In this talk Dr. David Perlmutter reviews recent research that reconstructs ancient human microbiomes by sequencing DNA preserved in dental calculus from archaeological skeletons. He explains how next‑generation sequencing of fossilized plaque reveals that the transition from hunter‑gatherer to Neolithic farming diets, and later the industrial revolution’s surge in refined flour and sugar, dramatically reshaped oral microbial communities—reducing diversity and increasing disease‑associated bacteria such as Streptococcus mutans and Porphyromonas gingivalis. Perlmutter also highlights modern factors that further disrupt the microbiome, especially the widespread use of broad‑spectrum antibiotics in children, which act as “weapons of mass microbial disruption.” He connects these microbial shifts to rising rates of chronic inflammatory conditions, including dental disease, gingivitis, dementia, coronary artery disease, and other systemic illnesses, arguing that understanding the ancestral microbiome provides a crucial baseline for interpreting today’s health challenges.
Chapters
Hello, I'm Dr. David Perlmutter. Have you ever wondered what the human microbiome must have been like in our ancestors? Probably you haven't, but truth of the matter is people are looking at that kind of stuff because it really reveals some very interesting information about things and how they have changed, how environmental influences have changed the human microbiome. So let's look at some research. This study is called Ancient Human Microbiomes and was published in the Journal of Human Evolution earlier in 2015. And it's really a very incredible study. What they did was they studied actually, and I'll take you there in just a moment, how the human microbiome has changed and concluded that industrialization, globalization, and modern sanitation. Because of these things, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. So this is the precedent that justifies why it is they felt it was necessary to study the human microbiome of our ancestors, applying these 2 techniques. Number one is what is called next-gen or next-generation sequencing, and A way of looking at the DNA sequencing of the bacteria that made up our microbiome. And they did it intriguingly by looking at what is called dental calculus. You know, when you go to the dentist and he or she, or the dental hygienist, removes that calcified material along the bottom of your tooth and between your teeth, that is actually fossilized bacterial DNA. Okay. Biofilm, and this is what the dentists normally clear out of your teeth. This is obviously a pretty aggressive case of dental calculus, but intriguingly, this is, in fossilized specimens, a rich source of genetic information that can give us some great clues as it relates to the state of the human microbiome. And that's exactly— what these researchers studied. And what they found was— and let me just read their quote— there's no doubt— I'm paraphrasing— that modern behavior and dietary changes are altering the microbial ecology of humans. While some of these changes could be beneficial, others are disruptive and may be a driving force behind the rapidly increasing rates of chronic inflammatory diseases in developed countries. Common medical interventions such as antibiotic therapy have dramatically reduced infectious disease burdens worldwide. However, rather than being targeted strikes against harmful bacteria alone, such therapies can also act as weapons of mass microbial disruption. So when we realize that almost every American child has been exposed to powerful broad-spectrum antibiotics, that this represents the number one drug for children 10 years of age and younger. With this new information, the effects of the— of these antibiotics on the microbiome, more and more researchers are challenging the wisdom of our aggressive usage of antibiotics. in terms of treating every cough or sniffle. Now, this next research called Sequencing Ancient Calcified Dental Plaque Shows Changes in the Oral Microbiota with Dietary Shifts of the Neolithic and Industrial Revolutions really puts into perspective how our modern diet has really changed the microbiome. And this was published in the journal Nature Genetics. And what these researchers found, they looked at 34 early European skeletons, and their conclusion was that the transition from hunter-gatherer to farming changed the oral microbial community to a, what they're calling, a disease-associated configuration, stating modern oral microbiotic ecosystems are markedly less diverse than historic populations, which might be contributing to chronic oral and other diseases in post-industrial lifestyles. Now, they looked at 2 particular bacteria, S. mutans and P. gingivalis, comparing the levels of these organisms in Mesolithic times versus modern times. And another way of looking at it would, of course, be these— another graph, just seeing that S. mutans, which is the bacterium that is involved with caries or cavities, dramatically increasing, and P. gingivalis, an organism that has been associated with gingivitis, also dramatically increasing. And I might just say that we're seeing significant correlations drawn between gingivitis and things like dementia and even coronary artery disease. Now, the conclusion of these researchers is that And I'll read this. 2 of the greatest dietary shifts in human evolution involve the adoption of carbohydrate-rich Neolithic farming diets beginning around 10,000 years before the present, and the more recent advent of industrial-produced flour and sugar, which occurred beginning in around 1850. Dental calculus on ancient teeth preserves a detailed genetic record throughout this period. So, you know, we marvel at our development of agriculture. But with the development of agriculture, there's been a dramatic increase in just the percentage carbohydrate that has made up the human diet. And then more recently, we've seen a dramatic increase in sugar consumption. So, It looks as if there really is no free ride when it comes to these dramatic dietary changes that have occurred with human evolution. And that what these researchers are identifying and calling our attention to is that these dramatic shifts in human nutrition with higher levels of carbohydrates and more recently, higher levels of monosaccharides or sugars, these are imparting dramatic changes in the oral microbiome. And as we now understand, there are shifts that are seen throughout the human systemic physiology that are associated with changes not only in the oral microbiome, of course, but also in the general intestinal microbiome as well. Very interesting information that really tends to point, for the first time, some causality, connecting the dots in terms of understanding Through the lens of the microbiome, how it is that this sudden change in human nutrition may be strongly related to our debilitating diseases. Interesting information for sure. I'm Dr. David Perlmutter.
