Proteomic evidence of dietary sources in ancient dental calculus.

Irina M. Velsko,Greger Larson,Meaghan Mackie,Camilla Speller ,Eros Chaves,Anita Radini,Malin Holst,Amy Z. Mundorff,Abigail Bouwman,Jessica Hendy,Sarah Fiddyment,Huiyun Rao,Román Fischer ,Richard Hagan,Krista McGrath,Matthew J. Collins,Courtney A. Hofman,Lauren Klaus,Christina Warinner,Christian Trachsel

doi:10.1098/rspb.2018.0977

Abstract

Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.

Highlights

Archaeological dental calculus is a rich source of ancient DNA and proteins, providing insights into past oral microbial communities [1,2] and ancient diets [3]
Proteomic evidence for the consumption of non-dairy animal products was limited to one putative faunal blood protein: a haemoglobin protein of likely ruminant origin identified in a single post-medieval individual (FAO14)
We identified putative plant proteins originating from oats (A. sativa), peas (P. sativum) and Brassicaceae in archaeological dental calculus and from potato (S. tuberosum), soybean (Glycine) and peanut (A. hypogaea) in modern individuals

Summary

Introduction

Archaeological dental calculus is a rich source of ancient DNA and proteins, providing insights into past oral microbial communities [1,2] and ancient diets [3]. Proteomic evidence for the consumption of non-dairy animal products was limited to one putative faunal blood protein: a haemoglobin protein of likely ruminant origin identified in a single post-medieval individual (FAO14) This underrepresentation of non-dairy derived animal proteins is strongly influenced by the fact that many of the most abundant proteins in muscle, skin, and bone (i.e. collagens, keratins, actin and myosin) are expressed by highly conserved genes with little or no sequence variation, and peptides deriving from these proteins may not be resolvable below the taxonomic level of class or order. Further research is necessary to identify the extent to which taphonomic (e.g. protein degradation), biological (e.g. AMY1 copy number variation, 7 amylase enzyme production) and dietary factors (e.g. starch consumption) influence its detection in dental calculus

Challenges and recommendations for dietary protein studies

Conclusion

Findings

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