Illumina High-throughput Sequencing Research Articles

Mechanism of the antifungal action of chloropicrin fumigation against Panax notoginseng root rot caused by Fusarium solani

Fusarium root rot caused by Fusarium solani severely damages the roots of Panax notoginseng (ginseng) seedlings eventually leading in most cases to the total loss of this valuable crop. Soil fumigants are generally better at controlling soil-borne diseases such as F. solani than fungicides which provide unacceptable control. Therefore, this study aimed at evaluating the efficacy of fumigant chloropicrin (Pic) against F. solani in both laboratory and field. Ultrastructural changes in the mycelia of F. solani in each treatment were indicative of structural changes at the cellular level by transmission electron microscopy (TEM). Bacterial and fungal communities and diversity were targeted for Illumina high-throughput sequencing. Results indicated that chloropicrin inhibited F. solani mycelial growth completely at a concentration of 1.2 μg/l. In addition, ultrastructural studies showed that Pic caused plasmolysis and plasma leakage, indicating that the cell membrane of F. solani was disrupted. In the field trials, Pic at 45 g/m2 yielded an excellent long-term control of target pathogens, and treated plots allowed P. notoginseng plants to maintain vigorous growth compared with the untreated controls. Illumina MiSeq sequencing results revealed that bacterial communities were affected more seriously by Pic than fungi. The beneficial microbes (such as Trichoderma and Chaetomium) gradually increased, and the harmful microbes (such as Fusarium) decreased in fumigated soil. Together, the promotion of beneficial microorganisms and the direct inhibition of F. solani by chloropicrin were the main mechanisms for the prevention and control of soil-borne diseases. Our results provide useful information understanding chloropicrin fumigation against soil-borne disease.

Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding.

Simple SummaryThe physicochemical conditions of thermal springs are one of the most significant barriers for detecting microbial life. According to the findings of various studies, high-throughput DNA sequencing technology can be utilized to perform more precise and detailed microbiome assessments. The main goal of this paper was to determine the microbiome in a thermal spring by metabarcoding environmental DNA obtained from four different sources and revealing how temperature and chemical composition affect the microbiome. This research also aimed to gather information that will aid in determining the best gene region and bioinformatic pipeline. The findings revealed a link between four different thermal springs’ physicochemical parameters and microbial composition and we found various manipulable steps in this study. This research is also first comprehensive thermal spring metabarcoding study conducted in Turkey.One of the most significant challenges for detecting microbial life in thermal springs by conventional techniques such as culturing is these places’ physicochemical (temperature, heavy metal content, pH, etc.) conditions. Data from several studies suggest that high-throughput DNA sequencing technologies can be used to perform more accurate and detailed microbiome analyses. The primary aim of this paper was to determine the microbiome in the thermal source by metabarcoding environmental DNA isolated from four different sources and reveal the reflection of differences caused by temperature and chemical content on the microbiome. DNA was extracted from water filtered with enclosed filters and using the Illumina high-throughput sequencing platform, V3 and V4 regions of the 16S rRNA gene were sequenced. The results showed a correlation between physicochemical conditions and microorganism composition of four different thermal springs. Springs with extremely high temperature (89–90 °C) were dominated by hyperthermophiles such as Hydrogenobacter and Thermus, while a spring with a high temperature (52 °C) was dominated by thermophiles such as Thermoanaerobaculum and Desulfurispora, and a spring with a low temperature (26 °C) and high salinity was dominated by halophiles and sulfur-oxidizers such as Hydrogenovibrio and Sulfirimonas. With this research, we observed many manipulable steps according to the work of interest. This study sought to obtain data that will help decide the right gene region and choose the optimal bioinformatic pipeline.

