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Microbial bioinformatics

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https://www.readbyqxmd.com/read/28101269/metagenomic-approaches-to-identify-novel-organisms-from-the-soil-environment-in-a-classroom-setting
#1
Sadia J Rahman, Trevor C Charles, Parjit Kaur
Molecular Microbial Metagenomics is a research-based undergraduate course developed at Georgia State University. This semester-long course provides hands-on research experience in the area of microbial diversity and introduces molecular approaches to study diversity. Students are part of an ongoing research project that uses metagenomic approaches to isolate clones containing 16S ribosomal ribonucleic acid (rRNA) genes from a soil metagenomic library. These approaches not only provide a measure of microbial diversity in the sample but may also allow discovery of novel organisms...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#2
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28066818/microbiome-helper-a-custom-and-streamlined-workflow-for-microbiome-research
#3
André M Comeau, Gavin M Douglas, Morgan G I Langille
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field...
January 2017: MSystems
https://www.readbyqxmd.com/read/28057680/an-informative-approach-on-differential-abundance-analysis-for-time-course-metagenomic-sequencing-data
#4
Dan Luo, Sara Ziebell, Lingling An
MOTIVATION: The advent of high-throughput next generation sequencing technology has greatly promoted the field of metagenomics where previously unattainable information about microbial communities can be discovered. Detecting differentially abundant features (e.g., species or genes) plays a critical role in revealing the contributors (i.e., pathogens) to the biological or medical status of microbial samples. However, currently available statistical methods lack power in detecting differentially abundant features contrasting different biological or medical conditions, in particular, for time series metagenomic sequencing data...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28055186/antimicrobials-inspired-by-nonribosomal-peptide-synthetase-gene-clusters
#5
Xavier Vila-Farres, John Chu, Daigo Inoyama, Melinda A Ternei, Christophe Lemetre, Louis J Cohen, Wooyoung Cho, Boojala Vijay B Reddy, Henry A Zebroski, Joel Stephen Freundlich, David S Perlin, Sean F Brady
Bacterial culture broth extracts have been the starting point for the development of numerous therapeutics. However, only a small fraction of bacterial biosynthetic diversity is accessible using this strategy. Here, we apply a discovery approach that bypasses the culturing step entirely by bioinformatically predicting small molecule structures from the primary sequences of the biosynthetic gene clusters. These structures are then chemically synthesized to give synthetic-bioinformatic natural products (syn-BNPs)...
January 5, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28054304/comparative-analysis-of-drosophila-melanogaster-gut-microbiota-with-respect-to-host-strain-sex-and-age
#6
Gangsik Han, Hyo Jung Lee, Sang Eun Jeong, Che Ok Jeon, Seogang Hyun
Microbiota has a significant impact on the health of the host individual. The complexity of the interactions between mammalian hosts and their microbiota highlights the value of using Drosophila melanogaster as a model organism, because of its relatively simple microbial community and ease of physiological and genetic manipulation. However, highly variable and sometimes inconsistent results regarding the microbiota of D. melanogaster have been reported for host samples collected from different geographical locations; discrepancies that may be because of the inherent physiological conditions of the D...
January 4, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28040177/regulation-of-the-synthesis-of-pulp-degrading-enzymes-in-bacillus-isolated-from-cocoa-fermentation
#7
Honoré G Ouattara, Sylvie Reverchon, Sébastien L Niamke, William Nasser
Pectin degrading enzymes are essential for quality of product from cocoa fermentation. Previously, we studied purified pectate lyases (Pel) produced by Bacillus strains from fermenting cocoa and characterized the cloned pel genes. This study aims to search for biological signals that modulates Pel production and regulators that influence pel gene expression. Strains were grown to the end of exponential phase in media containing various carbon sources. Pel enzymes production in Bacillus was unaffected by simple sugar content variation up to 2%...
May 2017: Food Microbiology
https://www.readbyqxmd.com/read/28039165/pbit-pipeline-builder-for-identification-of-drug-targets-for-infectious-diseases
#8
Gauri Shende, Harshala Haldankar, Ram Shankar Barai, Mohammed Husain Bharmal, Vinit Shetty, Susan Idicula-Thomas
: PBIT (Pipeline Builder for Identification of drug Targets) is an online webserver that has been developed for screening of microbial proteomes for critical features of human drug targets such as being non-homologous to human proteome as well as the human gut microbiota, essential for the pathogen's survival, participation in pathogen-specific pathways etc. The tool has been validated by analyzing 57 putative targets of Candida albicans documented in literature. PBIT integrates various in silico approaches known for drug target identification and will facilitate high-throughput prediction of drug targets for infectious diseases, including multi-pathogenic infections...
December 30, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28018236/host-microbiome-interaction-and-cancer-potential-application-in-precision-medicine
#9
REVIEW
Alejandra V Contreras, Benjamin Cocom-Chan, Georgina Hernandez-Montes, Tobias Portillo-Bobadilla, Osbaldo Resendis-Antonio
It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/28003808/microbiome-selection-could-spur-next-generation-plant-breeding-strategies
#10
Murali Gopal, Alka Gupta
"No plant is an island too…" Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28003256/recycler-an-algorithm-for-detecting-plasmids-from-de-novo-assembly-graphs
#11
Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir
MOTIVATION: Plasmids and other mobile elements are central contributors to microbial evolution and genome innovation. Recently, they have been found to have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their characterization through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing. Here, we attempt to ameliorate this situation by introducing a new circular element assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to be plasmids, phages and other circular elements...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27980708/bioinformatics-strategies-for-taxonomy-independent-binning-and-visualization-of-sequences-in-shotgun-metagenomics
#12
REVIEW
Karel Sedlar, Kristyna Kupkova, Ivo Provaznik
One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27966672/biology-of-archaea-from-a-novel-family-cuniculiplasmataceae-thermoplasmata-ubiquitous-in-hyperacidic-environments
#13
Olga V Golyshina, Ilya V Kublanov, Hai Tran, Alexei A Korzhenkov, Heinrich Lünsdorf, Taras Y Nechitaylo, Sergey N Gavrilov, Stepan V Toshchakov, Peter N Golyshin
The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed 'G-plasma'. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1-1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with 'G-plasma'. Organisms had largest genomes among Thermoplasmatales (1...
