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Microbial informatics

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https://www.readbyqxmd.com/read/27115645/bacterial-genomic-data-analysis-in-the-next-generation-sequencing-era
#1
Massimiliano Orsini, Gianmauro Cuccuru, Paolo Uva, Giorgio Fotia
Bacterial genome sequencing is now an affordable choice for many laboratories for applications in research, diagnostic, and clinical microbiology. Nowadays, an overabundance of tools is available for genomic data analysis. However, tools differ for algorithms, languages, hardware requirements, and user interface, and combining them as it is necessary for sequence data interpretation often requires (bio)informatics skills which can be difficult to find in many laboratories. In addition, multiple data sources, as well as exceedingly large dataset sizes, and increasingly computational complexity further challenge the accessibility, reproducibility, and transparency of the entire process...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/26829473/assembly-and-clustering-of-natural-antibiotics-guides-target-identification
#2
Chad W Johnston, Michael A Skinnider, Chris A Dejong, Philip N Rees, Gregory M Chen, Chelsea G Walker, Shawn French, Eric D Brown, János Bérdy, Dennis Y Liu, Nathan A Magarvey
Antibiotics are essential for numerous medical procedures, including the treatment of bacterial infections, but their widespread use has led to the accumulation of resistance, prompting calls for the discovery of antibacterial agents with new targets. A majority of clinically approved antibacterial scaffolds are derived from microbial natural products, but these valuable molecules are not well annotated or organized, limiting the efficacy of modern informatic analyses. Here, we provide a comprehensive resource defining the targets, chemical origins and families of the natural antibacterial collective through a retrobiosynthetic algorithm...
April 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/26442528/genomes-to-natural-products-prediction-informatics-for-secondary-metabolomes-prism
#3
Michael A Skinnider, Chris A Dejong, Philip N Rees, Chad W Johnston, Haoxin Li, Andrew L H Webster, Morgan A Wyatt, Nathan A Magarvey
Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products...
November 16, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/26364933/exploration-of-nonribosomal-peptide-families-with-an-automated-informatic-search-algorithm
#4
Lian Yang, Ashraf Ibrahim, Chad W Johnston, Michael A Skinnider, Bin Ma, Nathan A Magarvey
Microbial natural products are some of the most important pharmaceutical agents and possess unparalleled chemical diversity. Here we present an untargeted metabolomics algorithm that builds on our validated iSNAP platform to rapidly identify families of peptide natural products. By utilizing known or in silico-dereplicated seed structures, this algorithm screens tandem mass spectrometry data to elaborate extensive molecular families within crude microbial culture extracts with high confidence and statistical significance...
September 17, 2015: Chemistry & Biology
https://www.readbyqxmd.com/read/26350080/informatic-search-strategies-to-discover-analogues-and-variants-of-natural-product-archetypes
#5
Chad W Johnston, Alex D Connaty, Michael A Skinnider, Yong Li, Alyssa Grunwald, Morgan A Wyatt, Russell G Kerr, Nathan A Magarvey
Natural products are a crucial source of antimicrobial agents, but reliance on low-resolution bioactivity-guided approaches has led to diminishing interest in discovery programmes. Here, we demonstrate that two in-house automated informatic platforms can be used to target classes of biologically active natural products, specifically, peptaibols. We demonstrate that mass spectrometry-based informatic approaches can be used to detect natural products with high sensitivity, identifying desired agents present in complex microbial extracts...
March 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/26344171/progress-in-oral-personalized-medicine-contribution-of-omics
#6
Ingrid Glurich, Amit Acharya, Murray H Brilliant, Sanjay K Shukla
BACKGROUND: Precision medicine (PM), representing clinically applicable personalized medicine, proactively integrates and interprets multidimensional personal health data, including clinical, 'omics', and environmental profiles, into clinical practice. Realization of PM remains in progress. OBJECTIVE: The focus of this review is to provide a descriptive narrative overview of: 1) the current status of oral personalized medicine; and 2) recent advances in genomics and related 'omic' and emerging research domains contributing to advancing oral-systemic PM, with special emphasis on current understanding of oral microbiomes...
