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Navarrete-López, Paula, Victoria Asselstine, María Maroto, Marta Lombó, Ángela Cánovas i Alfonso Gutiérrez-Adán. "RNA Sequencing of Sperm from Healthy Cattle and Horses Reveals the Presence of a Large Bacterial Population". Current Issues in Molecular Biology 46, nr 9 (19.09.2024): 10430–43. http://dx.doi.org/10.3390/cimb46090620.
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RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and equine sperm cell preparations, low mapping rates to the reference genomes were observed, mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples, which led to a reduced sequencing depth of RNAs of interest. To explore the presence of bacteria, we aligned the unmapped reads to a complete database of bacterial genomes and identified bacteria-associated transcripts which were characterized. This analysis examines the limitations associated with sperm transcriptome profiling by reporting the nature of the RNA sequences among which bacterial RNA was found. These findings can aid researchers in understanding spermatozoal RNA-seq data and pave the way for the identification of molecular markers of sperm performance.
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Morcillo, Rafael, Juan Vílchez, Song Zhang, Richa Kaushal, Danxia He, Hailing Zi, Renyi Liu, Karsten Niehaus, Avtar Handa i Huiming Zhang. "Plant Transcriptome Reprograming and Bacterial Extracellular Metabolites Underlying Tomato Drought Resistance Triggered by a Beneficial Soil Bacteria". Metabolites 11, nr 6 (9.06.2021): 369. http://dx.doi.org/10.3390/metabo11060369.
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Water deficit is one of the major constraints to crop production and food security worldwide. Some plant growth-promoting rhizobacteria (PGPR) strains are capable of increasing plant drought resistance. Knowledge about the mechanisms underlying bacteria-induced plant drought resistance is important for PGPR applications in agriculture. In this study, we show the drought stress-mitigating effects on tomato plants by the Bacillus megaterium strain TG1-E1, followed by the profiling of plant transcriptomic responses to TG1-E1 and the profiling of bacterial extracellular metabolites. Comparison between the transcriptomes of drought-stressed plants with and without TG1-E1 inoculation revealed bacteria-induced transcriptome reprograming, with highlights on differentially expressed genes belonging to the functional categories including transcription factors, signal transduction, and cell wall biogenesis and organization. Mass spectrometry-based analysis identified over 40 bacterial extracellular metabolites, including several important regulators or osmoprotectant precursors for increasing plant drought resistance. These results demonstrate the importance of plant transcriptional regulation and bacterial metabolites in PGPR-induced plant drought resistance.
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Nobori, Tatsuya, André C. Velásquez, Jingni Wu, Brian H. Kvitko, James M. Kremer, Yiming Wang, Sheng Yang He i Kenichi Tsuda. "Transcriptome landscape of a bacterial pathogen under plant immunity". Proceedings of the National Academy of Sciences 115, nr 13 (12.03.2018): E3055—E3064. http://dx.doi.org/10.1073/pnas.1800529115.
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Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes in planta and determined high-resolution transcriptome patterns of the foliar bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana with a total of 27 combinations of plant immunity mutants and bacterial strains. Bacterial transcriptomes were analyzed at 6 h post infection to capture early effects of plant immunity on bacterial processes and to avoid secondary effects caused by different bacterial population densities in planta. We identified specific “immune-responsive” bacterial genes and processes, including those that are activated in susceptible plants and suppressed by plant immune activation. Expression patterns of immune-responsive bacterial genes at the early time point were tightly linked to later bacterial growth levels in different host genotypes. Moreover, we found that a bacterial iron acquisition pathway is commonly suppressed by multiple plant immune-signaling pathways. Overexpression of a P. syringae sigma factor gene involved in iron regulation and other processes partially countered bacterial growth restriction during the plant immune response triggered by AvrRpt2. Collectively, this study defines the effects of plant immunity on the transcriptome of a bacterial pathogen and sheds light on the enigmatic mechanisms of bacterial growth inhibition during the plant immune response.
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Passalacqua, Karla D., Anjana Varadarajan, Brian D. Ondov, David T. Okou, Michael E. Zwick i Nicholas H. Bergman. "Structure and Complexity of a Bacterial Transcriptome". Journal of Bacteriology 191, nr 10 (20.03.2009): 3203–11. http://dx.doi.org/10.1128/jb.00122-09.
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ABSTRACT Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and information on absolute abundance all provide valuable insights into gene function and regulation, but none has ever been determined on a genome-wide scale for any bacterium. Indeed, these aspects of the prokaryotic transcriptome have been explored on a large scale in only a few instances, and consequently little is known about the absolute composition of the mRNA population within a bacterial cell. Here we report the use of a high-throughput sequencing-based approach in assembling the first comprehensive, single-nucleotide resolution view of a bacterial transcriptome. We sampled the Bacillus anthracis transcriptome under a variety of growth conditions and showed that the data provide an accurate and high-resolution map of transcript start sites and operon structure throughout the genome. Further, the sequence data identified previously nonannotated regions with significant transcriptional activity and enhanced the accuracy of existing genome annotations. Finally, our data provide estimates of absolute transcript abundance and suggest that there is significant transcriptional heterogeneity within a clonal, synchronized bacterial population. Overall, our results offer an unprecedented view of gene expression and regulation in a bacterial cell.
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Cornforth, Daniel M., Justine L. Dees, Carolyn B. Ibberson, Holly K. Huse, Inger H. Mathiesen, Klaus Kirketerp-Møller, Randy D. Wolcott, Kendra P. Rumbaugh, Thomas Bjarnsholt i Marvin Whiteley. "Pseudomonas aeruginosa transcriptome during human infection". Proceedings of the National Academy of Sciences 115, nr 22 (14.05.2018): E5125—E5134. http://dx.doi.org/10.1073/pnas.1717525115.
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Laboratory experiments have uncovered many basic aspects of bacterial physiology and behavior. After the past century of mostly in vitro experiments, we now have detailed knowledge of bacterial behavior in standard laboratory conditions, but only a superficial understanding of bacterial functions and behaviors during human infection. It is well-known that the growth and behavior of bacteria are largely dictated by their environment, but how bacterial physiology differs in laboratory models compared with human infections is not known. To address this question, we compared the transcriptome of Pseudomonas aeruginosa during human infection to that of P. aeruginosa in a variety of laboratory conditions. Several pathways, including the bacterium’s primary quorum sensing system, had significantly lower expression in human infections than in many laboratory conditions. On the other hand, multiple genes known to confer antibiotic resistance had substantially higher expression in human infection than in laboratory conditions, potentially explaining why antibiotic resistance assays in the clinical laboratory frequently underestimate resistance in patients. Using a standard machine learning technique known as support vector machines, we identified a set of genes whose expression reliably distinguished in vitro conditions from human infections. Finally, we used these support vector machines with binary classification to force P. aeruginosa mouse infection transcriptomes to be classified as human or in vitro. Determining what differentiates our current models from clinical infections is important to better understand bacterial infections and will be necessary to create model systems that more accurately capture the biology of infection.
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Beisser, Daniela, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann i Jens Boenigk. "Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes". PeerJ 5 (10.01.2017): e2832. http://dx.doi.org/10.7717/peerj.2832.
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BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
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Chaudhuri, Roy R., Lu Yu, Alpa Kanji, Timothy T. Perkins, Paul P. Gardner, Jyoti Choudhary, Duncan J. Maskell i Andrew J. Grant. "Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome". Microbiology 157, nr 10 (1.10.2011): 2922–32. http://dx.doi.org/10.1099/mic.0.050278-0.
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C ampylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community.
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González-Torres, Pedro, Leszek P. Pryszcz, Fernando Santos, Manuel Martínez-García, Toni Gabaldón i Josefa Antón. "Interactions between Closely Related Bacterial Strains Are Revealed by Deep Transcriptome Sequencing". Applied and Environmental Microbiology 81, nr 24 (2.10.2015): 8445–56. http://dx.doi.org/10.1128/aem.02690-15.
