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Whole genome sequence microbiome

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https://www.readbyqxmd.com/read/28174737/metagenomic-characterization-of-microbial-communities-in-situ-within-the-deeper-layers-of-the-ileum-in-crohn-s-disease
#1
Chandra Sekhar Pedamallu, Ami S Bhatt, Susan Bullman, Sharyle Fowler, Samuel S Freeman, Jacqueline Durand, Joonil Jung, Fujiko Duke, Veronica Manzo, Diana Cai, Ashwin Ananthakrishnan, Akinyemi I Ojesina, Aruna Ramachandran, Dirk Gevers, Ramnik J Xavier, Atul K Bhan, Matthew Meyerson, Vijay Yajnik
BACKGROUND & AIMS: Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28122610/fast-and-simple-protein-alignment-guided-assembly-of-orthologous-gene-families-from-microbiome-sequencing-reads
#2
Daniel H Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P Cummings, Kay Nieselt, Rohan Williams
BACKGROUND: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28118849/distinguishing-potential-bacteria-tumor-associations-from-contamination-in-a-secondary-data-analysis-of-public-cancer-genome-sequence-data
#3
Kelly M Robinson, Jonathan Crabtree, John S A Mattick, Kathleen E Anderson, Julie C Dunning Hotopp
BACKGROUND: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28112736/maturation-of-the-infant-microbiome-community-structure-and-function-across-multiple-body-sites-and-in-relation-to-mode-of-delivery
#4
Derrick M Chu, Jun Ma, Amanda L Prince, Kathleen M Antony, Maxim D Seferovic, Kjersti M Aagaard
Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers...
January 23, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28081260/comparative-genome-sequencing-reveals-within-host-genetic-changes-in-neisseria-meningitidis-during-invasive-disease
#5
Johanna Klughammer, Marcus Dittrich, Jochen Blom, Vera Mitesser, Ulrich Vogel, Matthias Frosch, Alexander Goesmann, Tobias Müller, Christoph Schoen
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation...
2017: PloS One
https://www.readbyqxmd.com/read/28005526/introducing-ezbiocloud-a-taxonomically-united-database-of-16s-rrna-and-whole-genome-assemblies
#6
Seok-Hwan Yoon, Sung-Min Ha, Soonjae Kwon, Jeongmin Lim, Yeseul Kim, Hyungseok Seo, Jongsik Chun
The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is a premium need to enhance our efforts in exploring prokaryotic diversity and discovering new species as well as for routine identifications...
December 22, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27991530/comparative-metagenomics-reveals-taxonomically-idiosyncratic-yet-functionally-congruent-communities-in-periodontitis
#7
Shareef M Dabdoub, Sukirth M Ganesan, Purnima S Kumar
The phylogenetic characteristics of microbial communities associated with periodontitis have been well studied, however, little is known about the functional endowments of this ecosystem. The present study examined 73 microbial assemblages from 25 individuals with generalized chronic periodontitis and 25 periodontally healthy individuals using whole genome shotgun sequencing. Core metabolic networks were computed from taxa and genes identified in at least 80% of individuals in each group. 50% of genes and species identified in health formed part of the core microbiome, while the disease-associated core microbiome contained 33% of genes and only 1% of taxa...
December 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852235/enrichment-dynamics-of-listeria-monocytogenes-and-the-associated-microbiome-from-naturally-contaminated-ice-cream-linked-to-a-listeriosis-outbreak
#8
Andrea Ottesen, Padmini Ramachandran, Elizabeth Reed, James R White, Nur Hasan, Poorani Subramanian, Gina Ryan, Karen Jarvis, Christopher Grim, Ninalynn Daquiqan, Darcy Hanes, Marc Allard, Rita Colwell, Eric Brown, Yi Chen
BACKGROUND: Microbiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA)...
