Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs

The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. This finding, previously shown for Bacteria, was as well observed for the archaeal domain

A hydrogen‐oxidizing bacterium enriched from the open ocean resembling a symbiont

A new autotrophic hydrogen‐oxidizing Chromatiaceae bacterium, namely bacterium CTD079, was enriched from a water column sample at 1500 m water depth in the southern Pacific Ocean. Based on the phylogeny of 16S rRNA genes it was closely related to a scaly snail endosymbiont (99.2% DNA sequence identity) whose host so far is only known to colonize hydrothermal vents along the Indian ridge. The average nucleotide identity between the genomes of CTD079 and the snail endosymbiont was 91%. The observed differences likely reflect adaptations to their specific habitats. For example, CTD079 encodes additional enzymes like the formate dehydrogenase increasing the organism's spectrum of energy generation pathways. Other additional physiological features of CTD079 included the increase of viral defense strategies, secretion systems and specific transporters for essential elements. These important genome characteristics suggest an adaptation to life in the open ocean

Heat-stable metagenomic carbonic andydrases and their use

The present invention relates to polypeptides having carbonic anhydrase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides

A conceptual framework for evaluating national organ donation and transplantation programs

Conceptual frameworks are valuable resources that can be used to guide the planning, evaluation, and development of healthcare services. However, there are currently no comprehensive frameworks focused on organ donation and transplantation that identify the critical factors underlying a successful national program. To address this knowledge gap, we developed a conceptual framework that takes into account all major domains of influence, including political and societal aspects as well as clinical implementation. The framework was initially constructed based on a targeted review of the relevant medical literature. Feedback provided by a panel of international experts was incorporated into the framework via an iterative process. The final framework features 16 essential domains that are critical for initiating and maintaining a successful program and improving the health of patients with organ failure. Of particular note, these domains are subject to three overarching health system principles: responsiveness, efficiency, and equity. This framework represents a first attempt to develop a whole-system view of the various factors that contribute to the success of a national program. These findings provide a useful tool that can be adapted to any jurisdiction and used to plan, evaluate, and improve organ donation and transplantation programs

The national organ donation and transplantation program in Greece: gap analysis and recommendations for change

Greece has fallen far behind many comparable European countries in the field of organ donation and transplantation and has made little progress over the past decade. Despite efforts to improve its organ donation and transplantation program, systemic problems persist. In 2019, the Onassis Foundation commissioned a report to be prepared by the London School of Economics and Political Science that focused on the state of the Greek organ donation and transplantation program and proposed recommendations for its improvement. In this paper, we present our analysis of the Greek organ donation and transplantation program together with an overview of our specific recommendations. The analysis of the Greek program was undertaken in an iterative manner using a conceptual framework of best practices developed specifically for this project. Our findings were further developed via an iterative process with information provided by key Greek stakeholders and comparisons with case studies that featured successful donation and transplantation programs in Croatia, Italy, Portugal, Spain, and the United Kingdom. Because of their overall complexity, we used a systems-level approach to generate comprehensive and far-reaching recommendations to address the difficulties currently experienced by the Greek organ donation and transplantation program

How to structure a successful organ donation and transplantation system in eight (not so easy) steps: an Italian case study

Valuable information can be obtained from a systematic evaluation of a successful national transplant program. This paper provides an overview of Italy’s solid organ transplantation program which is coordinated by the National Transplant Network (Rete Nazionale Trapianti) and The National Transplant Center (Centro Nazionale Trapianti). The analysis is based on a system-level conceptual framework and identifies components of the Italian system that have contributed to improving rates of organ donation and transplantation. A narrative literature review was conducted and the findings were validated iteratively with input from subject matter experts. The results were organized into eight critical steps, including 1) generating legal definitions of living and deceased donation, 2) taking steps to ensure that altruistic donation and transplantation become part of the national culture and a point of pride, 3) seeking out existing examples of successful programs, 4) creating a situation in which it is easy to become a donor, 5) learning from mistakes, 6) working to diminish risk factors that lead to the need for organ donation, 7) increasing the rate of donations and transplantations via innovative strategies and policies, and 8) planning for a system that supports growth

Organ donation in Croatia: the iportance of a national champion, a comprehensive plan, and international collaborations

The Republic of Croatia is a global leader in organ donation and transplantation despite having fewer resources and more modest healthcare expenditures than other countries in the European Union. The results of an extensive literature review were combined with expert input in an iterative multi-step data collection and evaluation process designed to assess trends in Croatian organ donation and transplantation and identify key elements, policy changes, and drivers of the system that have contributed to its success. Multiple sources of evidence were used in this study, including primary documents, national and international transplantation reports, and insights from critical informants and content experts. The results highlight several key organizational reforms that have substantially improved the performance of the Croatian transplant program. Our findings emphasize the importance of strong central governance led by an empowered national clinical leader acting under the direct auspices of the Ministry of Health and a comprehensive and progressive national plan. The Croatian transplant system is notable for its integrated approach and efficient manner of managing scarce health resources. Collectively, the results suggest that Croatia has become nearly self-sufficient due to its systematic implementation of the guiding principles for organ donation and transplantation

Ten lessons from the Spanish model of organ donation and transplantation

The organ donation and transplantation program in Spain has long been considered the gold standard worldwide. An in-depth understanding of the Spanish program may promote the development and reform of transplant programs in other countries. Here, we present a narrative literature review of the Spanish organ donation and transplantation program supplemented by expert feedback and presented according to a conceptual framework of best practices in the field. Core features of the Spanish program include its three-tiered governing structure, close and collaborative relationships with the media, dedicated professional roles, a comprehensive reimbursement strategy, and intensive tailored training programs for all personnel. Several more sophisticated measures have also been implemented, including those focused on advanced donation after circulatory death (DCD) and expanded criteria for organ donation. The overall program is driven by a culture of research, innovation, and continuous commitment and complemented by successful strategies in prevention of end-stage liver and renal disease. Countries seeking ways to reform their current transplant systems might adopt core features and may ultimately aspire to include the aforementioned sophisticated measures. Countries intent on reforming their transplant system should also introduce programs that support living donation, an area of the Spanish program with potential for further improvement

Studying functions on coral reefs : past perspectives, current conundrums, and future potential

This work was funded by the Australian Research Council (DRB; grant number FL190100062).Function-based studies have opened a new chapter in our understanding of coral reefs. Unfortunately, we are opening this chapter as the world’s reefs rapidly transform. In this context, one of the most important roles of function-based studies is to inform coral reef conservation. At this critical juncture, we have a chance to reflect on where we have come from, and where we are going, in coral reef functional ecology, with specific consideration of what this means for our approaches to conserving reefs. As focal examples, we examine the role of corals on reefs, and the practice of culling crown-of-thorns starfish, from a functional perspective. We also consider how the papers in this special issue build on our current understanding. Ultimately, we highlight how robust scientific investigation, based on an understanding of ecosystem functions, will be key in helping us navigate reefs through the current coral reef crisis.Peer reviewe