Search Results (335)

Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans. Full article

The vertical stratification of oxygen concentration in deep reservoirs impacts nutrient cycling and ecosystem biodiversity. The Serra da Mesa reservoir, the largest in Brazil, was studied to evaluate the structure and production of the prokaryote community at five depths. Using ³H leucine incorporation and fluorescent in situ hybridization (FISH), the study focused on different depths near the dam, particularly within the euphotic zone. The water column was characterized into oxic, transitional, and hypoxic layers based on dissolved oxygen concentration. The highest densities and biomasses of prokaryotes were found at the euphotic zone’s depth limit, where bacterial production was low, suggesting inactive or slow-growing bacteria. Cell size differences and filamentous bacteria presence near the surface were observed, likely due to varying predation pressures. Prokaryote community composition differed across depths. At the subsurface level, with high dissolved organic carbon, alphaproteobacteria, betaproteobacteria, and Cytophaga–Flavobacter had similar densities, but the lowest bacterial biomass was recorded. The highest dissolved oxygen concentration depth had the lowest bacterial density, dominated by alphaproteobacteria and gammaproteobacteria. The study revealed that prokaryotic community structure and production vary with depth, indicating that microbial participation in layer dynamics is differentiated, with variations in abundance and distribution linked to oxygen concentrations. Full article

Abrupt dietary change can disrupt the intestinal balance in felines. This study aimed to assess the impact of heat-treated Bifidobacterium longum CECT-7384 combined with Fibersol-2 on the intestinal health of adult cats before and after dietary change. We selected 24 British shorthair cats, dividing them into two groups. From day 1 to day 14, the control group received a lower protein (33%) concentration (LPF) diet, while the treated group received the same LPF diet supplemented with 0.16% functional additives, consisting of Bifidobacterium longum CECT-7384 combined with Fibersol-2. Subsequently, from day 15 to day 28, the control group transitioned to a higher protein (40%) concentration (HPF) diet, while the treated group received the same HPF diet supplemented with 0.16% functional additives. Blood and fresh feces were collected on day 0, 14, 17, 21, and 28 of the experiment. The results suggest that the use of heat-treated Bifidobacterium longum CECT-7384 combined with Fibersol-2 may improve gastrointestinal function in cats by reducing serum LPS levels and fecal pH, while increasing fecal sIgA levels. In addition, the functional additive regulates the fecal microbiota and its function, promoting intestinal homeostasis and colonization with beneficial bacteria such as Blautia. Furthermore, on day 28, there was a significant difference in fecal microbiota beta diversity between the two groups. In summary, the addition of heat-treated Bifidobacterium longum CECT-7384 combined with Fibersol-2 contributes to improving the intestinal health of adult cats affected by abrupt dietary change. Full article

To expedite enrichment of anaerobic ammonia-oxidizing bacteria (AnAOB) as a way to reduce the start-up time, leading to a quicker transition into stable operation, the anaerobic ammonia oxidation (anammox) process was initiated by a biofilm reactor with polyurethane porous material. The enrichment of anammox bacteria was studied by progressively increasing the influent substrate concentration while simultaneously decreasing hydraulic retention time. Following a 73 d start-up and subsequent 103 d enrichment phase, the removal rates of ammonia and nitrite reached 97.87% and 99.96%, respectively, and the community was characterized by the development of brick-red anammox biofilms and granules. The predominant bacterial phyla within the reactor were Planctomycetota, Chloroflexi, and Proteobacteria, with relative abundances of 25.25%, 29.41%, and 14.3%, respectively, and the dominant genus was Candidatus brocadia, comprising 20.44% of the microbial community. These findings indicate that the polyurethane porous material biofilm reactor is conducive to the enrichment of AnAOB. After enrichment, the anaerobic microbial community exhibited significant richness and diversity, with anammox bacteria as the primary group. Full article

Natural curcumin is composed of three curcuminoids, namely curcumin (CUR), deme-thoxycurcumin (DMC) and bis-demethoxycurcumin (BDMC). These compounds are utilized in various biophotonics applications, including photodynamic therapy (PDT). This work aimed to evaluate the photodynamic action (alternative to antibiotics) of synthetic curcuminoids against Staphylococcus aureus. Herein, we evaluated an optimal proportion of the three curcuminoids mixed in solution to improve photoinactivation effects. Therefore, a set of computational calculations was carried out to understand the photodynamic action (stability and mechanism) of curcuminoids. Regarding computational analysis, the curcuminoid molecules were optimized using DFT with the hybrid exchange–correlation functional M06-2X, which includes long-range correction, and the 6-311++G(d,p) basis set. DMC and BDMC were more effective as photosensitizers than curcumin at a very low concentration of 0.75 µM, inactivating more than five orders of magnitude of S. aureus. Theoretical UV-vis absorption spectra showed that at maximum absorption wavelengths, electronic transitions of the π→π* type originated from H→L excitations. The BDMC was more stable than the other two curcuminoids after photobleaching, and the fluorescence emission was also higher, which could lead to its usage as a fluorescence dye to track bacteria. In fact, the results of electronic structure calculations proved that the stability order of curcuminoids is CUR < DMC < BDMC. The mixture of synthetic curcuminoids was more effective in the inactivation of S. aureus compared to curcumin by itself; for all proposed mixtures, an equal or superior reduction was achieved. Full article

