Seasonal and height dynamics of volatile organic compounds in rubber plantation: Impacts on ozone and secondary organic aerosol formation.

Rubber trees emit a range of volatile organic compounds (VOCs), including isoprene, monoterpenes, and sesquiterpenes, as part of their natural metabolism. These VOCs can significantly influence air quality through photochemical reactions that produce ozone and secondary organic aerosols (SOAs). This study examines the impact of VOCs detected in a rubber tree plantation in Northeastern Thailand on air quality, highlighting their role in atmospheric reactions that lead to the formation of ozone and SOAs. VOCs were collected at varying heights and seasons using Tenax-TA tubes paired with an atmospheric sampler pump and identified by gas chromatography-mass spectrometry. In total, 100 VOCs were identified, including alkanes, alkenes, terpenes, aromatics, and oxygenated VOCs. Principal Coordinate Analysis (PCoA) revealed distinct seasonal VOC profiles, with hydrocarbons, peaking in summer and terpenes in the rainy season. The Linear Mixed-Effects (LME) model indicates that VOC concentrations are more influenced by seasonal changes than by sampling heights. Secondary organic aerosol potential (SOAP) and ozone formation potential (OFP) of selected VOC species were also determined. The total SOAP ranged from 67.24 µg/m3 in summer to 17.87 µg/m3 in winter, while the total OFP ranged from 377.87 µg/m3 in summer to 139.39 µg/m3 in winter. Additionally, positive matrix factorization (PMF) analysis identified four main VOC sources: gasoline combustion (18.3 %), microbial activity (38.6 %), monoterpene emissions during latex production (15.0 %), and industrial sources (28.1 %). These findings provide essential information for managing air pollution in rubber tree plantations. By adopting focused air quality management strategies, plantation operators can mitigate the adverse effects of VOCs, promoting a healthier and more sustainable future.

Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease.

End-stage kidney disease (ESKD) is the final stage of chronic kidney disease (CKD), in which long-term damage has been caused to the kidneys to the extent that they are no longer able to filter the blood of waste and extra fluid. Peritoneal dialysis (PD) is one of the treatments that remove waste products from the blood through the peritoneum which can improve the quality of life for patients with ESKD. However, PD-associated peritonitis is an important complication that contributes to the mortality of patients, and the detection of bacterial pathogens is associated with a high culture-negative rate. The present study aimed to apply a metagenomic approach for the bacterial identification in the PD effluent (PDE) of patients with CKD based on 16S ribosomal DNA sequencing. As a result of this investigation, five major bacteria species, namely Escherichia coli, Phyllobacterium myrsinacearum, Streptococcus gallolyticus, Staphylococcus epidermidis and Shewanella algae, were observed in PDE samples. Taken together, the findings of the present study have suggested that this metagenomic approach could provide a greater potential for bacterial taxonomic identification compared with traditional culture methods, suggesting that this is a practical and culture-independent alternative approach that will offer a novel preventative infectious strategy in patients with CDK.

Modulation of the gut microbiota and short-chain fatty acid production by gac fruit juice and its fermentation in in vitro colonic fermentation.

This study aimed to investigate the effects of gac fruit juice and its probiotic fermentation (FGJ) utilizing Lactobacillus paracasei on the modulation of the gut microbiota and the production of short-chain fatty acids (SCFAs). We conducted a comparison between FGJ, non-fermented gac juice (GJ), and control samples through in vitro digestion and colonic fermentation using the human gut microbiota derived from fecal inoculum. Our findings revealed that both GJ and FGJ led to an increase in the viability of Lactobacilli, with FGJ exhibiting even higher levels compared to the control. The results from the 16S rDNA amplicon sequencing technique showed that both GJ and FGJ exerted positive impact on the gut microbiota by promoting beneficial bacteria, notably Lactobacillus mucosae and Bacteroides vulgatus. Additionally, both GJ and FGJ significantly elevated the levels of SCFAs, particularly acetic, propionic, and n-butyric acids, as well as lactic acid, in comparison to the control. Notably, FGJ exhibited a more pronounced effect on the gut microbiota compared to GJ. This was evident in its ability to enhance species richness, reduce the Firmicutes to Bacteroidetes (F/B) ratio, promote Akkermansia, and inhibit pathogenic Escherichia coli. Moreover, FGJ displayed enhanced production of SCFAs, especially acetic and lactic acids, in contrast to GJ. Our findings suggest that the probiotic fermentation of gac fruit enhances its functional attributes in promoting a balanced gut microbiota. This beverage demonstrates potential as a functional food with potential advantages for sustaining intestinal health.

Comprehensive analysis of miRNA profiling in Schistosoma mekongi across life cycle stages.

Schistosoma mekongi, a significant schistosome parasite, has various life stages, including egg, cercaria, female, and male, that play crucial roles in the complex life cycle. This study aimed to explore the microRNA (miRNA) profiles across these developmental stages to understand their potential functions and evolutionary significance, which have not been studied. Pre-processed sequencing reads of small RNA (sRNA) were obtained, and annotations were performed against the S. japonicum reference miRNA database. Results indicated marked variations in miRNA profiles across different life stages, with notable similarities observed between female and male S. mekongi. Principal Coordinate Analysis (PCoA) and unsupervised clustering revealed distinct miRNA signatures for each stage. Gene ontology (GO) analysis unveiled the potential roles of these miRNAs in various biological processes. The differential expression of specific miRNAs was prominent across stages, suggesting their involvement in crucial developmental processes. Furthermore, orthologous miRNA analysis against various worm species revealed distinct presence-absence patterns, providing insights into the evolutionary relationships of these miRNAs. In conclusion, this comprehensive investigation into the miRNA profiles of S. mekongi offers valuable insights into the functional and evolutionary aspects of miRNAs in schistosome biology.

