Abstract
During the last decade, paleoproteomics allowed us to open a direct window into the biological past, improving our understanding of the phylogenetic relationships of extant and extinct species, past human diseases, and reconstruction of the human diet. In particular, meta-proteomic studies, mainly carried out on ancient human dental calculus, provided insights into past oral microbial communities and ancient diets. On the contrary, very few investigations regard the analysis of ancient gut microbiota, which may enable a greater understanding of how microorganisms and their hosts have co-evolved and spread under the influence of changing diet practices and habitat. In this respect, this paper reports the results of the first-ever meta-proteomic analysis carried out on a gut tissue sample some 40,000 years old. Proteins were extracted by applying EVA (ethylene–vinyl acetate) films to the surface of the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), and then investigated via a shotgun MS-based approach. Proteomic and peptidomic analysis allowed in-depth exploration of its meta-proteome composition. The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones. Overall, the results of the meta-proteomic analysis here reported agreeing with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth and provided insight into its diet. The data have been deposited to the ProteomeXchange with identifier < PXD025518 > .
Highlights
The significant technological development, in terms of performance and sensitivity, of the mass spectrometers in the past 2 decades has expanded the application of MS-based approaches to the study of ancient proteins
Shotgun meta-proteomics applied to dental calculus is emerging as a powerful tool for disease and dietary characterization of ancient populations
Ancient proteins have been studied for their patterns of degradation and diagenetic chemical modifications (DCMs), and how these patterns can be used as markers for endogenous, ancient proteins as opposed to potential modern contaminants (Hill et al 2015; Cleland et al 2015; Cappellini et al 2012)
Summary
The significant technological development, in terms of performance and sensitivity, of the mass spectrometers in the past 2 decades has expanded the application of MS-based approaches to the study of ancient proteins. Dental calculus has become recognized as one of the richest sources of ancient biomolecules, preserving molecular evidence of oral bacteria, the human host, as well as consumed foodstuffs (Hardy et al 2009; Warinner et al 2014a, b, 2015) In this respect, shotgun meta-proteomics (i.e. characterization of proteins expressed from multiple organisms in a sample) applied to dental calculus is emerging as a powerful tool for disease and dietary characterization of ancient populations. A meta-proteomic approach allowed us to get insight into the gut microbiota composition, which may be reasonably related to the last meal of the mammoth, its diet and habitat
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