Appropriate crop rotation alleviates continuous cropping barriers by changing rhizosphere microorganisms in Panax notoginseng

Crop rotation is the most sustainable way to solve the CCO which is the main problem restricting the development of Chinese herbal medicine. In this study, we used Illumina high-throughput sequencing technology to study the effects of different interval years on rhizosphere microorganisms of Panax notoginseng at 1, 2 and 3 years intervals. The results showed that the number of beneficial bacteria increased while the pathogenic bacteria decreased during crop rotation. We also found that choosing the suitable crop is more effective than extending the rotation cycle duration. Phylogenetic analysis results showed that the preceding crop plays a decisive role in the rotation. Indicator, Random forest and Network all showed that crop rotation is to increase Trichoderma to combat CCOs. Our study indicated that job's tears is more suitable as the preceding crop of P. notoginseng. T. asperellum play a key role in crop rotation.

Abstract 1255: Identification of predictive biomarkers for neoadjuvant chemotherapy response in invasive breast cancer Latino patients

Abstract Purpose: Breast cancer (BC) is the leading cause of morbidity and mortality in women in Colombia, constituting a major public health issue. Importantly, not all breast cancer patients respond to neoadjuvant chemotherapy (NAC), leading to an incomplete pathological response and suggesting that there are tumor characteristics that may explain the differences in response. The overarching goal of this study is to identify gene expression profiles associated with an incomplete pathological response to NAC in Colombian women with invasive BC. Design: An integrative transcriptome analysis using Illumina high-throughput RNA sequencing was performed from 63 baseline and post-NAC (follow-up) paraffin-embedded samples from 46 different female patients with locally advanced BC (stage IIB to IIIC) treated at the Colombian National Cancer Institute. Gene expression data were obtained from 42 baseline and 21 follow-up samples. Two comparison analyses were conducted to identify differentially expressed genes (DEGs) first comparing baseline vs follow-up samples from nonresponders to NAC and second comparing to baseline samples from nonresponders vs responders to NAC. Additionally, enrichment analyses were performed in both comparative analyses. Results: From 46 patients included, 20 had a pathological complete response (pCR), while 26 did not show pCR. By investigating the gene expression profiling, 1546 significantly DEGs and 174 DEGs were identified among non-responders and Baseline analyses, respectively. From these analyses, 24 DEGs were found in common and apoptosis as the only shared enrichment pathway (p=0.001). In both analyses, Histone associated genes were downregulated in nonresponders (Histone 3, p=0,001 and Histone 2B, p<0,001). In addition, downregulation of Granzyme B and perforin were also found differentially expressed in apoptosis network pathways. CD8+ naïve T-cells, hematopoietic stem cells, Macrophages, Macrophages M1, Neurons, Th1 cells, activated dendritic cells and pro B cells were defined by the xCell algorithm and showed statistically significant association with non-response to NAC. Conclusions: Changes in histones and tumor microenvironment cell populations elicits local immune response, which contributed to therapeutic efficacy. Downregulation of Granzyme B and perforin could block mechanism of resistance to carcinogenesis, leading to non-response to NAC. Furthermore, patients with tumors containing higher gene signatures of these DEGs may benefit from NAC. Additional validations are needed to confirm these data. If confirmed, these data may be relevant in elucidating the mechanisms that lead to therapy resistance as well as in selecting patients that will benefit from NAC in Latino (Colombian) patients. Citation Format: Hedda Michelle Guevara-Nieto, Rafael Parra-Medina, Juan Carlos Mejia-Henao, Patricia Eugenia López-Correa, José Ismael Guío-Avila, Sandra Diaz-Casas, Jone Garai, Jovanny Zabaleta, Liliana López-Kleine, Alba Lucia Cómbita. Identification of predictive biomarkers for neoadjuvant chemotherapy response in invasive breast cancer Latino patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1255.

