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Coffee is a globally popular beverage and a significant agricultural economic crop in planted countries and regions. To understand the influence of primary processing on coffee, the microbial communities and chemical compounds were analyzed using high‐throughput sequencing and HPLC‐MS/MS metabolomics to confirm the dynamic changes of them during the dry processing of Coffea arabica from Yunnan, China. The results showed that Tatumella, Klebsiella, Gluconobacter, Brevundimonas, and Staphylococcus at the bacterial general level and Candida, Lachancea, Aschersonia, Cercospora, and Pichia at the fungi general level were the predominant microorganisms in the dry processing. During the dry process, Tatumella, Gluconobacter, and Candida showed a trend of increasing firstly and decreasing subsequently, while Klebsiella and Lachancea reached the highest at the end of processing. In contrast, Hannaella decreased gradually. Meanwhile, 1551 chemical compounds coming from 15 superclasses were detected. Furthermore, 129 differentially changed compounds (DCCs) including 91 upregulated DCCs with VIP > 1.0, p < 0.05, and FC > 1.5 and 38 downregulated DCCs with VIP > 1.0, p < 0.05, and FC < 0.67 were determined in finished samples versus raw materials. Among them, cis‐5‐caffeoylquinic acid and sesamose were very significantly DCCs. Therefore, this study can provide useful information for understanding the dry processing of coffee beans and its impact on coffee's quality properties. Tatumella, Klebsiella, Gluconobacter, Brevundimonas, and Staphylococcus at the bacterial general level and Candida, Lachancea, Aschersonia, Cercospora, and Pichia at the fungi general level were the predominant microorganisms during the dry processing of Coffea arabica. Meanwhile, 129 differentially changed compounds (DCCs) including 91 upregulated DCCs with VIP > 1.0, p < 0.05, and FC > 1.5, and 38 downregulated DCCs with VIP > 1.0, p < 0.05, and FC < 0.67, were determined in finished samples versus raw materials.

The bacterial diversity of salted mackerel “one‐night courtyard” at soft frozen area (−7℃–0℃) storage was studied. The fish samples at 0, 14, 21, 28, and 35 days were analysis for bacterial structure using high‐throughput sequencing technologies (HTS) and biogenic amines using high‐performance liquid chromatography (HPLC). The analysis results of HTS showed that the dominant bacteria species was varied gradually following with storage time. On the 0th, 21st, and 28th days of storage, dominant Vibrionaceae was accounting for 71.70%, 59.16%, and 70.68% of the total sequences analyzed, respectively. On the 14th and 35th days, Shewanellaceae was the dominant bacterial, accounting for 87.53% and 70.95% of the total sequences analyzed, respectively. In addition, 21st and 28th days, an abundance of Operational Taxonomic Units (OTUs) was top. The dominant bacterial of Proteobacteria, Firmicutes, was producer of biogenic amines. Furthermore, the analysis results of HPLC shown the total biogenic amines of maximum amount 363.01 mg/kg in the sample of HY.14 lower than 1000 mg/kg of the FDA regulation. The range ability of cadaverine was obvious following with the storage time. Cadaverine was 87.36 mg/kg on the 0th day, and it was maximum amount of 276.89 mg/kg on the 14th days. Putrescine was 20 mg/kg on the 0th day and maximum amount of 55.04 mg/kg on the 28thdays of storage. The tyramine was smallest amount of production, and the largest amount was 38.99 mg/kg on 28th, and the smallest amount was 11.97 mg/kg on 35th. Nevertheless, the maximum amount of histamine was 55.04 mg/kg on the 0th day and about 23.14 mg/kg of histamine was little change from 14th to 35th days of storage. Dominant bacteria affect the change of biogenic amines. The study can help understand the interaction between microbial flora and biogenic amines in the salted mackerel of one‐night courtyard. The variation trend of cadaverine, putrescine, and tyramine was consistent, first increase and then decrease, and among them, the content variation of cadaverine was obvious. Nevertheless, the amounts of histamine decreased gradually following with storage time. The study can help understand the interaction between microbial flora and biogenic amines in the salted mackerel fish of one‐night courtyard.

