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Microbiome 101 by Dr. Chris Mason

Chris Mason, PhD

Microbiome 101 by Chris Mason, PhD

Listen and read along as Chris Mason, PhD talks about the history of microbiome sequencing and research, how he started a career in the field, and where the science and technology is taking us in the future! 

Dr. Chris Mason:              00:00                    Afternoon, evening, wherever you may be. My name is Christopher Mason. I'm the Co-founder of Onegevity and also a faculty of Weill Cornell medicine where it built a laboratory that looks at genetic and also molecular phenotypes in people to see if we can better understand both disease and health. And today I'm here to tell you a bit about what we've been doing at Onegevity and looking at how we can understand the microbiome and the metagenome, which I'll tell you about as a better sort of window into health and disease and long-term wellness. I'll start with a bit of background first.

Dr. Chris Mason:              00:31                    So we've been doing lots of sequencing in my lab and around the world at this point for decades. And this has led to a really exciting, actually basically revolutionary time in genetics where we're generating more data than ever before, mainly because this chart has occurred in the past 15 years-- that the actual cost to sequence, say one whole human genome, you can see here has dropped down from the hundreds of millions of dollars down to about a thousand dollars today. And in some cases, even less. So, what this actually is really enabled is something faster as a technology change than Moore's law, which you can see here in white. It means that this is the fastest pace of technological change that's actually ever happened in human history, is that we can now sequence human genomes and do any sequencing of any piece of DNA or RNA much faster and much cheaper than ever before.

Dr. Chris Mason:              01:19                    And this has led to some really big headlines like Nature declaring in 2014 that we had now the thousand dollar genome was here and then just about two years ago saying we now have a hundred dollar genome that was coming soon because it's getting cheaper and cheaper. So, there was a lot of excitement and justifiably so, but embedding genomics into medical care from, for human genetics and it's getting better and better as time goes on. We're finding more applications of specific mutations that can lead to a better understanding of someone's risk for cardiovascular disease or for cancer or for psychiatric disease. And has really been quite a boom in genetics. And I'm a geneticist by training, so it's almost a time of euphoria actually I'd call it. But there's actually more than one genome. It's not just the human genome. And so, if you actually think of your body as a cellular democracy, your human cells are probably a minority party as far as we know. And that if you think of the estimate of the number of human cells, its range is anywhere from 51% to as much as 90% of your cells are bacterial cells in the literature. And what this means is that of course you treat one cell in your body-- that's not enough. You have to think about treating all the trillions of cells in your body, especially those majority party microbial cells: yeast, bacteria, and then also the viruses and other sorts of organisms that are in you, on you, and all around you.

Dr. Chris Mason:              02:40                    And if you were to think of this, basically as sort of visualization of this, it’s kind of what the world would look like if you were imagining it from a microbial perspective. So, in each droplet of air, and each droplet of water droplets that are floating through the air you see microbes and every time you leave your hand down on a surface, you leave microbes. You can see them on cups, on keyboards, on tables. Every time you move your hand, you leave a microbial trace. If you think about what's on your skin-- your skin has this essentially complete ecosystem of its own-- skin microbiome.

Dr. Chris Mason:              03:12                    When you breathe out, you can see the sort of small microbial features and aerosolized droplets carrying their microbes. You can see here that GI tract in this person, on your chair, again, the keyboard or the desk, each area has this little miniature ecosystem. And actually, even, for example, a cup. At the bottom of your cup, you have a well of microbes and you put a pen in and then poof! They'll pop out. It's really everywhere that we live and work and the places in which we really spend our lives has its own sort of ecosystem that we've now for the first time began to measure and visualize. And this is a great example or video from Jessica Green that shows that.

Dr. Chris Mason:              03:50                    So what's extraordinary about this is if you think again back to the human cells, we have many human cells, of course, they're important, but we're covered by these microbes. And if you were to step onto a scale, this would be about anywhere from two to four, even five pounds of bacteria in your body depending on how many humans’ cells you have and maybe how much you've had for breakfast that morning. Or you can see here that really this is an essential component of your biology, that this is really part of your ecosystem and what determines health and disease in ways I'll tell you about that today.

Dr. Chris Mason:              04:19                    So, what's been done in the past few years was to build a map of the human microbiome and basically what is the normal flora that is present in individuals. In this case, you can see this is work from the human microbiome project, and look at stool, cheek, tongue, nose, vagina, skin, different areas of the body-- all carry their own miniature sort of natural flora in their ecosystem that you can see represented here by these different colors.

