The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals

Ötzi the Iceman: forensic 3D reconstructions of a 5300-year-ago murder case

The cause of death of Ötzi the Iceman has been the subject of extensive investigation. A deep wound on his left shoulder and an arrowhead lodged between his rib cage and left scapula have been central to determining his final moments. While initial CT analyses concluded that exsanguination due to a lacerated left subclavian artery was the cause of death, recent research has suggested that the injury might not have been immediately fatal. This study re-analyzed the 2013 CT scans using a forensic approach to assess the shoulder injury in greater detail, by creating 3D models of the affected anatomical structures and calculating relevant tissue volumes. Additionally, forensic animation techniques were applied to reconstruct Ötzi's likely posture at the moment of impact. A previously unidentified hematoma with an approximate volume of 110 mL was observed, suggesting that death from blood loss alone may not have been immediate, although external hemorrhage cannot be excluded. Furthermore, forensic animation demonstrated that a straight trajectory of the arrow aligns with both the scapular lesion and arterial laceration, providing new insights into the injury mechanism. These results underscore the value of 3D segmentation and modeling in forensic pathology, offering enhanced reconstructions of traumatic events in both contemporary and archaeological contexts.

Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research

Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity and its associated ecosystem services, particularly in biodiversity hotspots where traditional assessments are challenging. Successful use of these data-driven technologies, however, requires access to appropriate reference data. We reviewed the >373,584 reference plant DNA barcodes in public repositories and found that they cumulatively cover a remarkable quarter of the ~435,000 extant land plant species (Embryophyta). Nevertheless, coverage gaps in tropical biodiversity hotspots reflect well-documented biases in biodiversity science - most reference specimens originated in the Global North. Currently, at least 17% of plant families lack any reference barcode data whatsoever, affecting tropical and temperate regions alike. Investigators often emphasise the importance of marker choice and the need to ensure protocols are technically capable of detecting and identifying a broad range of taxa. Yet persistent geographic and taxonomic gaps in the reference datasets show that these protocols rely upon risk undermining all downstream applications of the strategy, ranging from basic biodiversity monitoring to policy-relevant objectives - such as the forensic authentication of materials in illegal trade. Future networks of investigators could work strategically to improve data coverage, which will be essential in global efforts to conserve biodiversity while advancing more fair and equitable access to benefits arising from genetic resources.

Sixty years of research on bracken fern (Pteridium spp.) toxins: Environmental exposure, health risks and recommendations for bracken fern control

Bracken fern (Pteridium spp.) is a highly problematic plant worldwide due to its toxicity in combination with invasive properties on former farmland, in deforested areas and on disturbed natural habitats. The carcinogenic potential of bracken ferns has caused scientific and public concern for six decades. Its genotoxic effects are linked to illudane-type glycosides (ITGs), their aglycons and derivatives. Ptaquiloside is considered the dominating ITG, but with significant contributions from other ITGs. The present review aims to compile evidence regarding environmental pollution by bracken fern ITGs, in the context of their human and animal health implications. The ITG content in bracken fern exhibits substantial spatial, temporal, and chemotaxonomic variation. Consumption of bracken fern as food is linked to human gastric cancer but also causes urinary bladder cancers in bovines browsing on bracken. Genotoxic metabolites are found in milk and meat from bracken fed animals. ITG exposure may also take place via contaminated water with recent data pointing to concentrations at microgram/L-level following rain events. Airborne ITG-exposure from spores and dust has also been documented. ITGs may synergize with major biological and environmental carcinogens like papillomaviruses and Helicobacter pylori to induce cancer, revealing novel instances of chemical and biological co-carcinogenesis. Thus, the emerging landscape from six decades of bracken research points towards a global environmental problem with increasingly complex health implications.

Metaproteomic analysis of King Ghezo tomb wall (Abomey, Benin) confirms 19th century voodoo sacrifices

The palace of King Ghezo in Abomey, capital of the ancient kingdom of Dahomey (present-day Benin), houses two sacred huts which are specific funerary structures. It is claimed that the binder in their walls is made of human blood. In the study presented here, we conceived an original strategy to analyze the proteins present on minute amounts of the cladding sampled from the inner facade of the cenotaph wall and establish their origin. The extracted proteins were proteolyzed and the resulting peptides were characterized by high-resolution tandem mass spectrometry. Over 6397 distinct molecular entities were identified using cascading searches. Starting from without a priori searches of an extended generic database, the peptide repertoire was narrowed down to the most representative organisms-identified by means of taxon-specific peptides. A wide diversity of bacteria, fungi, plants, and animals were detected through the available protein material. This inventory was used to archaeologically reconstruct the voodoo rituals of consecration and maintenance of vitality. Several indicators attested to the presence of traces of human and poultry blood in the material taken. This study shows the essential advantages of paleoproteomics and metaproteomics for the study of ancient residues from archaeological excavations or historical monuments.

