Sequencing 700-year-old DNA

The field of archaeology has a fantastic, relatively new, weapon in its arsenal, as gene sequencing is providing some fantastic new insights about people living a very long time ago. But just what kind of things can be discerned from bodies that have spent centuries in the ground? Well, I can’t say I’m chomping at the bit to stand next to pile of corpses. So, we will need a couple of wise sages to walk us through the world of ancient DNA...

Will - The field of archeology has had a fantastic relatively new weapon added to its arsenal as gene sequencing is providing some fantastic new insights about people living a very long time ago. But just what kinds of things can be discerned from bodies that have spent centuries in the ground? Well, I can't say I'm chomping at the bit to stand next to a pile of corpses, so we'll need a couple of wise sages to walk us through the world of ancient DNA.

Christiana - Ancient DNA is what it sounds like. It's DNA that is ancient. So a loose definition would be anything that's over a hundred years old. DNA can come from multiple sources, it can come from skeletal remains, which is what I do a lot of my work on. Or it can come from soil, it can come from pottery, it can come from lots of different sources, but as long as it's over a hundred years old, it would qualify as ancient DNA.

Will - That's the University of Cambridge's Christiana Scheib, one of the leaders of the investigation. And who is our lucky specimen this time round?

Christiana - Today, we're going to be talking about an individual from the Augustinian Friary in Cambridge. And this is somebody who probably died between the years of 1330 and 1350. Yeah, we know a little bit about the people in this cemetery based on the archaeology and some of the historical records, and now also because of the genetic work that we've been doing as part of the After the Plague project.

Will - Those of you who are quick on the draw with your maths have already noted that 1350 is just shy of 700 years old, which begs the question, where do you look for DNA on a specimen that ancient?

Christiana - If we want to look at human DNA or pathogen DNA, we'll look at at teeth and we'll look at intact tooth roots, or in this case, what we're going to talk about today, dental calculus, which is a calcified film on the teeth, which we all get, and we usually get it cleaned off when we go to the dentist. But in earlier time periods, people didn't go regularly to the dentist, and so it builds up over time and it remains on the skeleton. Dental calculus forms in layers, and so theoretically you could get different time periods in a person's life as the dental calculus builds up over time. But generally, we're more looking at sort of the bulk. So we would take some dental calculus, we would scrape it off of the tooth and then put it through our normal sort of dental calculus ancient protocols, and we can look at the entirety of what might be inside the dental calculus of that person, which will reflect what was in their mouth throughout their life. If you do proteomics on the dental calculus, you can often get some food proteins or even sometimes some proteins from if they were using their mouth as a tool or processing some sort of fibres or other materials, you might be able to find that. We can also look at microfossils, which are tiny fossils that also get embedded into the calculus, which might show indications of usage of the mouth or being around. Sometimes you find charcoal indicating that people are around fires or there's a really good paper of some nuns actually, and they had this blue ink in their dental calculus that got incorporated, which gave a picture of them actually working on manuscripts. And so yeah, from the DNA, from the proteins from the microfossils, the dental calculus can give us a nice insight into the daily life of, of somebody in the past.

Will - So not only can they learn about the person themselves, but also even the microorganisms and other compounds that were present in their mouths. But if you are looking at skeletal remains, some of which were buried in so-called 'plague pits', do you have to be wary of any dormant illnesses being brought up with the samples?

Christiana - Ancient DNA is physically different from modern DNA in a few ways. Essentially over time, DNA chemically breaks down, and so as all organisms die, they start to break down. And so ancient DNA is characterised by short fragments, low amounts of DNA and also certain degradation changes in the actual bases in the DNA. And so even if we're looking at a plague pit or something where we know there's been disease, it's very unlikely that that disease would be still viable. It's not like the mummy or the most recent sort of Tomb Raider movie where they open up the tomb and everybody gets this disease. It doesn't really work like that.

