food and highly sanitized foods the diversity the terms of molecular diversity that's present in our food system in our food supply is actually quite low and that coupled with increased sanitation use of antibiotics C sections and formula has also dramatically reduced the diversity of microorganisms in our GI tract and when you put the combination of those two things together it's not surprising that a lot of these lifestyle diseases that we're genetically susceptible to that we have susceptible susceptibility to in our population it's not surprising they're growing in epidemic proportions in our culture and it's not as big surprise why that's such a burden on our health care is a study put out from the Institute of Medicine and the National Academy of Sciences this is the food system if you look at our food production system I challenge you to find the words health and nutrition in here I made it big so you could see it right I challenge you to find those words in there they're in there a little bit in policy nutrition here in health that's to keep the stuff from killing us that's not so much to promote health so our food system is driven by a whole lot of factors very few of which actually have anything to do with health or health care and that's despite the fact that health care now and health is a major outcome of our food system so this is the calories in the food supply the total food expenditures it's kind of nice to see those tracking together food away from home that would be some of that would be food while you're on the vehicle as well and obesity and I could plot multiple diseases on the same thing that are showing that same exact trend this is the system that we've created the system that we're in right now and we wonder why some of these diseases are increasing the way they are well this last year as was mentioned to you the Department of Food Science and Technology was moved out here to innovation camp never ask innovation campus and there's more than just the gut group within this department there are some remarkable groups in this department of food knowledge and research and resource program a wonderful applied research and engineering group with food processing center as well as natural product and food analysis and this this is even all the representation out here and with us being out here it really makes us start to think about how can we address this problem systematically how can we start approaching this systematically we have this well established gut group with these new facilities that are unique out here at innovation campus and one of the cool things that we have is a human clinical translational facility where we can do feeding studies here we can bring individuals and we can do feeding studies and we can also do some types of of small amounts of medical work on the individuals as well so that we can get biomedical information on individuals we can develop foods we can do feeding studies we have the analytical capabilities surrounding that and that's sitting right out here just off to our to our cell we have a very well established plant sciences and data sciences group and we have another remarkable facility sitting over here in the phenotype the plant phenotyping facility if you haven't seen that it's a fantastic facility to see it's also really cool at night when it's lit up with the with the blue lights as well if you've been by at night we have the agricultural engine of a land grant institution meaning that if we take a discovery we can turn it into something that like a plant or products derived from plants or animals and we can do that in a hurry we have a medical center that has very very unique expertise and very unique populations in which to study I'm going to come back to that one in a minute as well and we even have unique nonhuman primate facilities that exist over in Omaha and we also had this opportunity for capacity building and so this was campus level endeavors that were going on they're really stimulated us to start thinking about how can we put all this together systematically well where are the rate limiting gaps what are where we need to speed things up well first of all this number of food molecules with known effects is really small less than 10 so it's a small number of compounds that we know we can feed an individual and have predictable outcomes so we need to increase the number of these things dramatically secondly there they're not acting in by themselves they're acting in combinations and so they're having multifactorial interactions we understand how that works and then lastly we have individualized responses each individual responds a little bit differently we need to understand these three things and we need to approach this systematically how do we do that we do that by turning the university into it into a discovery and translation pipeline this is all sitting here it's all sitting around us we can do plant genotype we have this tremendous resource in plant genetic and a phenotypic diversity with all the breeding programs all the plant sciences will have to show you that in just a minute we can take that and use it to identify variants in these plants that actually cause perturbations in the microbiome we can be real systematic about identifying plants that have compounds in them that do that the next step then is to identify the actual molecules that are causing the perturbations and next thing you know we're holding a whole bunch of candidate molecules in our hands we can do all of this just with genetics up here on top the translation pipeline once we have those candidate molecules now we can test them in mouse models we can scale up then and move them into non-human primate models to use as a transition because there's a little bit of evolutionary distance between between primates and mice and then finally we can introduce them into healthy human populations as well as well and start to learn what these predictable outcomes will look like so this is just a group that that's starting to form right now this is a plant molecular diversity group that are looking at the genetic resource populations and targeted populations that we have in plants and we're using and developing and I'm sorry