Genetic Predisposition of Atherosclerotic Cardiovascular Disease in Ancient Human Remains

Background

Several computed tomographic studies have shown the presence of atherosclerosis in ancient human remains. However, while it is important to understand the development of atherosclerotic cardiovascular disease (ASCVD), genetic data concerning the prevalence of the disease-associated single nucleotide polymorphisms (SNPs) in our ancestors are scarce.

Objective

For a better understanding of the role of genetics in the evolution of ASCVD, we applied an enrichment capture sequencing approach to mummified human remains from different geographic regions and time periods.

Methods

Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.

Findings

Five out of 22 ancient individuals passed all filter steps for calculating a weighted polygenic risk score (PRS) based on 87 SNPs in 56 genes. PRSs were correlated to scores obtained from contemporary people from around the world and cover their complete range. The genetic results of the ancient individuals reflect their phenotypic results, given that the only two mummies showing calcified atherosclerotic arterial plaques on computed tomography scans are the ones exhibiting the highest calculated PRSs.

Conclusions

These data show that alleles associated with ASCVD have been widespread for at least 5,000 years. Despite some limitations due to the nature of aDNA, our approach has the potential to lead to a better understanding of the interaction between environmental and genetic influences on the development of ASCVD.

The Norsesquiterpene Glycoside Ptaquiloside as a Poisonous, Carcinogenic Component of Certain Ferns

Previous studies related to the ptaquiloside molecule, a carcinogenic secondary metabolite known from the world of ferns, are summarised. Ptaquiloside (PTA) belongs to the group of norsesquiterpenes of the illudane type. The name illudane refers to the fungal taxa from which the first representatives of the molecular group were identified. Ptaquiloside occurs mainly in Pteridium fern species, although it is also known in other fern taxa. The species of the genus Pteridium are common, frequent invasive species on all continents, and PTA is formed in smaller or larger amounts in all organs of the affected species. The effects of PTA and of their derivatives on animals and humans are of great toxicological significance. Its basic chemical property is that the molecule can be transformed. First, with the loss of sugar moiety, ptaquilosine is formed, and then, under certain conditions, a dienone derivative (pteridienone) may arise. The latter can alkylate (through its cyclopropane groups) certain molecules, including DNA, in animal or human organisms. In this case, DNA adducts are formed, which can later have a carcinogenic effect through point mutations. The scope of the PTA is interdisciplinary in nature since, for example, molecules from plant biomass can enter the body of animals or humans in several ways (directly and indirectly). Due to its physico-chemical properties (excellent water solubility), PTA can get from the plant into the soil and then into different water layers. PTA molecules that enter the soil, but mainly water, undergo degradation (hydrolytic) processes, so it is very important to clarify the toxicological conditions of a given ecosystem and to estimate the possible risks caused by PTA. The toxicoses and diseases of the animal world (mainly for ruminant farm animals) caused by PTA are briefly described. The intake of PTA-containing plants as a feed source causes not only various syndromes but can also enter the milk (and meat) of animals. In connection with the toxicological safety of the food chain, it is important to investigate the transport of carcinogenic PTA metabolites between organisms in a reassuring manner and in detail. This is a global, interdisciplinary task. The present review aims to contribute to this.

Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10-20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1-2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past.

A Healthier Smile in the Past? Dental Caries and Diet in Early Neolithic Farming Communities from Central Germany

Dental health is closely linked to an individual's health and diet. This bioarcheological study presents dental caries and stable isotope data obtained from prehistoric individuals (n = 101) from three Early Neolithic sites (c. 5500-4800 BCE) in central Germany. Dental caries and ante-mortem tooth loss (AMTL) were recorded and related to life history traits such as biological sex and age at death. Further, we correlate evidence on caries to carbon and nitrogen isotope data obtained from 83 individuals to assess the relationship between diet and caries. In 68.3% of the adults, carious lesions were present, with 10.3% of teeth affected. If AMTL is considered, the values increase by about 3%. The prevalence of subadults (18.4%) was significantly lower, with 1.8% carious teeth. The number of carious teeth correlated significantly with age but not sex. The isotopic data indicated an omnivorous terrestrial diet composed of domestic plants and animal derived protein but did not correlate with the prevalence of carious lesions. The combined evidence from caries and isotope analysis suggests a prevalence of starchy foods such as cereals in the diet of these early farmers, which aligns well with observations from other Early Neolithic sites but contrasts to Late Neolithic and Early Bronze Age populations in Germany.