EBV is a prevalent virus, infecting >90% of the world’s population. This is an oncogenic virus that causes ~200,000 cancer-related deaths annually. It is, in addition, a significant contributor to the burden of autoimmune diseases. Thus, EBV represents a significant public health burden. Upon infection, EBV remains dormant in host cells for long periods of time. However, the presence or episodic reactivation of the virus increases the risk of transforming healthy cells to malignant cells that routinely escape host immune surveillance or of producing pathogenic autoantibodies. Cancers caused by EBV display distinct molecular behaviors compared to those of the same tissue type that are not caused by EBV, presenting opportunities for targeted treatments. Despite some encouraging results from exploration of vaccines, antiviral agents and immune- and cell-based treatments, the efficacy and safety of most therapeutics remain unclear. Here, we provide an up-to-date review focusing on underlying immune and environmental mechanisms, current therapeutics and vaccines, animal models and emerging technologies to study EBV-associated diseases that may help provide insights for the development of novel effective treatments.

This study investigated the influences of aeration mode and influent carbon/nitrogen ratio on matrix oxygen concentration, pollutant removal, greenhouse gas emission, functional gene abundances and bacterial community in subsurface wastewater infiltration systems (SWISs). Intermittent or continuous aeration enhanced oxygen supply at 0.6 m depth in the matrix, which improved organics removal, nitrogen removal, the abundances of bacterial 16S rRNA, amoA, nxrA, narG, napA, nirK, nirS, norB, nosZ genes, bacterial community Alpha diversity, the relative abundances of Actinobacteria at 0.6 m depth, the relative abundances of Chloroflexi, Gemmatimonadetes, Bacteroidetes and Firmicutes at 0.9 and 1.2 m depth and reduced CH4 and N2O conversion efficiencies, the abundance of mcrA gene with carbon/nitrogen ratio of 12 and 16 compared with non-aeration. Increased carbon/nitrogen ratio resulted in higher TN removal efficiencies and lower CH4 and N2O conversion efficiencies in aeration SWISs than those in non-aeration SWIS. Intermittent aeration SWIS obtained high removal efficiencies of 83.2, 85.4 and 90.8% for TN, NH4+ -N and COD and low conversion efficiency of 0.21 and 0.65% for N2O and CH4 with optimal carbon/nitrogen ratio of 12. However, high TN (82.6%), NH4+ -N (84.9%) and COD (92.2%) removal efficiencies and low CH4 (0.67%) and N2O (0.23%) conversion efficiencies were achieved in continuous aeration SWIS with carbon/nitrogen ratio of 16.

Background The chicken gut microbiota is an important and complicated ecosystem for the host. They play an important role in converting food into nutrient and energy. The coding capacity of microbiome vastly surpasses that of the host’s genome, encoding biochemical pathways that the host has not developed. An optimal gut microbiota can increase agricultural productivity. This study aims to explore the composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range (outdoor, OD) and cage (indoor, ID) raising. Results Cecal samples were collected from 24 chickens across 4 groups (12-w OD, 12-w ID, 18-w OD, and 18-w ID). We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions to characterize the cecal microbiota of Dagu chicken and compare the difference of cecal microbiota between free-range and cage raising chickens. It was found that 34 special operational taxonomic units (OTUs) in OD groups and 4 special OTUs in ID groups. 24 phyla were shared by the 24 samples. Bacteroidetes was the most abundant phylum with the largest proportion, followed by Firmicutes and Proteobacteria. The OD groups showed a higher proportion of Bacteroidetes (>50 %) in cecum, but a lower Firmicutes/Bacteroidetes ratio in both 12-w old (0.42, 0.62) and 18-w old groups (0.37, 0.49) compared with the ID groups. Cecal microbiota in the OD groups have higher abundance of functions involved in amino acids and glycan metabolic pathway. Conclusion The composition and function of cecal microbiota in Dagu chicken under two feeding modes, free-range and cage raising are different. The cage raising mode showed a lower proportion of Bacteroidetes in cecum, but a higher Firmicutes/Bacteroidetes ratio compared with free-range mode. Cecal microbiota in free-range mode have higher abundance of functions involved in amino acids and glycan metabolic pathway.