Soil microbial community assembly model in response to heavy metal pollution

Heavy metal pollution affected the stability and function of soil ecosystem. The impact of heavy metals on soil microbial community and the interaction of microbial community has been widely studied, but little was known about the response of community assembly to the heavy metal pollution. In this study, we collected 30 soil samples from non (CON), moderately (CL) and severely (CH) contaminated fields. The prokaryotic community was studied using high-throughput Illumina sequencing of 16s rRNA gene amplicons, and community assembly were quantified using phylogenetic-bin-based null approach (iCAMP). Results showed that diversity and composition of both bacterial and archaeal community changed significantly in response to heavy metal pollution. The microbial community assembly tended to be more deterministic with the increase of heavy metal concentration. Among the assembly processes, the relative importance of homogeneous selection (deterministic process) increased significantly (increased by 16.2%), and the relative importance of drift and dispersal limitation (stochastic process) decreased significantly (decreased by 11.4% and 5.4%, respectively). The determinacy of bacterial and archaeal community assembly also increased with heavy metal stress, but the assembly models were different. The deterministic proportion of microorganisms tolerant to heavy metals, such as Thiobacillus, Euryarchaeota and Crenarchaeota (clustered in bin 32, bin59 and bin60, respectively) increased, while the stochastic proportion of microorganisms sensitive to heavy metals, such as Koribacteraceae (clustered in bin23) increased. Therefore, the heavy metal stress made the prokaryotic community be deterministic, however, the effects on the assembly process of different microbial groups differed obviously.

Variations in Marine Bacterial and Archaeal Communities during an Ulva prolifera Green Tide in Coastal Qingdao Areas.

Green tides caused by Ulva prolifera occur annually in the Yellow Sea, potentially influencing the marine microorganisms. Here, we focused on the variations in marine bacterial and archaeal communities during an U. prolifera green tide in coastal Qingdao areas with Illumina high-throughput sequencing analysis. Our results revealed that the diversity and structure of bacterial and archaeal communities, as well as the organization and structure of microbial co-occurrence networks, varied during the green tide. The decline phase may be favorable to the bacterial and archaeal diversity and richness. The bacterial community, as well as the archaeal community, showed clear variations between the outbreak and decline phases. A simpler and less connected microbial co-occurrence network was observed during the outbreak phase compared with the decline phase. Flavobacteriales and Rhodobacterales separately dominated the bacterial community during the outbreak and decline phase, and Marine Group II (MGII) dominated the archaeal community during the green tide. Combined with microbial co-occurrence network analysis, Flavobacteriales, Rhodobacterales and MGII may be important organisms during the green tide. Temperature, chlorophyll a content and salinity may have an important impact on the variations in bacterial and archaeal communities during the green tide.

The complete chloroplast genome of the Egyptian henbane (Hyoscyamus muticus L., Solanaceae)

Egyptian henbane (Hyoscyamus muticus L. Mant. Pl. 1767) is an important medicinal plant of the family Solanaceae. Its complete chloroplast (cp) genome was assembled using Illumina high-throughput sequencing technology to contribute to its conservation genetics studies. Here, we report the complete sequence of the chloroplast genome of H. muticus. The cp genome was 156,271 bp in length with an asymmetric base composition (30.9% A, 18.9% C, 18.6% G and 31.6% T). It encodes 132 genes comprising 87 protein-coding genes, 29 tRNA genes, and 8 rRNA genes. The overall GC content of the H. muticus chloroplast genome was 37.5%, and the corresponding values in the large single-copy (LSC), the small single-copy (SSC), and the inverted repeat (IR) regions were 35.5%, 31.5%, and 43.0%, respectively. The complete chloroplast genome sequence was deposited to the GenBank (NCBI, Accession number: MZ450974). The maximum likelihood phylogenetic analysis showed that the H. muticus and H. niger were clustered into one clade with strong support values, indicating their closer relationship.

The complete chloroplast genome sequence of Clerodendrum cyrtophyllum from Guangzhou, China

Clerodendrum cyrtophyllum is a well-known medicinal plant in southern China. Here, we presented the complete chloroplast (cp) genome of C. cyrtophyllum using Illumina high-throughput sequencing technology. The C. cyrtophyllum cp genome size is 152,004 bp with 38.13% GC content, including a pair of inverted repeat regions (IR, 51,592 bp) separated by a large single copy (LSC, 86,480 bp) and a small single copy region (SSC, 18,425 bp). It possesses 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis fully shows that C. cyrtophyllum is closely related to Clerodendrum bungei and Clerodendrum lindleyi. Overall, the complete cp genome sequence of C. cyrtophyllum provides a valuable resource for genetic diversity, phylogenetic relationship, and species identification.

