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https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#1
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
March 21, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#2
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28334194/swga-a-primer-design-toolkit-for-selective-whole-genome-amplification
#3
Erik L Clarke, Sesh A Sundararaman, Stephanie N Seifert, Frederic D Bushman, Beatrice H Hahn, Dustin Brisson
Motivation: Population genomic analyses are often hindered by difficulties in obtaining sufficient numbers of genomes for analysis by DNA sequencing. Selective whole-genome amplification (SWGA) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence acquisition. However, the process of designing sets of primers for this method has many degrees of freedom and would benefit from an automated process to evaluate the vast number of potential primer sets...
February 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#4
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28293230/a-new-functional-classification-of-glucuronoyl-esterases-by-peptide-pattern-recognition
#5
Jane W Agger, Peter K Busk, Bo Pilgaard, Anne S Meyer, Lene Lange
Glucuronoyl esterases are a novel type of enzymes believed to catalyze the hydrolysis of ester linkages between lignin and glucuronoxylan in lignocellulosic biomass, linkages known as lignin carbohydrate complexes. These complexes contribute to the recalcitrance of lignocellulose. Glucuronoyl esterases are a part of the microbial machinery for lignocellulose degradation and coupling their role to the occurrence of lignin carbohydrate complexes in biomass is a desired research goal. Glucuronoyl esterases have been assigned to CAZymes family 15 of carbohydrate esterases, but only few examples of characterized enzymes exist and the exact activity is still uncertain...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28284522/in-depth-analysis-of-rumen-microbial-and-carbohydrate-active-enzymes-profile-in-indian-crossbred-cattle
#6
V Lyju Jose, Ravi P More, Thulasi Appoothy, A Sha Arun
Rumen houses a plethora of symbiotic microorganisms empowering the host to hydrolyze plant lignocellulose. In this study, NGS based metagenomic approach coupled with bioinformatic analysis was employed to gain an insight into the deconstruction of lignocellulose by carbohydrate-active enzymes (CAZymes) in Indian crossbred Holstein-Friesian cattle. Cattle rumen metagenomic DNA was sequenced using Illumina-MiSeq and 1.9 gigabases of data generated with an average read length of 871 bp. Analysis of the assembled sequences by Pfam-based Carbohydrate-active enzyme Analysis Toolkit identified 17,164 putative protein-encoding CAZymes belonging to different families of glycoside hydrolases (7574), glycosyltransferases (5185), carbohydrate-binding modules (2418), carbohydrate esterases (1516), auxiliary activities (434) and polysaccharide lyases (37)...
February 28, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28279656/hepatic-induction-of-fatty-acid-binding-protein-4-plays-a-pathogenic-role-in-sepsis-in-mice
#7
Bingfang Hu, Yujin Li, Li Gao, Yan Guo, Yiwen Zhang, Xiaojuan Chai, Meishu Xu, Jiong Yan, Peipei Lu, Songrong Ren, Su Zeng, Yulan Liu, Wen Xie, Min Huang
Sepsis is defined as the host's deleterious systemic inflammatory response to microbial infections. Herein, we report an essential role of the fatty acid binding protein 4 (FABP4; alias adipocyte protein 2 or aP2), a lipid-binding chaperone, in sepsis response. Bioinformatic analysis of the Gene Expression Omnibus data sets showed the level of FABP4 was higher in the nonsurvival sepsis patients' whole blood compared to the survival cohorts. The expression of Fabp4 was induced in a liver-specific manner in cecal ligation and puncture (CLP) and lipopolysaccharide treatment models of sepsis...
March 6, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28276126/aquatic-adaptation-of-a-laterally-acquired-pectin-degradation-pathway-in-marine-gammaproteobacteria
#8
Jan-Hendrik Hehemann, Le Van Truong, Frank Unfried, Norma Welsch, Johannes Kabisch, Stefan E Heiden, Sabryna Junker, Dörte Becher, Andrea Thürmer, Rolf Daniel, Rudolf Amann, Thomas Schweder
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB...
March 9, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28272521/activity-screening-of-environmental-metagenomic-libraries-reveals-novel-carboxylesterase-families
#9
Ana Popovic, Tran Hai, Anatoly Tchigvintsev, Mahbod Hajighasemi, Boguslaw Nocek, Anna N Khusnutdinova, Greg Brown, Julia Glinos, Robert Flick, Tatiana Skarina, Tatyana N Chernikova, Veronica Yim, Thomas Brüls, Denis Le Paslier, Michail M Yakimov, Andrzej Joachimiak, Manuel Ferrer, Olga V Golyshina, Alexei Savchenko, Peter N Golyshin, Alexander F Yakunin
Metagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28261162/critical-issues-in-mycobiota-analysis
#10
Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G Thallinger, Gregor Gorkiewicz
Fungi constitute an important part of the human microbiota and they play a significant role for health and disease development. Advancements made in the culture-independent analysis of microbial communities have broadened our understanding of the mycobiota, however, microbiota analysis tools have been mainly developed for bacteria (e.g., targeting the 16S rRNA gene) and they often fall short if applied to fungal marker-gene based investigations (i.e., internal transcribed spacers, ITS). In the current paper we discuss all major steps of a fungal amplicon analysis starting with DNA extraction from specimens up to bioinformatics analyses of next-generation sequencing data...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28241020/investigation-of-the-fungal-community-structures-of-imported-wheat-using-high-throughput-sequencing-technology
#11
Yaqian Shi, Yinghui Cheng, Ying Wang, Guiming Zhang, Ruifang Gao, Caiyu Xiang, Jianjun Feng, Dingfeng Lou, Ying Liu
This study introduced the application of high-throughput sequencing techniques to the investigation of microbial diversity in the field of plant quarantine. It examined the microbial diversity of wheat imported into China, and established a bioinformatics database of wheat pathogens based on high-throughput sequencing results. This study analyzed the nuclear ribosomal internal transcribed spacer (ITS) region of fungi through Illumina Miseq sequencing to investigate the fungal communities of both seeds and sieve-through...
