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Shotgun sequence metagenome

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https://www.readbyqxmd.com/read/29347966/reprdb-and-pandb-minimalist-databases-with-maximal-microbial-representation
#1
Wei Zhou, Nicole Gay, Julia Oh
BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes...
January 18, 2018: Microbiome
https://www.readbyqxmd.com/read/29345635/genetic-risk-dysbiosis-and-treatment-stratification-using-host-genome-and-gut-microbiome-in-inflammatory-bowel-disease
#2
Ahmed Moustafa, Weizhong Li, Ericka L Anderson, Emily H M Wong, Parambir S Dulai, William J Sandborn, William Biggs, Shibu Yooseph, Marcus B Jones, J Craig Venter, Karen E Nelson, John T Chang, Amalio Telenti, Brigid S Boland
OBJECTIVES: Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS: Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals...
January 18, 2018: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/29335008/multi-omics-differentially-classify-disease-state-and-treatment-outcome-in-pediatric-crohn-s-disease
#3
Gavin M Douglas, Richard Hansen, Casey M A Jones, Katherine A Dunn, André M Comeau, Joseph P Bielawski, Rachel Tayler, Emad M El-Omar, Richard K Russell, Georgina L Hold, Morgan G I Langille, Johan Van Limbergen
BACKGROUND: Crohn's disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been confounded with patients' ongoing treatments. Additionally, most analyses of CD patients' microbiomes have focused on microbes in stool samples, which yield different insights than profiling biopsy samples. RESULTS: We sequenced the 16S rRNA gene (16S) and carried out shotgun metagenomics (MGS) from the intestinal biopsies of 20 treatment-naïve CD and 20 control pediatric patients...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29335005/in-depth-resistome-analysis-by-targeted-metagenomics
#4
Val F Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J Willems, Fernando de la Cruz, Teresa M Coque
BACKGROUND: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29332945/the-human-skin-microbiome
#5
REVIEW
Allyson L Byrd, Yasmine Belkaid, Julia A Segre
Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level...
January 15, 2018: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29322681/gut-microbiome-contributes-to-impairment-of-immunity-in-pulmonary-tuberculosis-patients-by-alteration-of-butyrate-and-propionate-producers
#6
Abhijit Maji, Richa Misra, Darshan B Dhakan, Vipin Gupta, Nitish K Mahato, Rituja Saxena, Parul Mittal, Nitin Thukral, Eshan Sharma, Anoop Singh, Richa Virmani, Mohita Gaur, Harshvardhan Singh, Yasha Hasija, Gunjan Arora, Anurag Agrawal, Anil Chaudhry, Jitendra P Khurana, Vineet K Sharma, Rup Lal, Yogendra Singh
Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs...
January 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29322618/genome-enabled-metabolic-reconstruction-of-dominant-chemosynthetic-colonizers-in-deep-sea-massive-sulfide-deposits
#7
Shingo Kato, Takazo Shibuya, Yoshihiro Takaki, Miho Hirai, Takuro Nunoura, Katsuhiko Suzuki
Deep-sea massive sulfide deposits remaining after ceasing of hydrothermal activity potentially provide energy for a chemosynthetic ecosystem in the dark, cold marine environments. Although yet-uncultivated bacteria in the phylum Nitrospirae and the class Deltaproteobacteria are known to dominate the microbial communities of sulfide deposits at and below the seafloor, their metabolic capabilities remain largely elusive. Here, we reveal the metabolic potential of these yet-uncultivated bacteria in hydrothermally inactive sulfide deposits collected at the Southern Mariana Trough by seafloor drilling...
January 10, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29311716/discovering-viral-genomes-in-human-metagenomic-data-by-predicting-unknown-protein-families
#8
Mauricio Barrientos-Somarribas, David N Messina, Christian Pou, Fredrik Lysholm, Annelie Bjerkner, Tobias Allander, Björn Andersson, Erik L L Sonnhammer
Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29302014/the-commensal-microbiome-is-associated-with-anti-pd-1-efficacy-in-metastatic-melanoma-patients
#9
Vyara Matson, Jessica Fessler, Riyue Bao, Tara Chongsuwat, Yuanyuan Zha, Maria-Luisa Alegre, Jason J Luke, Thomas F Gajewski
Anti-PD-1-based immunotherapy has had a major impact on cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients' microbiome, which has been shown to affect antitumor immunity and immunotherapy efficacy in preclinical mouse models. We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment, through an integration of 16S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria...
January 5, 2018: Science
https://www.readbyqxmd.com/read/29300319/surveillance-of-foodborne-pathogens-towards-diagnostic-metagenomics-of-fecal-samples
#10
REVIEW
Sandra Christine Andersen, Jeffrey Hoorfar
Diagnostic metagenomics is a rapidly evolving laboratory tool for culture-independent tracing of foodborne pathogens. The method has the potential to become a generic platform for detection of most pathogens and many sample types. Today, however, it is still at an early and experimental stage. Studies show that metagenomic methods, from sample storage and DNA extraction to library preparation and shotgun sequencing, have a great influence on data output. To construct protocols that extract the complete metagenome but with minimal bias is an ongoing challenge...
