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Endophytes are a unique group of microbes that live in different plant species, forming a symbiotic association and interacting with the host species and the environment. They have been isolated from diverse parts throughout plant kingdom and are very diverse, including viruses and protists other than bacteria and fungi. They have a significant effect on plant host growth and metabolism, as these endophytes produce various bioactive metabolites that enhance plant growth and resistance to abiotic and biotic stresses in the environment. Therefore, endophytes have great potential for use as biofertilizers and biocontrol agents in sustainable agriculture. They also produce various enzymes and biomolecules that can be used industrially. Bioremediation and biofuel production by these endophytes have also been explored. The review discusses the diversity and potential of endophytes, as well as the technical advances that can be used to increase this potential for large-scale industrial production and application. [ABSTRACT FROM AUTHOR]

Clostridium difficile is a Gram-positive, spore-forming bacterium, and major cause of nosocomial diarrhea. Related studies have identified numerous factors that influence virulence traits such as the production of the two primary toxins, toxin A (TcdA) and toxin B (TcdB), as well as sporulation, motility, and biofilm formation. However, multiple putative transcriptional regulators are reportedly encoded in the genome, and additional factors are likely involved in virulence regulation. Although the leucine-responsive regulatory protein (Lrp) has been studied extensively in Gram-negative bacteria, little is known about its function in Gram-positive bacteria, although homologs have been identified in the genome. This study revealed that disruption of the lone lrp homolog in C. difficile decelerated growth under nutrient-limiting conditions, increased TcdA and TcdB production. Lrp was also found to negatively regulate sporulation while positively regulate swimming motility in strain R20291, but not in strain 630. The C. difficile Lrp appeared to function through transcriptional repression or activation. In addition, the lrp mutant was relatively virulent in a mouse model of infection. The results of this study collectively demonstrated that Lrp has broad regulatory function in C. difficile toxin expression, sporulation, motility, and pathogenesis. [ABSTRACT FROM AUTHOR]

Arsenic is a toxic metalloid. Moderate levels of arsenic exposure from drinking water can cause various human health problems such as skin lesions, circulatory disorders and cancers. Thus, arsenic toxicity is a key focus area for environmental and toxicological investigations. Many arsenic-related genes in yeast have been identified by experimental strategies such as phenotypic screening and transcriptional profiling. These identified arsenic-related genes are valuable information for studying arsenic toxicity. However, the literature about these identified arsenic-related genes is widely dispersed and cannot be easily acquired by researchers. This prompts us to develop YARG (Yeast Arsenic-Related Genes) database, which comprehensively collects 3396 arsenic-related genes in the literature. For each arsenic-related gene, the number and types of experimental evidence (phenotypic screening and/or transcriptional profiling) are provided. Users can use both search and browse modes to query arsenic-related genes in YARG. We used two case studies to show that YARG can return biologically meaningful arsenic-related information for the query gene(s). We believe that YARG is a useful resource for arsenic toxicity research. YARG is available at . [ABSTRACT FROM AUTHOR]

Clostridium difficile is a Gram-positive, spore-forming anaerobic human gastrointestinal pathogen. C. difficile infection (CDI) is a major health concern worldwide, with symptoms ranging from diarrhea to pseudomembranous colitis, toxic megacolon, sepsis, and death. CDI onset and progression are mostly caused by intestinal dysbiosis and exposure to C. difficile spores. Current treatment strategies include antibiotics; however, antibiotic use is often associated with high recurrence rates and an increased risk of antibiotic resistance. Medium-chain fatty acids (MCFAs) have been revealed to inhibit the growth of multiple human bacterial pathogens. Components of coconut oil, which include lauric acid, have been revealed to inhibit C. difficile growth in vitro. In this study, we demonstrated that lauric acid exhibits potent antimicrobial activities against multiple toxigenic C. difficile isolates in vitro. The inhibitory effect of lauric acid is partly due to reactive oxygen species (ROS) generation and cell membrane damage. The administration of lauric acid considerably reduced biofilm formation and preformed biofilms in a dose-dependent manner. Importantly, in a mouse infection model, lauric acid pretreatment reduced CDI symptoms and proinflammatory cytokine production. Our combined results suggest that the naturally occurring MCFA lauric acid is a novel C. difficile inhibitor and is useful in the development of an alternative or adjunctive treatment for CDI. [ABSTRACT FROM AUTHOR]

