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Cultures of dairying: gene-culture-microbiome evolution and the ancient invention of dairy foods

Periodic Reporting for period 1 - DAIRYCULTURES (Cultures of dairying: gene-culture-microbiome evolution and the ancient invention of dairy foods)

Reporting period: 2018-11-01 to 2020-04-30

Global milk production exceeds 697 million metric tons – the volume equivalent of 278,800 Olympic size swimming pools – enough for every person on earth to consume a quarter litre of milk every single day. And yet, three quarters of the world’s population is genetically lactose intolerant. Milk is a fraught food, deeply entangled with politics, culture, economics, and history. At once celebrated as a super-food, vilified as unnatural, promoted as a cultural value, and decried as a danger, milk is a food whose history reflects the uneasy relationship between humans and food in the modern world. Public opinion of milk and dairy products has changed greatly over the past 50 years. As recently as the 1960s, milk was considered a basic food group in Europe and North America, a product so universal that the inability to digest milk was considered by the Western medical profession to be an unfortunate, but uncommon, disease alternately known as primary acquired lactase deficiency, adult hypolactasia, and lactose intolerance. Decades of subsequent research have shown that the ability to digest milk in adulthood is actually a derived trait found in only a few human populations (notably Europeans) with long histories of dairy pastoralism. In recent years, the pendulum has swung fully in the opposite direction with numerous media stories and organizations claiming that milk is an unnatural and harmful product with potential links to gastrointestinal illness, cancer, and cardiovascular disease. The growing public skepticism regarding milk as a dietary component relies in part on implicit and poorly defined assumptions about the nature of digestion, the role of microbes in human health, and the perceived “naturalness” of dairy as a human food. Importantly, what is generally missing entirely from public debate is an evidence-based accounting of the context and process by which dairying arose as a human food in the first place and the role it has subsequently played in the long arc of human history. The DAIRYCULTURES project seeks to enrich scientific and public understanding of dairy foods by systematically investigating the deep history of the biological and cultural relationships between humans, livestock, and microbes in a “gene-culture-microbiome coevolution” framework.

The prehistory of dairying presents a puzzling problem, a “milk paradox,” for archaeology. How and why did ancient peoples develop a staple food that is apparently poorly digested by most adult humans? And, once developed, how did this food spread on a continental scale? How are the Bronze Age steppe migrations of humans and their livestock related to the spread of dairying across Eurasia, and can we accurately trace the spread of dairying in the archaeological record? Is lactase persistence (LP) really the only important biological factor in the gene-culture co-evolution of dairying – or should we also be focusing on microbes? the The DAIRYCULTURES project focuses its attention on Mongolia, a country in which half of the population still leads a nomadic pastoralist lifestyle and where as much as 80% of the rural diet derives from dairy products. In addition to its rich dairying traditions today, Mongolia also has a long recorded history of dairying, including numerous references to dairy livestock and specific dairy products dating as far back as the 13th century in the Secret History of the Mongols. This combination of a rich dairy prehistory and a robust contemporary dairy tradition makes Mongolia an ideal biocultural laboratory in which to investigate “gene-culture-microbiome” coevolution.

There are three outstanding problems regarding our understanding of animal milk-based subsistence in traditional dairying societies like Mongolia. First, the origin of dairy domesticates and the time depth of dairying is poorly understood. Second, although recent advances have been made in the detection of milk proteins from dental calculus and archaeological food containers, current databases are patchy and incomplete in their coverage of milk protein sequences from various dairy species, making the identification of archaeological milk proteins challenging. Third, relatively little is known regarding the relationship between the gut microbiome and dairy digestion in traditional dairying societies, like Mongolia.

The DAIRYCULTURES project aims to address these problems by (1) establishing a genetic framework for domesticated sheep, goat, cattle, and yak ancestry lineages and the detection of past human and animal breed migrations, (2) establishing better tools, protocols, and resources for milk detection and characterization from archaeological materials, and (3) evaluating the role of the human gut microbiome in milk digestion and dairy gene-culture-microbiome coevolution in contemporary Mongolia.
The DAIRYCULTURES project has made significant progress towards project goals in several areas. All project staff have been hired, including students and postdocs in Germany as well as our fieldwork coordination team in Mongolia.

We have reconstructed the time depth of dairying in Mongolia, including the dairying history of five of Mongolia's seven dairy livestock. This work has included the development of new approaches for authenticating ancient milk proteins, as well as a systematic evaluation and optimization of of protein extraction protocols.

We have begun laboratory work on characterizing genetic diversity in ancient dairy livestock breeds.

The DAIRYCULTURES project has contributed to reconstructing the population history of ancient Mongolia, which allows us to contextualize major dairy technologies within a broader cultural and societal context.

To refine our understanding of dairy subsistence and milk intake in current Mongolian diets, we have empirically measured the macronutrient (including lactose) and micronutrient content of 15 major dairy foods consumed in Mongolia, and an additional 15 are currently undergoing analysis. With this dataset, we are able to accurately measure and predict lactose intake in contemporary nomadic herder diets.

We have made significant progress in identifying the relevant regulatory agencies and ethical commissions for conducting work on modern animal and human genetics. We have begun the process of establishing memoranda of understanding with partner Mongolian institutions and applying for ethical approvals for our study protocol.

We have developed and tested a field protocol for gut microbiome collection using FTA cards, which allows us to collect gut microbiome samples in remote locations. We have also evaluated a large panel of currently available metagenomics tools for taxonomic classification and functional inference.

We have created a public website for the project, and we are also in the process of creating a searchable database of ethnographic photos and videos related to Mongolian dairying practices that will be embedded in the website.

We have hosted two major conferences related to the project in Central Asia (Mongolia and Kyrgyzstan) and Portugal, as well as an interactive workshop to disseminate information about the project to potential study participants and members of the public in Mongolia.
Future anticipated results include the characterization and systematic comparison of the gut microbiome in Mongolian nomadic herders and urban dwellers, and the completion of genetic analysis of modern and archaeological dairy livestock.