Deep vertical rotary tillage increases the diversity of bacterial communities and alters the bacterial network structure in soil planted to corn

Deep vertical rotary tillage (DVRT) is a novel technique; however, its influence on soil bacterial diversity and community structure remains unclear. Herein, it was hypothesized that this tillage method significantly improves the bacterial diversity and alters the bacterial community structure and therefore it supports enhanced soil ecosystem functions in cultivated land. We investigated the soil bacterial communities and performed molecular ecological network analysis of cultivated land soils under different tillage regimes using high-throughput 16S rRNA gene Illumina sequencing. Soil samples were collected from the experimental field under 2 treatments: DVRT and conventional rotary tillage (CT) in Shizuishan City, Ningxia, China, in a 2-year field experiment. The α-diversity indices showed that DVRT resulted in higher bacterial diversity. In addition, the principal coordinate analysis results revealed a clear separation among the groups of cultivated land soils under the 2 treatment regimes. The key physicochemical factors that significantly influenced bacterial diversity and community structure were pH and total potassium concentration. The network analysis indicated that the bacterial network of DVRT soils consisted of more functionally interrelated bacterial modules than that of soils under CT, and the topological roles of characteristic bacteria and key bacteria were also different. In relation to CT, the relative abundances of organisms belonging to the functional groups of “Xenobiotics biodegradation and metabolism”, “Signal transduction”, and “Metabolism of cofactors and vitamins” were significantly increased in cultivated land soils under DVRT. It was concluded that DVRT treatment could improve bacterial diversity, alter the bacterial network structure, and enhance potential ecosystem functions in soils of cultivated land.

Comparative Transcriptome Analysis of Softening and Ripening-Related Genes in Kiwifruit Cultivars Treated with Ethylene.

This work presents the transcriptome analysis of green ‘Hayward’ (Actinidia deliciosa) and gold ‘Haegeum’ (Actinidia chinensis) kiwifruit cultivars after treatment with ethylene for three days at 25 °C. Illumina high-throughput sequencing platform was used to sequence total mRNAs and the transcriptome gene set was constructed by de novo assembly. A total of 1287 and 1724 unigenes were differentially expressed during the comparison of ethylene treatment with control in green ‘Hayward’ and gold ‘Haegeum’, respectively. From the differentially expressed unigenes, 594 and 906 were upregulated, and 693 and 818 were downregulated in the green and gold kiwifruit cultivars, respectively, when treated with ethylene. We also identified a list of genes that were expressed commonly and exclusively in the green and gold kiwifruit cultivars treated with ethylene. Several genes were expressed differentially during the ripening of kiwifruits, and their cumulative effect brought about the softening- and ripening-related changes. This work also identified and categorized genes related to softening and other changes during ripening. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) identified in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR) to validate the reliability of the expression profiles obtained from RNA-Seq. The data obtained from the present study will add to the information available on the molecular mechanisms of the effects of ethylene during the ripening of kiwifruits. This study will also provide resources for further studies of the genes related to ripening, helping kiwifruit breeders and postharvest technologists to improve ripening quality.

CUT&RUN for Chromatin Profiling in Caenorhabditis elegans.

