Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions

Duration of androgen deprivation therapy with postoperative radiotherapy for prostate cancer: a comparison of long-course versus short-course androgen deprivation therapy in the RADICALS-HD randomised trial

Background Previous evidence supports androgen deprivation therapy (ADT) with primary radiotherapy as initial treatment for intermediate-risk and high-risk localised prostate cancer. However, the use and optimal duration of ADT with postoperative radiotherapy after radical prostatectomy remains uncertain. Methods RADICALS-HD was a randomised controlled trial of ADT duration within the RADICALS protocol. Here, we report on the comparison of short-course versus long-course ADT. Key eligibility criteria were indication for radiotherapy after previous radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to add 6 months of ADT (short-course ADT) or 24 months of ADT (long-course ADT) to radiotherapy, using subcutaneous gonadotrophin-releasing hormone analogue (monthly in the short-course ADT group and 3-monthly in the long-course ADT group), daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as metastasis arising from prostate cancer or death from any cause. The comparison had more than 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 75% to 81% (hazard ratio [HR] 0·72). Standard time-to-event analyses were used. Analyses followed intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov , NCT00541047 . Findings Between Jan 30, 2008, and July 7, 2015, 1523 patients (median age 65 years, IQR 60–69) were randomly assigned to receive short-course ADT (n=761) or long-course ADT (n=762) in addition to postoperative radiotherapy at 138 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 8·9 years (7·0–10·0), 313 metastasis-free survival events were reported overall (174 in the short-course ADT group and 139 in the long-course ADT group; HR 0·773 [95% CI 0·612–0·975]; p=0·029). 10-year metastasis-free survival was 71·9% (95% CI 67·6–75·7) in the short-course ADT group and 78·1% (74·2–81·5) in the long-course ADT group. Toxicity of grade 3 or higher was reported for 105 (14%) of 753 participants in the short-course ADT group and 142 (19%) of 757 participants in the long-course ADT group (p=0·025), with no treatment-related deaths. Interpretation Compared with adding 6 months of ADT, adding 24 months of ADT improved metastasis-free survival in people receiving postoperative radiotherapy. For individuals who can accept the additional duration of adverse effects, long-course ADT should be offered with postoperative radiotherapy. Funding Cancer Research UK, UK Research and Innovation (formerly Medical Research Council), and Canadian Cancer Society

Adding 6 months of androgen deprivation therapy to postoperative radiotherapy for prostate cancer: a comparison of short-course versus no androgen deprivation therapy in the RADICALS-HD randomised controlled trial

Background Previous evidence indicates that adjuvant, short-course androgen deprivation therapy (ADT) improves metastasis-free survival when given with primary radiotherapy for intermediate-risk and high-risk localised prostate cancer. However, the value of ADT with postoperative radiotherapy after radical prostatectomy is unclear. Methods RADICALS-HD was an international randomised controlled trial to test the efficacy of ADT used in combination with postoperative radiotherapy for prostate cancer. Key eligibility criteria were indication for radiotherapy after radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to radiotherapy alone (no ADT) or radiotherapy with 6 months of ADT (short-course ADT), using monthly subcutaneous gonadotropin-releasing hormone analogue injections, daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as distant metastasis arising from prostate cancer or death from any cause. Standard survival analysis methods were used, accounting for randomisation stratification factors. The trial had 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 80% to 86% (hazard ratio [HR] 0·67). Analyses followed the intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov, NCT00541047. Findings Between Nov 22, 2007, and June 29, 2015, 1480 patients (median age 66 years [IQR 61–69]) were randomly assigned to receive no ADT (n=737) or short-course ADT (n=743) in addition to postoperative radiotherapy at 121 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 9·0 years (IQR 7·1–10·1), metastasis-free survival events were reported for 268 participants (142 in the no ADT group and 126 in the short-course ADT group; HR 0·886 [95% CI 0·688–1·140], p=0·35). 10-year metastasis-free survival was 79·2% (95% CI 75·4–82·5) in the no ADT group and 80·4% (76·6–83·6) in the short-course ADT group. Toxicity of grade 3 or higher was reported for 121 (17%) of 737 participants in the no ADT group and 100 (14%) of 743 in the short-course ADT group (p=0·15), with no treatment-related deaths. Interpretation Metastatic disease is uncommon following postoperative bed radiotherapy after radical prostatectomy. Adding 6 months of ADT to this radiotherapy did not improve metastasis-free survival compared with no ADT. These findings do not support the use of short-course ADT with postoperative radiotherapy in this patient population

The ancestral shape hypothesis: an evolutionary explanation for the occurrence of intervertebral disc herniation in humans