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ABSTRACTComparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, whether assemblages simply act as the arithmetic addition of their individual components. Here, we took advantage of transcriptome sequencing to address this question. For this, we analyzed the transcriptomes of two closely related strains of the extremely halophilic bacteriumSalinibacter rubergrown axenically and in coculture. These organisms dominate bacterial assemblages in hypersaline environments worldwide. The strains used here cooccurred in the natural environment and are 100% identical in their 16S rRNA genes, and each strain harbors an accessory genome representing 10% of its complete genome. Overall, transcriptomic patterns from pure cultures were very similar for both strains. Expression was detected along practically the whole genome albeit with some genes at low levels. A subset of genes was very highly expressed in both strains, including genes coding for the light-driven proton pump xanthorhodopsin, genes involved in the stress response, and genes coding for transcriptional regulators. Expression differences between pure cultures affected mainly genes involved in environmental sensing. When the strains were grown in coculture, there was a modest but significant change in their individual transcription patterns compared to those in pure culture. Each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation.
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Ding, Ting, i Yong Li. "Quorum sensing inhibitory effects of vanillin on the biofilm formation of Pseudomonas fluorescens P07 by transcriptome analysis". SDRP Journal of Food Science & Technology 5, nr 7 (2021): 275–92. http://dx.doi.org/10.25177/jfst.5.7.ra.10686.
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Pseudomonas fluorescens is an important psychrotrophic food-spoilage bacterium. Quorum sensing (QS) enables bacteria to control various physiological processes. Hence, targeting bacterial QS would be a novel method to improve food quality. In this study, P. fluorescens P07 was treated with vanillin, which showed strong QS inhibitory activity, and its resultant effects on swarming motility, biofilm formation, and extracellular polymeric substance (EPS) secretion were measured. The mechanisms underlying the inhibitory effects were then explored by transcriptomic analysis. The results showed that vanillin had inhibitory effects on swarming motility, biofilm formation, N-acyl-L-homoserine Lactone (AHLs) and EPS secretion of P. fluorescens P07. The result of transcriptionomic tests indicated that the decrease in bacterial biofilm formation was probably due to the influence of vanillin on mobility, adhesion, chemotaxis, EPS secretion, and QS system of the bacteria. Keywords: Pseudomonas fluorescens, quorum sensing, biofilm formation, transcriptome analysis, swarming motility
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Horlock, Anthony D., Rachel L. Piersanti, Rosabel Ramirez-Hernandez, Fahong Yu, Zhengxin Ma, KwangCheol C. Jeong, Martin J. D. Clift i in. "Uterine infection alters the transcriptome of the bovine reproductive tract three months later". Reproduction 160, nr 1 (lipiec 2020): 93–107. http://dx.doi.org/10.1530/rep-19-0564.
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Infection of the postpartum uterus with pathogenic bacteria is associated with infertility months later in dairy cattle. However, it is unclear whether these bacterial infections lead to long-term changes in the reproductive tract that might help explain this infertility. Here we tested the hypothesis that infusion of pathogenic bacteria into the uterus leads to changes in the transcriptome of the reproductive tract 3 months later. We used virgin Holstein heifers to avoid potential confounding effects of periparturient problems, lactation, and negative energy balance. Animals were infused intrauterine with endometrial pathogenic bacteria Escherichia coli and Trueperella pyogenes (n = 4) and compared with control animals (n = 6). Three months after infusion, caruncular and intercaruncular endometrium, isthmus and ampulla of the oviduct, and granulosa cells from ovarian follicles >8 mm diameter were profiled by RNA sequencing. Bacterial infusion altered the transcriptome of all the tissues when compared with control. Most differentially expressed genes were tissue specific, with 109 differentially expressed genes unique to caruncular endometrium, 57 in intercaruncular endometrium, 65 in isthmus, 298 in ampulla, and 83 in granulosa cells. Surprisingly, despite infusing bacteria into the uterus, granulosa cells had more predicted upstream regulators of differentially expressed genes than all the other tissues combined. In conclusion, there were changes in the transcriptome of the endometrium, oviduct and even granulosa cells, 3 months after intrauterine infusion of pathogenic bacteria. These findings imply that long-term changes throughout the reproductive tract could contribute to infertility after bacterial infections of the uterus.
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Su, Jing, Bo Yao, Rong Huang, Xiaoni Liu, Zhenfen Zhang i Yong Zhang. "Cross-Kingdom Pathogenesis of Pantoea alfalfae CQ10: Insights from Transcriptome and Proteome Analyses". Microorganisms 12, nr 11 (30.10.2024): 2197. http://dx.doi.org/10.3390/microorganisms12112197.
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In grassland agroecosystems, some plant pathogenic bacteria can cause disease in animals. These strains are known as plant and animal cross-kingdom pathogenic bacteria. In this study, we established an alfalfa root infection model and a mouse model via the gavage administration of the Pantoea alfalfae CQ10 (CQ10) bacterial suspension. It was confirmed that the CQ10 strain caused bacterial leaf blight of alfalfa. Mice inoculated with 0.4 mL of 109 cfu/mL bacterial suspension developed clinical symptoms 48 h later, such as diminished vitality, tendencies to huddle, and lack of appetite, including severe lesions in stomach, liver, kidney, and spleen tissues. CQ10 strains were isolated from mouse feces at different time points of inoculation. Thus, CQ10 is a plant and animal cross-kingdom pathogenic bacterium. Transcriptome and proteome analyses showed that biofilm and iron uptake are important virulence factors of the pathogen CQ10, among which Bap and Lpp regulating biofilm are the key cross-kingdom virulence genes of CQ10. From an evolutionary perspective, insights gained from this dual animal–plant pathogen system may help to elucidate the molecular basis underlying the host specificity of bacterial pathogens. The result provides a theoretical basis for the risk assessment, prevention, and control strategies of new pathogenic bacteria entering a new region.
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Xiao, Xi Ou, Wenqiu Lin, Enyou Feng i Xiongchang Ou. "Transcriptome and metabolome response of eggplant against Ralstonia solanacearum infection". PeerJ 11 (11.01.2023): e14658. http://dx.doi.org/10.7717/peerj.14658.
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Bacterial wilt is a soil-borne disease that represents ubiquitous threat to Solanaceae crops. The whole-root transcriptomes and metabolomes of bacterial wilt-resistant eggplant were studied to understand the response of eggplant to bacterial wilt. A total of 2,896 differentially expressed genes and 63 differences in metabolites were identified after inoculation with Ralstonia solanacearum. Further analysis showed that the biosynthesis pathways for phytohormones, phenylpropanoids, and flavonoids were altered in eggplant after inoculation with R. solanacearum. The results of metabolomes also showed that phytohormones played a key role in eggplant response to bacterial wilt. Integrated analyses of the transcriptomic and metabolic datasets indicated that jasmonic acid (JA) content and gene involved in the JA signaling pathway increased in response to bacterial wilt. These findings remarkably improve our understanding of the mechanisms of induced defense response in eggplant and will provide insights intothe development of disease-resistant varieties of eggplant.
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Rychel, Kevin, Katherine Decker, Anand V. Sastry, Patrick V. Phaneuf, Saugat Poudel i Bernhard O. Palsson. "iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning". Nucleic Acids Research 49, nr D1 (12.10.2020): D112—D120. http://dx.doi.org/10.1093/nar/gkaa810.
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Abstract Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their association to known genetic regulators. By grouping and analyzing genes based on observations from big data alone, iModulons can provide a novel perspective into how the composition of the transcriptome adapts to environmental conditions. Here, we present iModulonDB (imodulondb.org), a knowledgebase of prokaryotic transcriptional regulation computed from high-quality transcriptomic datasets using ICA. Users select an organism from the home page and then search or browse the curated iModulons that make up its transcriptome. Each iModulon and gene has its own interactive dashboard, featuring plots and tables with clickable, hoverable, and downloadable features. This site enhances research by presenting scientists of all backgrounds with co-expressed gene sets and their activity levels, which lead to improved understanding of regulator-gene relationships, discovery of transcription factors, and the elucidation of unexpected relationships between conditions and genetic regulatory activity. The current release of iModulonDB covers three organisms (Escherichia coli, Staphylococcus aureus and Bacillus subtilis) with 204 iModulons, and can be expanded to cover many additional organisms.
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O’Flaherty, Sarah, Natalia Cobian i Rodolphe Barrangou. "Impact of Pomegranate on Probiotic Growth, Viability, Transcriptome and Metabolism". Microorganisms 11, nr 2 (5.02.2023): 404. http://dx.doi.org/10.3390/microorganisms11020404.