Biofilms, aggregates of bacteria enclosed in a self-produced matrix, have been implicated in various pediatric respiratory infections, including acute otitis media (AOM), otitis media with effusion (OME), adenoiditis, protracted bacterial bronchitis, and pulmonary exacerbations in cystic fibrosis. These infections are prevalent in children and often associated with biofilm-producing pathogens, leading to recurrent and chronic conditions. Biofilms reduce antibiotic efficacy, contributing to treatment failure and disease persistence. This narrative review discusses biofilm production by respiratory pathogens such as Streptococcus pneumoniae, non-typeable Haemophilus influenzae, Pseudomonas aeruginosa, and Staphylococcus aureus. It examines their mechanisms of biofilm formation, antibiotic resistance, and the challenges they present in clinical treatment. Various antibiofilm strategies have shown promise in vitro and in animal studies, including the use of N-acetylcysteine, enzymes like dispersin B, and agents disrupting quorum sensing and biofilm matrix components. However, their clinical application, particularly in children, remains limited. Traditional treatments for biofilm-associated diseases have not significantly evolved, even with biofilm detection. The transition from experimental findings to clinical practice is complex and requires robust clinical trials and standardized biofilm detection protocols. Addressing biofilms in pediatric respiratory infections is crucial for improving treatment outcomes and managing recurrent and chronic diseases effectively. Full article

Ribosomes are not totally globular machines. Instead, they comprise prominent structural protrusions and a myriad of tentacle-like projections, which are frequently made up of ribosomal RNA expansion segments and N- or C-terminal extensions of ribosomal proteins. This is more evident in higher eukaryotic ribosomes. One of the most characteristic protrusions, present in small ribosomal subunits in all three domains of life, is the so-called beak, which is relevant for the function and regulation of the ribosome’s activities. During evolution, the beak has transitioned from an all ribosomal RNA structure (helix h33 in 16S rRNA) in bacteria, to an arrangement formed by three ribosomal proteins, eS10, eS12 and eS31, and a smaller h33 ribosomal RNA in eukaryotes. In this review, we describe the different structural and functional properties of the eukaryotic beak. We discuss the state-of-the-art concerning its composition and functional significance, including other processes apparently not related to translation, and the dynamics of its assembly in yeast and human cells. Moreover, we outline the current view about the relevance of the beak’s components in human diseases, especially in ribosomopathies and cancer. Full article

Anammox, a reaction in which microorganisms oxidize ammonia under anaerobic conditions, is used in the industry to remove ammonium from wastewater in an environmentally friendly manner. This process does not produce intermediate products such as nitrite or nitrate, which can act as secondary pollutants in soil and water environments. For industrial applications, anammox bacteria should be obtained from the environment and cultivated. Anammox bacteria generally exhibit a slow growth rate and may not produce a large number of cells due to their anaerobic metabolism. Additionally, their habitats appear to be limited to specific environments, such as oxidation-reduction transition zones. Consequently, most of the anammox bacteria that are used or studied originate from marine environments. In this study, anammox bacterial evidence was found in rice paddy soil and cultured under various conditions of aerobic, microaerobic, and anaerobic batch incubations to determine whether enrichment was possible. The anammox-specific gene (hzsA) and microbial community analyses were performed on the incubated soils. Although it was not easy to enrich anammox bacteria due to co-occurrence of denitrification and nitrification based on the chemistry data, potential existence of anammox bacteria was assumed in the terrestrial paddy soil environment. For potential industrial uses, anammox bacteria could be searched for in rice paddy soils by applying optimal enrichment conditions. Full article

