The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow‐up.

As atmospheric [CO2] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO2 (eCO2) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO2. Although many genes were found to be commonly expressed by the two genotypes under eCO2, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO2. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO2 with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO2 in these coffee genotypes.

Antibiotics are notable weapons in fighting bacteria. Nowadays, however, the effectiveness of antibiotics is severely hindered by the increasing levels of antibiotic resistances in pathogenic bacterial populations, which can persist due to the selective pressure caused by antibiotic exposure. Arguably, the main cause of antibiotic resistances endurance in nature is antibiotic misuse, such as via overusing, inappropriate prescribing as well as the uncontrolled use in agriculture and livestock. There is also a lack of knowledge on appropriate antibiotic usage by the general public. Public scientific literacy and more research on therapeutic practices are fundamental to tackle this problem. Here, we present SimulATe a software which allows the simulation of the effects of antibiotic therapies on bacterial populations during human infections. This software can be used to develop students’ scientific literacy, using infections and antibiotic treatments as context to engage students in scientific practices, and discussions on antibiotic treatment onset and duration or on its use in immunosuppressed or critically ill individuals. SimulATe’s features also allow it to be used for research purposes allowing the simulation of real scenarios and exploration of their outcomes across the parameters’ landscape.