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Despite rising interest in understanding intestinal bacterial survival in situ, relatively little attention has been devoted to deciphering the interaction between bacteria and functional food ingredients. Here, we examined the interplay between diverse beneficial Lactobacillaceae species and a pomegranate (POM) extract and determined the impact of this functional ingredient on bacterial growth, cell survival, transcription and target metabolite genesis. Three commercially available probiotic strains (Lactobacillus acidophilus NCFM, Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum Lp-115) were used in growth assays and flow cytometry analysis, indicating differential responses to the presence of POM extract across the three strains. The inclusion of POM extract in the growth medium had the greatest impact on L. acidophilus cell counts. LIVE/DEAD staining determined significantly fewer dead cells when L. acidophilus was grown with POM extract compared to the control with no POM (1.23% versus 7.23%). Whole-transcriptome analysis following exposure to POM extract showed markedly different global transcriptome responses, with 15.88% of the L. acidophilus transcriptome, 19.32% of the L. rhamnosus transcriptome and only 2.37% of the L. plantarum transcriptome differentially expressed. We also noted strain-dependent metabolite concentrations in the medium with POM extract compared to the control medium for punicalagin, ellagic acid and gallic acid. Overall, the results show that POM extract triggers species-specific responses by probiotic strains and substantiates the rising interest in using POM as a prebiotic compound.
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Chetal, Kashish, i Sarath Chandra Janga. "OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes". BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/318217.
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Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons—codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets.Description. We present operomeDB, a database which provides an ensemble of all the predicted operons for bacterial genomes using available RNA-sequencing datasets across a wide range of experimental conditions. Although several studies have recently confirmed that prokaryotic operon structure is dynamic with significant alterations across environmental and experimental conditions, there are no comprehensive databases for studying such variations across prokaryotic transcriptomes. Currently our database contains nine bacterial organisms and 168 transcriptomes for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading, and querying of data. In addition, because of its ability to load custom datasets, users can also compare their datasets with publicly available transcriptomic data of an organism.Conclusion. OperomeDB as a database should not only aid experimental groups working on transcriptome analysis of specific organisms but also enable studies related to computational and comparative operomics.
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Li, Tongda, Ross Mann, Jatinder Kaur, German Spangenberg i Timothy Sawbridge. "Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions". Plants 10, nr 9 (30.08.2021): 1802. http://dx.doi.org/10.3390/plants10091802.
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Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.
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Guo, Lizhen, Min Tang, Shiqi Luo i Xin Zhou. "Screening and Functional Analyses of Novel Cecropins from Insect Transcriptome". Insects 14, nr 10 (29.09.2023): 794. http://dx.doi.org/10.3390/insects14100794.
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Antibiotic resistance is a significant and growing threat to global public health. However, antimicrobial peptides (AMPs) have shown promise as they exhibit a broad spectrum of antibacterial activities with low potential for resistance development. Insects, which inhabit a wide range of environments and are incredibly diverse, remain largely unexplored as a source of novel AMPs. To address this, we conducted a screening of the representative transcriptomes from the 1000 Insect Transcriptome Evolution (1KITE) dataset, focusing on the homologous reference genes of Cecropins, the first identified AMPs in insects known for its high efficiency. Our analysis identified 108 Cecropin genes from 105 insect transcriptomes, covering all major hexapod lineages. We validated the gene sequences and synthesized mature peptides for three identified Cecropin genes. Through minimal inhibition concentration and agar diffusion assays, we confirmed that these peptides exhibited antimicrobial activities against Gram-negative bacteria. Similar to the known Cecropin, the three Cecropins adopted an alpha-helical conformation in membrane-like environments, efficiently disrupting bacterial membranes through permeabilization. Importantly, none of the three Cecropins demonstrated cytotoxicity in erythrocyte hemolysis tests, suggesting their safety in real-world applications. Overall, this newly developed methodology provides a high-throughput bioinformatic pipeline for the discovery of AMP, taking advantage of the expanding genomic resources available for diverse organisms.
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Yun, Ki Wook, Rebecca Wallihan, Alexis Juergensen, Asuncion Mejias i Octavio Ramilo. "Community-Acquired Pneumonia in Children: Myths and Facts". American Journal of Perinatology 36, S 02 (25.06.2019): S54—S57. http://dx.doi.org/10.1055/s-0039-1691801.
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AbstractCommunity-acquired pneumonia (CAP) is the leading cause of death in children < 5 years of age worldwide. It is also one of the most frequent infectious diseases in children, leading to large antibiotic use and hospitalization even in the industrialized countries. However, the optimal management of CAP in children is still not well defined. Currently, respiratory viruses are considered the most frequent etiologic agents, but detection of viruses in the upper respiratory tract does not guarantee causation of pneumonia, nor precludes the presence of a bacterial pathogen. In both the upper and lower respiratory tract, respiratory viruses and pathogenic bacteria interact. Emerging evidence indicates that dual viral–bacterial infections function synergistically in many cases and together likely enhance the severity of CAP. Therefore, new and advanced technologies capable of sensitively and specifically discriminating viral, bacterial, and viral–bacterial coinfections are needed. Instead of focusing on the pathogen, analysis of host immune transcriptome profiles from children with CAP can potentially offer diagnostic signatures, help to assess disease severity, and eventually, prognostic indicators. An optimized management strategy by using molecular pathogen testing and transcriptome profiling will facilitate prompt, more appropriate, and targeted therapies, which in turn will lead to improved clinical outcomes in children with CAP.
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Youngblom, Madison A., Tracy M. Smith, Holly J. Murray i Caitlin S. Pepperell. "Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth". PLOS Pathogens 20, nr 4 (18.04.2024): e1012124. http://dx.doi.org/10.1371/journal.ppat.1012124.
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Mycobacterium tuberculosis (M. tb), the causative agent of tuberculosis (TB), is a leading global cause of death from infectious disease. Biofilms are increasingly recognized as a relevant growth form during M. tb infection and may impede treatment by enabling bacterial drug and immune tolerance. M. tb has a complicated regulatory network that has been well-characterized for many relevant disease states, including dormancy and hypoxia. However, despite its importance, our knowledge of the genes and pathways involved in biofilm formation is limited. Here we characterize the biofilm transcriptomes of fully virulent clinical isolates and find that the regulatory systems underlying biofilm growth vary widely between strains and are also distinct from regulatory programs associated with other environmental cues. We used experimental evolution to investigate changes to the transcriptome during adaptation to biofilm growth and found that the application of a uniform selection pressure resulted in loss of strain-to-strain variation in gene expression, resulting in a more uniform biofilm transcriptome. The adaptive trajectories of transcriptomes were shaped by the genetic background of the M. tb population leading to convergence on a sub-lineage specific transcriptome. We identified widespread upregulation of non-coding RNA (ncRNA) as a common feature of the biofilm transcriptome and hypothesize that ncRNA function in genome-wide modulation of gene expression, thereby facilitating rapid regulatory responses to new environments. These results reveal a new facet of the M. tb regulatory system and provide valuable insight into how M. tb adapts to new environments.
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Raad, Nicole, Hannes Luidalepp, Michel Fasnacht i Norbert Polacek. "Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli". International Journal of Molecular Sciences 22, nr 4 (8.02.2021): 1703. http://dx.doi.org/10.3390/ijms22041703.
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Almost two-thirds of the microbiome’s biomass has been predicted to be in a non-proliferating, and thus dormant, growth state. It is assumed that dormancy goes hand in hand with global downregulation of gene expression. However, it remains largely unknown how bacteria manage to establish this resting phenotype at the molecular level. Recently small non-protein-coding RNAs (sRNAs or ncRNAs) have been suggested to be involved in establishing the non-proliferating state in bacteria. Here, we have deep sequenced the small transcriptome of Escherichia coli in the exponential and stationary phases and analyzed the resulting reads by a novel biocomputational pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 12,000 small transcripts enriched during both growth stages. Differential expression analysis reveals distinct sRNAs enriched in the stationary phase that originate from various genomic regions, including transfer RNA (tRNA) fragments. Furthermore, expression profiling by Northern blot and RT-qPCR analyses confirms the growth phase-dependent expression of several enriched sRNAs. Our study adds to the existing repertoire of bacterial sRNAs and suggests a role for some of these small molecules in establishing and maintaining stationary phase as well as the bacterial stress response. Functional characterization of these detected sRNAs has the potential of unraveling novel regulatory networks central for stationary phase biology.