The enteric nervous system (ENS) interacts bidirectionally with the local immune system, responding to inflammation within the gastrointestinal (GI) tract. In a previous study using the same samples, several gene targets were identified as being differentially expressed in the inflamed colonic tissue of pigs challenged with dextran sodium sulphate (DSS). Additionally, animals in the basal DSS group, exhibited reduced growth and increased fecal and pathology scores, while the relative abundance of beneficial taxa was reduced and harmful bacteria increased. While changes in the innate immune response and barrier function are widely cited regarding inflammatory bowel disease (IBD), the effects of inflammation on the local structures of the enteric nervous system (ENS) are less well understood. Hence, the objectives of this study were to: (1) evaluate the expression of a range of functionally diverse neuroactive receptors, transporters and neurotrophic factors in RNA derived from the colonic tissue from the same pigs; (2) examine associations with these neuroactive components and inflammatory, barrier function and matrix remodeling targets. Mature pigs were split into two experimental groups: (1) basal diet (n = 10); (2) basal diet + DSS (n = 11). The pigs were orally challenged with DSS once daily for four days and sacrificed humanely. Colonic tissue was collected for gene expression analysis. Most of the targets evaluated in this study were present at low levels or in some cases were undetectable by QPCR, including the dopamine receptor DRD5 and the serotonin receptor HTR3A. The dopamine receptors (DRD1, DRD3, DRD4), serotonin receptor (HTR4), and other selected neuroactive receptors (GRM7, GABRA2) were down-regulated in the DSS-challenged animals relative to the basal group (p < 0.05). Most notably, DRD2, was up-regulated four-fold, suggesting an active process involving this receptor (p < 0.05). Relationships with (previously published) gene expression data from the same samples suggest that DRD1 and DRD2 are influenced by different pathways and may also be interlinked with matrix remodeling and, more specifically, genes relevant to the epithelial to mesenchymal transition (CDH1, CDH2, IL6, IL13, IL10, MMP1, MMP2) an important fibrotic process in the pathogenesis of IBD. Full article

Probiotics face harsh conditions during their transit through the gastrointestinal tract (GIT) of fish because of low-pH environments and intestine fluid. Therefore, the evaluation of probiotic viability under simulated gastrointestinal conditions is an important step to consider for probiotic supplementation in fish feed prior to in vivo trials. Therefore, this study aimed to evaluate the effect of stomach and intestinal simulated conditions on the viability of encapsulated Lactococcus lactis A12 using an in vitro digestion model for tilapia. A Box Behnken design was used to evaluate the potential effect of three factors, namely stomach pH, residence time in the stomach, and enzyme quantity, on the viability of encapsulated Lactococcus lactis A12. As the main results, low pH (4.00), long residence time (4 h), and enzyme quantity (2.68 U of total protease activity) led to lower final cell counts after the phases of the stomach and intestine. Encapsulated probiotic bacteria showed higher viability (p < 0.05) and antibacterial activity (p < 0.05) against the pathogen Streptococcus agalactiae than non-encapsulated bacteria. The results suggest that L. lactis A12 survives in GIT conditions and that the proposed in vitro model could be used to explore the viability of probiotic bacteria intended for fish feed supplementation. Full article

Fish were kept for six weeks at three different initial stocking densities and water O₂ concentrations (low-LD, 8.5 kg/m³ and 95–70% O₂ saturation; medium-MD, 17 kg/m³ and 55–75% O₂ saturation; high-HD, 25 kg/m³ and 60–45% O₂ saturation), with water temperature increasing from 19 °C to 26–27 °C. The improvement in growth performance with the decrease in stocking density was related to changes in skin and intestinal mucosal microbiomes. Changes in microbiome composition were higher in skin, with an increased abundance of Alteromonas and Massilia in HD fish. However, these bacteria genera were mutually exclusive, and Alteromonas abundance was related to a reactive behavior and systemic growth regulation via the liver Gh/Igf system, while Massilia was correlated to a proactive behavior and a growth regulatory transition towards muscle rather than liver. At the intestinal level, microbial abundance showed an opposite trend for two bacteria taxa, rendering in a low abundance of Reyranella and a high abundance of Prauserella in HD fish. This trend was correlated with up-regulated host gene expression, affecting the immune response, epithelial cell turnover, and abiotic stress response. Most of the observed responses are adaptive in nature, and they would serve to infer new welfare indicators for increased stress resilience. Full article

The increasing emergence of multidrug-resistant (MDR) pathogens causes difficult-to-treat infections with long-term hospitalizations and a high incidence of death, thus representing a global public health problem. To manage MDR bacteria bugs, new antimicrobial strategies are necessary, and their introduction in practice is a daily challenge for scientists in the field. An extensively studied approach to treating MDR infections consists of inducing high levels of reactive oxygen species (ROS) by several methods. Although further clinical investigations are mandatory on the possible toxic effects of ROS on mammalian cells, clinical evaluations are extremely promising, and their topical use to treat infected wounds and ulcers, also in presence of biofilm, is already clinically approved. Biochar (BC) is a carbonaceous material obtained by pyrolysis of different vegetable and animal biomass feedstocks at 200–1000 °C in the limited presence of O₂. Recently, it has been demonstrated that BC’s capability of removing organic and inorganic xenobiotics is mainly due to the presence of persistent free radicals (PFRs), which can activate oxygen, H₂O₂, or persulfate in the presence or absence of transition metals by electron transfer, thus generating ROS, which in turn degrade pollutants by advanced oxidation processes (AOPs). In this context, the antibacterial effects of BC-containing PFRs have been demonstrated by some authors against Escherichia coli and Staphylococcus aureus, thus giving birth to our idea of the possible use of BC-derived PFRs as a novel method capable of inducing ROS generation for antimicrobial oxidative therapy. Here, the general aspects concerning ROS physiological and pathological production and regulation and the mechanism by which they could exert antimicrobial effects have been reviewed. The methods currently adopted to induce ROS production for antimicrobial oxidative therapy have been discussed. Finally, for the first time, BC-related PFRs have been proposed as a new source of ROS for antimicrobial therapy via AOPs. Full article

