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- Database of Metagenomes of Sediments from Estuarine Aquaculture Farms in Portugal—AquaRAM Project CollectionPublication . Nogueira, Teresa; Silva, Daniel G.; Lopes, Susana; Botelho, AnaAquaculture farms and estuarine environments close to human activities play a critical role in the interaction between aquatic and terrestrial surroundings and animal and human health. The AquaRAM project aimed to study estuarine aquaculture farms in Portugal as a reservoir of antibiotic resistance genes and the potential of its spread due to mobile genetic elements. We have assembled a collection of metagenomic data from 30 sediment samples from oysters, mussels, and gilt-head sea bream aquaculture farms. This collection includes samples of the estuarine environment of three rivers and one lagoon located from the north to the south of Portugal, namely, the Lima River in Viana do Castelo, Aveiro Lagoon in Aveiro, Tagus River in Alcochete, and Sado River in Setúbal. Statistical data from the raw metagenome files, as well as the file sizes of the assembled nucleotide and protein sequences, are also presented. The link to the statistics and the download page for all the metagenomes is also listed below.
- Evolution of Animal Microbial Communities in Response to Environmental StressPublication . Nogueira, Teresa; Botelho, Ana; Bowler, Lucas; Inácio, João
- Os coronavírus dos animais e do HomemPublication . Duarte, Margarida; Nogueira, Teresa; Botelho, Ana; Cavaco, Sandra; Duarte, Ana; Santos, Patricia; Sousa, Rita; Portela, Sara
- Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in AquaculturesPublication . Nogueira, Teresa; Botelho, AnaThe shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union’s 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.
- Editorial: Evolution of Animal Microbial Communities in Response to Environmental StressPublication . Nogueira, Teresa; Botelho, Ana; Bowler, Lucas; Inácio, João
- Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the ResistomePublication . Silva, Daniel G.; Domingues, Célia P. F.; Figueiredo, João F.; Dionisio, Francisco; Botelho, Ana; Nogueira, TeresaIt is recognized that the spread of antibiotic resistance (AR) genes among aquatic environments, including aquaculture and the human environment, can have detrimental effects on human and animal health and the ecosystem. Thus, when transmitted to the human microbiome or pathogens, resistance genes risk human health by compromising the eventual treatment of infections with antibiotic therapy. This study aimed to define the resistance profile of aquaculture farms and their potential risk for spreading. Twenty-four sediments from oyster and gilthead sea bream aquaculture farms located in three Portuguese river estuaries (17 sediments from Sado, 4 from Aveiro, and 3 from Lima) were studied by comparative metagenomic analysis. The computation of the diversity of genes conferring resistance per antibiotic class revealed a significant increase in aminoglycosides, beta-lactams, disinfectants, quinolones, and tetracyclines counts. In all geographic locations under study, the most diverse AR genes confer resistance to the macrolides, tetracyclines and oxazolidinones classes, all of which are medically important for human and animal therapies, as well as resistance to disinfectants. The diversity of mobile genetic elements correlated with the number of AR genes such as tetracyclines, suggesting that AR could be easily mobilized among bacterial genomes and microbiomes.
- CORONAVIRUS ANIMAUX ET HUMAINS: Évolution and pathogénicité du virus prévention des maladiesPublication . Duarte, Margarida; Nogueira, Teresa; Botelho, Ana; Cavaco, Sandra; Duarte, Ana; Santos, Patricia; Sousa, Rita; Portela, SaraThe most recently discovered Human coronavirus, Severe Acute Respiratory Syndrome - Coronavirus - 2 (SARS-CoV-2), is certainly the best-known coronavirus of all, as it is considered a successful invader. First identified in late 2019, it generated the current pandemic of coronavirus disease of 2019 (COVID-19) when it spread across the planet in only a few months. Like some other members of the same family of viruses, SARS-CoV-2 can infect different types of human cells, however, the epithelia of the lungs and larynx are the main targets thus preferentially causing respiratory infections. Mortality associated with COVID-19 alongside the impacts on health, education, the economy and individual and social well-being are currently a concern for the whole world. These are not only due to the effects of the disease, but also the pandemic control measures imposed by governments across the world, namely mandatory isolation, and we are still looking to adapt to this new way of life alongside a virus that was previously unknown. However, humans and other animal species have long lived side by side with other coronaviruses, many of which unknown to most people, some quite harmless whilst other potentially lethal. In that sense, this is no different. This book aims to assemble and disseminate information about the origin, evolution and pathogenesis of animal and human coronaviruses in a simple and accessible way, and through this clarify readers’ doubts and fears as well as the rationale underlying transmission prevention actions. The main text of the manuscript is accompanied by two types of additional information for optional consultation; more in-depth information about some of the mentioned concepts (know more) and a set of questions & answers, providing the reader with the opportunity to clarify doubts relating to the content of each section. For the preparation of this book, we counted on the collaboration of technicians, researchers and academics in the areas of microbiology, epidemiology, animal health and public health. During the production and editing process, a board game and cards (Beat Corona) were also produced. These further explored some of the concepts mentioned in this book, including behaviours related to life in society and their implications in the transmission of diseases caused by coronaviruses, including COVID-19. This game can be used as a pedagogical resource in the classroom context, or as a mere leisure and learning activity.
- The Social Distancing Imposed To Contain COVID-19 Can Affect Our Microbiome: a Double-Edged Sword in Human HealthPublication . Domingues, Célia P. F.; Rebelo, João S.; Dionisio, Francisco; Botelho, Ana; Nogueira, TeresaHygienic measures imposed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and contain COVID-19 have proven effective in controlling the pandemic. In this article, we argue that these measures could impact the human microbiome in two different and disparate ways, acting as a double-edged sword in human health. New lines of research have shown that the diversity of human intestinal and oropharyngeal microbiomes can shape pulmonary viral infection progression. Here, we suggest that the disruption in microbial sharing, as it is associated with dysbiosis (loss of bacterial diversity associated with an imbalance of the microbiota with deleterious consequences for the host), may worsen the prognosis of COVID-19 disease. In addition, social detachment can also decrease the rate of transmission of antibiotic-resistant bacteria. Therefore, it seems crucial to perform new studies combining the pandemic control of COVID-19 with the diversity of the human microbiome.
- COVID-19 lockdowns may reduce resistance genes diversity in the human microbiome and the need for antibioticsPublication . Rebelo, João S.; Domingues, Célia P. F.; Dionisio, Francisco; Gomes, Manuel C.; Botelho, Ana; Nogueira, TeresaRecently, much attention has been paid to the COVID-19 pandemic, yet bacterial resistance to antibiotics remains a serious and unsolved public health problem, which kills thousands of people annually, being an insidious and silent pandemic. In this study, we explored the idea of confinement and the tightening of the hygiene measures to contain the spreading of coronavirus, to simulate the effect that it has on lowering the spreading of pathogenic bacteria in a human network, and on the need to use antibiotics. For that, we used computational biology to generate simulations