The evolutionary history of the human oral microbiota and its implications for modern health

Abstract

Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.

The making of the oral microbiome in Agta hunter-gatherers

“…We applied genomic control to correct for cryptic relatedness and population stratification and minimize false positives induced by inflated association test statistics 81 . To do so, we estimated the genomic inflation factor as the median value of the likelihood ratio test (LRT) values divided by 0.456 (median of a χ 2 (1) distribution) and recalculated the p-values after dividing the LRT values by the genomic inflation factor 82 . Threshold of significance was set at FDR 10%, and only genomic positions having at least three samples for the major homozygous genotype and for the heterozygous genotype were considered.…”

Mars: new insights and unresolved questions

“…The microbiomes of modern humans living in urban settings are less diverse than those of ancient indigenous peoples as shown by a range of recent seminal studies (De Filippo et al, 2010;Clemente et al, 2015;Eisenhofer et al, 2020;Sprockett et al, 2020;Weyrich, 2021). Diversity within the human microbiome is reduced when our lifestyle isolates us from contact with biodiverse soils (Blum et al, 2019) and the microbiomes of astronauts are known to become impoverished due to isolation and from Earth's biosphere (Sugita and Cho, 2015).…”

Microbiomics: Were we all wrong before?

“…As we continue to investigate the pathogenesis of periodontal diseases in the omics era, Laura Weyrich, 19 a paleomicrobiologist, takes the position that tracing the evolutionary history of oral microbiota and the factors that shape its origins will likely unlock information to mitigate disease today. Humans likely diverged from other bipedal hominids about 200 000 years ago, 20 providing ample time for the separation, diversification, and adaptation of our oral microbiota from other primates.…”