The gut microbiota plays a crucial role in regulating energy metabolism, facilitating nutrient absorption, and supporting immune function, thereby assisting the host in adapting to seasonal dietary changes. Here, we compare the gut microbiome composition of wild gray snub-nosed monkeys during winter (from October to December) and spring (from January to March) to understand differences in seasonal nutrient intake patterns. Snub-nosed monkeys are foregut fermenters and consume difficult-to-digest carbohydrates and lichen. To examine the digestive adaptations of gray snub-nosed monkeys, we collected 14 fresh fecal samples for DNA analysis during the winter and spring. Based on 16S rRNA sequencing, metagenomic sequencing, and functional metagenomic analyses, we identified that Firmicutes, Actinobacteria, Verrucomicrobia, and Bacteroidetes constitute a keystone bacterial group in the gut microbiota during winter and spring and are responsible for degrading cellulose. Moreover, the transition in dietary composition from winter to spring was accompanied by changes in gut microbiota composition, demonstrating adaptive responses to varying food sources and availability. In winter, the bacterial species of the genera Streptococcus were found in higher abundance. At the functional level, these bacteria are involved in fructose and mannose metabolism and galactose metabolism c-related pathways, which facilitate the breakdown of glycogen, starch, and fiber found in fruits, seeds, and mature leaves. During spring, there was an increased abundance of bacteria species from the Prevotella and Lactobacillus genera, which aid the digestion of protein-rich buds. Combined, these findings reveal how the gut microbiota adjusts to fluctuations in energy balance and nutrient intake across different seasons in this critically endangered species. Moreover, we also identified Pseudomonas in two samples; the presence of potential pathogens within the gut could pose a risk to other troop members. Our findings highlight the necessity of a conservation plan that focuses on protecting vegetation and implementing measures to prevent disease transmission for this critically endangered species. Full article

Soil microorganisms are a crucial component of forest ecosystems because of their involvement in the decomposition of organic matter and nutrient cycling and their influence on plant growth and development. Soil type is a fundamental characteristic of soil. In the transitional forest regions from subtropical to temperate zones in China, various soil types can be found, including yellow-brown soils, brown soils, and cinnamon soils. However, the composition and distribution patterns of soil bacterial and fungal communities in different soil types remain uncertain. This study selected a 4.8-hectare plot in Baiyun Mountain Forest National Park, China. To explore the spatial distribution and ecological processes of soil microbial communities across three different soil types, Illumina sequencing was conducted. Results showed that the composition and assembly of bacterial and fungal communities varied substantially among different soil types. Bacteria were more influenced by environmental factors than fungi. Fungal communities consistently demonstrated greater stability compared to bacterial communities across the three soil types. Light was the main environmental factor driving the variation in the assembly of microbial communities among different soil types. This study demonstrates that there are differences in the composition and structure of soil microbial communities among different soil types, providing important insights into the management and sustainable development of soil microorganisms in temperate forests. Full article

This study aimed to analyse the impact of a simulated human digestion process on the composition and functional properties of dietary fibres derived from pomegranate-peel, tomato-peel, broccoli-stem and grape-stem by-products. For this purpose, a computer-controlled simulated digestion system consisting of three bioreactors (simulating the stomach, small intestine and colon) was utilised. Non-extractable phenols associated with dietary fibre and their influence on antioxidant capacity and antiproliferative activity were investigated throughout the simulated digestive phases. Additionally, the modifications in oligosaccharide composition, the microbiological population and short-chain fatty acids produced within the digestion media were examined. The type and composition of each dietary fibre significantly influenced its functional properties and behaviour during intestinal transit. Notably, the dietary fibre from the pomegranate peel retained its high phenol content throughout colon digestion, potentially enhancing intestinal health due to its strong antioxidant activity. Similarly, the dietary fibre from broccoli stems and pomegranate peel demonstrated anti-proliferative effects in both the small and the large intestines, prompting significant modifications in colonic microbiology. Moreover, these fibre types promoted the growth of bifidobacteria over lactic acid bacteria. Thus, these results suggest that the dietary fibre from pomegranate peel seems to be a promising functional food ingredient for improving human health. Full article