Weight Loss and Fat Metabolism during Multi-Day High-Altitude Sojourns: A Hypothesis Based on Adipocyte Signaling

Several publications and random observations have reported weight loss in high-altitude sojourners of both sexes. This could be a result of multiple adaptations, which hypoxia and mountaineering provoke on a cellular and organic level. Several publications have discussed the effect on appetite-regulating hormones to be one of the main contributing factors. We aimed to review the available data and show the current state of knowledge regarding nutritional aspects in high altitude with a special focus on fatty dietary forms. To reach this aim we conducted a literature search via PubMed according to the PRISMA 2020 protocol to identify relevant studies. We found that very few studies cover this field with scientifically satisfying evidence. For final analysis, reviews as well as papers that were not clearly related to the topic were excluded. Six articles were included discussing hormonal influences and the impact of exercise on appetite regulation as well as genetic factors altering metabolic processes at altitude. Leptin expression seems to be the biggest contributor to appetite reduction at altitude with an initial increase followed by a decrease in the course of time at high altitude. Its expression is greatly dependent on the amount of white adipose tissue. Since the expression of leptin is associated with an increased β-oxidation of fatty acids, a high-fat diet could be advantageous at a certain time point in the course of high-altitude sojourns.

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

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.

Presence of the carcinogen ptaquiloside in fern-based food products and traditional medicine: Four cases of human exposure

Ptaquiloside (PTA) is a natural carcinogen present in many ferns. Brackens (Pteridium sp.) contain PTA and are classified by WHO/IARC as ‘ … possibly carcinogenic to humans’, however, these ferns are used in food, traditional medicine and as food supplements around the world. This study aimed to outline the presence of PTA in different human exposure routes by using and validating an LC-MS based protocol to test the contents of PTA in commercial products, the degradation product Pterosin B (PtB) and wild specimens from Europe, Asia and North America. The Limit of Detection of the protocol was 0.024 μg g⁻¹ for PTA and 0.028 μg g⁻¹ for PtB. PTA and PtB were present in most wild specimens (PTA: BD – 6300 ± 520 μg g⁻¹; PtB: BD - 449 ± 1 μg g⁻¹) while commercial products made from fronds, as well as fronds prepared as traditional Chinese medicine, were in the range 44 ± 3 to 666 ± 33 μg g⁻¹ for PTA and BD to 1653 ± 184 μg g⁻¹ for PtB. This study did not find PTA/PtB in rhizomes and products made thereof nor in homoeopathic products based on bracken. Boiling or drying bracken showed to reduce PTA some degree but cannot remove it completely. Interestingly, crosiers with no PTA/PtB were found in the USA, indicating a potential for commercial production of PTA-free fronds.

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Ptaquiloside is a natural carcinogen found in fern-based food products and natural remedies.

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Bracken ferns collected in the wild contain ptaquiloside after processing.

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Commercial dried bracken fronds (leaves) contain high levels of ptaquiloside.

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Commercial products based on rhizomes and some natural remedies contain no ptaquiloside.

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Presence of no-ptaquiloside ferns indicate potential of growing non-toxic cultivars.

Paleogenomics of the prehistory of Europe: human migrations, domestication and disease

A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.

DNA methylation profiling in mummified human remains from the eighteenth-century

Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we were able to detect characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions matched the fact that the specimen was lung tissue from a 28-year-old woman. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.