developing and using an in vitro screen of the microbiome so we can identify the differences here that are perturbing or cause different perturbations in these microbiome and we can use genetics then to map back and identify the actual genes and pathways that are causing this perturbation this can be done extremely systematically all be done through high throughput high throughput automated systems we can also now combine our scale up and study once we've identified these compounds we can scale up studies and notabiotic mice that are carrying human gut microbiome so they're mice that resemble a human GI tract we can study their their ability to modify the the microbiome and non-human primates and then lastly we can study them and healthy human populations and so we can start to scale this across both mice all the way up into humans to really understand this responder non-responder business and how can we take an individual and predict which category they'll be in we can learn to do that at all different scales and this involves several different individuals here on campus as well as our friends at the University of Nebraska Omaha in particular Jeff French and Sid Byredi who have access to these animal populations and have very specialized resources and resource populations present over in Omaha that can be used for this and lastly we have groups at the Medical Center and the the group that we've we've been working with the most here is Dr. Eric Rush and Tanner Hegelstrom that are involved in the Monroe Meyer Institute and that's a genetic medicine group and the genetic medicine group interacts with lots of different groups over in Omaha so it was a nice portal into the into the clinics over there but one of the studies or one of the diseases that we're starting to look at in addition to looking at the inflammatory bowel disease and metabolic diseases is a particular type of disease called cardiomyopathy and this is a familial form so it's an inherited form of cardiomyopathy and cardiomyopathy occurs when you get a swelling of the left ventricle in the heart and this ultimately leads to heart defect and heart dysfunction and these individuals have very poor outcomes by the age of 30 to 50 years of age so about 30% of these cases are familial and there's a whole bunch of genes that have been identified that will cause this type of dysfunction just simply if you have a mutation in one of these genes but several of those genes I'm sorry I should mention that just because you have the mutation doesn't mean you'll come down with a disease what's called incomplete penetrance and so there's a sort of missing factor to the equation here and the question is whether microbiome could be part of that and when you look at several of these diseases or several of these genes that are involved in that disease the ones in green here are actually highly expressed in the colon and suggested to it that in addition to heart defects we could also have these individuals with disruptions in their colon function disruptions and gut permeability and secondary dysbiosis contributing to the disease now the reason we also chose this disease is it's a little bit risky but the reason we also chose it was because if in fact this is the case imagine being able to treat one of these individuals now we're not gonna cure the disease but imagine if you will being able to treat one of these individuals and perhaps extend their life by simply changing their diet that's a completely different way of thinking about treating these diseases and that's what gets us excited about this and I know it's been a big deck of slides and we're just about done because this is the one I think that really gets us going but I want to say you know after you've seen all this that Nebraska should be the one to lead this cultural change it's gonna take a cultural change to think about producing these kinds of foods because we've usually been focused on production and yield traits that's the typical focus of our food production but how about health promoting traits and not just simple traits but but traits that are involved in making foods that are clinically proven to have beneficial beneficial effects on health and this can be targeted for multiple types of targets not just the western disease challenges that we face here but third world challenges food animal production even challenges the same system can be targeted all of these and that targeting starts all the way back in here in the screen so it's going to cause it's going to cost a bit for us to think about them to do this it's going to cause and require a bit of cultural change in terms of thinking about why we make the foods that we should and I say we should lead the world and how to make the food that we should not just by making the food that we can let's make the food we should make here in Nebraska not just the food we can make let's make it for the right reason and put it in all the right places I think that's our challenge and it's it's it's not by accident that we're standing and we're all sitting here in Nebraska Innovation Campus while we think about that challenge that this is the place to do it I don't know about you but I'm just going to say are you in who's in real quick just there's a whole bunch of people I need to thank that are listed on this slide and I just want to point out a just a couple of people very very quickly and I'll let it sit up here for people to look at but I definitely want to thank Bob Hutkins who has been a mentor to me and a colleague for for many many years here at this institution that's been fantastic to work with him Daniel Pomp who is now at North Carolina who's also been a fantastic mentor to me both on the academic side and to some degree on on the business side as well Charlie Casper who was was one of the individuals that actually suggested I come to Nebraska several years ago and was a mentoring he goes all the way back to my days at Iowa State as well as Tom Stillhub he had Princeton and Bill Haldenwang who was my graduate mentor so just want to pass that out real quick thanks so thank you Annie for your timely informative presentation as chair of the research council it's my pleasure to moderate our question