2015: Journal of Oral Microbiology
https://www.readbyqxmd.com/read/26319390/utilizing-de-bruijn-graph-of-metagenome-assembly-for-metatranscriptome-analysis
#7
Yuzhen Ye, Haixu Tang
MOTIVATION: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities)...
April 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26241506/bioinformatics-of-antimicrobial-resistance-in-the-age-of-molecular-epidemiology
#8
REVIEW
Andrew G McArthur, Gerard D Wright
Antimicrobial resistance is a global health challenge and has an evolutionary trajectory ranging from proto-resistance in the environment to untreatable clinical pathogens. Resistance is not static, as pathogenic strains can move among patient populations and individual resistance genes can move among pathogens. Effective treatment of resistant infections, antimicrobial stewardship, and new drug discovery increasingly rely upon genotype information, powered by decreasing costs of DNA sequencing. These new approaches will require advances in microbial informatics, particularly in development of reference databases of molecular determinants such as our Comprehensive Antibiotic Resistance Database and clinical metadata, new algorithms for prediction of resistome and resistance phenotype from genotype, and new protocols for global collection and sharing of high-throughput molecular epidemiology data...
October 2015: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/25914197/microbial-metaproteomics-for-characterizing-the-range-of-metabolic-functions-and-activities-of-human-gut-microbiota
#9
REVIEW
Weili Xiong, Paul E Abraham, Zhou Li, Chongle Pan, Robert L Hettich
The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host...
October 2015: Proteomics
https://www.readbyqxmd.com/read/25844058/mass-spectral-similarity-for-untargeted-metabolomics-data-analysis-of-complex-mixtures
#10
Neha Garg, Clifford Kapono, Yan Wei Lim, Nobuhiro Koyama, Mark J A Vermeij, Douglas Conrad, Forest Rohwer, Pieter C Dorrestein
While in nucleotide sequencing, the analysis of DNA from complex mixtures of organisms is common, this is not yet true for mass spectrometric data analysis of complex mixtures. The comparative analyses of mass spectrometry data of microbial communities at the molecular level is difficult to perform, especially in the context of a host. The challenge does not lie in generating the mass spectrometry data, rather much of the difficulty falls in the realm of how to derive relevant information from this data. The informatics based techniques to visualize and organize datasets are well established for metagenome sequencing; however, due to the scarcity of informatics strategies in mass spectrometry, it is currently difficult to cross correlate two very different mass spectrometry data sets from microbial communities and their hosts...
February 1, 2015: International Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/25714718/sewage-reflects-the-microbiomes-of-human-populations
#11
Ryan J Newton, Sandra L McLellan, Deborah K Dila, Joseph H Vineis, Hilary G Morrison, A Murat Eren, Mitchell L Sogin
UNLABELLED: Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples...
2015: MBio
https://www.readbyqxmd.com/read/25487354/automated-identification-of-depsipeptide-natural-products-by-an-informatic-search-algorithm
#12
Michael A Skinnider, Chad W Johnston, Rostyslav Zvanych, Nathan A Magarvey
Nonribosomal depsipeptides are a class of potent microbial natural products, which include several clinically approved pharmaceutical agents. Genome sequencing has revealed a large number of uninvestigated natural-product biosynthetic gene clusters. However, while novel informatic search methods to access these gene clusters have been developed to identify peptide natural products, depsipeptide detection has proven challenging. Herein, we present an improved version of our informatic search algorithm for natural products (iSNAP), which facilitates the detection of known and genetically predicted depsipeptides in complex microbial culture extracts...
January 19, 2015: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/25278581/clinical-microbiology-informatics
#13
REVIEW
Daniel D Rhoads, Vitali Sintchenko, Carol A Rauch, Liron Pantanowitz
The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing...
October 2014: Clinical Microbiology Reviews
https://www.readbyqxmd.com/read/25256301/cmeias-jfrad-a-digital-computing-tool-to-discriminate-the-fractal-geometry-of-landscape-architectures-and-spatial-patterns-of-individual-cells-in-microbial-biofilms
#14
Zhou Ji, Kyle J Card, Frank B Dazzo
Image analysis of fractal geometry can be used to gain deeper insights into complex ecophysiological patterns and processes occurring within natural microbial biofilm landscapes, including the scale-dependent heterogeneities of their spatial architecture, biomass, and cell-cell interactions, all driven by the colonization behavior of optimal spatial positioning of organisms to maximize their efficiency in utilization of allocated nutrient resources. Here, we introduce CMEIAS JFrad, a new computing technology that analyzes the fractal geometry of complex biofilm architectures in digital landscape images...
