Alterations in the composition of the lung microbiome associated with adverse clinical outcomes, known as dysbiosis, have been implicated with disease severity and exacerbations in COPD.
To ...characterise longitudinal changes in the lung microbiome in the AERIS study (Acute Exacerbation and Respiratory InfectionS in COPD) and their relationship with associated COPD outcomes.
We surveyed 584 sputum samples from 101 patients with COPD to analyse the lung microbiome at both stable and exacerbation time points over 1 year using high-throughput sequencing of the 16S ribosomal RNA gene. We incorporated additional lung microbiology, blood markers and in-depth clinical assessments to classify COPD phenotypes.
The stability of the lung microbiome over time was more likely to be decreased in exacerbations and within individuals with higher exacerbation frequencies. Analysis of exacerbation phenotypes using a Markov chain model revealed that bacterial and eosinophilic exacerbations were more likely to be repeated in subsequent exacerbations within a subject, whereas viral exacerbations were not more likely to be repeated. We also confirmed the association of bacterial genera, including
and
, with disease severity, exacerbation events and bronchiectasis.
Subtypes of COPD have distinct bacterial compositions and stabilities over time. Some exacerbation subtypes have non-random probabilities of repeating those subtypes in the future. This study provides insights pertaining to the identification of bacterial targets in the lung and biomarkers to classify COPD subtypes and to determine appropriate treatments for the patient.
Results, NCT01360398.
Strategies for 21st-century environmental management and conservation under global change require a strong understanding of the biological mechanisms that mediate responses to climate- and ...human-driven change to successfully mitigate range contractions, extinctions, and the degradation of ecosystem services. Biodiversity responses to past rapid warming events can be followed in situ and over extended periods, using cross-disciplinary approaches that provide cost-effective and scalable information for species' conservation and the maintenance of resilient ecosystems in many bioregions. Beyond the intrinsic knowledge gain such integrative research will increasingly provide the context, tools, and relevant case studies to assist in mitigating climate-driven biodiversity losses in the 21st century and beyond.
Knowledge of global patterns of biodiversity, ranging from intraspecific genetic diversity (GD) to taxonomic and phylogenetic diversity, is essential for identifying and conserving the processes that ...shape the distribution of life. Yet, global patterns of GD and its drivers remain elusive. Here we assess existing biodiversity theories to explain and predict the global distribution of GD in terrestrial mammal assemblages. We find a strong positive covariation between GD and interspecific diversity, with evolutionary time, reflected in phylogenetic diversity, being the best predictor of GD. Moreover, we reveal the negative effect of past rapid climate change and the positive effect of inter-annual precipitation variability in shaping GD. Our models, explaining almost half of the variation in GD globally, uncover the importance of deep evolutionary history and past climate stability in accumulating and maintaining intraspecific diversity, and constitute a crucial step towards reducing the Wallacean shortfall for an important dimension of biodiversity.
Criticism has been levelled at climate‐change‐induced forecasts of species range shifts that do not account explicitly for complex population dynamics. The relative importance of such dynamics under ...climate change is, however, undetermined because direct tests comparing the performance of demographic models vs. simpler ecological niche models are still lacking owing to difficulties in evaluating forecasts using real‐world data. We provide the first comparison of the skill of coupled ecological‐niche‐population models and ecological niche models in predicting documented shifts in the ranges of 20 British breeding bird species across a 40‐year period. Forecasts from models calibrated with data centred on 1970 were evaluated using data centred on 2010. We found that more complex coupled ecological‐niche‐population models (that account for dispersal and metapopulation dynamics) tend to have higher predictive accuracy in forecasting species range shifts than structurally simpler models that only account for variation in climate. However, these better forecasts are achieved only if ecological responses to climate change are simulated without static snapshots of historic land use, taken at a single point in time. In contrast, including both static land use and dynamic climate variables in simpler ecological niche models improve forecasts of observed range shifts. Despite being less skilful at predicting range changes at the grid‐cell level, ecological niche models do as well, or better, than more complex models at predicting the magnitude of relative change in range size. Therefore, ecological niche models can provide a reasonable first approximation of the magnitude of species' potential range shifts, especially when more detailed data are lacking on dispersal dynamics, demographic processes underpinning population performance, and change in land cover.
We compare for the first time the skill of demographic models vs. simpler ecological niche models in predicting documented shifts in the ranges of 20 British breeding bird species across a 40‐year period of observed climate change. We show that more complex demographic models, which account for dispersal and metapopulation dynamics, tend to have higher predictive accuracy in forecasting observed species range shifts than structurally simpler models that only account for variation in climate. However, simpler ecological niche models do as well, or better, than more complex models at predicting the magnitude of relative change in range size.
In the face of increasing cumulative effects from human and natural disturbances, sustaining coral reefs will require a deeper understanding of the drivers of coral resilience in space and time. Here ...we develop a high‐resolution, spatially explicit model of coral dynamics on Australia's Great Barrier Reef (GBR). Our model accounts for biological, ecological and environmental processes, as well as spatial variation in water quality and the cumulative effects of coral diseases, bleaching, outbreaks of crown‐of‐thorns starfish (Acanthaster cf. solaris), and tropical cyclones. Our projections reconstruct coral cover trajectories between 1996 and 2017 over a total reef area of 14,780 km2, predicting a mean annual coral loss of −0.67%/year mostly due to the impact of cyclones, followed by starfish outbreaks and coral bleaching. Coral growth rate was the highest for outer shelf coral communities characterized by digitate and tabulate Acropora spp. and exposed to low seasonal variations in salinity and sea surface temperature, and the lowest for inner‐shelf communities exposed to reduced water quality. We show that coral resilience (defined as the net effect of resistance and recovery following disturbance) was negatively related to the frequency of river plume conditions, and to reef accessibility to a lesser extent. Surprisingly, reef resilience was substantially lower within no‐take marine protected areas, however this difference was mostly driven by the effect of water quality. Our model provides a new validated, spatially explicit platform for identifying the reefs that face the greatest risk of biodiversity loss, and those that have the highest chances to persist under increasing disturbance regimes.