and answer session just as a reminder please use the microphone we're asking questions so that those viewing via the web stream can hear your questions and I'll start off with a question if you don't mind yeah so a curiosity for an individual under constant conditions how stable is actually the gut microbiome could fluctuation the microbiome be correlated with diseases that also have kind of a fluctuation so our microbiome as as we're developing early in life is relatively unstable but by the time you reach adulthood it's almost stable as a brick so there's some daily changes and fluctuations that happen that with our diet with small changes you might have in your diet you have a whopping dose of antibiotics or something that'll make it but a short-term change but those are typically short-term changes and it comes back to it's a very resilient ecosystem thanks in your research did you serve sterile grain to those mice and what did you sample PCs or just the output from the to determine the microbiome so typically we're sampling what's easy which is fecal material especially if we're doing hundreds to thousands of animals in an experiment if it's a small number we're doing a very detailed experiment and it's a terminal experiment then the animals are sacrificed and then some of the tissues can be gathered and we can look at more internal parts and depending upon the nature of the experiment the feed may or may not be sterilized so there may be things coming in on the feed as well in the experiments but with germ free animals or animals that have been conventionalized those use feed that is sterilized I said germ free animals are the mice are weird what do you tell us meaning that their immune systems don't develop properly their gut tissues don't look the way normal in terms of in terms of their their structure their microstructures that they're formed metabolically they're a little bit different they eat more they have to eat more so there's some very different characteristics those animals have we have a question from one of our viewers on the live web stream I'm wondering about the impact of this work on our students has there been an increase in undergraduate interest in these new fields in food science and technology is the gut microbiome becoming a new recruiting tool Dr. Benson's enthusiasm must have a positive influence on students if only enthusiasm was what it took to get students through school we're certainly doing everything we can to start introducing these concepts into our courses and I'll say one of the challenges that it causes is within a discipline we face this in every discipline there's a certain amount of disciplinary material that has to be broadcast to the students and has to be taught to the students and a lot of these studies you're seeing are very interdisciplinary and so it gets to be difficult to make sure the students get enough of the discipline as well as some of the newer stuff so of course we injected every opportunity we get in our enthusiasm is usually there does the current business plan for the land grant university systems and its close ties to industrial agriculture permit it to meet your challenge that's a good question Harvey I think that's part of our part of our challenge as an academic institution even though there is the land grant mission part of our challenge as an academic institution is to create that culture where economics is not the sole driving force and I think we have to really start considering the fact that long-term economics will be a driving force you can see how it was driving in terms of the outcomes of our current food system health care is a huge burden on our culture right now and I would suggest that we should be the ones that change it this isn't going to be done in a medical school you won't find a medical school that'll have the capabilities to reach all the way back to the agricultural engines like we can here to land grant institution so I think that we're not only poised to do it but we must be the ones to do it and the gut microbiome is typically characterized in the domain of bacteria could you comment a little bit on the other domains of life yeah so the the archaea are present there they're small in terms of number but large in terms of impact and so those guys are involved in hydrogen cycling and depending upon which type of host you may be involved in definitely involved in participating in methane production as well but certainly involved in the hydrogen cycling other forms of life that we find there the phage we know that are these are viruses that attack bacteria phage are also there and very abundant and probably contributing as well although we don't really understand how they're contributing to the structure of the system we understand how phage do it much better out in the ocean than we do in in our guts as far as higher organism fungi they seem to be Heather Helen Adams who's sitting right next you could tell you a lot more about that than I could but the fungal content seems to be a minor component with the exception of perhaps Canada and we don't really understand yet what they're doing if they're doing much at all that's the representation at least in humans in one of your tests you showed that you gave the test animals a high fat diet yes but the different fats have such dramatically different effects can you be more specific as to what kind of fat you gave them and it depends on which diet you're after which experiment you're asking about there's multiple experiments we've talked about in there and yes we certainly take that into effect so different ratios are very those are very carefully calibrated diets that the animals are given well if there's no further questions please join me in thanking Dr. Benson again Andy what a fantastic presentation we're very appreciative of you taking time and and you know preparing your presentation but explaining in a way that we can all understand very very very exciting so as a token of our appreciation we have a tradition of giving you something that you can look at every day and smile so this is a framed copy of the poster that you've seen around the campus and so this is for your own office and thank you very very much thank you