2017: PloS One
https://www.readbyqxmd.com/read/28235585/omics-in-fish-mucosal-immunity
#12
Salinas Irene, Susana Magadán
The mucosal immune system of fish is a complex network of immune cells and molecules that are constantly surveilling the environment and protecting the host from infection. A number of "omics" tools are now available and utilized to understand the complexity of mucosal immune systems in non-traditional animal models. This review summarizes recent advances in the implementation of "omics" tools pertaining to the four mucosa-associated lymphoid tissues in teleosts. Genomics, transcriptomics, proteomics, and "omics" in microbiome research require interdisciplinary collaboration and careful experimental design...
February 21, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28231302/bioinformatic-prediction-of-g-protein-coupled-receptor-encoding-sequences-from-the-transcriptome-of-the-foreleg-including-the-haller-s-organ-of-the-cattle-tick-rhipicephalus-australis
#13
Sergio Munoz, Felix D Guerrero, Anastasia Kellogg, Andrew M Heekin, Ming-Ying Leung
The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28211005/resequencing-and-annotation-of-the-nostoc-punctiforme-attc-29133-genome-facilitating-biofuel-and-high-value-chemical-production
#14
Luis E Moraes, Matthew J Blow, Erik R Hawley, Hailan Piao, Rita Kuo, Jennifer Chiniquy, Nicole Shapiro, Tanja Woyke, James G Fadel, Matthias Hess
Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28188552/enhanced-biodegradation-of-low-and-high-density-polyethylene-by-novel-bacterial-consortia-formulated-from-plastic-contaminated-cow-dung-under-thermophilic-conditions
#15
Sinosh Skariyachan, Anagha Shamsundar Setlur, Sujay Yashwant Naik, Ashwini Amaresh Naik, Makam Usharani, Kiran S Vasist
The current study aimed to devise eco-friendly, safe, and cost-effective strategies for enhanced degradation of low- and high-density polyethylene (LDPE and HDPE) using newly formulated thermophilic microbial consortia from cow dung and to assess the biodegradation end products. The plastic-degrading bacteria from cow dung samples gathered from highly plastic-acclimated environments were enriched by standard protocols. The degradation ability was comprehended by zone of clearance method, and the percentage of degradation was monitored by weight reduction process...
February 10, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28187415/estimation-of-biomass-composition-from-genomic-and-transcriptomic-information
#16
Sophia Santos, Isabel Rocha
Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genome-scale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments...
November 27, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28184370/metaproteomics-as-a-complementary-approach-to-gut-microbiota-in-health-and-disease
#17
REVIEW
Bernardo A Petriz, Octávio L Franco
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28174747/a-disease-associated-microbial-and-metabolomics-state-in-relatives-of-pediatric-inflammatory-bowel-disease-patients
#18
Jonathan P Jacobs, Maryam Goudarzi, Namita Singh, Maomeng Tong, Ian H McHardy, Paul Ruegger, Miro Asadourian, Bo-Hyun Moon, Allyson Ayson, James Borneman, Dermot P B McGovern, Albert J Fornace, Jonathan Braun, Marla Dubinsky
BACKGROUND & AIMS: Microbes may increase susceptibility to inflammatory bowel disease (IBD) by producing bioactive metabolites that affect immune activity and epithelial function. We undertook a family based study to identify microbial and metabolic features of IBD that may represent a predisease risk state when found in healthy first-degree relatives. METHODS: Twenty-one families with pediatric IBD were recruited, comprising 26 Crohn's disease patients in clinical remission, 10 ulcerative colitis patients in clinical remission, and 54 healthy siblings/parents...
November 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28174738/microgeographic-proteomic-networks-of-the-human-colonic-mucosa-and-their-association-with-inflammatory-bowel-disease
#19
Xiaoxiao Li, James LeBlanc, David Elashoff, Ian McHardy, Maomeng Tong, Bennett Roth, Andrew Ippoliti, Gildardo Barron, Dermot McGovern, Keely McDonald, Rodney Newberry, Thomas Graeber, Steve Horvath, Lee Goodglick, Jonathan Braun
BACKGROUND & AIMS: Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosal-luminal interface to study the disease-related biology of the human colonic mucosa. METHODS: We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28167213/metagenomics-approach-to-the-study-of-the-gut-microbiome-structure-and-function-in-zebrafish-danio-rerio-fed-with-gluten-formulated-diet
#20
Hyunmin Koo, Joseph A Hakim, Mickie L Powell, Ranjit Kumar, Peter G Eipers, Casey D Morrow, Michael Crowley, Elliot J Lefkowitz, Stephen A Watts, Asim K Bej
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine...
February 3, 2017: Journal of Microbiological Methods
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