[The Iceman : Life scenarios and pathological findings from 30 years of research on the glacier mummy "Ötzi"]

The comprehensive investigation of the excellently preserved mummy of Ötzi, the Iceman, and his equipment over the last 30 years has provided a wealth of information about the life and disease of this late Neolithic individual. This research has indicated that his origin was from a local southern Alpine population, that he grew up in the valleys of the Southern Alps, and that he had considerable local mobility. He had well-balanced nutrition with a mixed vegetable and animal diet. He was very mobile in the alpine terrain and of athletic constitution. The Iceman suffered from mild to moderate degenerative joint disease primarily of the right hip joint, slight spondylosis of the cervical and lumbar spine, a minor focal (premature) arteriosclerosis, lung anthracosis and possibly silicosis, previous pleuritic inflammation (possibly of post-specific origin), intestinal infections of the stomach by Helicobacter pylori and Trichuris trichiura worm infestation in the intestines, a mild osteomalacia of cancellous bone, and diverse pathologies of his teeth with dental caries and periodontitis, as well as hair anomalies. The presence of borreliosis is still under debate. As potential remedies, the Iceman carried some anthelmintic substances with him: a birch polypore and an anthelmintic fern. The numerous tattoos may also have had therapeutic effects. Finally, the last days of Ötzi could be reconstructed quite precisely: his gastrointestinal content indicates that the Iceman moved from Alpine heights to a lower location and then again up to the glacier region where he died. During this journey he encountered two attacks: the first, several days before his death, lead to a stabbing wound in his right hand; the second was an arrow hit that wounded the Iceman lethally at his left axilla by laceration of the subclavian artery.

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

Liquid chromatography and mass spectrometry for the analysis of acylglycerols in art and archeology

Lipid characterization in art and archeology, together with the study of lipid degradation processes, is an important research area in heritage science. Lipid-based materials have been used as food since ancient times, but also employed as illuminants and as ingredients in cosmetic, ritual, and pharmaceutical preparations. Both animal and plant lipids have also been processed to produce materials used in art and crafts, such as paint binders, varnishes, waterproofing agents, and coatings. Identifying the origin of the lipid materials is challenging when they are found in association with artistic historical objects. This is due to the inherent complex composition of lipids, their widespread occurrence, and the chemical alterations induced by ageing. The most common approach for lipid characterization in heritage objects entails profiling fatty acids by gas chromatography/mass spectrometry after saponification or transesterification. New developments in high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) for the characterization of acylglycerols, together with more efficient sample treatments, have fostered the introduction of liquid chromatography for characterizing the lipid profile in heritage objects. This review reports the latest developments and applications of HPLC-MS for the characterization of lipid materials in the field of heritage science. We describe the various approaches for sample pretreatment and highlight the advantages and limitations of HPLC-MS in the analysis of paint and archeological samples. © 2020 John Wiley & Sons Ltd.

Comprehensive coverage of human last meal components revealed by a forensic DNA metabarcoding approach

Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. While the identification of food components of plant and animal origin has traditionally been conducted by macro- and microscopical approaches in case of incomplete digestion, molecular methods provide the potential to increase sensitivity and taxonomic resolution. In particular, DNA metabarcoding (PCR-amplification and next generation sequencing of complex DNA mixtures) has seen a rapid growth in the field of wildlife ecology to assess species’ diets from faecal and gastric samples. Despite clear advantages, molecular approaches have not yet been established in routine human forensics to investigate the last meal components of deceased persons. In this pilot study we applied for the first time a DNA metabarcoding approach to assess both plant and vertebrate components of 48 human stomach content samples taken during medicolegal autopsies. We obtained a final dataset with 34 vertebrate and 124 vegetal unique sequences, that were clustered to 9 and 33 operational taxonomic units (OTUs), respectively. Our results suggest that this approach can provide crucial information about circumstances preceding death, and open promising perspectives for biomedical dietary surveys based on digested food items found in the gastrointestinal tract.

How Modern Mass Spectrometry Can Solve Ancient Questions: A Multi-Omics Study of the Stomach Content of the Oldest Human Ice Mummy, the 5300-Year-Old Iceman or Oetzi

In the past 40 years, mass spectrometry has seen a stunning development regarding increased sensitivity, resolution, and accuracy, especially for biomolecule analysis. These days without any doubt mass spectrometry is the most powerful analytical tool as a standalone technique or in conjunction with separation techniques such as high-performance liquid chromatography (HPLC), gas chromatography (GC), or capillary electrophoresis (CE). It is literally used to analyze any kind of small or large molecules ranging from basic elements to metabolites, pesticides, toxins, small or large molecule drugs, oligonucleotides, peptides, proteins, and many other molecule classes.Here, various modern mass spectrometry techniques such as LC-MS , GC-MS, ICP-MS, and elemental bio-imaging are briefly described how they were used for the first complex multi-omics study of the oldest human ice mummy, the 5300-year-old Iceman or Oetzi. The study comprised of mass spectrometry-driven proteomics (protein profiling and characterization), metabolomics, lipidomics, glycomics, and metallomics.