January 4, 2018: Genes
https://www.readbyqxmd.com/read/29297318/16spip-a-comprehensive-analysis-pipeline-for-rapid-pathogen-detection-in-clinical-samples-based-on-16s-metagenomic-sequencing
#11
Jiaojiao Miao, Na Han, Yujun Qiang, Tingting Zhang, Xiuwen Li, Wen Zhang
BACKGROUND: Pathogen detection in clinical samples based on 16S metagenomic sequencing technology in microbiology laboratories is an important strategy for clinical diagnosis, public health surveillance, and investigations of outbreaks. However, the implementation of the technology is limited by its accuracy and the time required for bioinformatics analysis. Therefore, a simple, standardized, and rapid analysis pipeline from the receipt of clinical samples to the generation of a test report is needed to increase the use of metagenomic analyses in clinical settings...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29296020/linking-soil-biology-and-chemistry-in-biological-soil-crust-using-isolate-exometabolomics
#12
Tami L Swenson, Ulas Karaoz, Joel M Swenson, Benjamin P Bowen, Trent R Northen
Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29281673/taxonomic-differences-of-gut-microbiomes-drive-cellulolytic-enzymatic-potential-within-hind-gut-fermenting-mammals
#13
Emma C L Finlayson-Trick, Landon J Getz, Patrick D Slaine, Mackenzie Thornbury, Emily Lamoureux, Jamie Cook, Morgan G I Langille, Lois E Murray, Craig McCormick, John R Rohde, Zhenyu Cheng
Host diet influences the diversity and metabolic activities of the gut microbiome. Previous studies have shown that the gut microbiome provides a wide array of enzymes that enable processing of diverse dietary components. Because the primary diet of the porcupine, Erethizon dorsatum, is lignified plant material, we reasoned that the porcupine microbiome would be replete with enzymes required to degrade lignocellulose. Here, we report on the bacterial composition in the porcupine microbiome using 16S rRNA sequencing and bioinformatics analysis...
2017: PloS One
https://www.readbyqxmd.com/read/29277868/comparative-metagenomics
#14
Andrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da Silva, Emmanuel Dias-Neto, João C Setubal
Thanks in large part to newer, better, and cheaper DNA sequencing technologies, an enormous number of metagenomic sequence datasets have been and continue to be generated, covering a huge variety of environmental niches, including several different human body sites. Comparing these metagenomes and identifying their commonalities and differences is a challenging task, due not only to the large amounts of data, but also because there are several methodological considerations that need to be taken into account to ensure an appropriate and sound comparison between datasets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29235707/tales-from-the-tomb-the-microbial-ecology-of-exposed-rock-surfaces
#15
Tess E Brewer, Noah Fierer
Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology, and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analyzed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29227468/metagenomic-binning-and-association-of-plasmids-with-bacterial-host-genomes-using-dna-methylation
#16
John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno, Xue-Song Zhang, Austin Davis-Richardson, Ronald Canepa, Eric W Triplett, Jeremiah J Faith, Robert Sebra, Eric E Schadt, Gang Fang
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29225146/microbial-diversity-within-the-airway-microbiome-in-chronic-pediatric-lung-diseases
#17
Andrea Hahn, Stephanie Warnken, Marcos Pérez-Losada, Robert J Freishtat, Keith A Crandall
The study of the airway microbiome in children is an area of emerging research, especially in relation to the role microbial diversity may play in acute and chronic inflammation. Three such pediatric airway diseases include cystic fibrosis, asthma, and chronic lung disease of prematurity. In cystic fibrosis, the presence of Pseudomonas spp. is associated with decreased microbial diversity. Decreasing microbial diversity is also associated with poor lung function. In asthma, early viral infections appear to drive changes in bacterial diversity which may be associated with asthma risk...
December 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29223543/metagenomic-sequencing-of-environmental-dna-reveals-marine-faunal-assemblages-from-the-west-antarctic-peninsula
#18
Dominique A Cowart, Katherine R Murphy, C-H Christina Cheng
The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods...
December 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29211769/arsenic-exposure-and-intestinal-microbiota-in-children-from-sirajdikhan-bangladesh
#19
Xiaoxi Dong, Natalia Shulzhenko, Julien Lemaitre, Renee L Greer, Kate Peremyslova, Quazi Quamruzzaman, Mahmudar Rahman, Omar Sharif Ibn Hasan, Sakila Afroz Joya, Mostofa Golam, David C Christiani, Andriy Morgun, Molly L Kile
BACKGROUND: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk of many diseases in which gut microbiota have been shown to play a role. We examined the association between arsenic exposure from drinking water and the composition of intestinal microbiota in children exposed to low and high arsenic levels during prenatal development and early life. RESULTS: 16S rRNA gene sequencing revealed that children with high arsenic exposure had a higher abundance of Proteobacteria in their stool compared to matched controls with low arsenic exposure...
2017: PloS One
https://www.readbyqxmd.com/read/29197179/metagenomic-investigation-of-idiopathic-meningoencephalomyelitis-in-dogs
#20
L L Hoon-Hanks, S McGrath, K L Tyler, C Owen, M D Stenglein
BACKGROUND: Meningoencephalomyelitis of unknown origin (MUO) is a common and life-threatening neuroinflammatory disease in dogs. Features of the disease are suggestive of an underlying immune-mediated process, but the association of this disease with a pathogen is still unknown. HYPOTHESIS/OBJECTIVES: To search for candidate etiologic agent associated with cases if MUO using next generation metagenomic sequencing. ANIMALS: Twenty-two dogs diagnosed with either MUO (11/22; 10 CSF and 3 brain), or noninflammatory CNS diseases inconsistent with MUO (11/22; 11 CSF and 2 brain) that served as negative controls...
December 2, 2017: Journal of Veterinary Internal Medicine
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