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Morad, Golnaz, Ashish V. Damania, Brenda Melendez, Matthew C. Wong, Pranoti V. Sahasrabhojane, Sarah B. Johnson, Manoj Chelvanambi i in. "Abstract 1283: Digital spatial profiling of metastatic brain tumors reveals association of the tumor microbiome with immune alterations in the tumor microenvironment". Cancer Research 84, nr 6_Supplement (22.03.2024): 1283. http://dx.doi.org/10.1158/1538-7445.am2024-1283.
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Abstract Introduction: Metastatic brain tumors are associated with significant morbidity and mortality. The microbiome has emerged as a novel hallmark of cancer, with a prominent role in tumor immunity and response to treatment. However, the role of the microbiome in brain tumors, and in particular brain metastasis, is largely unknown. We hypothesized that distinct microbial communities are associated with alterations in the tumor microenvironment in metastatic brain tumors. Methods: To evaluate the role of different microbial communities in brain metastasis, matched stool, saliva, and tumor samples were collected prospectively from patients with metastatic brain tumors who underwent surgical tumor resection at the University of Texas MD Anderson Cancer Center. Stool and saliva samples were sequenced via metagenomic shotgun sequencing and tumor samples were analyzed through 16S rRNA gene sequencing. The tumor microbiome was further characterized through confocal and electron microscopy and culture techniques. Lastly, we conducted digital spatial profiling using the NanoString GeoMx® platform to determine the spatial association of the tumor microbiome with tumor and immune transcriptome. Spatial single-cell transcriptome analysis of bacteria-positive and bacteria-negative cells within the tumor microenvironment is currently in progress using the CosMx® platform (NanoString Inc.). Results: Our computational and experimental analyses demonstrated that bacterial signals could be detected in metastatic brain tumors and exhibit an intracellular localization. Interestingly, we found that the tumor bacterial signatures in brain metastases were composed of commensal oral bacterial taxa but had limited overlap with the gut microbiome. Spatial transcriptome analysis demonstrated that tumor areas with high bacterial signal were associated with innate-immune mediated anti-bacterial responses, suggesting an active host response to intra-tumoral bacteria in metastatic brain tumors. Conclusion: Overall, this work demonstrates the presence of intracellular bacterial signal coupled with an anti-bacterial response within the tumor microenvironment of brain metastases. These findings offer a new perspective on the dynamic interaction between cancer, microbiome, and the brain microenvironment and can inform future mechanistic and translational studies to improve the outcome of brain tumor patients. Citation Format: Golnaz Morad, Ashish V. Damania, Brenda Melendez, Matthew C. Wong, Pranoti V. Sahasrabhojane, Sarah B. Johnson, Manoj Chelvanambi, Florentia Dimitriou, Jillian S. Losh, Nadim J. Ajami, Sherise D. Ferguson, Jennifer A. Wargo. Digital spatial profiling of metastatic brain tumors reveals association of the tumor microbiome with immune alterations in the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1283.
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Dickson, Mackenzie J., Jeanette V. Bishop, Thomas R. Hansen, I. Martin Sheldon i John J. Bromfield. "The endometrial transcriptomic response to pregnancy is altered in cows after uterine infection". PLOS ONE 17, nr 3 (31.03.2022): e0265062. http://dx.doi.org/10.1371/journal.pone.0265062.
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Pregnancy induces changes in the transcriptome of the bovine endometrium from 15 days after insemination. However, pregnancy is less likely to occur if cows had a postpartum bacterial infection of the uterus, even after the resolution of disease. We hypothesized that uterine bacterial infection alters the endometrial transcriptomic signature of pregnancy after the resolution of disease. To examine the endometrial transcriptomic signature of pregnancy, cows were inseminated 130 days after intrauterine infusion of pathogenic Escherichia coli and Trueperella pyogenes, subsequently endometrium was collected 16 days after insemination for RNA sequencing. We found 171 pregnancy regulated genes in cows 146 days after bacterial infection. When comparing our findings with previous studies that described the endometrial transcriptomic signature of pregnancy in healthy cows, 24 genes were consistently differentially expressed in pregnancy, including MX1, MX2 and STAT1. However, 12 pregnancy regulated genes were found only in the endometrium of healthy cows, including ISG15 and TRANK1. Furthermore, 28 pregnancy regulated genes were found only in the endometrium of cows following bacterial infection and these were associated with altered iNOS, TLR, and IL-7 signaling pathways. Although 94 predicted upstream regulators were conserved amongst the studies, 14 were found only in the endometrium of pregnant healthy cows, and 5 were found only in cows following bacterial infection, including AIRE, NFKBIA, and DUSP1. In conclusion, there were both consistent and discordant features of the endometrial transcriptomic signature of pregnancy 146 days after intrauterine bacterial infusion. These findings imply that there is an essential transcriptomic signature of pregnancy, but that infection induces long-term changes in the endometrium that affect the transcriptomic response to pregnancy.
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Wang, Bo, Xi-Cheng Wang, Zhuang-Wei Wang, Zhen-Xiao Chen i Wei-Min Wu. "The Responses of a Grapevine Rhizosphere System to Mulching Using Amplicon Sequencing and Transcriptomic Analysis". Agronomy 13, nr 6 (20.06.2023): 1656. http://dx.doi.org/10.3390/agronomy13061656.
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Although mulching is a widely used agronomic practice, its effects on the rhizosphere remain poorly understood. Here, we employed amplicon and transcriptomic sequencing to investigate variations in a grapevine rhizosphere system under mulch treatment (rice straw + felt + plastic film). Analyzing 16S and intergenic spacer (ITS) rRNA sequences indicated that the Shannon and Simpson indices of the bacterial and fungal communities increased markedly under mulch treatment. The bacterial and fungal compositions varied significantly between the control and mulch treatments. Mulching enriched for potentially beneficial microbes that confer disease resistance to plants or participate in nitrogen metabolism (Kaistobacter, Ammoniphilus, Lysobacter, Ammoniphilus, Alicyclobacillus, Aquicella, Nitrospira, Chaetomium, and Microascus), whereas more potentially pathogenic microbes (Fusarium and Gibberella) were detected in the control. Moreover, certain bacteria and fungi exhibited different correlations with the root transcriptome functions of the MEBlue module. The complexity of the bacterial and fungal co-occurrence networks increased with higher node numbers, positive and negative links after mulching. Following mulching, the rhizosphere showed elevated pH, organic matter, and catalase activities, and decreased sucrase and cellulase and β-glucosidase activities. Our results provide comprehensive data showing how a grapevine rhizosphere system responded to mulching treatment and shed important insight into mulching practices for fruit trees.
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Chan, Kok-Gan, Kumutha Priya, Chien-Yi Chang, Ahmad Yamin Abdul Rahman, Kok Keng Tee i Wai-Fong Yin. "Transcriptome analysis ofPseudomonas aeruginosaPAO1 grown at both body and elevated temperatures". PeerJ 4 (19.07.2016): e2223. http://dx.doi.org/10.7717/peerj.2223.
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Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogenPseudomonas aeruginosaPAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some keyP. aeruginosaPAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.
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Ebersole, J., S. Kirakodu, J. Chen, R. Nagarajan i O. A. Gonzalez. "Oral Microbiome and Gingival Transcriptome Profiles of Ligature-Induced Periodontitis". Journal of Dental Research 99, nr 6 (19.02.2020): 746–57. http://dx.doi.org/10.1177/0022034520906138.
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This investigation evaluated the relationship of the oral microbiome and gingival transcriptome in health and periodontitis in nonhuman primates ( Macaca mulatta). Subgingival plaque samples and gingival biopsies were collected from healthy sites and at sites undergoing ligature-induced periodontitis. Microbial samples were analyzed with 16S amplicon sequencing to identify bacterial profiles in young (3 to 7 y) and adult (12 to 23 y) animals. The gingival transcriptome was determined with a microarray analysis and focused on the expression level of 452 genes that are associated with the development of inflammation and innate and adaptive immune responses. Of the 396 total operational taxonomic units (OTUs) identified across the samples, 81.8% were detected in the young group and 99.5% in the adult group. Nevertheless, 58 of the OTUs composed 88% of the signal in adults, and 49 OTUs covered 91% of the OTU readouts in the young group. Correlation analyses between the microbiome members and specific gingival genes showed a high number of significant bacteria-gene correlations in the young healthy tissues, which decreased by 75% in diseased tissues. In contrast, these correlations increased by 2.5-fold in diseased versus healthy tissues of adult animals. Complexes of bacteria were delineated that related to specific sets of immune genes, differing in health and disease and in the young versus adult animals. The correlated gene profiles demonstrated selected pathway overrepresentation related to particular bacterial complexes. These results provide novel insights into microbiome changes with disease and the relationship of these changes to specific gene profiles and likely biologic activities occurring in healthy and diseased gingival tissues in this human-like periodontitis model.
