Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era

Objectives

Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.

Materials and Methods

Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250–1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.

Results

Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.

Discussion

We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.     

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo‐) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro‐) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high‐throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome‐scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.     

A cross-sectional analysis of the prevalence of dental anxiety and its relation to the oral health-related quality of life in patients with dental treatment needs at a university clinic in Switzerland

doi: 10.1111/j.1741‐2358.2011.00465.x A cross‐sectional analysis of the prevalence of dental anxiety and its relation to the oral health‐related quality of life in patients with dental treatment needs at a university clinic in Switzerland Objectives: The aim of this observational, cross‐sectional study was to analyse the relationship between dental anxiety (DA) and health‐related quality of life aspects associated with oral conditions of a population with dental treatment needs in Switzerland. Methods: The measurements of DA were collected by means of two questionnaires, the Dental Anxiety Scale (DAS) and a Visual Analogue Scale (VAS). Oral health‐related quality of life (OHRQoL) was assessed with the Oral Health Impact Profile (OHIP). The sample included 223 patients enrolled at a university clinic which specialises in oral prosthetic rehabilitation and temporomandibular disorders. Of them, 78.9% were at or above the age of 50. Results: No gender or age dependencies were observed. A comparison of answers regarding OHRQoL and DA revealed a significant interdependence (p = 0.0118); highly anxious patients were 3.55 times more likely to suffer from poor quality of life compared with less anxious ones. Conclusion: This cross‐sectional study of mostly elderly patients seeking dental treatment in Switzerland found that increased DA was associated with an impaired OHRQoL. The average DA was slightly higher than the results of other industrialised countries and the average OHRQoL was reduced.     

A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA

We have used a systematic protocol for extracting, quantitating, sexing and validating ancient human mitochondrial and nuclear DNA of one male and one female Beothuk, a Native American population from Newfoundland, which became extinct approximately 180 years ago. They carried mtDNA haplotypes, which fall within haplogroups X and C, consistent with Northeastern Native populations today. In addition we have sexed the male using a novel-sexing assay and confirmed the authenticity of his Y chromosome with the presence of the Native American specific Y-QM3 single nucleotide polymorphism (SNP). This is the first ancient nuclear SNP typed from a Native population in the Americas. In addition, using the same teeth we conducted a stable isotopes analysis of collagen and dentine to show that both individuals relied on marine sources (fresh and salt water fish, seals) with no hierarchy seen between them, and that their water sources were pooled or stored water. Both mtDNA sequence data and Y SNP data hint at possible gene flow or a common ancestral population for both the Beothuk and the current day Mikmaq, but more importantly the data do not lend credence to the proposed idea that the Beothuk (specifically, Nonosabasut) were of admixed (European-Native American) descent. We also analyzed patterns of DNA damage in the clones of authentic mtDNA sequences; there is no tendency for DNA damage to occur preferentially at previously defined mutational hotspots, suggesting that such mutational hotspots are not hypervariable because they are more prone to damage.     

Ancient DNA reveals a migration of the ancient Di‐qiang populations into Xinjiang as early as the early Bronze Age

Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty‐nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y‐chromosomal DNA analyses combined with the archaeological studies revealed that the Di‐qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age. Am J Phys Anthropol 157:71–80, 2015. © 2014 Wiley Periodicals, Inc.     

基于Web of Science的阴道菌群研究现状和热点的可视化分析与展望

探索阴道菌群近10年来的研究现状并预测其发展趋势。

在Web of Science数据库中检索近10年阴道菌群相关的文献,运用可视化软件VOSviewer进行共词分析、文献耦合、合著分析等。

阴道菌群领域发文量呈整体上升趋势,目前的主要热点研究分为阴道菌群的多样性、传染病学、细胞生物和基因学、阴道菌群与生殖的关联四大方面。

文献可视化研究展现了阴道菌群的研究现状和发展趋势,为相关研究人员提供了借鉴。

     

通过烟台午台遗址人牙结石淀粉粒探究人类对植物资源的利用

本研究通过对山东烟台市午台遗址人牙结石淀粉粒的分析,发现了来自禾本科的粟(Setaria italica L.)、小麦族(Triticeae)、壳斗科栎属(Quercus sp.)、豆科(Fabaceae)及块根块茎类植物的淀粉粒,数量较为丰富,种属来源较为多样,显示了午台遗址先民利用植物性食物资源的多样性。研究表明午台先民除了利用粟黍类农作物作为主要食物资源外,还广泛采集一些野生果类和块根块茎类作为食物的补充。本研究中发现了大遗存中没有发现的壳斗科栎属等,弥补了大遗存研究的不足。     