The microbial communities inhabiting mud volcanoes have received more attention due to their noteworthy impact on the global methane cycle. However, the impact of temporal effects of volcanic eruptions on the microbial community's diversity and functions remain poorly characterized. This study aimed to underpin the temporal variations in the bacterial community's diversity and PICRUSt-predicted functional profile changes of mud volcanic sites located in southern Taiwan using 16S rRNA gene sequencing. The physicochemical analysis showed that the samples were slightly alkaline and had elevated levels of Na+, Cl−, and SO42−. Comparatively, the major and trace element contents were distinctly higher, and tended to be increased in the long-period samples. Alpha diversity metrics revealed that the bacterial diversity and abundance were lesser in the initial period, but increased over time. Instead, day 96 and 418 samples showed reduced bacterial abundance, which may have been due to the dry spell that occurred before each sampling. The initial-period samples were significantly abundant in haloalkaliphilic marine-inhabiting, hydrocarbon-degrading bacterial genera such as Marinobacter, Halomonas, Marinobacterium, and Oceanimonas. Sulfur-reducing bacteria such as Desulfurispirillum and Desulfofarcimen were found dominant in the mid-period samples, whereas the methanogenic archaeon Methanosarcina was abundant in the long-period samples. Unfortunately, heavy precipitation encountered during the mid and long periods may have polluted the volcanic site with animal pathogens such as Desulfofarcimen and Erysipelothrix. The functional prediction results showed that lipid biosynthesis and ubiquinol pathways were significantly abundant in the initial days, and the super pathway of glucose and xylose degradation was rich in the long-period samples. The findings of this study highlighted that the temporal effects of a mud volcanic eruption highly influenced the bacterial diversity, abundance, and functional profiles in our study site. [ABSTRACT FROM AUTHOR]

The outbreak of airborne pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA) through bioaerosol, and their molecular characterization around domestic poultry farming areas, was not completely understood. This imposes risk of a MRSA-associated health threat for the relevant livestock food production units. To address this issue, the present study investigated the role of bioaerosol in transmitting MRSA strains in poultry house settings by combining molecular typing, phylogenetic classification, antibiotic susceptibility, and virulence gene distribution patterns. The present study highlights that all 18 bioaerosol and stool samples collected were MRSA positive, with a unique set of virulence factors. Out of 57 isolated MRSA isolates, 68.4% and 19.3% consisted of SCCmec I and IV elements, respectively, which are commonly linked with hospital-acquired and livestock-associated MRSA strains. It is worth noting that the exfoliative toxin eta and etb genes were carried by 100% and 70.2% of all isolates, respectively. Only 17.5% of strains showed the presence of enterotoxin entC. These MRSA isolates were resistant to chloramphenicol (C), ciprofloxacin (CIP), clindamycin (DA), erythromycin (E), and tetracycline (T), signifying their multi-drug resistance traits. A cluster of phylogenetic analysis described that 80.7% and 15.8% of total isolates belonged to Staphylococcus aureus protein A (spa) type t002 and t548. Whereas 3.5% were reflected as a new spa type. Additionally, as per the chi-squared test score value, these two spa types (t002 and t548) have a distribution correlation with HA-MRSA and LA-MRSA in all the samples (p < 0.005, chi-squared test; degree of freedom = 1). Ultimately, this study highlights the prevalence of MRSA colonization in the conventional poultry farm environment, showing the risk of bioaerosol transmission, which needs epidemiological attention and prevention strategies. [ABSTRACT FROM AUTHOR]

Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination. [ABSTRACT FROM AUTHOR]

Despite advances in the characterization of colorectal cancer (CRC), it still faces a poor prognosis. There is growing evidence that gut microbiota and their metabolites potentially contribute to the development of CRC. Thus, microbial dysbiosis and their metabolites associated with CRC, based on stool samples, may be used to advantage to provide an excellent opportunity to find possible biomarkers for the screening, early detection, prevention, and treatment of CRC. Using 16S rRNA amplicon sequencing coupled with statistical analysis, this study analyzed the cause–effect shift of the microbial taxa and their metabolites that was associated with the fecal gut microbiota of 17 healthy controls, 21 polyps patients, and 21 cancer patients. The microbial taxonomic shift analysis revealed striking differences among the healthy control, polyps and cancer groups. At the phylum level, Synergistetes was reduced significantly in the polyps group compared to the healthy control and cancer group. Additionally, at the genus level and in association with the cancer group, a total of 12 genera were highly enriched in abundance. In contrast, only Oscillosprira was significantly higher in abundance in the healthy control group. Comparisons of the polyps and cancer groups showed a total of 18 significantly enriched genera. Among them, 78% of the genera associated with the cancer group were in higher abundance, whereas the remaining genera showed a higher abundance in the polyps group. Additionally, the comparison of healthy control and polyp groups showed six significantly abundant genera. More than 66% of these genera showed a reduced abundance in the polyps group than in healthy controls, whereas the remaining genera were highly abundant in the polyps group. Based on tumor presence and absence, the abundance of Olsenella and Lactobacillus at the genus level was significantly reduced in the patient group compared to healthy controls. The significant microbial function prediction revealed an increase in the abundance of metabolites in the polyps and cancer groups compared to healthy controls. A correlation analysis revealed a higher contribution of Dorea in the predicted functions. This study showed dysbiosis of gut microbiota at the taxonomic level and their metabolic functions among healthy subjects and in two stages of colorectal cancer, including adenoma and adenocarcinoma, which might serve as potential biomarkers for the early diagnosis and treatment of CRC. [ABSTRACT FROM AUTHOR]