In vitro evaluation of the anti­breast cancer properties and gene expression profiles of Thai traditional formulary medicine extracts.

Breast cancer is a leading cause of cancer-related deaths worldwide. Moreover, standard treatments are limited, so new alternative treatments are required. Thai traditional formulary medicine (TTFM) utilizes certain herbs to treat different diseases due to their dominant properties including anti-fungal, anti-bacterial, antigenotoxic, anti-inflammatory and anti-cancer actions. However, very little is known about the anti-cancer properties of TTFM against breast cancer cells and the underlying molecular mechanism has not been elucidated. Therefore, the present study, evaluated the metabolite profiles of TTFM extracts, the anti-cancer activities of TTFM extracts, their effects on the apoptosis pathway and associated gene expression profiles. Liquid chromatography with tandem mass spectroscopy analysis identified a total of 226 compounds within the TTFM extracts. Several of these compounds have been previously shown to have an anti-cancer effect in certain cancer types. The MTT results demonstrated that the TTFM extracts significantly reduced the cell viability of the breast cancer 4T1 and MDA-MB-231 cell lines. Moreover, an apoptosis assay, demonstrated that the TTFM extracts significantly increased the proportion of apoptotic cells. Furthermore, the RNA-sequencing results demonstrated that 25 known genes were affected by TTFM treatment in 4T1 cells. TTFM treatment significantly up-regulated Slc5a8 and Arhgap9 expression compared with untreated cells. Moreover, Cybb, and Bach2os were significantly downregulated after TTFM treatment compared with untreated cells. Reverse transcription-quantitative PCR demonstrated that TTFM extract treatment significantly increased Slc5a8 and Arhgap9 mRNA expression levels and significantly decreased Cybb mRNA expression levels. Moreover, the mRNA expression levels of Bax and Casp9 were significantly increased after TTFM treatment in 4T1 cells compared with EpH4-Ev cells. These findings indicated anti-breast cancer activity via induction of the apoptotic process. However, further experiments are required to elucidate how TTFM specifically regulates genes and proteins. This study supports the potential usage of TTFM extracts for the development of anti-cancer drugs.

Comparison of circulating bacterial profiles between mild and severe COVID-19 patients.

Recent reports revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients can develop bacteremia; however, the circulating bacterial profile is not well studied. Therefore, this study has aimed to investigate circulating bacterial profile in mild (n = 15) and severe (n = 13) SARS-CoV-2-infected patients as well as healthy controls (n = 10), using 16S rDNA (V4) sequencing approach. The alpha diversity indexes and Bray-Curtis dissimilarity matrix revealed that the bacterial profiles between the two conditions are significantly different. Correspondingly, the relative abundance indicates that the predominant bacterial phylum in both conditions was Proteobacteria. At genus level, the dominant bacterial genera in the mild patients belonged to Sphingomonas, Stenotrophomonas, and Achromobacter, while bacterial genera belonging to Enhydrobacter, Comamonas, and Acinetobacter were dominant in the severe patients. Furthermore, Linear discriminant analysis (LDA) Effect Size (LEfSe). revealed that Stenotrophomonas, Delftia, Achromobacter, and Neisseria were enriched in the mild condition, while Agrobacterium, Comamonas, Pseudomonas, Corynebacterium, Alkaliphilus, and Kocuria were enriched in the severe patients. These results revealed a distinct circulating bacterial profile in the mild and severe SARS-CoV-2-infected patients, which may provide an insight for further therapeutic strategy.

Genome characterization and mutation analysis of human influenza A virus in Thailand.

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/ H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

Revolutionized virome research using systems microbiology approaches.

Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.

Bacterial microbiota in upper respiratory tract of COVID-19 and influenza patients.

The upper respiratory tract is inhabited by diverse range of commensal microbiota which plays a role in protecting the mucosal surface from pathogens. Alterations of the bacterial community from respiratory viral infections could increase the susceptibility to secondary infections and disease severities. We compared the upper respiratory bacterial profiles among Thai patients with influenza or COVID-19 by using 16S rDNA high-throughput sequencing based on MiSeq platform. The Chao1 richness was not significantly different among groups, whereas the Shannon diversity of Flu A and Flu B groups were significantly lower than Non-Flu & COVID-19 group. The beta diversity revealed that the microbial communities of influenza (Flu A and Flu B), COVID-19, and Non-Flu & COVID-19 were significantly different; however, the comparison of the community structure was similar between Flu A and Flu B groups. The bacterial classification revealed that Enterobacteriaceae was predominant in influenza patients, while Staphylococcus and Pseudomonas were significantly enriched in the COVID-19 patients. These implied that respiratory viral infections might be related to alteration of upper respiratory bacterial community and susceptibility to secondary bacterial infections. Moreover, the bacteria that observed in Non-Flu & COVID-19 patients had high abundance of Streptococcus, Prevotella, Veillonella, and Fusobacterium. This study provides the basic knowledge for further investigation of the relationship between upper respiratory microbiota and respiratory disease which might be useful for better understanding the mechanism of viral infectious diseases.