This episode of "Matters Microbial" features Dr. Laura Weyrich, who discusses the fascinating field of the paleo-oral microbiome. Dr. Weyrich elaborates on how her research group analyzes ancient DNA (aDNA) preserved in the dental calculus of Neanderthals and ancient humans to reconstruct the oral microbial communities of the past. A significant portion of the discussion is dedicated to the critical importance of rigorous scientific controls to prevent contamination and the complex ethics involved in studying ancient human remains. Key findings reveal that pre-agricultural humans and Neanderthals possessed healthier oral microbiomes compared to modern populations. The transition to agriculture and the dietary shifts of the Industrial Revolution precipitated a move towards disease-associated microbial communities, creating an "evolutionary mismatch" in the mouths of people today. The ultimate goal of this research is to translate these ancient insights into modern therapies, such as Oral Microbiome Transplants, to improve both oral and systemic health.
Unlocking the Past: Ancient DNA and the Secrets of the Oral Microbiome
0:00 - Introduction and Classroom Discoveries: Host Dr. Mark Martin opens the episode with a remembrance for microbiologist Dr. Kimberly Walker and shares updates from his microbiology course, including the diverse microbial life found inside student water bottles and creative "Luxart" made with glowing bacteria.
4:53 - Welcome Dr. Laura Weyrich and the Paleo-Microbiome: Dr. Weyrich is introduced, and she explains the concept of studying the "paleo microbiome"βthe communities of microbes that lived in and on ancient humans and our extinct relatives.
6:28 - The Challenge of Studying Ancient DNA (aDNA): The conversation delves into the methods for studying microbes from the deep past, primarily by extracting remnant DNA. Most ancient DNA, however, is highly fragmented and degraded.
8:05 - The Critical Importance of Controls: Dr. Weyrich emphasizes that the most significant challenge in aDNA research is preventing contamination from modern DNA in reagents, the lab environment, or even the researchers themselves. She stresses the need for extensive controls, such as exposing swabs to the lab air, to ensure the ancient DNA signals are real.
12:25 - A Field of Self-Correction: Early attempts at aDNA research, such as claims of isolating ancient yeast from amber, were often flawed due to a lack of controls. The field has since become extremely rigorous, highlighting how science is a process that corrects itself over time.
17:21 - The Ethics of Ancient DNA Research: The discussion addresses the profound ethical responsibilities of studying ancient human remains, particularly the need for collaboration and engagement with Indigenous communities whose ancestors are the subjects of study.
21:28 - Dental Calculus: A Microbial Time Capsule: Dr. Weyrich identifies dental calculus (calcified dental plaque) as the best source for ancient oral DNA. This rock-hard substance fossilizes during an individual's life, perfectly preserving a snapshot of their oral microbes.
25:33 - Microbiome Shifts with Agriculture and Industry: Research shows ancient hunter-gatherers and Neanderthals had excellent oral health. The oral microbiome shifted dramatically with the advent of agriculture (introducing more carbohydrates) and again during the Industrial Revolution (with processed sugar), leading to communities adapted to cause diseases like cavities and gum disease.
29:42 - An "Evolutionary Mismatch" in Modern Mouths: Today's oral microbiome is in a "disease state." Practices like toothbrushing are necessary to combat microbes that are mismatched with our evolutionary history. The goal of Dr. Weyrich's research is to find ways to restore a healthier, more ancestral-like microbial community.
31:40 - The Mouth-Body Connection: Poor oral health and periodontal disease are strongly linked to systemic health issues, including heart disease, diabetes, and Alzheimer's disease, underscoring the importance of a healthy oral microbiome.
33:42 - The Future is Pro-Microbial: Oral Microbiome Transplants: Dr. Weyrich's lab is developing Oral Microbiome Transplants (OMT), a therapy that involves transferring a healthy microbial community from a donor to a recipient. This aims to use beneficial microbes to outcompete pathogens and prevent disease.
43:48 - Neanderthal Microbial Insights: Studies show that Neanderthals and ancient humans shared or exchanged oral microbes. Counterintuitively, Neanderthals had remarkably good teeth, meaning they produced less of the dental calculus that is so valuable for this research.
1:05:06 - Key Advice for Future Scientists: Dr. Weyrich concludes by encouraging listeners and students to always challenge dogma, recognize that science is a continuous learning process, and to find and follow their scientific passions.
Summary of References
An obituary for microbiologist Dr. Kimberly Walker, a friend of the host and a previous guest on the podcast.
A link to Episode #9 of Matters Microbial, featuring a discussion with citizen scientist Sebastian Cocioba about creating accessible scientific tools.
An academic article on the ethics of DNA research on human remains, proposing five globally applicable guidelines for respectful and responsible study.
Two review articles providing an overview of the field of ancient DNA (aDNA), detailing its history, technological advancements, and broad applications in understanding human evolution, domestication, and ancient pathogens.
Two articles, one co-authored by Dr. Weyrich, addressing the critical importance of proper controls for studying low-biomass samples to avoid misinterpretation due to contaminating DNA from lab reagents (the "kitome").
A recent study using ancient DNA from human bones to successfully detect Yersinia pestis, the bacterium that causes plague, in Neolithic individuals.
An academic review providing a comprehensive overview of the modern human oral microbiome, covering its diversity, structure, and role in both oral and systemic health.
A news article describing how ancient DNA can be recovered from dental calculus, allowing researchers to reconstruct the genomes of extinct microbes and study their functions.
An article by Dr. Weyrich and colleagues detailing their research on the British oral microbiome from ~2200 BCE to 1853 CE, revealing shifts in microbial communities associated with major lifestyle changes, diet, and events like the Second Plague Pandemic.
Two YouTube videos, one providing a general overview of Neanderthal life, culture, and extinction, and another featuring Dr. Weyrich describing her research program on the paleo-microbiome.
An article co-authored by Dr. Weyrich on the behavior, diet, and diseases of Neanderthals as inferred from the ancient DNA found in their dental calculus.
Links to Dr. Weyrich's university faculty page and her research lab's website, providing more information on her work and publications.
Glossary of Terms
Ancient DNA (aDNA): Genetic material recovered from ancient biological specimens, such as bones, teeth, or preserved tissues. It is typically fragmented and damaged.
Dental Calculus: Hardened, calcified dental plaque that forms on teeth. It is an excellent preservative of DNA from oral microbes, food particles, and host cells from ancient individuals.
Luxart: Art created using living, bioluminescent (glowing) bacteria on a petri dish as the "paint."
Microbiome: The community of all microorganisms (such as bacteria, fungi, and viruses) that live in a particular environment, especially a part of the body like the mouth or gut.
Neanderthal: An extinct species of archaic human who lived in Eurasia until about 40,000 years ago. They were close relatives of modern humans.
Oral Microbiome Transplant (OMT): A therapeutic procedure involving the transfer of a healthy, diverse community of oral microbes from a donor to a recipient to prevent or treat oral diseases.
Paleo-microbiome: The study of the microbiomes of ancient organisms, including extinct hominins, reconstructed using ancient DNA.
PCR (Polymerase Chain Reaction): A laboratory technique used to make millions of copies of a specific DNA segment, allowing scientists to amplify tiny amounts of DNA for analysis.
Periodontal Disease: A serious gum infection that damages the soft tissue and, without treatment, can destroy the bone that supports the teeth.
Siderophore: Small molecules produced by certain microorganisms to scavenge for iron from their environment. Mentioned in the context of student projects.
Streptococcus: A genus of bacteria commonly found in the human mouth. Some species, like Streptococcus mutans, are strongly associated with causing dental caries (cavities).