Global compositional and functional states of the human gut microbiome in health and disease.

The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.

Role of Whole-Genome Sequencing in Characterizing the Mechanism of Action of para-Aminosalicylic Acid and Its Resistance.

para-Aminosalicylic acid (PAS) remains one of the drugs of last resort for the treatment of tuberculosis, but its mechanism of action is still not completely understood. The main aim of this project was to identify new potential mechanisms of action and resistance to PAS by performing whole-genome sequencing on PAS-resistant laboratory mutants. A new variant in the folC gene was identified, as well as some other mutations that require further study.

Role of Cellular Metabolism during Candida-Host Interactions.

Microscopic fungi are widely present in the environment and, more importantly, are also an essential part of the human healthy mycobiota. However, many species can become pathogenic under certain circumstances, with Candida spp. being the most clinically relevant fungi. In recent years, the importance of metabolism and nutrient availability for fungi-host interactions have been highlighted. Upon activation, immune and other host cells reshape their metabolism to fulfil the energy-demanding process of generating an immune response. This includes macrophage upregulation of glucose uptake and processing via aerobic glycolysis. On the other side, Candida modulates its metabolic pathways to adapt to the usually hostile environment in the host, such as the lumen of phagolysosomes. Further understanding on metabolic interactions between host and fungal cells would potentially lead to novel/enhanced antifungal therapies to fight these infections. Therefore, this review paper focuses on how cellular metabolism, of both host cells and Candida, and the nutritional environment impact on the interplay between host and fungal cells.

Host-mycobiome metabolic interactions in health and disease.

Fungal communities (mycobiome) have an important role in sustaining the resilience of complex microbial communities and maintenance of homeostasis. The mycobiome remains relatively unexplored compared to the bacteriome despite increasing evidence highlighting their contribution to host-microbiome interactions in health and disease. Despite being a small proportion of the total species, fungi constitute a large proportion of the biomass within the human microbiome and thus serve as a potential target for metabolic reprogramming in pathogenesis and disease mechanism. Metabolites produced by fungi shape host niches, induce immune tolerance and changes in their levels prelude changes associated with metabolic diseases and cancer. Given the complexity of microbial interactions, studying the metabolic interplay of the mycobiome with both host and microbiome is a demanding but crucial task. However, genome-scale modelling and synthetic biology can provide an integrative platform that allows elucidation of the multifaceted interactions between mycobiome, microbiome and host. The inferences gained from understanding mycobiome interplay with other organisms can delineate the key role of the mycobiome in pathophysiology and reveal its role in human disease.

Integrative functional analysis uncovers metabolic differences between Candida species.

Candida species are a dominant constituent of the human mycobiome and associated with the development of several diseases. Understanding the Candida species metabolism could provide key insights into their ability to cause pathogenesis. Here, we have developed the BioFung database, providing an efficient annotation of protein-encoding genes. Along, with BioFung, using carbohydrate-active enzyme (CAZymes) analysis, we have uncovered core and accessory features across Candida species demonstrating plasticity, adaption to the environment and acquired features. We show a greater importance of amino acid metabolism, as functional analysis revealed that all Candida species can employ amino acid metabolism. However, metabolomics revealed that only a specific cluster of species (AGAu species-C. albicans, C. glabrata and C. auris) utilised amino acid metabolism including arginine, cysteine, and methionine metabolism potentially improving their competitive fitness in pathogenesis. We further identified critical metabolic pathways in the AGAu cluster with biomarkers and anti-fungal target potential in the CAZyme profile, polyamine, choline and fatty acid biosynthesis pathways. This study, combining genomic analysis, and validation with gene expression and metabolomics, highlights the metabolic diversity with AGAu species that underlies their remarkable ability to dominate they mycobiome and cause disease.

Improving the Potency of N-Aryl-2,5-dimethylpyrroles against Multidrug-Resistant and Intracellular Mycobacteria.

A series of N-phenyl-2,5-dimethylpyrrole derivatives, designed as hybrids of the antitubercular agents BM212 and SQ109, have been synthesized and evaluated against susceptible and drug-resistant mycobacteria strains. Compound 5d, bearing a cyclohexylmethylene side chain, showed high potency against M. tuberculosis including MDR-TB strains at submicromolar concentrations. The new compound shows bacteriostatic activity and low toxicity and proved to be effective against intracellular mycobacteria too, showing an activity profile similar to isoniazid.

Alcaloides aporfínicos con actividad antituberculosa aislados de Ocotea discolor Kunth (Lauraceae) / Aporphine alkaloids with antitubercular activity isolated from Ocotea discolor Kunth (Lauraceae) / Alcalóides aporfirínicos com atividade antituberculosa isolados de Ocotea discolor Kunth (Lauraceae)

Resumen La tuberculosis causa miles de muertes a nivel mundial y, actualmente, los fármacos usados no son suficientes y en ocasiones son obsoletos para su tratamiento. Por tanto, se hace necesaria la búsqueda de nuevos compuestos que ayuden a combatirla. Se evaluó la actividad antituberculosis de los alcaloides ocoxilonina (1), ocoteina (2), dicentrina (3) y 1,2-metilendioxi-3, 10,11-trimetoxiaporfina (4), aislados de la madera de Ocotea discolor. Las estructuras fueron identificadas por medio del análisis de los datos espectroscópicos de resonancia magnética nuclear (NMR 1D - 1H, 13C, 2D -COSY, HSQC y HMBC), espectros de masas y comparación con datos de la literatura. Todos los compuestos aislados demostraron actividad antituberculosa, con un rango de variación en la concentración mínima inhibitoria entre 140 y 310 μM, siendo la ocoteina (2) la más activa contra la cepa virulenta de Mycobacterium tuberculosis H37Rv.

Abstract Tuberculosis disease causes thousands of deaths worldwide and, currently, the used drugs are either not enough or obsolete for its treatment Therefore, new compounds that combat this disease are been seek Thus, the antituberculosis activity of the alkaloids ocoxilonine (1), ocoteine (2), dicentrine (3) and 1,2-methylenedioxy-3,10,11-trimethoxy aporphine (4), isolated from Ocotea discolor wood was evaluated Their structures were identified by analysis of nuclear magnetic resonance spectroscopic data (NMR 1D - 1H, 13C, 2D - COSY, HSQC and HMBC), mass spectra, and comparison with literature data All the isolated compounds showed antituberculosis activity, with a variation range in the minimum inhibitory concentration between 140 to 310 μM, being ocoteine (2) the most active compound against the virulent strain Mycobacterium tuberculosis H37Rv.

Resumo Devido a que a tuberculose provoca milhares de mortes em todo o mundo e a que, atualmente os medicamentos usados são inadequados e obsoletos para o tratamento desta doença, é preciso buscar novos compostos que ajudem a combatê-la. Assim, foi avaliada a atividade antituberculosis dos alcaloides ocoxilonina (1), ocoteina (2), dicentrina (3) y 1,2-metilendioxi-3,10,11-trimetoxiaporfina (4), isolados a partir da madeira de Ocotea discolor. Estas estruturas foram identificadas pela elucidação dos dados espectroscópicos (NMR 1D - 1H, 13C, 2D -COSY, HSQC e HMBC), espectros de massas e por comparação com os dados da literatura. Todos os compostos isolados demonstraram atividade antituberculosis, com um intervalo de variação na concentração inibitória mínima entre 140 e 310 μM sendo a ocoteína (2) o composto mais ativo contra a variedade virulenta Mycobacterium tuberculosis H37Rv.