December 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27959634/emerging-concepts-and-technologies-for-the-discovery-of-microorganisms-involved-in-human-disease
#14
Susan Bullman, Matthew Meyerson, Aleksandar D Kostic
Established infectious agents continue to be a major cause of human morbidity and mortality worldwide. However, the causative agent remains unknown for a wide range of diseases; many of these are suspected to be attributable to yet undiscovered microorganisms. The advent of unbiased high-throughput sequencing and bioinformatics has enabled rapid identification and molecular characterization of known and novel infectious agents in human disease. An exciting era of microbe discovery, now underway, holds great promise for the improvement of global health via the development of antimicrobial therapies, vaccination strategies, targeted public health measures, and probiotic-based preventions and therapies...
December 5, 2016: Annual Review of Pathology
https://www.readbyqxmd.com/read/27955641/microbial-phenomics-information-extractor-micropie-a-natural-language-processing-tool-for-the-automated-acquisition-of-prokaryotic-phenotypic-characters-from-text-sources
#15
Jin Mao, Lisa R Moore, Carrine E Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Ranade, Hong Cui
BACKGROUND: The large-scale analysis of phenomic data (i.e., full phenotypic traits of an organism, such as shape, metabolic substrates, and growth conditions) in microbial bioinformatics has been hampered by the lack of tools to rapidly and accurately extract phenotypic data from existing legacy text in the field of microbiology. To quickly obtain knowledge on the distribution and evolution of microbial traits, an information extraction system needed to be developed to extract phenotypic characters from large numbers of taxonomic descriptions so they can be used as input to existing phylogenetic analysis software packages...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27943589/paleomicrobiology-to-investigate-copper-resistance-in-bacteria-isolation-and-description-of-cupriavidus-necator-b9-in-the-soil-of-a-medieval-foundry
#16
David C Gillan, Van Camp Camille, Max Mergeay, Ann Provoost, Nicolas Thomas, Laurent Vermard, Gabriel Billon, Ruddy Wattiez
Remains of a medieval foundry were excavated by archaeologists in 2013 in Verdun (France). Ancient workshops specialized in brass and copper alloys were found with an activity between 13th to 16th c. Levels of Cu, Zn and Pb reached 20000, 7000 and 6000 mg kg(-1) (dw), respectively, in several soil horizons. The objective of the present work was to examine the microbial community in this contaminated site. A total of 8-22 10(6) reads were obtained by shotgun metagenomics in 4 soil horizons. Bioinformatic analyses suggest the presence of complex bacterial communities dominated by Proteobacteria...
December 10, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27940320/mir-212-3p-inhibits-lps-induced-inflammatory-response-through-targeting-hmgb1-in-murine-macrophages
#17
Weiwei Chen, Xiaoying Ma, Peng Zhang, Qifeng Li, Xin Liang, Jianwen Liu
Sepsis is a major cause of mortality in seriously ill patients characterized by a series of severe systemic inflammatory responses due to an infection. Thus, there is a critically need to search more accurate biomarkers and targets for diagnosis and treatment of sepsis. Our study showed that miR-212-3p was up-regulated in LPS-treated macrophage RAW264.7 cells. Overexpression of miR-212-3p in RAW264.7 cells led to suppression of pro-inflammatory cytokines (TNF-α and IL-6) induced by LPS. Bioinformatic predictions and experimental researches both revealed that HMGB1 was a direct target of miR-212-3p...
December 8, 2016: Experimental Cell Research
https://www.readbyqxmd.com/read/27939730/viral-micrornas-identified-in-human-dental-pulp
#18
Sheng Zhong, Afsar Naqvi, Eric Bair, Salvador Nares, Asma A Khan
INTRODUCTION: MicroRNAs (miRs) are a family of noncoding RNAs that regulate gene expression. They are ubiquitous among multicellular eukaryotes and are also encoded by some viruses. Upon infection, viral miRs (vmiRs) can potentially target gene expression in the host and alter the immune response. Although prior studies have reported viral infections in human pulp, the role of vmiRs in pulpal disease is yet to be explored. The purpose of this study was to examine the expression of vmiRs in normal and diseased pulps and to identify potential target genes...
January 2017: Journal of Endodontics
https://www.readbyqxmd.com/read/27924593/analysis-of-16s-rrna-gene-amplicon-sequences-using-the-qiime-software-package
#19
Blair Lawley, Gerald W Tannock
The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27903821/construction-of-a-minimal-genome-as-a-chassis-for-synthetic-biology
#20
REVIEW
Bong Hyun Sung, Donghui Choe, Sun Chang Kim, Byung-Kwan Cho
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput '-omics' research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300-500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis...
November 30, 2016: Essays in Biochemistry
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