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    Carbon tax ethics
    (John Wiley & Sons, Inc., 2023-09-06) Mintz-Woo, Kian
    Ideal carbon tax policy is internationally coordinated, fully internalizes externalities, redistributes revenues to those harmed, and is politically acceptable, generating predictable market signals. Since nonideal circumstances rarely allow all these conditions to be met, moral issues arise. This paper surveys some of the work in moral philosophy responding to several of these issues. First, it discusses the moral drivers for estimates of the social cost of carbon. Second, it explains how national self-interest can block climate action and suggests international policies—carbon border tax adjustments and carbon clubs—that can help address these concerns. Third, it introduces some of the social science literature about the political acceptability of carbon taxes before addressing a couple common public concerns about carbon taxes. Finally, it introduces four carbon revenue usage options, arguing that redistributive and climate compensation measures are most morally justified.
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    The impact of primer design on amplicon-based metagenomic profiling accuracy: detailed insights into bifidobacterial community structure
    (MDPI, 2020-01) Mancabelli, Leonardo; Milani, Christian; Lugli, Gabriele A.; Fontana, Federico; Turroni, Francesca; van Sinderen, Douwe; Ventura, Marco; Horizon 2020; Science Foundation Ireland
    Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological processes important for preservation of the health status of the host. The most widespread microbiota profiling method is based on amplification and sequencing of a variable portion of the 16S rRNA gene as a universal taxonomic marker among members of the Bacteria domain. Despite its popularity and obvious advantages, this 16S rRNA gene-based approach comes with some important limitations. In particular, the choice of the primer pair for amplification plays a major role in defining the accuracy of the reconstructed bacterial profiles. In the current study, we performed an in silico PCR using all currently described 16S rRNA gene-targeting primer pairs (PP) in order to assess their efficiency. Our results show that V3, V4, V5, and V6 were the optimal regions on which to design 16S rRNA metagenomic primers. In detail, PP39 (Probio_Uni/Probio_Rev), PP41 (341F/534R), and PP72 (970F/1050R) were the most suitable primer pairs with an amplification efficiency of >98.5%. Furthermore, the Bifidobacterium genus was examined as a test case for accurate evaluation of intra-genus performances at subspecies level. Intriguingly, the in silico analysis revealed that primer pair PP55 (527f/1406r) was unable to amplify the targeted region of any member of this bacterial genus, while several other primer pairs seem to rather inefficiently amplify the target region of the main bifidobacterial taxa. These results highlight that selection of a 16S rRNA gene-based PP should be done with utmost care in order to avoid biases in microbiota profiling results.
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    Mobilome and resistome reconstruction from genomes belonging to members of the Bifidobacterium genus
    (MDPI, 2019-12) Mancino, Walter; Lugli, Gabriele A.; van Sinderen, Douwe; Ventura, Marco; Turroni, Francesca; Horizon 2020 Framework Programme; Science Foundation Ireland
    Specific members of the genus Bifidobacterium are among the first colonizers of the human/animal gut, where they act as important intestinal commensals associated with host health. As part of the gut microbiota, bifidobacteria may be exposed to antibiotics, used in particular for intrapartum prophylaxis, especially to prevent Streptococcus infections, or in the very early stages of life after the birth. In the current study, we reconstructed the in silico resistome of the Bifidobacterium genus, analyzing a database composed of 625 bifidobacterial genomes, including partial assembled strains with less than 100 genomic sequences. Furthermore, we screened bifidobacterial genomes for mobile genetic elements, such as transposases and prophage-like elements, in order to investigate the correlation between the bifido-mobilome and the bifido-resistome, also identifying genetic insertion hotspots that appear to be prone to horizontal gene transfer (HGT) events. These insertion hotspots were shown to be widely distributed among analyzed bifidobacterial genomes, and suggest the acquisition of antibiotic resistance genes through HGT events. These data were further corroborated by growth experiments directed to evaluate bacitracin A resistance in Bifidobacterium spp., a property that was predicted by in silico analyses to be part of the HGT-acquired resistome.
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    Bifidobacterium breve UCC2003 exopolysaccharide modulates the early life Microbiota by acting as a potential dietary substrate
    (MDPI, 2020) Püngel, Deborah; Treveil, Agatha; Dalby, Matthew J.; Caim, Shabhonam; Colquhoun, Ian J.; Booth, Catherine; Ketskemety, Jennifer; Korcsmaros, Tamas; van Sinderen, Douwe; Lawson, Melissa A. E.; Hall, Lindsay J.; Wellcome Trust; H2020 Marie Skłodowska-Curie Actions; Science Foundation Ireland
    BACKGROUND: Bifidobacterium represents an important early life microbiota member. Specific bifidobacterial components, exopolysaccharides (EPS), positively modulate host responses, with purified EPS also suggested to impact microbe-microbe interactions by acting as a nutrient substrate. Thus, we determined the longitudinal effects of bifidobacterial EPS on microbial communities and metabolite profiles using an infant model colon system. METHODS: Differential gene expression and growth characteristics were determined for each strain; Bifidobacterium breve UCC2003 and corresponding isogenic EPS-deletion mutant (B. breve UCC2003del). Model colon vessels were inoculated with B. breve and microbiome dynamics monitored using 16S rRNA sequencing and metabolomics (NMR). RESULTS: Transcriptomics of EPS mutant vs. B. breve UCC2003 highlighted discrete differential gene expression (e.g., eps biosynthetic cluster), though overall growth dynamics between strains were unaffected. The EPS-positive vessel had significant shifts in microbiome and metabolite profiles until study end (405 h); with increases of Tyzzerella and Faecalibacterium, and short-chain fatty acids, with further correlations between taxa and metabolites which were not observed within the EPS-negative vessel. CONCLUSIONS: These data indicate that B. breve UCC2003 EPS is potentially metabolized by infant microbiota members, leading to differential microbial metabolism and altered metabolite by-products. Overall, these findings may allow development of EPS-specific strategies to promote infant health.
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    Delineation of a lactococcal conjugation system reveals a restriction-modification evasion system
    (John Wiley & Sons, Inc., 2023-06) Ortiz Charneco, Guillermo; Kelleher, Philip; Buivydas, Andrius; Dashko, Sofia,; de Waal, Paul P.; van Peij, Noël N. M. E.; Roberts, Richard John; Mahony, Jennifer; van Sinderen, Douwe; Science Foundation Ireland
    Plasmid pUC11B is a 49.3-kb plasmid harboured by the fermented meat isolate Lactococcus lactis subsp. lactis UC11. Among other features, pUC11B encodes a pMRC01-like conjugation system and tetracycline-resistance. In this study, we demonstrate that this plasmid can be conjugated at high frequencies to recipient strains. Mutational analysis of the 22 genes encompassing the presumed pUC11B conjugation cluster revealed the presence of several genes with essential conjugation functions, as well as a gene, trsR, encoding a putative transcriptional repressor of this conjugation cluster. Furthermore, plasmid pUC11B encodes an anti-restriction protein, TrsAR, which facilitates higher conjugation frequencies when pUC11B is transferred into recipient strains containing Type II or Type III RM systems. These findings demonstrate how RM mechanisms can be circumvented when they act as a biological barrier for conjugation events.