Background: Recent studies suggest there is a relationship between intervertebral disc herniation and vertebral shape. The nature of this relationship is unclear, however. Humans are more commonly afflicted with spinal disease than are non-human primates and one suggested explanation for this is the stress placed on the spine by bipedalism. With this in mind, we carried out a study of human, chimpanzee, and orangutan vertebrae to examine the links between vertebral shape, locomotion, and Schmorl’s nodes, which are bony indicators of vertical intervertebral disc herniation. We tested the hypothesis that vertical disc herniation preferentially affects individuals with vertebrae that are towards the ancestral end of the range of shape variation within Homo sapiens and therefore are less well adapted for bipedalism. Results: The study employed geometric morphometric techniques. Two-dimensional landmarks were used to capture the shapes of the superior aspect of the body and posterior elements of the last thoracic and first lumbar vertebrae of chimpanzees, orangutans, and humans with and without Schmorl’s nodes. These data were subjected to multivariate statistical analyses. Canonical Variates Analysis indicated that the last thoracic and first lumbar vertebrae of healthy humans, chimpanzees, and orangutans can be distinguished from each other (p0.4590). The Procrustes distance between pathological humans and chimpanzees was found to be smaller than the one between pathological and healthy humans. This was the case for both vertebrae. Pair-wise MANOVAs of Principal Component scores for both the thoracic and lumbar vertebrae found significant differences between all pairs of taxa (p0.367). Together, these results suggest that human vertebrae with Schmorl’s nodes are closer in shape to chimpanzee vertebrae than are healthy human vertebrae. Conclusions: The results support the hypothesis that intervertebral disc herniation preferentially affects individuals with vertebrae that are towards the ancestral end of the range of shape variation within H. sapiens and therefore are less well adapted for bipedalism. This finding not only has clinical implications but also illustrates the benefits of bringing the tools of evolutionary biology to bear on problems in medicine and public health.Anthropology, Department ofArts, Faculty ofNon UBCReviewedFacult

3D shape analyses of extant primate and fossil hominin vertebrae support the ancestral shape hypothesis for intervertebral disc herniation

Background: Recently we proposed an evolutionary explanation for a spinal pathology that afflicts many people, intervertebral disc herniation (Plomp et al. [2015] BMC Evolutionary Biology 15, 68). Using 2D data, we found that the bodies and pedicles of lower vertebrae of pathological humans were more similar in shape to those of chimpanzees than were those of healthy humans. Based on this, we hypothesized that some individuals are more prone to intervertebral disc herniation because their vertebrae exhibit ancestral traits and therefore are less well adapted for the stresses associated with bipedalism. Here, we report a study in which we tested this “Ancestral Shape Hypothesis” with 3D data from the last two thoracic and first lumbar vertebrae of pathological Homo sapiens, healthy H. sapiens, Pan troglodytes, and several extinct hominins. Results: We found that the pathological and healthy H. sapiens vertebrae differed significantly in shape, and that the pathological H. sapiens vertebrae were closer in shape to the P. troglodytes vertebrae than were the healthy H. sapiens vertebrae. Additionally, we found that the pathological human vertebrae were generally more similar in shape to the vertebrae of the extinct hominins than were the healthy H. sapiens vertebrae. These results are consistent with the predictions of the Ancestral Shape Hypothesis. Several vertebral traits were associated with disc herniation, including a vertebral body that is both more circular and more ventrally wedged, relatively short pedicles and laminae, relatively long, more cranio-laterally projecting transverse processes, and relatively long, cranially-oriented spinous processes. We found that there are biomechanical and comparative anatomical reasons for suspecting that all of these traits are capable of predisposing individuals to intervertebral disc herniation. Conclusions: The results of the present study add weight to the hypothesis that intervertebral disc herniation in H. sapiens is connected with vertebral shape. Specifically, they suggest that individuals whose vertebrae are towards the ancestral end of the range of shape variation within H. sapiens have a greater propensity to develop the condition than other individuals. More generally, the study shows that evolutionary thinking has the potential to shed new light on human skeletal pathologies.Arts, Faculty ofNon UBCAnthropology, Department ofReviewedFacult

Diverse and Dynamic Dietary Patterns in Early Colonial Cuba: New Insights from Multiple Isotope Analyses

The European conquest and colonization of the Caribbean precipitated massive changes in indigenous cultures and societies of the region. One of the earliest changes was the introduction of new plant and animal foods and culinary traditions. This study presents the first archaeological reconstruction of indigenous diets and foodways in the Caribbean spanning the historical divide of 1492. We use multiple isotope datasets to reconstruct these diets and investigate the potential relationships between dietary and mobility patterns at multiple scales. Dietary patterns are assessed by isotope analyses of different skeletal elements from the archaeological skeletal population of El Chorro de Maíta, Cuba. This approach integrates carbon and nitrogen isotope analyses of bone and dentine collagen with carbon and oxygen isotope analyses of bone and enamel apatite. The isotope results document extreme intrapopulation dietary heterogeneity but few systematic differences in diet between demographic/social groups. Comparisons with published isotope data from other precolonial and colonial period populations in the Caribbean indicate distinct dietary and subsistence practices at El Chorro de Maíta. The majority of the local population consumed more animal protein resources than other indigenous populations in the Caribbean, and their overall dietary patterns are more similar to colonial period enslaved populations than to indigenous ones

Distinct clones of Yersinia pestis caused the black death

International audienceFrom AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18(th) century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to conclusions that it must have been caused by other pathogens. It has also been disputed whether plague had the same etiology in northern and southern Europe. Here we identified DNA and protein signatures specific for Y. pestis in human skeletons from mass graves in northern, central and southern Europe that were associated archaeologically with the Black Death and subsequent resurgences. We confirm that Y. pestis caused the Black Death and later epidemics on the entire European continent over the course of four centuries. Furthermore, on the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route. These two clades are ancestral to modern isolates of Y. pestis biovars Orientalis and Medievalis. Our results clarify the etiology of the Black Death and provide a paradigm for a detailed historical reconstruction of the infection routes followed by this disease