High arsenic concentration in groundwater is influenced by redox reactions in As-bearing iron (oxy)hydroxide minerals and elevated total organic carbon, resulting in arsenic contamination and enrichment in groundwater after introduction of seawater into an aquifer. In this study, hydrochemical and isotopic (S, O and C) techniques were used to relate arsenic contamination and seawater flooding/intrusion in groundwater aquifers in the Chianan Plain, southwestern Taiwan. Thirty-three samples (30 from groundwater and 3 from river water) were collected from April–June of 2014. Most of the groundwater samples collected from the Chianan Plain were dominated by As(III), indicating that reducing conditions prevailed within the aquifers. The δ18O-δD plots of most of the groundwater samples from the Chianan Plain are generally lined on the global meteoric water line (GMWL), but the δ18O and δD isotopic compositions of the river water samples show enriched signals. Salinity and sulfate concentrations of river water and shallow groundwater have been found to increase after seawater flooding/intrusion. The δ18O and δD isotopic compositions of the river water showed a gradual trend toward those of seawater. The trend in the isotopic compositions of the river and groundwater samples indicated a mixing of seawater and meteoric water. Up to the present, the groundwater levels in the coastal areas of the Chianan Plain have dropped to zero meters in elevation parallel to sea level due to excessive groundwater withdrawal, resulting in seawater intrusion into the aquifers in Budai, Yichu, and Beimen in the Plain. Moreover, high salinity (48.1‰) occurred only in the Beimen 2B shallow groundwater at a depth of 60 m is a result of seawater flooding infiltration from the nearby salinized Pachang River. The δ34S [SO 4 ] /δ18O [SO 4 ] isotopic ratios (2.63–2.82) of low-As (concentration < 50 μg/L) river water samples were similar to those of marine sulfate minerals dissolved in seawater, but were variable (0 − 2.93) among the high-As (concentration ≧ 50 μg/L) groundwater samples from the Chianan Plain. Sulfates in seawater were introduced into the coastal aquifers of the Chianan Plain under the Holocene marine transgression, wherein the mixing of paleo- and modern-sulfates due to seawater intrusion might have occurred or are occurring. The release of sulfur and arsenic (mostly arsenite) in the Chianan Plain groundwater under reducing environments indicating redox reactions in sulfates and iron (oxy)hydroxide minerals may change the isotopic (S and O in sulfate) compositions in groundwater, resulting in enrichment of δ34S [SO 4 ] and δ18O [SO 4 ]. Salinity can promote arsenic release in groundwater and thus enrich the δ34S [SO 4 ] and δ18O [SO 4 ] isotopic compositions, in which 6.0–22.8‰ δ34S [SO 4 ] and 9.3–15.5‰ δ18O [SO 4 ] occur in shallow fresh groundwater (depth < 60 m) but up to 27.7‰ δ34S [SO 4 ] and 20.4‰ δ18O [SO 4 ] occur in shallow saline groundwater, in comparison to 0‰ δ34S [SO 4 ] and 5.4–6.5‰ δ18O [SO 4 ] in deep fresh groundwater (depth between 60 and 318 m) and up to 38.5‰ δ34S [SO 4 ] and 18.7‰ δ18O [SO 4 ] in deep brackish groundwater. This study provides insights suggesting that the As-containing iron(II) minerals are oxidized to iron(III) minerals and then re-reduced to iron(II) which leads to As release. Unlabelled Image • A rsenic enrichment in groundwater occurred after introduction of seawater. • The trend of δD [H 2 O] /δ18O [H 2 O] indicated a mixing of seawater and meteoric water. • Enriched δ34S [SO 4 ] and δ18O [SO 4 ] in groundwater occurred under reducing conditions. • As-contained Fe-oxide/hydroxide minerals are major aqueous As source in groundwater. • Redox reactions can change the isotopic composition of dissolved sulfate. [ABSTRACT FROM AUTHOR]