April 2015: Microbial Ecology
https://www.readbyqxmd.com/read/24939130/metaproteomics-extracting-and-mining-proteome-information-to-characterize-metabolic-activities-in-microbial-communities
#15
Paul E Abraham, Richard J Giannone, Weili Xiong, Robert L Hettich
Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches...
2014: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/24800368/sampling-bacterial-biodiversity-from-a-highly-contaminated-stream-flowing-through-a-densely-populated-urban-area-in-karachi
#16
Syed Faaiz Enam, Humaira Qureshi, Sohail A Qureshi
BACKGROUND: Few studies have attempted to understand the complexity of microbial populations in Pakistan where infectious diseases are prevalent. This study was undertaken to assess bacterial biodiversity in Nehr-e-Khayyam a heavily polluted stream connected to the Arabian Gulf, which runs through a densely populated urban area in Karachi, Pakistan. METHODS: Employing a universal pair of oligonucleotides capable of amplifying species-specific segments of 16S rRNA gene from all Eubacteria, we generated a library of PCR products using total DNA purified from the collected sample, cloned the amplifers into pGEM-T-Easy and sequenced each recombinant clone...
April 2011: Journal of Ayub Medical College, Abbottabad: JAMC
https://www.readbyqxmd.com/read/24719854/comparative-metagenomic-analysis-of-human-gut-microbiome-composition-using-two-different-bioinformatic-pipelines
#17
Valeria D'Argenio, Giorgio Casaburi, Vincenza Precone, Francesco Salvatore
Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies...
2014: BioMed Research International
https://www.readbyqxmd.com/read/24515391/treatment-of-microbial-biofilms-in-the-post-antibiotic-era-prophylactic-and-therapeutic-use-of-antimicrobial-peptides-and-their-design-by-bioinformatics-tools
#18
REVIEW
Mariagrazia Di Luca, Giuseppe Maccari, Riccardo Nifosì
The treatment for biofilm infections is particularly challenging because bacteria in these conditions become refractory to antibiotic drugs. The reduced effectiveness of current therapies spurs research for the identification of novel molecules endowed with antimicrobial activities and new mechanisms of antibiofilm action. Antimicrobial peptides (AMPs) have been receiving increasing attention as potential therapeutic agents, because they represent a novel class of antibiotics with a wide spectrum of activity and a low rate in inducing bacterial resistance...
April 2014: Pathogens and Disease
https://www.readbyqxmd.com/read/24377417/global-catalogue-of-microorganisms-gcm-a-comprehensive-database-and-information-retrieval-analysis-and-visualization-system-for-microbial-resources
#19
Linhuan Wu, Qinglan Sun, Hideaki Sugawara, Song Yang, Yuguang Zhou, Kevin McCluskey, Alexander Vasilenko, Ken-Ichiro Suzuki, Moriya Ohkuma, Yeonhee Lee, Vincent Robert, Supawadee Ingsriswang, François Guissart, Desmeth Philippe, Juncai Ma
BACKGROUND: Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities...
2013: BMC Genomics
https://www.readbyqxmd.com/read/23848071/-progress-in-the-knowledge-of-the-intestinal-human-microbiota
#20
Virginia Robles-Alonso, Francisco Guarner
New sequencing technologies together with the development of bio-informatics allow a description of the full spectrum of the microbial communities that inhabit the human intestinal tract, as well as their functional contributions to host health. Most community members belong to the domain Bacteria, but Archaea, Eukaryotes (yeasts and protists), and Viruses are also present. Only 7 to 9 of the 55 known divisions or phyla of the domain Bacteria are detected in faecal or mucosal samples from the human gut. Most taxa belong to just two divisions: Bacteroidetes and Firmicutes, and the other divisions that have been consistently found are Proteobacteria, Actinobacteria, Fusobacteria, and Verrucomicrobia...
May 2013: Nutrición Hospitalaria: Organo Oficial de la Sociedad Española de Nutrición Parenteral y Enteral
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