Dr. Chris Mason:              04:45                    And so what's extraordinary about this is not just that they're there but they're actually contributing a fair amount to our biology. It's estimated that maybe a third or so of the small molecules in your blood either are made by the microbiome or are processed by the microbiome. And what's even more exciting is actually that there's a lot of evidence that even if you take drugs that are not antibiotics, like say something for depression or something for diabetes, these drugs actually impact the gut microbiome as well. So, when you treat the human cells, you're treating all the bacterial cells as well.

Dr. Chris Mason:              05:19                    The other kind of interesting thing about the microbiome that's come up in the past few years is that we found out that many organisms actually work on your behalf. So, this is a case of some work by Michael Fischbach and Mohammed Donia that showed that they can look at this normal bacterial data and actually find, like in the vaginal microbiome, new antibiotics that are present, that can be used therapeutically. So really, you could almost have self-medicating bacteria' you don't have to ask them to work on your behalf, they'll just do it cause they're hanging out in you or on your, around you. And so this gives you almost sort of the microbiome protection in some cases and almost like superpowers from the microbiome and other kids were, the microbiome has gotten really exciting as thinking about fecal microbiome transplants, which if you've not heard of these, they are exactly what they sound like. They're extraordinarily powerful in treating Clostridium difficile infections, which are really reticent infections, hard to get rid of.

Dr. Chris Mason:              06:13                    It's also led to some really interesting headlines where when you transplant a microbiome from one person to another of the gut microbiome, you think about coming to grips with the stool microbiome. As this is kind of an unfortunately titled headline for example, but it's also led to patients coming together and saying, well, I've heard that that person has really good microbiome inside of them, and I'd like to have that transplanted. This led to some people that make the power of, which is an extraordinary website of people getting together to think about really safe, accessible, microbiome transplants for all who need it. They're sharing stories and sometimes they're sharing samples and it's getting interesting, but they're not crazy. The success rate for C. diff infections is anywhere from 85 to 95% in some of the higher rates for treatment. It can even help treat ulcerative colitis, so it's really been an extraordinary effort to deploy a pretty unique but powerful therapeutic mechanism for really persistent gut disorders.

Dr. Chris Mason:              07:09                    This led to a lot of really great work from OpenBiome, which is actually a nonprofit that says, "well, we can't just have people sending each other random stool samples in the mail. We should actually test it, make sure there are no pathogens. Regulate it, make sure it's being done correctly." And when they launched, they needed both samples and they needed some funding and they said, well, listen, if we could just get enough samples, we can treat a lot of people. You could argue that sometimes the thing you leave behind-- this might be the most important thing you do all day and that you just flush it away.

Dr. Chris Mason:              07:36                    So they launched a campaign also to get samples and to get funding. They called the Care Campaign, which is one of my favorite names and "sharing is caring", being the principle. And they even noted that if you are actually regular enough, you could make about $13,000 a year from what you would normally just flush away. And so it was actually a really kind of extraordinary ability to think about what is the value of something if you can use it therapeutically, but it is a donation-- kind of tissue but also of a drug, right? It thinks about what I just told you. It is a tissue in an ecosystem that makes and processes drugs, yet it's also a collection of cells like tissue and the way it's been regulated, so far is that it's been mostly as a tissue not as a drug, which makes it easier to transplant. Which has just been very good for, in general, the use of it for therapeutic purposes.

Dr. Chris Mason:              08:23                    So if you look now where we've been in the past three, four years, it actually means that at this point, the microbiome has been linked to almost everything-- it has been linked to obesity and how you process food, spilling into inflammatory bowel disease, and now almost more than a dozen different diseases have been linked to the microbiome. And some of them are very, very obvious. You can think of, for example, acne or you can think of gastric ulcers like Helicobacter pylori or potentially anything in the gut. But what's been more surprising is actually things like autism, depression, neuropsychiatric disorders. And this is through what's called through the vagus nerve, the brain-gut access, where there's so much communication between the gut and the brain and a lot of the neuropeptides that are made in your gut also transit through your body.

Dr. Chris Mason:              09:06                    And so there really is this continual exchange between the gut microbiome and neuropsychiatric conditions. And in general, your physiology. It's such a key component of your health that some people call it the second brain of your body. And so, it's been linked to all of these diseases.

Dr. Chris Mason:              09:23                    But now this begs the question of it seems like it's important, but really what is the best way than to measure this very important component of my physiology, and health, and potentially a risk for disease. And we've looked a lot at this from work in my laboratory and with collaborators to say, what are the differences between say shotgun sequencing and 16s. And we've found in some cases, there can be really large differences between this method, which is called 16S, which is a way where you only amplify one section of the ribosomal RNA, the fragment called 16S.

