 I am an archeological geneticist, I focus on ancient DNA in the past but what I'm really interested in is not just the DNA from a particular skeleton but I want to know about their whole life, I want to know about their life history, the diseases they had, the diets they ate but unfortunately very little of that preserves in the archeological record and this frustrated me for a very long period of time. And then I hit upon something really interesting, it's called dental calculus. You probably know it by the name tooth tartar, it's more common name. What it is, it's the dental plaque on the surface of your teeth that mineralizes while you're alive. It actually is the only part of your body that actually fossilizes during life and this entraps and preserves these materials on your teeth for very long time. And what's interesting is that dental plaque is very sticky, lots of things get entrapped in it and so we actually have this amazing record of behaviors, of all sorts of things that otherwise don't preserve at all right there sitting on the surface of your teeth that we can then go and mine out of the past. This fascinates me that we now have a window into this invisible world. When I started this research very few people were thinking about dental calculus. It wasn't very interesting, it's tooth tartar. What would you do with that? But the more I started investigating it, the more I started realizing that it preserves DNA for extraordinary periods of time, it preserves proteins for very long periods of time. Also little things like microfossils, fragments of textiles, fragments of food particles, even things like paints that a person might have used during their lifetime become trapped and then encased in dental calculus and preserve. And as a scientist we can now use a wide variety of tools to mine those bits of information out and recover entire aspects not only of the genome of the individual which is also present in dental calculus but of all the things they did, the illnesses they had, the life they lived and the things they ate throughout their life. All the things that we wish we had a window to that don't preserve under conventional means we can get at through dental calculus. Initially we applied many methods in part because I didn't know where to begin, this was a material that has hardly been studied in fact for the past 50 years most of the research that's been done on dental calculus is just how to get rid of it, how dentists can more effectively remove it. There was very little known about the actual biology of the system so we had to be quite exploratory on our methods. We applied several different ones so for example we applied metagenomics, we specifically shotgun metagenomics, this is where you extract all of the DNA in a sample and then sequence all of it. This is a very new technique using next generation sequencing, it's only been available for less than 10 years and we applied this. It's computationally very difficult, generates lots and lots of data, terabytes of data so it's very complicated to analyze but it gives you an incredibly detailed window into the DNA that's preserved. We also applied a very new technique called shotgun proteomics where we applied tandem mass spectrometry. This is, it's only very recently that the instruments have become fast enough and sensitive enough to be able to do a bulk extraction of all the proteins that we can recover and then to sequence those or identify the proteins that were originally present. This was a particularly interesting aspect of the study to me because we were the first to apply this to an oral sample to a calculus sample in this ancient context but actually was the first time it had ever been done for even modern dental plaques. This was really pioneering, it was very very exciting. We also applied a number of other methods, conventional microscopy, light microscopy and scanning electron microscopy, rayman spectroscopy, all of these were coming together to try to understand the biology of the system, what minerals were present, what types of microfossils might be entrapped. We had very rich information but I was particularly excited about the metagenomic and the proteomic data. We found really rich sources of biomolecules in here. In the archaeological record in general ancient DNA and ancient proteins tend not to preserve very well. What we found in calculus is a very different story so we now know as a result of this work that dental calculus is the richest source of ancient DNA known in the entire record. In fact it's on average about a hundred to a thousand times more DNA in calculus than skeleton material from the same skeleton so it's really really rich and the same is true for proteins. We don't just find a narrow range of proteins which is what we typically find from dentin or bone. We find this incredible array of proteins that come from the bacteria that come from the human itself and also from diet. With the human proteins actually we don't just get run-of-the-mill proteins we get very exciting proteins like immune associated proteins and so we're able to reconstruct this entire relationship between the microbes and the host right there on the surface of the teeth. So the findings actually far exceeded my expectations. When I started this research my highest hope was that we might recover some oral bacteria that we might be able to associate with say dental caries. What I had no idea was that the ancient DNA and proteins that were preserved would allow us to reconstruct the entire ancient oral microbiome of this individual and the host response. We have an entire suite of immune proteins that were present and identified that we know are directly involved in response to microbial infections. So here we had in this particular case we had someone with periodontal disease and we could see the bacteria involved the host response all encapsulated and fossilized for us in time this detailed relationship. This is incredibly important if you think about how today we're starting to realize the tremendous importance of the microbiome in our overall health one question has always been well how could we ever look in the past where would we ever get it from and it turns out dental calculus is a fantastic reservoir of the microbiome sitting right there in our mouth in the mouths of these ancient people. We can go to almost any period in the past we can radiocarbon