In this study, we develop a spatially explicit model of coral cover that accounts for the cumulative impact of multiple disturbances from 1998 to 2017 across Australia's Great Barrier Reef. We identify the environmental drivers of coral growth for six major benthic communities, as well as anthropogenic correlates of reef resilience.
An emerging research program on population and geographic range dynamics of Australia's mammals illustrates an approach to better understand and respond to geographic range collapses of threatened ...wildlife in general. In 1788, Europeans colonized an Australia with a diverse and largely endemic mammal fauna, where many species that are now extinct or threatened were common and widespread. Subsequent population declines, range collapses and extinctions were caused by introduced predators and herbivores, altered land use, modified fire regimes and the synergies between these threats. Declines in population and range size continue for many Australian mammals despite legislative protection and conservation interventions. Here, we propose an approach that integrates museum data and other historical records into process‐explicit macroecological models to better resolve mammal distributions and abundances as they were at European arrival. We then illustrate how this integrative approach can identify the likely synergistic mechanisms causing mammal population declines across these and other landscapes. This emerging research approach, undertaken with fine temporal and spatial resolution, but at large geographic scales, will provide valuable insights into the different pathways to, and drivers of, extinction. Such insights may, in turn, underpin conservation strategies based on a process‐explicit understanding of population decline and range collapse under alternative scenarios of impending climate and environmental change. Given that similar information is available for other regional biotas, the approach we describe here can be adapted to conserve threatened wildlife in other regions across the globe.
Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early Holocene are uncertain, with intense debate on the roles of human hunting, ...climatic change, and their synergy. Obstacles to a resolution have included an overreliance on correlative rather than process‐explicit approaches for inferring drivers of distributional and demographic change. Here, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia and in its expansion in North America using process‐explicit macroecological models. The approach integrates modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, species‐specific population ecology, and the growth and spread of anatomically modern humans. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years require high dispersal abilities, large maximum densities, and a small Allee effect. Analyses of validated process‐explicit projections indicate that climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses show that the range collapse and extinction of the muskox in Europe (~13,000 years ago) was likely caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities probably combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene–Holocene transition signals a vulnerability of this species to future increased warming. By better establishing the ecological processes that shaped the distribution of the muskox through space and time, we show that process‐explicit macroecological models have important applications for the future conservation and management of this iconic species in a warming Arctic.
We reconstructed 21,000 years of climate‐ and human‐driven range dynamics of muskox by integrating modern occurrence records, fossil records, paleoclimate reconstructions, ancient DNA sequences, human expansion models and spatially explicit process‐explicit macroecological models. Models that could reconcile inferences of demographic change from fossils were used to determine the likely chains of causality responsible for the contemporary distribution of muskox. We show that climatic change was a primary driver of the structure and dynamics of the distribution of muskox, with human activities, and their interactions with climatic changes, being important in some regions.
Drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, hampering assessments of subsequent modification of island biodiversity. We ...developed and tested a new statistical-simulation approach for reconstructing the pattern and pace of human migration across islands at high spatiotemporal resolutions. Using Polynesian colonisation of New Zealand as an example, we show that process-explicit models, informed by archaeological records and spatiotemporal reconstructions of past climates and environments, can provide new and important insights into the patterns and mechanisms of arrival and establishment of people on islands. We find that colonisation of New Zealand required there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding rapidly over both North and South Islands. These verified spatiotemporal reconstructions of colonisation dynamics provide new opportunities to explore more extensively the potential ecological impacts of human colonisation on New Zealand's native biota and ecosystems.
Background Rectal neuroendocrine tumors (RNETs) are often discovered on screening colonoscopy. Indications for staging and definitive resection are inconsistent in current guidelines. We evaluated ...the role of grade in guiding staging and procedural decision-making. Methods Patients with biopsy confirmed RNETs between 2004 and 2015 were reviewed. Baseline characteristics, staging investigations (biochemical and imaging), and endoscopic/surgical treatment were recorded. Associations between grade, preoperative staging, interventions, and survival were determined using Fisher-Freeman-Halton Exact, log-rank, and Kaplan-Meier analysis. Results Amongst 139 patients with RNETs, 9% were aged greater than or equal to 75 years and 44% female. Tumor grade was: 73% grade 1 (G1), 18%, grade 2 (G2) and 9% grade 3 (G3). Staging investigations were performed in 52% of patients. All serum chromogranin A and 97% of 24-hour urine 5-hydroxyindoleacetic acid tests were normal. The large majority of staging computed tomography (CT) scans were negative (76%) with subgroup analysis showing no G1 patients with CT identified distant disease compared with 38% of G2 and 50% of G3 patients (p < 0.001). G1 patients were more likely to achieve R0/R1 resections compared to G2 (95% vs. 50%, p < 0.001) and G1 patients had significantly better 5-year overall survival (G1: 98%, G2: 67%, G3: 10%, p < 0.001). Conclusion Tumor grade is important in preoperative workup and surgical decision-making. Biochemical staging may be omitted but staging CT should be considered for patients with grade greater than or equal to 2 lesions. Anatomic resections should be considered for patients with grade 2 disease. Keywords: Rectal neuroendocrine tumors, Preoperative staging, Chromogranin A, Urine 5-HIAA, Operative decision-making, Tumor grade, Recurrence, Survival
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