Background Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates. Results Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins. Conclusions Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus. Electronic supplementary material The online version of this article (10.1186/s40168-019-0717-3) contains supplementary material, which is available to authorized users.

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), Viking sailors reached Greenland, North America, and large parts of western Eurasia, and left a legacy that persists today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BCE) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

High resolution incremental isotopic analysis of the dentine from early forming teeth, especially first molars (M1s), provides a means to assess the effects of poor childhood nutrition and healthcare on individuals in an assemblage where there are no infants to study. This approach is applied to an 18th and 19th century cemetery population associated with St Saviour's Almshouse burial ground in Southwark, London, to assess whether, or how, early dietary history, including weaning age, influenced health and nutritional status. The results show a general pattern in which non-breast milk foods were introduced before or by 6 months of age, as indicated by elevated δ(15) N during this period. Almost all individuals for which we also have second molar (M2) records, showed lower δ(15) N values from a very young age (>1 year) until approximately 8-10 years, compared to adult values. The overall results show a significant difference in δ(1) (3) C (p = 0 to 4sf, F = 17.327) and a weaker statistical difference in δ(15) N between males and females (p = 0.019, F = 5.581). One possible cause of this is a difference in the diet of males and females early in life, or alternatively, a greater susceptibility of males to nutritional deprivation compared to females. The latter argument is strengthened by a significant difference in the incidence of enamel hypoplasia between the males and females, with 7.7% of male teeth showing defects, compared to 3.9% of females.

The cemetery is located in the south-west of Pottenbrunn, on plot "Steinfeld" (15°41´05"/48°13´55"). Discovered in 1930, it had already yielded objects dating to the early La Tène period. In 1981, road construction revealed further finds which initiated rescue excavations by the Bundesdenkmalamt (State Office for Protection of Historical Monuments) under the guidance of J.-W. Neugebauer (Ramsl 2002a(Ramsl , 13) in 1981(Ramsl and 1982. A total of 42 graves with 45 burials (single and double inhumations, and cremations) have been documented. Some burials were severely disturbed (by ancient activities such as grave robbing and/or contemporary construction work), and some were set within fenced enclosures ("Grabgärten"). Three (of 22) samples of charcoal and bone fragments taken by Peter Stadler (Department of Prehistory, Natural History Museum Vienna) in the course of the FWFproject "Absolute Chronology for Early Civilisations in Austria and Central Europe" returned AMS dates of 410-200 cal BCE (grave 520), 550-200 cal BCE (grave 565) and 380-350 cal BCE (grave 1005) (Ramsl 2002b, 359). The cremation burials were not included in the initial osteological analysis, but 31 inhumed individuals were studied (Gerold 2002). Petrous bones from three of these were successfully analyzed for aDNA. Sample I11699 (female) derived from an individual (inv. no. 26.238) aged c. 20 years in grave 89 which, despite disturbance in antiquity, was accompanied by fibulae and ceramic vessels. Sample I11701 (male) derived from an individual (inv. no. 26.249) aged c. 18 years in grave 570, which also included shears, fibulae, and ceramic vessels. Evidence for bone porosity in the mandible and maxilla suggest possible Vitamin C deficiency, while enamel hypoplasia points to malnutrition or illness during childhood. Sample I11708 (female) derived from an individual (inv.no. 26.250) aged c. 25-35 years in grave 574/2, who was richly adorned with fibulae, bronze, iron and silver-rings, an amber ring, a bracelet, a glass bead, and a worked bone artefact.