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Olovnikov, Ivan, Ken Chan, Ravi Sachidanandam, Dianne K. Newman i Alexei A. Aravin. "Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA". Molecular Cell 51, nr 5 (wrzesień 2013): 594–605. http://dx.doi.org/10.1016/j.molcel.2013.08.014.
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Basu, Anindya, Biswajit Mishra i Susanna Su Jan Leong. "Global transcriptome analysis reveals distinct bacterial response towards soluble and surface-immobilized antimicrobial peptide (Lasioglossin-III)". RSC Advances 5, nr 96 (2015): 78712–18. http://dx.doi.org/10.1039/c5ra14862f.
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Choe, Donghui, Richard Szubin, Saugat Poudel, Anand Sastry, Yoseb Song, Yongjae Lee, Suhyung Cho, Bernhard Palsson i Byung-Kwan Cho. "RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics". PLOS Genetics 17, nr 9 (27.09.2021): e1009821. http://dx.doi.org/10.1371/journal.pgen.1009821.
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RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies.
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Hantus, Charlotte E., Isabella J. Moppel, Jenna K. Frizzell, Anna E. Francis, Kyogo Nagashima i Lisa M. Ryno. "L-Rhamnose Globally Changes the Transcriptome of Planktonic and Biofilm Escherichia coli Cells and Modulates Biofilm Growth". Microorganisms 12, nr 9 (19.09.2024): 1911. http://dx.doi.org/10.3390/microorganisms12091911.
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L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. Our results reveal that L-rhamnose significantly affects growth kinetics and biofilm formation, particularly reducing biofilm growth in rich media at 37 °C. Transcriptomic analysis through RNA-seq showed that L-rhamnose modulates gene expression differently depending on the temperature and media conditions, promoting a planktonic state by upregulating genes involved in rhamnose transport and metabolism and downregulating genes related to adhesion and biofilm formation. These findings highlight the nuanced role of L-rhamnose in bacterial adaptation and survival, providing insight into potential applications in controlling biofilm-associated infections and industrial biofilm management.
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Skvortsov, T. A., D. V. Ignatov, K. B. Majorov, A. S. Apt i T. L. Azhikina. "Mycobacterium tuberculosis Transcriptome Profiling in Mice with Genetically Different Susceptibility to Tuberculosis". Acta Naturae 5, nr 2 (15.06.2013): 62–69. http://dx.doi.org/10.32607/20758251-2013-5-2-62-69.
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Whole transcriptome profiling is now almost routinely used in various fields of biology, including microbiology. In vivo transcriptome studies usually provide relevant information about the biological processes in the organism and thus are indispensable for the formulation of hypotheses, testing, and correcting. In this study, we describe the results of genome-wide transcriptional profiling of the major human bacterial pathogen M. tuberculosis during its persistence in lungs. Two mouse strains differing in their susceptibility to tuberculosis were used for experimental infection with M. tuberculosis. Mycobacterial transcriptomes obtained from the infected tissues of the mice at two different time points were analyzed by deep sequencing and compared. It was hypothesized that the changes in the M. tuberculosis transcriptome may attest to the activation of the metabolism of lipids and amino acids, transition to anaerobic respiration, and increased expression of the factors modulating the immune response. A total of 209 genes were determined whose expression increased with disease progression in both host strains (commonly upregulated genes, CUG). Among them, the genes related to the functional categories of lipid metabolism, cell wall, and cell processes are of great interest. It was assumed that the products of these genes are involved in M. tuberculosis adaptation to the host immune system defense, thus being potential targets for drug development.
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Bergamo, Alberta, Marco Gerdol, Alberto Pallavicini, Samuele Greco, Isabelle Schepens, Romain Hamelin, Florence Armand, Paul J. Dyson i Gianni Sava. "Lysozyme-Induced Transcriptional Regulation of TNF-α Pathway Genes in Cells of the Monocyte Lineage". International Journal of Molecular Sciences 20, nr 21 (5.11.2019): 5502. http://dx.doi.org/10.3390/ijms20215502.
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Lysozyme is one of the most important anti-bacterial effectors in the innate immune system of animals. Besides its direct antibacterial enzymatic activity, lysozyme displays other biological properties, pointing toward a significant anti-inflammatory effect, many aspects of which are still elusive. Here we investigate the perturbation of gene expression profiles induced by lysozyme in a monocyte cell line in vitro considering a perspective as broad as the whole transcriptome profiling. The results of the RNA-seq experiment show that lysozyme induces transcriptional modulation of the TNF-α/IL-1β pathway genes in U937 monocytes. The analysis of transcriptomic profiles with IPA® identified a simple but robust molecular network of genes, in which the regulation trends are fully consistent with the anti-inflammatory activity of lysozyme. This study provides the first evidence in support of the anti-inflammatory action of lysozyme on the basis of transcriptomic regulation data resulting from the broad perspective of a whole-transcriptome profiling. Such important effects can be achieved with the supplementation of relatively low concentrations of lysozyme, for a short time of exposure. These new insights allow the potential of lysozyme in pharmacological applications to be better exploited.
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Kobayashi, Karin, i Hiromi Nishida. "Transcriptome Analysis of Sake Yeast in Co-Culture with kuratsuki Kocuria". Fermentation 10, nr 5 (10.05.2024): 249. http://dx.doi.org/10.3390/fermentation10050249.
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Kuratsuki bacteria enter the sake production process and affect the flavor and taste of sake. This study compared gene expression in the sake yeast Saccharomyces cerevisiae in co-culture with kuratsuki Kocuria to that in monoculture. Among the 5922 genes of S. cerevisiae, 71 genes were upregulated more than 2-fold, and 61 genes were downregulated less than 0.5-fold in co-culture with kuratsuki Kocuria. Among the stress-induced genes, fourteen were upregulated, and six were downregulated. Among the fourteen upregulated genes, six were induced in response to replication stress. Although the G1 cyclin gene CLN3 was upregulated by more than 2-fold, eight genes that were induced in response to meiosis and/or sporulation were also upregulated. Fourteen metabolism-related genes, for example, the glyceraldehyde-3-phosphate dehydrogenase genes TDH1, TDH2, and TDH3, were downregulated by less than 0.5-fold in co-culture with kuratsuki Kocuria. The gene expression patterns of S. cerevisiae co-cultured with kuratsuki Kocuria differed from those co-cultured with lactic acid bacteria. Therefore, S. cerevisiae responded differently to different bacterial species. This strongly suggests that kuratsuki bacteria affect gene expression in sake yeast, thereby affecting the flavor and taste of sake.
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Patel, Arjun, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V. Sastry, Svetlana Maurya, Kevin Rychel, David J. Gonzalez i Bernhard O. Palsson. "Proteome allocation is linked to transcriptional regulation through a modularized transcriptome". Nature Communications 15, nr 1 (19.06.2024). http://dx.doi.org/10.1038/s41467-024-49231-y.
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AbstractIt has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigate whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions can be modularized in the same way to reveal novel relationships between their compositions. We find that; (1) the modules of the proteome and the transcriptome are comprised of a similar list of gene products, (2) the modules in the proteome often represent combinations of modules from the transcriptome, (3) known transcriptional and post-translational regulation is reflected in differences between two sets of modules, allowing for knowledge-mapping when interpreting module functions, and (4) through statistical modeling, absolute proteome allocation can be inferred from the transcriptome alone. Quantitative and knowledge-based relationships can thus be found at the genome-scale between the proteome and transcriptome in bacteria.
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Lim, Hyun Gyu, Ye Gao, Kevin Rychel, Cameron Lamoureux, Xuwen A. Lou i Bernhard O. Palsson. "Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase". mSystems, 26.12.2024. https://doi.org/10.1128/msystems.01315-24.