The diversity of protists was researched in the Alboran Sea (SW Mediterranean Sea) by means of high-throughput sequencing technologies based on the amplification of the V9 region of 18S rRNA. Samples were collected at different depths in seven stations following an environmental gradient from a coastal upwelling zone to the core of an oligotrophic anticyclonic gyre (AG). Sampling was performed during summer, when the water column was stratified. The superphyla Alveolata, Stramenopila and Rhizaria accounted for 84% of the total operational taxonomic units (OTUs). The most diverse groups were Dinophyceae (21% of OTUs), Marine Alveolates-II (MALV-II; 20%), Ciliophora (9%) and MALV-I (6%). In terms of read abundance, the predominant groups were Dinophyceae (29%), Bacillariophyta (14%), MALV-II (11%) and Ciliophora (11%). Samples were clustered into three groups according to the sampling depth and position. The shallow community in coastal stations presented distinguishable patterns of diatoms and ciliates compared with AG stations. These results indicate that there was a strong horizontal coupling between phytoplankton and ciliate communities. Abundance of Radiolaria and Syndiniales increased with depth. Our analyses demonstrate that the stratification disruption produced by the AG caused shifts in the trophic ecology of the plankton assemblages inducing a transition from bottom-up to top-down control.

The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.

Background American ginseng ( Panax quinquefolius L.) is renowned worldwide for its eutherapeutic effects. The replantation of American ginseng usually fails due to problems associated with continuous cropping. An imbalance in the microbial community is thought to be responsible for this, but the overall changes in microbial communities under a continuous cropping system are unclear. Methods This study used quantitative polymerase chain reaction combined with high-throughput sequencing methods to confirm changes in a microbial community under continuous cropping of American ginseng. Results Copy numbers of bacteria and fungi significantly declined by 47.7 and 45.5%, respectively, upon American ginseng cropping over 3 years. A total of 66,391 classified sequences were obtained from high-throughput sequencing analyses of 16S and 18S rRNA in six soil samples. A decline in bacterial diversity and an increase in fungal diversity were observed in the continuous cropping soils of American ginseng compared to those of traditional crops. Compared with soils used for traditional crops, the relative abundance of bacterial and fungal groups changed in soils subjected to continuous cropping with American ginseng. Conclusions Our results revealed that the diversity and composition of soil bacterial and fungal communities changed in the continuous cropping of American ginseng compared to those of traditional crops. Those data provided comprehensive insight into microbial communities at the agro-ecosystem scale and contributed to the understanding of micro-ecological environments in the rhizosphere of medicinal plants.

More and more Chinese families are using dishwashers, consumers have paid special attention to the sterilization and disinfection function of dishwashers in recent years. However, there is still a lack of research on the distribution of microorganisms in dishwashers nationwide in China. In order to better upgrade the sterilization and disinfection functions of dishwashers, the plate culture method and high-throughput sequencing technology were used to comprehensively analyze the microbiology of household dishwashers in different cities of China in spring, summer, autumn and winter in this study. A total of 1109 strains of bacteria were isolated from dishwashing machine samples by culturable method, including 706 strains of bacteria distributed in 72 genera, 403 strains of fungi distributed in 52 genera.The most frequently isolated bacteria were Bacillus , Pseudomonas , Brevibacillus , Exiguobacterium , and Acinetobacter . The most frequently isolated fungi were Aspergillus , Penicillium , Exophiala , Fusarium, and Candida . A total of 3779 OTUs were obtained from bacteria and 1541 OTUs were obtained from fungi by amplicon sequencing. The results of culture-independent analysis were consistent with those of culturable analysis. This study laid a foundation for the directional screening of superior microbial resources in dishwashers. It provided data support for the further upgrading of the sterilization and disinfection function of the dishwasher.