Dr. Chris Mason:              09:55                    And basically, instead of say 23S, this one region of the ribosome RNA is present in almost all bacteria, which is why it gets used. But the problem is it's specific to bacteria. So, what we've noted here is that not only is it specific to bacteria, it will miss lots of things. You can see here, for example, if you use shotgun sequencing, which is what we use at Onegevity, it's actually different and far superior to the other methods. In this case, if you just use 16S for bacteria or 18S for eukaryotes or some parasites, or internal tandem sequencing or spacer sequencing, we can look at fungi for example. But none of these methods, which are targeted methods, will reveal to you all of the more dynamic and functional elements of a sample, including things like antibiotic resistance and antimicrobial resistance you can see down here.

Dr. Chris Mason:              10:48                    So the reason we really deploy shotgun sequencing and, and empirically, based on our data sets, is because it is the best way to get the most comprehensive look at what's present in your sample. The only disadvantage is that you have to sequence deeper to get it because you're not just looking at one kingdom or domain of life. But generally we actually really, and we published on this, this is the most comprehensive way to examine any microbiome sample or really any DNA sample that could come from anywhere in the world.

Dr. Chris Mason:              11:20                    So we've been also working with the FDA in this to generalize, and create standards. This is something called the International Metagenomics and Microbiome Standards Alliance (IMMSA). It is the best practices in microbiome research and making sure that we use positive controls, and negative controls, optimized methods, and we do this because it's a nontrivial method. When you get fragments of DNA and you want to map them to all known species. We found that there are dozens and dozens of tools on this, but we have, I'm done, you know, benchmarking and characterization of what are the ways to computationally analyze in the metagenomic sample-- of all those species. And we've seen here that we have a way to balance the false positives and false negatives and give what is effectively near clinical level action-ability and measurement accuracy of all the species that you can find.

Dr. Chris Mason:              12:13                    So this is some work that we've done, but we've also applied this in more unique environments. So for example, there's no real microbiome standard for the subway. Maybe at one time. I saw a woman here, she was grabbing the pole with this, I think very suspiciously used paper towel, for example. You could see I once caught someone wearing a lab glove on the subway. Again, terrified to touch what's on the steel railing. And it's extraordinary that when everyone generally thinks of bacteria, they don't think of most of the good things they think of the bad things. They generally are very afraid and sort of filled with this fear of the microbiome. But whenever possible in both in science and in life and also in business, it's good to replace fear with the knowledge if something is actually there.

Dr. Chris Mason:              12:57                    And so we've applied this not only to work in the lab but also to work in the subway that we wanted to know what's actually there and have a sense of mapping of what's around in the world around us. The other reason I got really interested in microbiome research and about 10 years ago was that my daughter, when she got old enough to ride the subway, actually managed to at one point grab a pole and even lick the subway pole, which was this extraordinary moment of parental terror, realizing that clearly, a microbiome transition had just happened. And I desperately wanted to know what it was.

Dr. Chris Mason:              13:31                    And what I ended up doing is thinking, well, we don't know what's there, but I looked in the literature or tried to find out there was actually no information about what's present on the surface that's touched by millions of people every day. And I thought, well, you know, we should, we should do this! We should make then a microbial map of the metropolis or what the New Yorker called the "metropolome" and build a map and try and make almost like a smart city. So, we launched a project back in 2013 to actually catalog all five boroughs in New York City and every single subway station and annotate, and map, and sequence everything at a city scale for a metagenomic genomic profile.

Dr. Chris Mason:              14:06                    And so in this case, we sequenced over 10 billion reads, fragments of DNA. And then this is also how we process samples at Onegevity-- we basically take fragments of DNA, use multiple algorithms to get high, accurately confirmation of species and strains, and then map them. And when, one thing you'll see if any of you get a Onegevity report or any of your clients, is that you'll get things that are known, but you also often get unknown organisms-- things that are not yet known. But I'm really excited because we can now map them and start to look for them again in healthy patients or those patients with any sort of diseases or problems. But we made maps for every single species we could find and also built out distributions of things that we couldn't find in.

Speaker 1:                          14:47                    This paper is published in 2015. And so what's extraordinary is we saw not only the bacteria, but we can also use the information to look for antibiotic-resistant bacteria, which we confirmed here with culturing methods. But the sequencing information actually gives you not only sort of the presence of a guess at what's there for antibiotic resistance, but the density of those DNA fragments tells you what's the most likely driver of that antibiotic resistance, which you can see here. And so we could actually confirm on two kinds of media that TetK was the driving gene for antibiotic resistance in these samples. And so we found this at the antibiotic resistance level. We can see across the city very distinct maps of sort of microbial density all around the city.