Cleavage under targets and release using nuclease (CUT&RUN) is a recently developed chromatin profiling technique that uses a targeted micrococcal nuclease cleavage strategy to obtain high-resolution binding profiles of protein factors or to map histones with specific post-translational modifications. Due to its high sensitivity, CUT&RUN allows quality binding profiles to be obtained with only a fraction of the starting material and sequencing depth typically required for other chromatin profiling techniques such as chromatin immunoprecipitation. Although CUT&RUN has been widely adopted in multiple model systems, it has rarely been utilized in Caenorhabditis elegans, a model system of great importance to genomic research. Cell dissociation techniques, which are required for this approach, can be challenging in C. elegans due to the toughness of the worm's cuticle and the sensitivity of the cells themselves. Here, we describe a robust CUT&RUN protocol for use in C. elegans to determine the genome-wide localization of protein factors and specific histone marks. With a simple protocol utilizing live, uncrosslinked tissue as the starting material, performing CUT&RUN in worms has the potential to produce physiologically relevant data at a higher resolution than chromatin immunoprecipitation. This protocol involves a simple dissociation step to uniformly permeabilize worms while avoiding sample loss or cell damage, resulting in high-quality CUT&RUN profiles with as few as 100 worms and detectable signal with as few as 10 worms. This represents a significant advancement over chromatin immunoprecipitation, which typically uses thousands or hundreds of thousands of worms for a single experiment. The protocols presented here provide a detailed description of worm growth, sample preparation, CUT&RUN workflow, library preparation for high-throughput sequencing, and a basic overview of data analysis, making CUT&RUN simple and accessible for any worm lab. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Growth and synchronization of C. elegans Basic Protocol 2: Worm dissociation, sample preparation, and optimization Basic Protocol 3: CUT&RUN chromatin profiling Alternate Protocol: Improving CUT&RUN signal using a secondary antibody Basic Protocol 4: CUT&RUN library preparation for Illumina high-throughput sequencing Basic Protocol 5: Basic data analysis using Linux.

Response of Gut Microbiota, Digestive Enzyme Ability, and Immune Function to Starvation in the Oriental River Prawn Macrobrachium nipponense

In order to evaluate the interplay of nutritional status and the digestive capacity, immune function, and gut microbiota in the oriental river prawn Macrobrachium nipponense, a 14-day starvation trial was conducted to detect the effects of starvation on the activities of digestive enzymes and immune enzymes and the structure of prawn gut microbiota. The adult prawns were randomly assigned to a control group (F group) and starvation group (S group) with three replicates. The F group was normally fed with commercial diet, and the S group was starved for 14 days. The result showed that digestive enzyme activities of trypsin and lipase in the hepatopancreas of the S group were significantly lower than those of the F group after 4 d of starvation ( P < 0.05 ), while the activity of amylase significantly increased after 14 d of starvation ( P < 0.05 ). Moreover, the results of the histological analysis of prawn gut showed that both the height of epithelial cells and microvilli of intestine in the S group were obviously decreased than those in the F group ( P < 0.05 ) after 14 d of starvation. The activities of immune-related enzymes including superoxide dismutase, catalase, and acid phosphatase in the hepatopancreas of the S group significantly decreased after 4 d of starvation, and lysozyme activity of the F group was lower than that of the S group after 7 d of starvation ( P < 0.05 ). In addition, the results of Illumina high-throughput sequencing showed that a total of 14,285 OTUs were obtained and classified into 30 phyla, among which Actinobacteria and Proteobacteria were the predominant microflora in the intestinal microbial communities of both groups. However, the relative abundance of opportunistic pathogens was significantly increased in the S group, while the relative abundance of beneficial bacterium was decreased ( P < 0.05 ). The bacterial richness with the Chao estimator was significantly higher in the F group than in the S group ( P < 0.05 ). Both the results of principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS) demonstrated that the intestinal microbiota of the F group was separate from those of the S group. The result of functional prediction of the metabolic pathways showed that the intestinal microbiota was enriched in the KEGG pathways of amino acid, carbohydrate, fatty acid, and lipid biosynthesis and degradation at level 2. This result implied that the microbiota of shrimp gut decreased nutrition metabolism under the stress of starvation. Meanwhile, comparing to the F group, the immune-related pathway of enterobacterial common antigen biosynthesis was markedly reduced in the S group ( P < 0.05 ). The result of redundancy analysis (RDA) further confirmed that the activities of digestive and immune enzymes were correlated with the microbial community structure. Finally, the structural equation modeling highlighted that changes in the activities of digestive and immune enzymes were directly related to the gut bacterial community and notably affected prawn growth.