Impact of socio-demographic variables, oral hygiene practices, oral habits and diet on dental caries experience of Indian elderly: a community-based study

A number of factors influence the caries experience and the pattern of restorative care especially in the older age group. Objective: To evaluate the dental caries experience and restorative treatment needs of an elderly Indian population and to study the impact of socio‐demographic variables, oral hygiene practices, oral habits and dietary practices on them. Design: A community‐based study. Setting: An urban area in the south zone of Delhi and a cluster of four villages in its neighbourhood. Subjects: A total of 1240 elderly subjects, 716 urban and 524 rural, were included in the study. Results: Of the 1052 dentate elderly subjects, 676 (64.2%) had decayed teeth (66.7% root caries and 33.3% coronal caries), 69 (6.6%) had filled teeth and 17 (1.6%) had recurrent decay. Restorations were indicated in 233 (22.2%) subjects, endodontic treatment in 51 (4.8%) and extractions in 424 (40.3%). Urban–rural differences in caries experience were statistically significant. Multivariate regression analysis showed that dental caries was associated with literacy level, oral hygiene practices, oral health perception and diet, while previous restorative treatment was correlated only with location (urban–rural) and presence or absence of systemic diseases. Conclusion: Dental caries prevalence was high amongst the studied elderly population and significant differences were observed in those living in a rural compared with an urban setting. Only a small percentage of elderly had evidence of previous restorative treatment whereas their unmet treatment need was significant.     

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

It is now well recognized that considering species evolutionary history is crucial for understanding the processes driving community assembly (Cavender‐Bares et al. 2009 ). Considerable efforts have been made to integrate phylogenetics and community ecology into a single theoretical framework. Yet, assessing phylogenetic structure at the community scale remains a great challenge, in particular for poorly known organisms. While DNA metabarcoding is increasingly used for assessing taxonomic composition of complex communities from environmental samples, biases and limitations of this technique can preclude the retrieval of information on phylogenetic community structure. In this issue of Molecular Ecology, Andújar et al. (2015) demonstrate that shotgun sequencing of bulk samples of soil beetles and subsequent reconstruction of mitochondrial genomes can provide a solid phylogenetic framework to estimate species diversity and gain insights into the mechanisms underlying the spatial turnover of soil mesofaunal assemblages. This work highlights the enormous potential of ‘metagenome skimming’ not only for improving the current standards of DNA‐based biodiversity assessment but also for opening up the application of phylogenetic community ecology to hyperdiverse and poorly known biota, which was heretofore inconceivable.     

洞察景观环境影响蜜蜂之新视角: 肠道微生物

作为生态服务提供者的传粉蜜蜂与景观生态息息相关, 而以农田为主的景观组成显著降低了传粉蜜蜂的多样性。目前调查研究显示, 农田的扩张与蜜蜂多样性下降相关, 且农药残留对蜜蜂损害严重。景观中的开花植物决定了蜜蜂的食物(营养)组成, 其中花粉蛋白含量与蜜蜂的生长发育紧密相关。尽管研究已证实景观环境会显著影响蜜蜂蜂群的发展和个体的生长繁殖能力, 但未来还需要加强景观组成变化直接作用于蜜蜂的机制研究。另一方面, 大量研究表明蜜蜂肠道共生菌是影响宿主健康的重要因素: 可促进宿主吸收营养和抵抗病原菌。作为传粉者, 蜜蜂接触到的主要外部环境——花粉和花蜜都含有特殊的微生物, 很多研究暗示花源微生物是蜜蜂肠道菌来源之一。研究表明景观环境相关的食物(营养)、农药残留以及环境微生物都会显著影响肠道微生物。现有少量的研究证明不同景观的蜜蜂肠道微生物有差异, 景观环境可能通过作用于蜜蜂肠道微生物进而影响蜜蜂健康。然而不同景观环境中的微生物, 尤其是花源微生物和蜜蜂肠道菌之间的关联有待证明。景观对蜜蜂肠道微生物的影响值得研究, 希望可以从肠道菌的视角鉴别对蜜蜂友好的景观环境, 进而指导土地合理利用和蜜蜂保护。     

Ancient DNA from pollen: a genetic record of population history in Scots pine

Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.