Dr. Chris Mason:              15:28                    And even here we saw a really interesting area where a station that had been flooded by hurricane sandy had 10 species unique to that-- that we didn't see anywhere else in the rest of the city. Which really kind of points to what happened back in 2012 --the city had been submerged under water in some cases and we wondered before this station got opened up to the public, could we find a persistent, sort of molecular echo of the cold ocean water that was still there in the subway station. So, we have actually swabbed the station. And then also it could find species like Shewanella frigidimarina, which was previously thought to be an Antarctic species, but now we could find it in the New York City subway station. And what's notable is it makes something called Eicosapentaenoic acid or EPA, which is normally found in fish. And actually, interestingly, if you have low levels of this in your diet, you might even be at a higher risk of suicide. So this could be one example of almost a good bacteria that are still floating around the New York City subway system that was likely deposited by the cold ocean water. So a very interesting sort of map what's there.

Dr. Chris Mason:              16:27                    And so what this work has been built on is first a curiosity of what's there. But then also now it's really been focused a lot on what are these organisms making and how can we think about optimizing this, not just for mapping cities but also mapping the small cities inside people's guts. But, fundamentally, this blue area of the chart is something that's really driven a lot of curiosity and work in our lab. And so in particular, this is the question of what have we been missing, what is it we're not mapping.

Dr. Chris Mason:              16:51                    And so we've worked with the Bill and Melinda Gates Foundation to build a global distribution of the epigenetic map of the different antibiotic and antimicrobial resistance. This is now a global project called the Metagenics and Design of Subways and Urban Biomes. And using essentially a global network of teams to build out what's present on these public services that really represents skin microbiome. And basically, several times a year we have people all around the world in collaborating cities and sites that go out and basically collect samples within an automated and annotated, and uniform protocol and build up this sort of a map of what's happening around the earth's cities. So we've done this now in the past three years. We're ramping up to the fourth year shortly. And you can see here that we have thousands of samples that represent effectively what is the normal microbiome that is interacting with the skin and what's present in our cities, both as a function of discovery and also for public health.

Dr. Chris Mason:              17:47                    What these data have already shown us is that you can use shotgun sequence data to actually increase the size of life and do what's called metagenome assembled genomes, meaning the sequence data helps let you actually stitch together what are the genome is present in a sample which we've been using here. And we're also using this as a way to actually track and map and then predict where the antimicrobial resistance is going next. And the final thing we'd be doing is to see what might be driving it. And in particular, we've seen over the counter antibiotic resistance, and antibiotics are used as driving this resistance.

Dr. Chris Mason:              18:21                    So in particular, if you look at what's present in chromosomes or in plasmids, for different classes of antibiotics, this is the density of the antibiotic resistance markers we see. And what's the W.H.O. annotated dose for different cities. We can see that there's an increasing trend and significant trend of how much is being used in different cities around the world and what's particularly driving this, which is an interesting feature of antimicrobial stewardship, it's called.

Dr. Chris Mason:              18:46                    So in the last couple of sections, don't think about other places we've been taking this technology. One of them is to go a little bit higher. So I'm particularly just recently we published a profile looking at twin astronauts when one of them is up in space. This was called the NASA twin study where we were one of the teams looking at the integrative biology of space travel over two years. And one thing that we did observe is that the microbiome did a shift in flight. You can see here in red that you have many, many species, each one of these colors of different species and they were maintained over time. But the ratio and the density of different species did change. And so this is something that's called the Firmicutes to Bacteroidetes ratio-- it did shift in flight, indicating that there's some response at that, the human side and even the microbial side of what Trevor Noah called the "space genes" in his show.

Dr. Chris Mason:              19:34                    So it's been a very, kind of an intriguing back and forth to think about how much of the body is plastic and what goes back to normal. But this actually was difficult. It'd be just frankly much easier if we could just sequence in space. So we launched the mission with Aaron Burton and collaborators at NASA to say, 'well, we should just go the sequence in space instead of bringing everything back!' And so we needed was a small sequencer. And fortunately, we had something called the nanopore sequencer, which as DNA moves through a poor, it changes the conductance of this membrane and actually then leads to a way to discern whether you have ACG or T on your small nanopore device.