The effects of grazer exclosure duration on soil microbial communities on the Qinghai-Tibetan Plateau

While determining the response of soil microbes to grazer exclosure duration is critical to understanding ecosystem restoration processes, few studies have focused on this issue. With seasonal grazing as a control, microbes of alpine grassland soils under 5, 13, 22, and 39 years of grazer exclosure situated in the eastern part of the Qinghai-Tibetan Plateau, were examined. Microbial diversity was determined through Illumina high-throughput sequencing of the 16S rRNA gene and an internal transcription spacer (ITS). We found that soil bacterial α-diversity showed insignificant differences between seasonal grazing and grazer exclosure and among the grazer exclosures of different durations, while fungal α-diversity under the 5-year grazer exclosure was significantly different from those under the other treatments. Soil microbial community profiles under the 13-, 22-, and 39-year grazer exclosures were significantly different compared to those under the seasonal grazing or 5-year grazer exclosure. Briefly, longer exclosure durations led to a higher relative abundance of multiple copiotrophic microbial lineages (e.g., β-Proteobacteria, Rhizobiales, and Frankiales), whereas several oligotrophic microbial lineages (e.g., Chloroflexi, Leotiomycetes, and Xylariales) gradually and significantly decreased. Functional predictions suggest that as grazer exclosure duration was extended, the relative abundance of nitrogen fixers increased, while the proportions of plant pathogenic fungi decreased. This indicates that long-term grazer exclosure duration may contribute to enhanced soil nitrogen fixation and grassland health by maintaining plant growth and decreasing the risk of plant disease. However, this may have a resource cost as plant productivity and soil organic carbon both decreased with the extension of grazer exclosure duration. Therefore, the agroecology effect of grazer exclosure duration on the diversity and abundance of soil nitrogen fixing bacteria and plant pathogen fungi, should be given more attention in the cold and humid portion of the Qinghai-Tibetan Plateau.

Engineered manganese redox cycling in anaerobic–aerobic MBBRs for utilisation of biogenic manganese oxides to efficiently remove micropollutants

Freshly formed manganese oxides (MnOx) can oxidise various organic pollutants, but its reactivity is short-lived and therefore continuous pollutant removal by MnOx is not feasible. In this study, an engineered cycle of manganese reduction followed by oxidation was implemented in a two-stage moving bed biofilm reactor (staged MBBR), aiming to replenish MnOx for continuous micropollutant removal. In the anaerobic reactor, added MnO2 was reduced to Mn2+ by microbially-mediated reaction with organic matter in the sewage. The reduced Mn2+ was then re-oxidised to biogenic manganese oxides (BioMnOx) in the aerobic reactor, which precipitated into the suspended biofilm. Part of the BioMnOx was regularly recycled to the anaerobic reactor for the next round of manganese reduction. Mass balance assessment shows that manganese redox cycling functioned well during continuous operation, and BioMnOx was continuously regenerated within the aerobic reactor. A specific Mn-oxidising bacteria belonging to Stenotrophomonas sp. was isolated from suspended biofilm of the aerobic reactor and identified, and Illumina high-throughput sequencing analysis reveals a microbial community shift in the staged MBBR during manganese redox cycling. Furthermore, both batch and continuous-flow experiments show that specific micropollutants such as bezafibrate, diclofenac and sulfamethoxazole were efficiently removed (over 80%) by the staged MBBR.