November 16, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27813268/dissemination-of-clostridium-difficile-in-food-and-the-environment-significant-sources-of-c-difficile-community-acquired-infection
#9
REVIEW
K Warriner, C Xu, M Habash, S Sultan, S J Weese
Clostridium difficile is a significant pathogen with over 300 000 cases reported in North America annually. Previously, it was thought that C. difficile was primarily a clinically associated infection. However, through the use of whole genome sequencing it has been revealed that the majority of cases are community acquired. The source of community-acquired C. difficile infections (CDI) is open to debate with foodborne being one route considered. Clostridium difficile fits the criteria of a foodborne pathogen with respect to being commonly encountered in a diverse range of foods that includes meat, seafood and fresh produce...
November 4, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27760173/filtration-and-normalization-of-sequencing-read-data-in-whole-metagenome-shotgun-samples
#10
Philippe Chouvarine, Lutz Wiehlmann, Patricia Moran Losada, David S DeLuca, Burkhard Tümmler
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes...
2016: PloS One
https://www.readbyqxmd.com/read/27696646/diet-induced-changes-of-redox-potential-underlie-compositional-shifts-in-the-rumen-archaeal-community
#11
Nir Friedman, Eran Shriker, Ben Gold, Thomer Durman, Raphy Zarecki, Eytan Ruppin, Itzhak Mizrahi
Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here, we addressed these questions in the rumen microbiome ecosystem - a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the degradation of the ingested plant material. Our dietary intervention experiments revealed that diet affects the most abundant taxa within the microbiome and that a specific group of methanogenic archaea of the order Methanomicrobiales is highly sensitive to its changes...
October 1, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27558918/a-robust-ambient-temperature-collection-and-stabilization-strategy-enabling-worldwide-functional-studies-of-the-human-microbiome
#12
Ericka L Anderson, Weizhong Li, Niels Klitgord, Sarah K Highlander, Mark Dayrit, Victor Seguritan, Shibu Yooseph, William Biggs, J Craig Venter, Karen E Nelson, Marcus B Jones
As reports on possible associations between microbes and the host increase in number, more meaningful interpretations of this information require an ability to compare data sets across studies. This is dependent upon standardization of workflows to ensure comparability both within and between studies. Here we propose the standard use of an alternate collection and stabilization method that would facilitate such comparisons. The DNA Genotek OMNIgene∙Gut Stool Microbiome Kit was compared to the currently accepted community standard of freezing to store human stool samples prior to whole genome sequencing (WGS) for microbiome studies...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27479330/virtual-microfluidics-for-digital-quantification-and-single-cell-sequencing
#13
Liyi Xu, Ilana L Brito, Eric J Alm, Paul C Blainey
We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial cells and human microbiome samples in the virtual microfluidics system, and demonstrated whole-genome sequencing of single-cell MDA products with excellent coverage uniformity and markedly reduced chimerism compared with products of liquid MDA reactions...
September 2016: Nature Methods
https://www.readbyqxmd.com/read/27460902/a-snapshot-of-the-microbiome-of-amblyomma-tuberculatum-ticks-infesting-the-gopher-tortoise-an-endangered-species
#14
Khemraj Budachetri, Daniel Gaillard, Jaclyn Williams, Nabanita Mukherjee, Shahid Karim
The gopher tortoise tick, Amblyomma tuberculatum, has a unique relationship with the gopher tortoise, Gopherus polyphemus, found in sandy habitats across the southeastern United States. We aimed to understand the overall bacterial community associated with A. tuberculatum while also focusing on spotted fever group Rickettsia. These tortoises in the Southern Mississippi region are a federally threatened species; therefore, we have carefully trapped the tortoises and removed the species-specific ticks attached to them...
October 2016: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/27422831/enrichment-of-root-endophytic-bacteria-from-populus-deltoides-and-single-cell-genomics-analysis
#15
Sagar M Utturkar, W Nathan Cude, Michael S Robeson, Zamin K Yang, Dawn M Klingeman, Miriam L Land, Steve L Allman, Tse-Yuan S Lu, Steven D Brown, Christopher W Schadt, Mircea Podar, Mitchel J Doktycz, Dale A Pelletier
UNLABELLED: Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots...
