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Badillo-Sanchez D, Serrano Ruber M, Davies-Barrett A, Jones DJ, Hansen M, Inskip S. Metabolomics in archaeological science: A review of their advances and present requirements. SCIENCE ADVANCES 2023; 9:eadh0485. [PMID: 37566664 PMCID: PMC10421062 DOI: 10.1126/sciadv.adh0485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/11/2023] [Indexed: 08/13/2023]
Abstract
Metabolomics, the study of metabolites (small molecules of <1500 daltons), has been posited as a potential tool to explore the past in a comparable manner to other omics, e.g., genomics or proteomics. Archaeologists have used metabolomic approaches for a decade or so, mainly applied to organic residues adhering to archaeological materials. Because of advances in sensitivity, resolution, and the increased availability of different analytical platforms, combined with the low mass/volume required for analysis, metabolomics is now becoming a more feasible choice in the archaeological sector. Additional approaches, as presented by our group, show the versatility of metabolomics as a source of knowledge about the human past when using human osteoarchaeological remains. There is tremendous potential for metabolomics within archaeology, but further efforts are required to position it as a routine technique.
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Affiliation(s)
| | - Maria Serrano Ruber
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Anna Davies-Barrett
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Donald J. L. Jones
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester, UK
- The Leicester van Geest MultiOmics Facility, University of Leicester, Leicester, UK
| | - Martin Hansen
- Environmental Metabolomics Lab, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Sarah Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
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Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Míguez A, Manghi P, Cemper-Kiesslich J, Rosendahl W, Kusebauch U, Morrone SR, Hoopmann MR, Rota-Stabelli O, Rattei T, Moritz RL, Oeggl K, Segata N, Zink A, Reschreiter H, Kowarik K. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Curr Biol 2021; 31:5149-5162.e6. [PMID: 34648730 PMCID: PMC8660109 DOI: 10.1016/j.cub.2021.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.
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Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy.
| | - Mohamed S Sarhan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander Schoenafinger
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy; Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Stefania Zingale
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Aitor Blanco-Míguez
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Jan Cemper-Kiesslich
- Interfaculty Department of Legal Medicine & Department of Classics, University of Salzburg, Ignaz-Harrer-Straße 79, 5020 Salzburg, Austria
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159 Mannheim, Germany; Curt-Egelhorn-Zentrum Archäomtrie, D6,3, 61859 Mannheim, Germany
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all'Adige (TN), Italy
| | - Thomas Rattei
- CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Klaus Oeggl
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Nicola Segata
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Hans Reschreiter
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria
| | - Kerstin Kowarik
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria.
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Abstract
The compositional space of a set of 120 diverse beer samples was profiled by rapid flow-injection analysis (FIA) Fourier transform ion cyclotron mass spectrometry (FTICR-MS). By the unrivaled mass resolution, it was possible to uncover and assign compositional information to thousands of yet unknown metabolites in the beer matrix. The application of several statistical models enabled the assignment of different molecular pattern to certain beer attributes such as the beer type, the way of adding hops and the grain used. The dedicated van Krevelen diagrams and mass difference networks displayed the structural connectivity of the annotated sum formulae. Thereby it was possible to provide a base of knowledge of the beer metabolome far above database-dependent annotations. Typical metabolic signatures for beer types, which reflect differences in ingredients and ways of brewing, could be extracted. Besides, the complexity of isomeric compounds, initially profiled as single mass values in fast FIA-FTICR-MS, was resolved by selective UHPLC-ToF-MS2 analysis. Thereby structural hypotheses based on FTICR’s sum formulae could be confirmed. Benzoxazinoid hexosides deriving from the wheat’s secondary metabolism were uncovered as suitable marker substances for the use of whole wheat grains, in contrast to merely wheat starch or barley. Furthermore, it was possible to describe Hydroxymethoxybenzoxazinone(HMBOA)-hexosesulfate as a hitherto unknown phytoanticipin derivative in wheat containing beers. These findings raise the potential of ultrahigh resolution mass spectrometry for rapid quality control and inspection purposes as well as deep metabolic profiling, profound search for distinct hidden metabolites and classification of archeological beer samples.
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