Rice washing drainage (RWD) embedded in poly(vinyl alcohol)/sodium alginate as denitrification inoculum for high nitrate removal rate with low biodiversity

Immobilization technology with low maintenance is a promising alternative to enhance nitrate removal from water. In this study, washing rice drainage (RWD) was immobilized by poly(vinyl alcohol)/sodium alginate (PVA/SA) to obtain RWD-PVA/SA gel beads as inoculum for denitrification. When initial nitrate concentration was 50 mg N/L, nitrate was effectively removed at rates of 50–600 mg/(L∙d) using acetate as carbon source (C/N = 1.25). Arrhenius activation energy (Ea) of nitrate oxidoreductase was 28.64 kJ/mol for the RWD-PVA/SA gel beads. Temporal and spatial variation in microbial community structures were revealed along with RWD storage and in the reactors by Illumina high-throughput sequencing technology. RWD-PVA/SA gel beads has a simple (operational taxonomic units (OTUs) 〈100). Dechloromonas, Pseudomonas, Flavobacterium and Acidovorax were the most four dominant genera in the denitrification reactors inoculated with RWD-PVA/SA gel beads. This study provides an inoculum for denitrification with high nitrate removal performance and simple microbial community structures.

Oligotrophic Bacterial Community Structure Associated with Muscovite Mineral Is Rich in Proteobacterial Microbiomes Revealed through Next-Generation Sequencing

The microbial life indigenous to mineral deposits are generally regarded as extremophiles as they are tolerant to extreme conditions. The microorganisms that thrive in such environments survive by modifying their metabolic pathway or mechanisms. The microbiome associated with ore deposits remain poorly studied. The present study is the first attempt to explore the taxonomic composition of the bacterial community associated with the muscovite ore deposit from Southern India by using high throughput Illumina sequencing employing the V3 and V4 region of the16S rDNA and bioinformatics channel. A total of 20 bacterial phyla with 55 classes, 96 orders, 192 families, 382 genera and 462 species were recovered in the study. The alpha diversity index suggests that muscovite ore deposits harbored highly variable bacterial communities. Among the bacterial communities, Proteobacteria (33%), Actinobacteria (29.9%), Firmicutes (25.4%), Bacteroidetes (5.5%) and Chloroflexi (2.7%) were the dominate phyla. A total of 156 abundant species and 306 rare species were observed and is an indication of the presence of novel species. This study helps to understand the survival strategy of oligotrophs, which are an important aspect of microbial ecology.

Distinct Platelet Ribonucleic Acid Signatures in Patients with Pulmonary Hypertension.

Rationale: Pulmonary hypertension encompasses progressive disorders leading to right ventricular dysfunction and early death. Late detection is an important cause of poor clinical outcomes. However, biomarkers that accurately predict the presence of pulmonary hypertension are currently lacking. Objectives: In this study, we provide evidence that blood platelets contain a distinctive ribonucleic acid (RNA) profile that may be exploited for the detection of pulmonary hypertension. Methods: Blood platelet RNA was isolated prospectively from 177 prevalent patients with different subtypes of pulmonary hypertension as well as 195 control subjects clinically not suspected of pulmonary hypertension. Sequencing libraries were created using SMARTer (Switching Mechanism at 5' end of RNA Template) copy desoxyribonucleic acid amplification and sequenced on the Illumina High Throughput Sequencing platform. RNA-sequencing reads were mapped to the human reference genome, and intron-spanning spliced RNA reads were selected. Differential spliced RNA panels were calculated by analysis of variance statistics. A particle swarm optimization-enhanced classification algorithm was built employing a development (n = 213 samples) and independent validation series (n = 159 samples). Results: We detected a total of 4,014 different RNAs in blood platelets from patients with pulmonary hypertension (n = 177) and asymptomatic control subjects (n = 195). Gene ontology analysis revealed enhanced RNA concentrations for genes related to RNA processing, translation, and mitochondrial function. A particle swarm optimization-selected RNA panel of 408 distinctive differentially spliced RNAs mediated detection of pulmonary hypertension with 93% sensitivity, 62% specificity, 77% accuracy, 0.89 (95% confidence interval, 0.83-0.93) area under the curve, and a negative predictive value of 91% in the independent validation series. The prediction score was independent of age, sex, smoking, pulmonary hypertension subtype, and the use of pulmonary hypertension-specific medication or anticoagulants. Conclusions: A platelet RNA panel may accurately discriminate patients with pulmonary hypertension from asymptomatic control subjects. In the light of current diagnostic delays, this study is the starting point for further development and evaluation of a platelet RNA-based blood test to ultimately improve early diagnosis and clinical outcomes in patients with pulmonary hypertension.