Dr. Chris Mason:              20:09                    And this is even something that's been attached to the phone. Somebody called a SmidgION. But we got together to start to plan the mission and we work on first a patch. So we knew we could start the mission and that worked out okay. So we said, okay, we're going to go to space. We're getting ready for this. Then we wanted to try to see if we could first get it to work in zero gravity. So we tried to work on the parabolic flight simulator. Which you can see here, Dr. Andrew Feinberg doing some of the first testings of its time seeing if we could do pipetting in zero gravity. And then also try sequencers in zero gravity. You can imagine that you don't want the tips of your pipette like that to float around. It's also worth noting that when you're molecular biology or microbiology, you generally want your tube to stay in the same place, which is not the case in zero gravity.

Dr. Chris Mason:              20:53                    But when you get to the bottom of the flight, everything does crash back down. And Doctor Feinberg was a good sport about it. Managed to load the flow cell. We had a successful proof of principle, a sequencing in zero gravity to which should work. And then we also published this to show that DNA sequencing was ready for liftoff. Then Dr. Kate Rubin's made it up to space shortly thereafter. Was one of the first astronauts and virologists to make it up to the space station. We managed to get supplies up to the space station no problem. And then just a few years ago, we managed to do the first sequencing in zero gravity. Dr. Rubin's doing it for the first time in space. NASA added that music. That was not me the record, but you can see you're excited that the sequencer was working and we managed to sequence and space for the first time, which some people called the dawn of genomics in space.

Speaker 1:                          21:43                    We also managed to get this genome sequenced and then assembled, representing the first that has been sequenced and assembled from data that was not made on this planet. And what we're doing now is actually working to track infections and mapping on the space station in real time. So if there is an infection or anything that needs to be tracked, we can actually sequence it in real time. And we use them the same algorithms for that study as we do for work at mapping microbes in people here on earth as well.

Dr. Chris Mason:              22:10                    So I want to close with a thought of-- that's a bit of background about microbiome research and what can be done today, but then think about not just measuring microbiomes, for saying what's wrong with people? But think about how we can be more protective of it or defensive.

Dr. Chris Mason:              22:23                    And so this has come up in some ideas of something called the genome project. It's this idea of genome engineering or microbiome engineering. And I actually think fundamentally this is one of the best tests of our understanding of biology-- is can we try and engineer or tweak something and then actually predict that may work? And so this is exactly what we've been doing, clinical trials and some of our work at Onegevity. Can we have not just precision medicine, but be more predictive with our medicine and maintain health and hopefully prevent disease, or if you do get diseased figured ways to move back away towards health. So particularly the platform that we've developed builds not just on the microbiome, it's actually multi-omics data integration as well as longitudinal profiling that builds into the health intelligence platform. It includes all the data and methods in public data sets of which I've just described, a lot of the algorithms and methods I've also just described, but basically it gives us one of the things that are really key to the platform-- which is the Gutbio kit, which gives you this metagenomics plus analysis. So, as I described, it's not just 16S profiling. It detects all these features in your gut as well as potential new biochemical, basically pathways inside your gun. And in general, we're working on ways to make it so you have an easier way to collect the sample. We also have methods for drawing blood to do metabolomics, and also genome sequencing combined, as well-- and all these modalities into one platform.

Dr. Chris Mason:              23:44                    And also it's continually learning. So the AI platform as both working on the microbiome data and also the other molecular data to improve stratification as well as the predictions--- what we think will work based on certain people's genetic and multi-omic profiles.

Dr. Chris Mason:              23:59                    In particular, when you think about engineering the gut microbiome, what you need are products. And what's really powerful about this is our partnership with Thorne. We have prebiotics, probiotics, different vitamins, different supplementation regimes that we can try to see what's actually working the best and then predict based on the data we have, what will work the best for a specific person. So, we've been testing dozens of these formulas already. There's a total of 312 that are in the catalog. And so we're in the process of working through the ones that we already know that work well for IBS or other gut disorders, but also trying them for other sorts of potential indicators with some of our clinical trials. And really it's a partnership between having really good science, really well-regulated, rigorous manufacturing processes that are here in the U.S. that we can vouch for and watch every step of the way. They've gone through NSF approval that actually we have to have for the official partnership with the US Olympic team and with Mayo Clinic.

Speaker 1:                          24:56                    So, these are the things that doctors are ordering already, but now we want to bring some of the same real focus in functional medicine that we've been doing in the clinic, in our labs, and bring this out to anyone and everyone who wants it and can actually use it in their life to improve their health and hopefully maintain it.

Dr. Chris Mason:              25:13                    So with that as a backdrop, I want to say thanks and feel free to reach out if you have any other questions and have a great morning, afternoon, or evening, wherever you may be.