Will - So the nature of DNA decay is somewhat of a blessing when it comes to reducing the risk of disease, but it's a double-edged sword, of course. As this breakdown means, sample sizes are absolutely tiny. So with the odds not really in their favour, what was discovered when they got their teeth into the ancient DNA? Illumina's Michal Szpak, who worked on the sequencing samples, is here to take us through it.

Michal - So what did we find? Well, we found the presence of the Y chromosome so we could confirm it was a male individual. Actually 80% of the data couldn't be matched, but that's not unusual. And you know, it's for various reasons. So partially due to gaps in the reference database, but also naturally occurring variation. But also the, ancient nature of the ancient DNA, so you know, the damage and chemical modifications that Christiana was talking about. And then, from those reads that could be assigned to a species, 99% were bacteria. And of that, around 85 to 90% were oral bacteria commonly found in the human mouth, which is consistent with the sample origin. So we are happy about that and almost 50% were sulphate reducing bacteria involved in gum disease. But we also found a number of less common but nastier bacteria also causing gum disease and dental infections such as Tannerella forsythia for example, but also Streptococcus pyogenes, which is infrequent, but usually pathogenic. It infects human throat and mouth and skin often causing scarlet fever and skin rashes. But also dental abscess.

Will - So a lot of common mouth bacteria, some uncommon a bit nastier bacteria, but little to no presence of the real nasties at the time, smallpox, typhoid, leprosy, what have you. So first of all, well done to this individual for potentially avoiding all of those horrible diseases, but it does mean that the cause of death remains a mystery.

Michal - Yes, you know, the cause of death could be natural. We didn't find anything obvious. You know, none of the bacteria that we found are likely to cause death. It kind of looks like a pretty normal oral microbiota. It's not unheard of for commensal bacteria to cause infections. They're part of normal microbiota, meaning many people carry them without any symptoms, but in some cases they can lead to serious illness or in extreme cases even death. You know, as, for example, as seen in some forms of streptococcal infections. We found some streptococcus, but it's rather unclear which strain. So it is very, very unlikely that any of those would cause death.

Christiana - We normally wouldn't look for cause of death in oral dental calculus. Normally if you're looking at ancient pathogen DNA, you're looking at something septic, so something that would've been in the bloodstream. So if we're gonna find Yersinia pestis, that's going to be inside the dental pulp chamber or inside of a bone somewhere where you're actually getting the remains of what was in the bloodstream at the time of death. And so even if we found a streptococcal strain inside the dental pulp cavity, instead of say in the dental calculus, you still wouldn't be able to say for sure that 'oh, it was some sort of infection.'

Will - Even so, it is a treasure trove of information, and this field of sequencing has the potential to uncover a whole lot more going forward.

Michal - There's been a lot of buzz around ancient environmental DNA found in the soil dirt and sentiments, which can preserve very well, under right conditions, and serve as a great source of DNA in the absence of skeletal remains especially. Well, in fact the oldest DNA ever sequenced was from 2 million years old sediments in Greenland. So I think more sampling and sequencing around the world would give us a better picture of past ecological turnovers, and I think that would be quite exciting.

Will - And one last question to ponder. With increased oral hygiene around the globe, are future archeologists going to find dental calculus less useful?

Christiana - I would say it depends. You know, there are still people who don't brush their teeth as much and also if you have some other condition. For example, we see this in the skeletal records, individuals who've had some sort of paralysis and are not able to scrape that off or who don't have good care at the end of their life. Not everybody ruthlessly cleans off all of their dental calculus and their plaque every single day. So it doesn't rule it out. It probably makes it a bit less likely but it's not going to make it impossible to find these sorts of things in the future.

Michal - I definitely, personally know quite a few people who have very obvious dental calculus in plaque, so I think it's going to be with us for quite some time.

Will - So, is our take home message, please go and brush your teeth to confuse future archeologists and I guess also help your health out too.

Michal - Please make it harder for future archeologists. Indeed.