Ancient protein analysis in archaeology

The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.

Decorated bodies for eternal life: A multidisciplinary study of late Roman Period stucco-shrouded portrait mummies from Saqqara (Egypt)

This study focuses on the multidisciplinary investigation of three stucco-shrouded mummies with mummy portrait from Egypt dating from the late 3^rd to the middle of the 4^th century AD, corresponding to the late Roman Period. These three mummies were excavated in the early 17^th and late 19^th centuries in the Saqqara necropolis near the ancient Egyptian capital of Memphis. Two of them experienced an interesting collection history, when they became part of the collection of the Elector of Saxony and King of Poland August II in Dresden, Germany, in 1728. The investigation includes information about the mummies’ discovery, collection history and shroud decoration obtained through Egyptological expertise. In addition, information on the state of preservation, technique of artificial mummification, age at death, sex, body height and health of the deceased was achieved through computed tomography (CT) analysis. Research yielded an adult male, a middle-aged female and a young female. Due to the rather poorly preserved bodies of the male and middle-aged female, a specific technique of artificial mummification could not be ascertained. Brain and several internal organs of the well-preserved young female were identified. Wooden boards, beads of necklaces, a hairpin, and metal dense items, such as lead seals, nails and two coins or medallions were discovered. Paleopathological findings included carious lesions, Schmorl’s nodes, evidence of arthritis and a vertebral hemangioma. The study revealed insights on the decoration and burial preparation of individuals of upper socioeconomic status living in the late Roman Period, as well as comprehensive bioanthropological information of the deceased.

The Wonderful World of Poo: The Turdome and Beyond

Defecate: it is something we all do, it is something we joke about, yet for many in real life it is a subject that is taboo. However, it is now being realised that faeces are a veritable scientific goldmine, have many potential uses, and may even save your life! In this article I will review the history behind the use of faecal material and look at some of its emerging playing fields, in particular its role in medical diagnosis. I will discuss faecal proteomics and other omics technologies (Proteogenomics: The Omics Pipeline), including studies on the microbiome, in order to understand, diagnose, and treat gastrointestinal tract pathologies and other diseases, and show how these technologies will play a role in the move towards personalized medicine.

Helicobacter pylori in ancient human remains

The bacterium Helicobacter pylori (H. pylori) infects the stomachs of approximately 50% of all humans. With its universal occurrence, high infectivity and virulence properties it is considered as one of the most severe global burdens of modern humankind. It has accompanied humans for many thousands of years, and due to its high genetic variability and vertical transmission, its population genetics reflects the history of human migrations. However, especially complex demographic events such as the colonisation of Europe cannot be resolved with population genetic analysis of modern H. pylori strains alone. This is best exemplified with the reconstruction of the 5300-year-old H. pylori genome of the Iceman, a European Copper Age mummy. Our analysis provided precious insights into the ancestry and evolution of the pathogen and underlined the high complexity of ancient European population history. In this review we will provide an overview on the molecular analysis of H. pylori in mummified human remains that were done so far and we will outline methodological advancements in the field of ancient DNA research that support the reconstruction and authentication of ancient H. pylori genome sequences.

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

Molecular Reconstruction of the Diet in Human Stool Samples

Understanding dietary effects on the gut microbial composition is one of the key questions in human microbiome research. It is highly important to have reliable dietary data on the stool samples to unambiguously link the microbiome composition to food intake. Often, however, self-reported diet surveys have low accuracy and can be misleading. Thereby, additional molecular biology-based methods could help to revise the diet composition. The article by Reese et al. [A. T. Reese, T. R. Kartzinel, B. L. Petrone, P. J. Turnbaugh, et al., mSystems 4(5):e00458-19, 2019, https://doi.org/10.1128/mSystems.00458-19] in a recent issue of mSystems describes a DNA metabarcoding strategy targeting chloroplast DNA markers in stool samples from 11 human subjects consuming both controlled and freely selected diets. The aim of this study was to evaluate the efficiency of this molecular method in detecting plant remains in the sample compared to the written dietary records. This study displays an important first step in implementing molecular dietary reconstructions in stool microbiome studies which will finally help to increase the accuracy of dietary metadata.