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ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.
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Nagai, Motoki, Masaomi Kurokawa i Bei-Wen Ying. "The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli". DNA Research 27, nr 3 (1.06.2020). http://dx.doi.org/10.1093/dnares/dsaa018.
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Abstract The growth rate, representing the fitness of a bacterial population, is determined by the transcriptome. Chromosomal periodicity, which is known as the periodic spatial pattern of a preferred chromosomal distance in microbial genomes, is a representative overall feature of the transcriptome; however, whether and how it is associated with the bacterial growth rate are unknown. To address these questions, we analysed a total of 213 transcriptomes of multiple Escherichia coli strains growing in an assortment of culture conditions varying in terms of temperature, nutrition level and osmotic pressure. Intriguingly, Fourier transform analyses of the transcriptome identified a common chromosomal periodicity of transcriptomes, which was independent of the variation in genomes and environments. In addition, fitting of the data to a theoretical model, we found that the amplitudes of the periodic transcriptomes were significantly correlated with the growth rates. These results indicated that the amplitude of periodic transcriptomes is a parameter representing the global pattern of gene expression in correlation with the bacterial growth rate. Thus, our study provides a novel parameter for evaluating the adaptiveness of a growing bacterial population and quantitatively predicting the growth dynamics according to the global expression pattern.
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Jacob, Cristián, André C. Velásquez, Nikhil A. Josh, Matthew Settles, Sheng Yang He i Maeli Melotto. "Dual Transcriptomic Analysis Reveals Metabolic Changes Associated with Differential Persistence of Human Pathogenic Bacteria in Leaves of Arabidopsis and Lettuce". G3 Genes|Genomes|Genetics, 22.09.2021. http://dx.doi.org/10.1093/g3journal/jkab331.
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Abstract Understanding the molecular determinants underlying the interaction between the leaf and human pathogenic bacteria is key to provide the foundation to develop science-based strategies to prevent or decrease the pathogen contamination of leafy greens. In this study, we conducted a dual RNA-sequencing analysis to simultaneously define changes in the transcriptomic profiles of the plant and the bacterium when they come in contact. We used an economically relevant vegetable crop, lettuce (Lactuca sativa L. cultivar Salinas), and a model plant, Arabidopsis thaliana Col-0, as well as two pathogenic bacterial strains that cause disease outbreaks associated with fresh produce, Escherichia coli O157: H7 and Salmonella enterica serovar Typhimurium 14028 s (STm 14028 s). We observed commonalities and specificities in the modulation of biological processes between Arabidopsis and lettuce and between O157: H7 and STm 14028 s during early stages of the interaction. We detected a larger alteration of gene expression at the whole transcriptome level in lettuce and Arabidopsis at 24 hours post inoculation with STm 14028 s compared to that with O157: H7. In addition, bacterial transcriptomic adjustments were substantially larger in Arabidopsis than in lettuce. Bacterial transcriptome was affected at a larger extent in the first 4 hours compared to the subsequent 20 hours after inoculation. Overall, we gained valuable knowledge about the responses and counter-responses of both bacterial pathogen and plant host when these bacteria are residing in the leaf intercellular space. These findings and the public genomic resources generated in this study are valuable for additional data mining.
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Ibberson, Carolyn B., i Marvin Whiteley. "The Staphylococcus aureus Transcriptome during Cystic Fibrosis Lung Infection". mBio 10, nr 6 (19.11.2019). http://dx.doi.org/10.1128/mbio.02774-19.
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ABSTRACT Laboratory models have been invaluable for the field of microbiology for over 100 years and have provided key insights into core aspects of bacterial physiology such as regulation and metabolism. However, it is important to identify the extent to which these models recapitulate bacterial physiology within a human infection environment. Here, we performed transcriptomics (RNA-seq), focusing on the physiology of the prominent pathogen Staphylococcus aureus in situ in human cystic fibrosis (CF) infection. Through principal-component and hierarchal clustering analyses, we found remarkable conservation in S. aureus gene expression in the CF lung despite differences in the patient clinic, clinical status, age, and therapeutic regimen. We used a machine learning approach to identify an S. aureus transcriptomic signature of 32 genes that can reliably distinguish between S. aureus transcriptomes in the CF lung and in vitro. The majority of these genes were involved in virulence and metabolism and were used to improve a common CF infection model. Collectively, these results advance our knowledge of S. aureus physiology during human CF lung infection and demonstrate how in vitro models can be improved to better capture bacterial physiology in infection. IMPORTANCE Although bacteria have been studied in infection for over 100 years, the majority of these studies have utilized laboratory and animal models that often have unknown relevance to the human infections they are meant to represent. A primary challenge has been to assess bacterial physiology in the human host. To address this challenge, we performed transcriptomics of S. aureus during human cystic fibrosis (CF) lung infection. Using a machine learning framework, we defined a “human CF lung transcriptome signature” that primarily included genes involved in metabolism and virulence. In addition, we were able to apply our findings to improve an in vitro model of CF infection. Understanding bacterial gene expression within human infection is a critical step toward the development of improved laboratory models and new therapeutics.
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Lamouche, Florian, Anaïs Chaumeret, Ibtissem Guefrachi, Quentin Barrière, Olivier Pierre, Florence Guérard, Françoise Gilard i in. "From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis inAeschynomeneNodules Using theBradyrhizobiumsp. Strain ORS285bclAMutant". Journal of Bacteriology 201, nr 17 (10.06.2019). http://dx.doi.org/10.1128/jb.00191-19.
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ABSTRACTSoil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process inBradyrhizobiumsp. strain ORS285, a symbiont ofAeschynomenespp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, thebclAnodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules ofAeschynomene afrasperaandAeschynomene indicainfected with the wild type or thebclAmutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.IMPORTANCELegume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis ofBradyrhizobiumwild-type andbclAmutant bacteria in culture and in symbiosis withAeschynomenehost plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.
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Tan, Lu, Zhihao Guo, Yanwen Shao, Lianwei Ye, Miaomiao Wang, Xin Deng, Sheng Chen i Runsheng Li. "Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing". Nucleic Acids Research, 16.07.2024. http://dx.doi.org/10.1093/nar/gkae601.
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Abstract Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping. Here, we showed that pre-processing of bacterial total RNA (size selection followed by ribosomal RNA depletion and polyadenylation) guaranteed high throughputs of sequencing data and considerably increased the amount of mRNA reads. This way, complex transcriptome architectures were reconstructed for Escherichia coli and Staphylococcus aureus and extended the boundaries of 225 known E. coli operons and 89 defined S. aureus operons. Utilizing unmodified in vitro-transcribed (IVT) RNA libraries as a negative control, several Nanopore-based computational tools globally detected putative modification sites in the E. coli and S. aureus transcriptomes. Combined with Next-Generation Sequencing-based N6-methyladenosine (m6A) detection methods, 75 high-confidence m6A candidates were identified in the E. coli protein-coding transcripts, while none were detected in S. aureus. Altogether, we demonstrated the potential of Nanopore DRS in systematic and convenient transcriptome and epitranscriptome analysis.
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Zhang, Yi, Mengqi Ni, Yunhui Bai, Qiao Shi, Jinbin Zheng i Zhaoxia Cui. "Full-Length Transcriptome Analysis Provides New Insights Into the Diversity of Immune-Related Genes in Portunus trituberculatus". Frontiers in Immunology 13 (7.04.2022). http://dx.doi.org/10.3389/fimmu.2022.843347.