September 15, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27391011/gutss-an-alignment-free-sequence-comparison-method-for-use-in-human-intestinal-microbiome-and-fecal-microbiota-transplantation-analysis
#16
Mitchell J Brittnacher, Sonya L Heltshe, Hillary S Hayden, Matthew C Radey, Eli J Weiss, Christopher J Damman, Timothy L Zisman, David L Suskind, Samuel I Miller
BACKGROUND: Comparative analysis of gut microbiomes in clinical studies of human diseases typically rely on identification and quantification of species or genes. In addition to exploring specific functional characteristics of the microbiome and potential significance of species diversity or expansion, microbiome similarity is also calculated to study change in response to therapies directed at altering the microbiome. Established ecological measures of similarity can be constructed from species abundances, however methods for calculating these commonly used ecological measures of similarity directly from whole genome shotgun (WGS) metagenomic sequence are lacking...
2016: PloS One
https://www.readbyqxmd.com/read/27306663/natural-history-of-the-infant-gut-microbiome-and-impact-of-antibiotic-treatment-on-bacterial-strain-diversity-and-stability
#17
Moran Yassour, Tommi Vatanen, Heli Siljander, Anu-Maaria Hämäläinen, Taina Härkönen, Samppa J Ryhänen, Eric A Franzosa, Hera Vlamakis, Curtis Huttenhower, Dirk Gevers, Eric S Lander, Mikael Knip, Ramnik J Xavier
The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life...
June 15, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/27291330/can-molecular-dna-based-techniques-unravel-the-truth-about-diabetic-foot-infections
#18
REVIEW
M Malone, I B Gosbell, H G Dickson, K Vickery, B A Espedido, S O Jensen
Diabetes foot infections are a common condition and a major causal pathway to lower extremity amputation. Identification of causative pathogens is vital in directing antimicrobial therapy. Historically, clinicians have relied upon culture-dependent techniques that are now acknowledged as both being selective for microorganisms that thrive under the physiological and nutritional constraints of the microbiology laboratory and that grossly underestimate the microbial diversity of a sample. The amplification and sequence analysis of the 16S rRNA gene has revealed a diversity of microorganisms in diabetes foot infections, extending the view of the diabetic foot microbiome...
June 12, 2016: Diabetes/metabolism Research and Reviews
https://www.readbyqxmd.com/read/27237775/comparison-of-microbial-dna-enrichment-tools-for-metagenomic-whole-genome-sequencing
#19
Matthew Thoendel, Patricio R Jeraldo, Kerryl E Greenwood-Quaintance, Janet Z Yao, Nicholas Chia, Arlen D Hanssen, Matthew P Abdel, Robin Patel
Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus...
August 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27217714/association-of-primary-open-angle-glaucoma-with-mitochondrial-variants-and-haplogroups-common-in-african-americans
#20
David W Collins, Harini V Gudiseva, Benjamin Trachtman, Anita S Bowman, Anna Sagaser, Prithvi Sankar, Eydie Miller-Ellis, Amanda Lehman, Victoria Addis, Joan M O'Brien
PURPOSE: To estimate the population frequencies of all common mitochondrial variants and ancestral haplogroups among 1,999 subjects recruited for the Primary Open-Angle African American Glaucoma Genetics (POAAGG) Study, including 1,217 primary open-angle glaucoma (POAG) cases and 782 controls, and to identify ancestral subpopulations and mitochondrial mutations as potential risk factors for POAG susceptibility. METHODS: Subject classification by characteristic glaucomatous optic nerve findings and corresponding visual field defects, as defined by enrolling glaucoma specialists, stereo disc photography, phlebotomy, extraction of total DNA from peripheral blood or saliva, DNA quantification and normalization, PCR amplification of whole mitochondrial genomes, Ion Torrent deep semiconductor DNA sequencing on DNA pools ("Pool-seq"), Sanger sequencing of 3,479 individual mitochondrial DNAs, and bioinformatic analysis...
2016: Molecular Vision
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