Seventy-five mosses and liverworts found frozen with the late Neolithic Tyrolean Iceman: Origins, taphonomy and the Iceman's last journey

The Iceman site is unique in the bryology of the Quaternary. Only 21 bryophytes (mosses and liverworts) grow now in the immediate vicinity of the 5,300 year old Iceman discovery site at 3,210m above sea level in the Ötztal Alps, Italy. By contrast 75 or more species including at least ten liverworts were recovered as subfossils frozen in, on and around the Iceman from before, at and after his time. About two thirds of the species grow in the nival zone (above 3,000m above sea level) now while about one third do not. A large part of this third can be explained by the Iceman having both deliberately and inadvertently carried bryophytes during his last, fatal journey. Multivariate analyses (PCA, RDA) provide a variety of explanations for the arrivals of the bryophytes in the rocky hollow where the mummy was discovered. This is well into the nival zone of perennial snow and ice with a very sparse, non-woody flora and very low vegetation cover. Apart from the crucial anthropochory (extra-local plants), both hydrochory (local species) and zoochory (by wild game such as ibex of both local and extra-local species) have been important. Anemochory of mainly local species was of lesser importance and of extra-local species probably of little or no importance. The mosses Neckera complanata and several other ecologically similar species as well as a species of Sphagnum (bogmoss) strongly support the claim that the Iceman, took northwards up Schnalstal, South Tyrol, as the route of the last journey. A different species of bogmoss, taken from his colon is another indication the Iceman’s presence at low altitude south of Schnalstal during his last hours when he was first high up, low down and finally at over 3,000m.

Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept

Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.

Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to characterize diets, but such approaches have not previously been widely applied to humans. Here, we present data derived from sequencing of a chloroplast DNA marker (the P6 loop of the trnL [UAA] intron) in stool samples collected from 11 individuals consuming both controlled and freely selected diets. The DNA metabarcoding strategy resulted in successful PCR amplification in about 50% of samples, which increased to a 70% success rate in samples from individuals eating a controlled plant-rich diet. Detection of plant taxa among sequenced samples yielded a recall of 0.86 and a precision of 0.55 compared to a written diet record during controlled feeding of plant-based foods. The majority of sequenced plant DNA matched common human food plants, including grains, vegetables, fruits, and herbs prepared both cooked and uncooked. Moreover, DNA metabarcoding data were sufficient to distinguish between baseline and treatment diet arms of the study. Still, the relatively high PCR failure rate and an inability to distinguish some dietary plants at the sequence level using the trnL-P6 marker suggest that future methodological refinements are necessary. Overall, our results suggest that DNA metabarcoding provides a promising new method for tracking human plant intake and that similar approaches could be used to characterize the animal and fungal components of our omnivorous diets.

IMPORTANCE Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.

Possible evidence for care and treatment in the Tyrolean Iceman

The Tyrolean Iceman is the world's oldest glacier mummy. He was found in September 1991 in the Italian part of the Ötztal Alps. Since his discovery a variety of morphological, radiological and molecular analyses have been performed that revealed detailed insights into his state of health. Despite the various pathological conditions found in the Iceman, little is known about possible forms of care and treatment during the Copper Age in Northern Italy. A possible approach to this topic is the presence of tattoos on the mummified body. In previous work, it was already believed that the tattoos were administered as a kind of treatment for his lower back pain and degenerative joint disease of his knees, hip and wrist. In other studies, the tattoos of the Iceman have been related to an early form of acupuncture. We carefully re-evaluated the various health issues of the Iceman, including joint diseases, gastrointestinal problems and arterial calcifications and compared them to the location and number of tattoos. Together with the finding of medically effective fungi and plants, such as the birch polypore or fern in his equipment and intestines, we suggest that care and treatment was already common during the Iceman's time.

Spending too little in hard times

People's decisions to consume and save resources are critical to their wellbeing. Previous experiments find that people typically spend too much because of how they discount the future. We propose that people's motive to preserve their savings can instead cause them to spend too little in hard times. We design an economic game in which participants can store resources for the future to survive in a harsh environment. A player's income is uncertain and consumption yields diminishing returns within each day, creating tradeoffs between spending and saving. We compare participants' decisions to a heuristic that performed best in simulations. We find that participants spent too much after windfalls in income, consistent with previous research, but they also spent too little after downturns, supporting the resource preservation hypothesis. In Experiment 2, we find that by varying the income stream, the downturn effect can be isolated from the windfall effect. In Experiments 3-4, we find the same downturn effect in games with financial and political themes.