Although it is now clear that the human microbiome plays a critical role in making us human, in keeping us healthy, and in making us sick, we know remarkably little about the diversity, variation, and evolution of the human microbiome both today and in the past, say researchers writing in the Journal of Human Evolution​.

Indeed, while the past two decades of research have helped to uncover a mass of new data on the human microbiome, even the most extensive sampling of the modern microbiota will provide limited insight into the evolution of the human microbiome and the influence of gut microbes on pre-industrial human health.

“Although considerable effort has been invested in characterizing healthy gut and oral microbiomes, recent investigations of rural, non-Western populations have raised questions about whether the microbiota we currently define as normal have been shaped by recent influences of modern Western diet, hygiene, antibiotic exposure, and lifestyle,” ​said the research team – led by Christina Warinner from the University of Oklahoma. “The process of industrialization has dramatically reduced our direct interaction with natural environments and fundamentally altered our relationship with food and food production.”​

“But we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterising this change,”​ they suggested.

“By contrast, the direct investigation of ancient microbiomes from discrete locations and time points in the past would provide a unique view into the coevolution of microbes and hosts, host microbial ecology, and changing human health states through time,”​ they suggest.

An altered microbiome?​

According to Warinner and her colleagues, the lack of historical data on the make-up of the ancestral human microbiome means that researchers are left with many questions: “When and how did our bacterial communities become distinctly human? And what does this mean for our microbiomes today and in the future?”​

Indeed, the team noted that is it unknown how modern Western diets, hygiene practices, and antibiotic exposure has impacted ‘normal’ microbiome functions. They questioned whether humans are still in ‘mutualistic symbiosis’ with our microbiomes, or wheteher ‘diseases of civilization’ such as heart disease, obesity, type II diabetes, asthma, allergies, and osteoporosis are evidence that our microbiomes “are out of ecological balance and teetering on dysbiosis?”​

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“At an even more fundamental level, who are the members of the human microbiome, how did they come to inhabit us, and how long have they been there? Who is ‘our microbial self’?”​

Look to the past to move forward​

According to the team, with the exception of frozen and mummified remains, only two microbiomes routinely produce substrates that persist after death in archaeological contexts: faecal material that may desiccate or mineralize to produce coprolites, and dental calculus’ which calcifies during life in such a way that by the time of death it is already in a semi-fossilized and resists decomposition.

However, they warned that characterising ancient human microbiomes is more complex than a simple binary present to past comparison, and will instead require a time-series approach linked to major moments in human development and innovation, from migrations out of Africa, admixture with archaic humans, refining tool technologies, domesticating, and industrializing.

“Our goal now should be to discover if and how each of these pivotal moments in human history and prehistory reflect moments where our relationship with microbes was changed,”​ they suggested. “Fortuitously, substrates such as dental calculus appear to preserve well and are nearly as ubiquitous as the skeletal material itself, with globally diverse distributions through time”​

Indeed, they noted that there is now a ‘wealth’ of ancient human microbiome information available, which is providing a more complete picture of human biology and evolution.

“Ancient microbiome research provides an additional pathway to understanding human biology that cannot be achieved by studies of extant individuals and related species alone,”​ said the authors.

“Although reconstructing the ancestral microbiome by studying our ancestors directly is not without challenges, this approach provides a more direct picture of human-microbe coevolution.”​

Source: Journal of Human Evolution​​

Published online ahead of print, doi: 10.1016/j.jhevol.2014.10.016​

“Ancient human microbiomes”​

Authors: Christina Warinner, et al​