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Generally, invertebrates were thought to solely rely on their non-specific innate immune system to fight against invading microorganisms. However, increasing studies have implied that the innate immune response of invertebrates displayed diversity and specificity owing to the hyper-variable immune molecules in organisms. In order to get an insight into the diversity of immune-related genes in Portunus trituberculatus, a full-length transcriptome analysis of several immune-related tissues (hemocytes, hepatopancreas and gills) in P. trituberculatus was performed and the diversity of several immune-related genes was analyzed. The full-length transcriptome analysis of P. trituberculatus was conducted using a combination of SMRT long-read sequencing and Illumina short-read sequencing. A total of 17,433 nonredundant full-length transcripts with average length of 2,271 bp and N50 length of 2,841 bp were obtained, among which 13,978 (80.18%) transcripts were annotated. Moreover, numerous transcript variants of various immune-related genes were identified, including pattern recognition receptors, antimicrobial peptides, heat shock proteins (HSPs), antioxidant enzymes and vital molecules in prophenoloxidase (proPO)-activating system. Based on the full-length transcriptome analysis, open reading frames (ORFs) of four C-type lectins (CTLs) were cloned, and tissue distributions showed that the four CTLs were ubiquitously expressed in all the tested tissues, and mainly expressed in hepatopancreas and gills. The transcription of the four CTLs significantly increased in several immune-related tissues (hemocytes, hepatopancreas and gills) of P. trituberculatus challenged with Vibrio alginolyticus and displayed different profiles. Moreover, the four CTLs displayed distinct bacterial binding and antibacterial activities. The recombinant protein PtCTL-1 (rPtCTL-1) and rPtCTL-3 displayed bacterial binding and antibacterial activities against all tested bacteria. rPtCTL-2 only showed bacterial binding and antibacterial activities against V. alginolyticus. No obvious bacterial binding or antibacterial activities for PtCTL-4 was observed against the tested bacteria. This study enriches the transcriptomic information on P. trituberculatus and provides new insights into the innate immune system of crustaceans. Additionally, our study provided candidates of antibiotic agents for the prevention and treatment of bacteriosis.
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Chen, Weiqin, Leilei Mao, Qingpi Yan, Lingmin Zhao, Lixing Huang, Jiaonan Zhang i Yingxue Qin. "Comparative transcriptome analysis explored the molecular mechanisms of a luxR‐type regulator regulating intracellular survival of Aeromonas hydrophila". Journal of Fish Diseases, 31.03.2024. http://dx.doi.org/10.1111/jfd.13949.
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AbstractAeromonas hydrophila is not a traditional intracellular bacterium. However, previous studies revealed that pathogenic A. hydrophila B11 could temporarily survive for at least 24 h in fish phagocytes, and the regulation of intracellular survival in bacteria was associated with regulators of the LuxR‐type. The mechanisms of luxR08110 on the A. hydrophila's survival in macrophages were investigated using comprehensive transcriptome analysis and biological phenotype analysis in this study. The results showed that after luxR08110 was silenced, the intracellular survival ability of bacteria was significantly diminished. Comparative transcriptome analysis revealed that luxR08110 was a critical regulator of A. hydrophila, which regulated the expression of over 1200 genes, involving in bacterial flagellar assembly and chemotaxis, ribosome, sulphur metabolism, glycerolipid metabolism, and other mechanisms. Further studies confirmed that after the inhibition of expression of luxR08110, the motility, chemotaxis and adhesion of A. hydrophila significantly decreased. Moreover, compared with the wild‐type strain, the survival rates of silencing strain were all considerably reduced under both H2O2 and low pH stress conditions. According to both transcriptome analysis and phenotypic tests, the luxR08110 of A. hydrophila could act as global regulator in bacteria intracellular survival. This regulator regulated intracellular survival of A. hydrophila mainly through two ways. One way is to regulate bacterial flagellar synthesis and further affects the motility, chemotaxis and adhesion of bacteria. The other way is to regulate sulphur and glycerolipid metabolisms, thus affecting bacterial energy production and the ability to resist environmental stress.
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Wang, Zi, Miao Sun, Yongqiang Wang, Jinchuan Shi, Wei Gao, Dongxu Han, Fanjun Zeng i in. "Regulation of ofloxacin resistance in Escherichia coli strains causing calf diarrhea by quorum-sensing acyl-homoserine lactone signaling molecules". Frontiers in Veterinary Science 12 (5.02.2025). https://doi.org/10.3389/fvets.2025.1540132.
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Escherichia coli is a major pathogen responsible for calf diarrhea. However, it has developed resistance to many antimicrobial drugs for their inappropriate usage. The bacterial quorum sensing system transmits information between bacteria, it's important in regulating bacterial virulence, drug and acid resistance and so on. This system can found in Gram-negative bacteria and operates through acyl-homoserine lactone (AHL) signaling molecules. In this study, a type I quorum sensing AHL, N-Octanoyl-L-Homoserine lactone (C8), was added to E. coli growth medium to investigate its regulatory functions in drug resistance. After screening out the strains of E. coli that showed an obvious regulatory effect to the drug ofloxacin (OFX), transcriptomic sequencing was performed on the E. coli strains from the sub-inhibitory concentration group that concentration plus C8 group, and the control group. It shows that C8 significantly influenced resistance to OFX and the minimum inhibitory concentration of OFX in the tested strain was significantly increased. To Analyze transcriptome sequencing results identified 415 differentially expressed genes between the control and sub-inhibitory concentration groups, of which 201 were up-regulated and 214 were down. There were 125 differentially expressed genes between bacteria treated with a sub-inhibitory concentration of OFX and those treated with C8, of which 102 were up-regulated and 23 were down. Finally, It found that to adding the C8 significantly increased the resistance of tested bacteria to OFX. Data from transcriptome sequencing on differently expressed genes helps to explain how the type I quorum sensing system controls drug resistance in E. coli.
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Heom, Kellie A., Chatarin Wangsanuwat, Lazarina V. Butkovich, Scott C. Tam, Annette R. Rowe, Michelle A. O'Malley i Siddharth S. Dey. "Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures". mSystems, 19.10.2023. http://dx.doi.org/10.1128/msystems.00281-23.
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ABSTRACT Bacterial mRNA sequencing is inefficient due to the abundance of ribosomal RNA that is challenging to deplete. While commercial kits target rRNA from common bacterial species, they are frequently inefficient when applied to divergent species, including those from environmental isolates. Similarly, other methods typically employ large probe sets that tile the entire length of rRNAs; however, such approaches are infeasible when applied to many species. Therefore, we present EMBR-seq+, which requires fewer than 10 oligonucleotides per rRNA by combining rRNA blocking primers with RNase H-mediated depletion to achieve rRNA removal efficiencies of up to 99% in diverse bacterial species. Furthermore, in more complex microbial co-cultures between Fibrobacter succinogenes strain UWB7 and anaerobic fungi, EMBR-seq+ depleted both bacterial and fungal rRNA, with a fourfold improvement in bacterial rRNA depletion compared with a commercial kit, thereby demonstrating that the method can be applied to non-model microbial mixtures. Notably, for microbes with unknown rRNA sequences, EMBR-seq+ enables rapid iterations in probe design without requiring to start experiments from total RNA. Finally, efficient depletion of rRNA enabled systematic quantification of the reprogramming of the bacterial transcriptome when cultured in the presence of the anaerobic fungi Anaeromyces robustus or Caecomyces churrovis . We observed that F. succinogenes strain UWB7 downregulated several lignocellulose-degrading carbohydrate-active enzymes in the presence of anaerobic gut fungi, suggesting close interactions between two cellulolytic species that specialize in different aspects of biomass breakdown. Thus, EMBR-seq+ enables efficient, cost-effective, and rapid quantification of the transcriptome to gain insights into non-model microbial systems. IMPORTANCE Microbes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.
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Tseng, Peng-Wei, Hau-Wen Li, Chih Chen, Yung-Che Tseng, Ching-Fong Chang i Guan-Chung Wu. "Transcriptomic profile of symbiotic accessory nidamental gland during female maturation in bigfin reef squid". Frontiers in Marine Science 9 (9.01.2023). http://dx.doi.org/10.3389/fmars.2022.1026742.
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The bigfin reef squid, Sepioteuthis lessoniana, are a valuable commercial species in East Asian regions such as Taiwan and Japan. A lack of genomic information limits the application of potential aquaculture techniques, especially in breeding when considering the hatching rate of offspring. In some squids and cuttlefishes, symbiotic bacteria are transmitted from the accessory nidamental gland (ANG) to the jelly coat of eggs. In Hawaiian bobtail squid, these parent-delivered mutualistic bacteria play an important role in preventing lethal biofouling of the eggs and accelerating the hatch rate of offspring. The bacterial consortium, which is housed in the female squids ANG, are governed by host selection during female maturation. Immune functions are typically used to explain the regulatory mechanism of symbioses by host selection. In this study, we evaluated the transcripts featured in bacterial selection and maintenance during ANG development using RNA-seq. Different developmental stages of ANGs (stages 1–4) were sequenced. The de novo transcriptome assembly resulted in 524,918 unigenes. Two groups, non-pigmentation group (stage 1 and stage 3) and pigmentation group (stage 4), were clustered by transcriptome-wide expression profile analysis. The gene expression analyses indicated that 9,475 differential expression genes (DEGs) in three different phases and 1,363 (14.3%) DEGs were matched in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Furthermore, KEGG-enriched analysis results suggested that immune responses are a dominant pathway in the non-pigmentation group (stage 1 and stage 3) whereas lipid metabolism and metabolism of flora fermentation are dominant in the pigmentation group (stage 4). Although the host immunity plays an important role during bacterial colonization of the ANG in bigfin reef squid, our results showed that most immune-related genes had a reduced transcriptomic level in the pigmentation group compared with the non-pigmentation group. Therefore, our results provide new insight to understand the regulatory mechanisms of initial bacterial colonization and later bacterial pigmentation in the bigfin reef squid.