date the skeleton and have a snapshot of the oral microbiome. This is fantastic one of the questions we want to know what is the ancestral state of the microbiome you know if we think that today in industrialized societies we have a very disturbed microbiome that we have to know what it used to look like in order to make that comparison where does it come from it turns out we can actually get that information from dental calculus it's really rich so we were able to reconstruct this community of bacteria that's one thing we were also able to recover specific genomes from different organisms for different microbes one in particular I found really interesting is tannerola forcithia it's very associated with chronic periodontal disease and we had so many genetic sequences from it that we could actually reconstruct its entire genome and determine that the particular string that this individual had in medieval Germany lacked a conjugative transpose on which is a genetic element that conveys tetracycline resistance today and this person didn't have it so that was very exciting when we looked at the proteins we found it was just so interesting we found salivary amylase which is something you expect to find it's in saliva it helps you digest starch we also find this enormous range of immune proteins mostly associated with neutrophils which is a particular cell type that's engaged in defending you from dental plaque and other microbial infections and we also found dietary proteins in another study we looked at a larger number of samples and were able to trace milk consumption all the way back to the bronze age by picking out milk proteins from dental calculus so I find this incredibly exciting we can get angles of health and we can get angles of diet and also microscopically we see traces of things like fibers so if you think about clothing for example they don't preserve well in the archaeological record and yet we can go into the dental calculus of individuals and see bits of cotton bits of flax bits of hemp and we can then infer what types of clothing people were wearing if they were using people who were working with clothing or have clothing and that they're holding in their teeth while they're working on different fabrics so it's this real window into the past that we've never quite had anything like it the relevance of these findings is that we now have a new source of human life history behavior health and diet in the past that that was under our noses the whole time and we didn't know about and now is revealing complex information on a scale that we we'd never expected this is providing information about how the human oral microbiome has evolved and changed through time we can use this to see how changes in human behavior changes in human society may have impacted our microbiome which then may impact our health we also now have this incredible window into microbes ancient microbes that we can radiocarbon date put a date on and see how individual microbes change through time um we've had a long history of coalition with many of these microbes we don't understand these relationships very well some of them are actually quite protective against disease for us and we now have a way of actually going into the archaeological record and finding these microbes we can actually do archaeological microbiology this is a completely new area so I think this is very very exciting looking at how microbes evolve through time and how our relationship has changed with them in terms of moving forward we're still trying to explore how far we can go with this technology and everywhere we look we keep finding new and exciting things so one aspect is we noticed early on that we could recover human DNA from calculus but we didn't know what could we do with it is there enough to do any kind of interesting research with so we we recently conducted a study where we showed you could recover whole mitochondrial genomes from calculus this is really exciting in cases where you might not be able to analyze the skeletal material for one reason or another we're also really interested in understanding whether or not calculus might provide an unusual or even a better preservational environment for DNA in general than dentin or bone the fact that it calcifies during life effectively sealing off that DNA seems to have a protective effect on it doesn't seem to decompose or undergo the same kind of decay that the rest of the body goes under it's what's very protected so this reservoir aspect of it is very interesting to me we're also now starting to apply this to many many more skeletons we want to know how far back in the past can we go our initial study focused on the medieval period because we wanted a system that we we understood to a pretty good degree we wanted to know if the findings made no sense we know enough about the medieval period to know what we expected to find and we did find it this gave us a lot of confidence in our results and now we can take that information and start applying it to deeper and deeper periods in the past and so we're exploring in many many directions we're also further exploring proteins it seems like almost every year a new mass spectrometer comes out that can recover even more information and as we start to apply these technologies our protein counts are going from 40 to 80 to 100 to 200 to sometimes we even get 700 protein identifications in a single sample this is including health information host information dietary information we're really really excited about this and we're starting to pick up dietary items but otherwise we would never see and what's also really exciting about the protein work is not only can we say oh this person was eating oats or this person was eating something related to a cow which you would get from genomic information we can say oh this is specifically oat seed or this is specifically cow milk and when it comes to milk we can not only say that it's milk we can say it's cow milk it's sheep milk it's goat milk we can actually distinguish it so proteins because they're tissue specific we can actually say what specific foods we're eating and that gets really exciting this is a completely new area so right now we're pushing the limits of all the technologies that we have at our fingertips um to try to reach the limit which we haven't reached yet of how much we how much information we can really extract from this material