Analysis of Bacterial Community Composition and Ecological Function during Soft Rot Process in Pitaya (Hylocereus spp.) Stems

The soft rot in pitaya (Hylocereus spp.) stems seriously affected the harvest of pitaya fruits, but the dynamic change characteristics of bacterial community in pitaya stems during soft rot stages had not been revealed. In this study, we analyzed the bacterial community composition of different soft rot stages and visualized functional annotations of the core bacterial community in five soft rot periods via the Illumina high-throughput sequencing technology, MetaCoMET online network platform, and FAPROTAX database. The results showed that the dominant bacteria in healthy and diseased pitaya stems were Proteobacteria and Firmicutes. Pseudomonas, Enterobacter, Sphingomonas, and Sphingobacterium were the core bacteria microbiomes during the infection stages. Meanwhile, the ecological function analysis results showed that the Enterobacter and Pseudomonas bacteria may play an important role in causing soft rot of pitaya stems. Therefore, the results shown in this paper could provide a useful reference for the study on microecological mechanism of soft rot of pitaya stems.

The complete chloroplast genome of Solanum sisymbriifolium (Solanaceae), the wild eggplant

Solanum sisymbriifolium is a critical wild eggplant resource with resistance to many serious diseases that affect eggplant production. In this study, the chloroplast genome of S. sisymbriifolium was successfully sequenced using Illumina high-throughput sequencing technology. The length of the complete chloroplast genome is 155,771 bp, and its GC content is 37.76%. There is a large single-copy region (86,404 bp), a small single-copy region (18,525 bp), and a pair of inverted repeat regions (25,421 bp) in the chloroplast genome. A total of 128 coding genes were annotated in the entire chloroplast genome, including 83 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The phylogenetic tree of 17 complete chloroplast genomes shows that S. sisymbriifolium is closely related to Solanum wrightii.

Comparative study on the mutation spectrum of tissue DNA and blood ctDNA in patients with non-small cell lung cancer

BackgroundTo study the mutations detected in tissue DNA and blood circulating tumor DNA (ctDNA) of patients with advanced lung cancer and analyze the correlations between gene mutations, clinical features, and treatment.MethodsTargeted next-generation sequencing (NGS) technology based on probe hybrid capture and Illumina high-throughput sequencing was used to detect the DNA of tumor tissue samples (n=24) and blood samples (n=15) of ctDNA from 28 lung cancer patients with a clear pathological diagnosis. For mutations, the detection range included 4 types of mutations (point mutations, small indels, copy number variations) in all exon regions and partial intron regions of the 556 genes panel.ResultsThe most frequently detected mutant genes in 24 lung cancer tissue samples were TP53 (58.3%, 14/24), EGFR (33.3%, 8/24), LRP1B (25.0%, 6/24), KRAS (20.8%, 5/24), and ARID1A (16.7%, 4/24). The common mutant genes detected in 15 ctDNA samples were TP53 (60%, 5/15), EGFR (33.3%, 5/15), LRP1B (20.0%, 3/15), ERBB4 (3/15), and ARID1A (13.3%, 2/15). Among the 28 patients, 11 patients underwent both tissue DNA and ctDNA detection. The average co-mutation frequency of paired tissue DNA with ctDNA was 38.9% (0–83.3%), and the median value was 37.5%.ConclusionsTissue DNA and ctDNA samples could detect genetic mutations and be consistent. Therefore, ctDNA detection as a method for disease diagnosis and evaluation of tumor molecular status may be helpful for the clinical diagnosis and treatment of lung cancer patients.