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Zhang, Zhiyuan, Yuanyuan Pan, Wajid Hussain, Guozhong Chen i Erguang Li. "BBSdb, an open resource for bacterial biofilm-associated proteins". Frontiers in Cellular and Infection Microbiology 14 (1.08.2024). http://dx.doi.org/10.3389/fcimb.2024.1428784.
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Bacterial biofilms are organized heterogeneous assemblages of microbial cells encased within a self-produced matrix of exopolysaccharides, extracellular DNA and proteins. Over the last decade, more and more biofilm-associated proteins have been discovered and investigated. Furthermore, omics techniques such as transcriptomes, proteomes also play important roles in identifying new biofilm-associated genes or proteins. However, those important data have been uploaded separately to various databases, which creates obstacles for biofilm researchers to have a comprehensive access to these data. In this work, we constructed BBSdb, a state-of-the-art open resource of bacterial biofilm-associated protein. It includes 48 different bacteria species, 105 transcriptome datasets, 21 proteome datasets, 1205 experimental samples, 57,823 differentially expressed genes (DEGs), 13,605 differentially expressed proteins (DEPs), 1,930 ‘Top 5% differentially expressed genes’, 444 ‘Threshold-based DEGs’ and a predictor for prediction of biofilm-associated protein. In addition, 1,781 biofilm-associated proteins, including annotation and sequences, were extracted from 942 articles and public databases via text-mining analysis. We used E. coli as an example to represent how to explore potential biofilm-associated proteins in bacteria. We believe that this study will be of broad interest to researchers in field of bacteria, especially biofilms, which are involved in bacterial growth, pathogenicity, and drug resistance.Availability and implementation: The BBSdb is freely available at http://124.222.145.44/#!/.
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Xiang, Xueyan, Davide Poli, Bernard M. Degnan i Sandie M. Degnan. "Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont". Marine Biotechnology, 27.07.2022. http://dx.doi.org/10.1007/s10126-022-10138-8.
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AbstractInvestigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.
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Lyou, Eun Sun, Min Sung Kim, Soo Bin Kim, MinJi Park, Kyong-Dong Kim, Won Hee Jung i Tae Kwon Lee. "Single-cell phenotypes revealed as a key biomarker in bacterial–fungal interactions: a case study of Staphylococcus and Malassezia". Microbiology Spectrum, listopad 2023. http://dx.doi.org/10.1128/spectrum.00437-23.
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ABSTRACT Microbial interactions are determined by competition, cooperation, and inaction, depending on the transcriptional response to the metabolites secreted by each other. The consequence of these interactions is reflected in the cell phenotype by the composition of cell materials, including lipids, nucleotides, and proteins. We studied the phenotypic plasticity of single cells involved in microbial interactions using Raman spectroscopy and evaluated the types of interactions by linking phenotypes to transcriptional profiles. We used a membrane-based co-culture system to induce chemical interactions between skin-dominant bacteria and fungi, Staphylococcus and Malassezia. Staphylococcus species exhibited an amensalism interaction with Malassezia based on growth and cell viability. Malassezia co-cultured with S. epidermidis and S. aureus resulted in significant changes in the Raman spectra of nucleic acids and proteins in the Raman phenotypes, respectively. The observed differences in phenotypes during co-culture with Malassezia were significantly associated with changes in transcriptomic profiles, which demonstrated variations in the defense/resistance and biofilm-formation mechanisms of S. epidermidis, whereas no meaningful changes were observed for the transcriptome of S. aureus . These approaches provide a robust, simple, and reproducible method for comprehending bacterial–fungal interactions. IMPORTANCE Evaluating bacterial–fungal interactions is important for understanding ecological functions in a natural habitat. Many studies have defined bacterial–fungal interactions according to changes in growth rates when co-cultivated. However, the current literature lacks detailed studies on phenotypic changes in single cells associated with transcriptomic profiles to understand the bacterial-fungal interactions. In our study, we measured the single-cell phenotypes of bacteria co-cultivated with fungi using Raman spectroscopy with its transcriptomic profiles and determined the consequence of these interactions in detail. This rapid and reliable phenotyping approach has the potential to provide new insights regarding bacterial–fungal interactions.
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Ying, Bei-Wen, Yuki Matsumoto, Kazuki Kitahara, Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Toshihiko Kishimoto i Tetsuya Yomo. "Bacterial transcriptome reorganization in thermal adaptive evolution". BMC Genomics 16, nr 1 (16.10.2015). http://dx.doi.org/10.1186/s12864-015-1999-x.
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Homberger, Christina, Lars Barquist i Jörg Vogel. "Ushering in a new era of single-cell transcriptomics in bacteria". microLife, 21.09.2022. http://dx.doi.org/10.1093/femsml/uqac020.
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Abstract Transcriptome analysis of individual cells by single-cell RNA-seq (scRNA-seq) has become routine for eukaryotic tissues, even being applied to whole multi-cellular organisms. In contrast, developing methods to read the transcriptome of single bacterial cells has proven more challenging, despite a general perception of bacteria as much simpler than eukaryotes. Bacterial cells are harder to lyse, their RNA content is about two orders of magnitude lower than that of eukaryotic cells, and bacterial mRNAs are less stable than their eukaryotic counterparts. Most importantly, bacterial transcripts lack functional poly(A) tails, precluding simple adaptation of popular standard eukaryotic scRNA-seq protocols that come with the double advantage of specific mRNA amplification and concomitant depletion of rRNA. However, thanks to very recent breakthroughs in methodology, bacterial scRNA-seq is now feasible. This short review will discuss recently published bacterial scRNA-seq approaches (MATQ-seq, microSPLiT, PETRI-seq) and a spatial transcriptomics approach based on multiplexed in situ hybridization (par-seqFISH). Together, these novel approaches will not only enable a new understanding of cell-to-cell variation in bacterial gene expression, they also promise a new microbiology by enabling high-resolution profiling of gene activity in complex microbial consortia such as the microbiome or pathogens as they invade, replicate and persist in host tissue.
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Huang, Xiaoli, Minghao Li, Jincheng Wang, Lili Ji, Yi Geng, Yangping Ou, Shiyong Yang, Lizi Yin, Liangyu Li i Defang Chen. "Effect of Bacterial Infection on the Edibility of Aquatic Products: The Case of Crayfish (Procambarus clarkii) Infected With Citrobacter freundii". Frontiers in Microbiology 12 (29.09.2021). http://dx.doi.org/10.3389/fmicb.2021.722037.
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Aquatic products are one of the world’s essential protein sources whose quality and safety are threatened by bacterial diseases. This study investigated the possible effects of bacterial infection on the main edible part, the muscle, in the case of crayfish infected with Citrobacter freundii. The histopathological analysis confirmed that crayfish was sensitive to C. freundii and muscle was one of the target organs. The transcriptome results showed impaired intercellular junctions, downregulation of actin expression, and inhibition of metabolic pathways. Furthermore, transcriptomic results suggest that C. freundii mainly affect muscle structure and nutrition. Subsequent validation experiments confirmed structural damage and nutrient loss in C. freundii infected crayfish muscle. Besides, the spoilage tests showed that C. freundii did not accelerate muscle spoilage and the bacteria had a limited impact on food safety. Therefore, although C. freundii may not be a specific spoilage bacterium, it still affects the edible taste and nutritional value of crayfish muscle. The findings of this study might contribute to further research on C. freundii infection and provide a warning about the adverse effects of bacterial infection on aquatic products.