keyword
MENU ▼
Read by QxMD icon Read
search

Metagenome

keyword
https://www.readbyqxmd.com/read/28937980/methanobrevibacter-attenuation-via-probiotic-intervention-reduces-flatulence-in-adult-human-a-non-randomised-paired-design-clinical-trial-of-efficacy
#1
Minseok Seo, Jaeyoung Heo, Joon Yoon, Se-Young Kim, Yoon-Mo Kang, Jihyun Yu, Seoae Cho, Heebal Kim
TRIAL DESIGN: The aim of this study was to investigate which of the gut microbes respond to probiotic intervention, as well as study whether they are associated with gastrointestinal symptoms in a healthy adult human. For the experimental purpose, twenty-one healthy adults were recruited and received probiotic mixture, which is composed of five Lactobacilli strains and two Bifidobacteria strains, once a day for 60 days. Defecation survey and Bioelectrical Impedance Analysis were conducted pre- and post-administration to measure phenotypic differences...
2017: PloS One
https://www.readbyqxmd.com/read/28936406/gut-microbiome-based-therapeutics-in-liver-cirrhosis-basic-consideration-for-the-next-step
#2
REVIEW
Hiroshi Fukui
Infections account for significant morbidity and mortality in liver cirrhosis and most are related to the gut microbiome. Fecal dysbiosis, characterized by an overgrowth of potentially pathogenic bacteria and a decrease in autochthonous non-pathogenic bacteria, becomes prominent with the progression of liver cirrhosis. In cirrhotic patients, disruption of the intestinal barrier causes intestinal hyperpermeability (i.e. leaky gut), which is closely related to gut dysmotility, dysbiosis and small intestinal bacterial overgrowth and may induce pathological bacterial translocation...
September 28, 2017: Journal of Clinical and Translational Hepatology
https://www.readbyqxmd.com/read/28935725/small-circular-rep-encoding-single-stranded-dna-genomes-in-peruvian-diarrhea-virome
#3
Eda Altan, Juana Del Valle Mendoza, Xutao Deng, Tung G Phan, Mohammadreza Sadeghi, Eric L Delwart
Metagenomic analysis of diarrhea samples revealed the presence of numerous human enteric viruses and small circular Rep-encoding single-stranded DNA (CRESS-DNA) genomes. One such genome was related to smacoviruses, while eight others were related to genomes reported in the feces of different mammals. The tropism of these CRESS-DNA viruses remains unknown.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935667/upregulation-of-herv-k-is-linked-to-immunity-and-inflammation-in-pulmonary-arterial-hypertension
#4
Toshie Saito, Kazuya Miyagawa, Shih-Yu Chen, Rasa Tamosiuniene, Lingli Wang, Orr Sharp, Erik Samayoa, Daisuke Harada, Jan-Renier A J Moonen, Aiqin Cao, Pin-I Chen, Jan K Hennigs, Mingxia Gu, Caiyun G Li, Ryan D Leib, Dan Li, Christopher M Adams, Patricia A Del Rosario, Matthew A Bill, Francois Haddad, Jose G Montoya, William Robinson, Wendy J Fantl, Garry P Nolan, Roham T Zamanian, Mark R Nicolls, Charles Y Chiu, Maria E Ariza, Marlene Rabinovitch
Background -Immune dysregulation has been linked to occlusive vascular remodeling in pulmonary arterial hypertension (PAH) that is hereditary, idiopathic or associated with other conditions. Circulating autoantibodies, lung perivascular lymphoid tissue and elevated cytokines have been related to PAH pathogenesis but without clear understanding of how these abnormalities are initiated, perpetuated and connected in the progression of disease. We therefore set out to identify specific target antigens in PAH lung immune complexes as a starting point toward resolving these issues to better inform future application of immunomodulatory therapies...
September 21, 2017: Circulation
https://www.readbyqxmd.com/read/28935108/discovery-of-new-glycosidases-from-metagenomic-libraries
#5
Zach Armstrong, Peter Rahfeld, Stephen G Withers
Microorganisms routinely perform complex enzymatic transformations of natural material; thus, their enzymes have the potential to tackle medical and industrial challenges. However, a vast number of microbes are recalcitrant to cultivation. Functional screening of environmental DNA allows us to tap into the seemingly boundless diversity of enzymes encoded by microbial populations. In this chapter, we describe methods for the isolation of environmental DNA, generation of metagenomic libraries, and the functional screening of these libraries for new glycosidases...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28934976/desman-a-new-tool-for-de-novo-extraction-of-strains-from-metagenomes
#6
Christopher Quince, Tom O Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E Darling, Gavin Collins, A Murat Eren
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934964/comprehensive-benchmarking-and-ensemble-approaches-for-metagenomic-classifiers
#7
Alexa B R McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J Prill, Elizabeth Hénaff, Noah Alexander, Samuel S Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi, Nick Greenfield, Rita R Colwell, Gail L Rosen, Christopher E Mason
BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934322/comparative-metagenomics-approaches-to-characterize-the-soil-fungal-communities-of-western-coastal-region-saudi-arabia
#8
Tarek A A Moussa, Hassan S Al-Zahrani, Omar A Almaghrabi, Tamer S Abdelmoneim, Michael P Fuller
A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota-99.31%, Basidiomycota-0.59%, Chytridiomycota-0.04%, Glomeromycota-0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota-74...
2017: PloS One
https://www.readbyqxmd.com/read/28933074/-genomic-research-of-traditional-chinese-medicines-in-vivo-metabolism
#9
Shui-Ming Xiao, Rui Bai, Xiao-Yan Zhang
Gene is the base of in vivo metabolism and effectiveness for traditional Chinese medicines (TCM), and the gene expression, regulation and modification are used as the research directions to perform the TCM multi-component, multi-link and multi-target in vivo metabolism studies, which will improve the research on TCM metabolic proecess, effect target and molecular mechanism. Humans are superorganisms with 1% genes inherited from parents and 99% genes from various parts of the human body, mainly coming from the microorganisms in intestinal flora...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932683/rhizospheric-metagenome-of-the-terrestrial-mangrove-fern-acrostichum-from-indian-sunderbans
#10
Sayak Ganguli, Sabdar Rahaman, Abhishek R Bera, Vineet Vishal, Shelvia Malik, K Roopalakshmi, Pankaj K Singh
This study reports the analyses of the rhizospheric microbiome of the terrestrial mangrove fern Acrostichum aureum Linn. from the Indian Sunderbans. Samples were collected using standard protocols and 16S rRNA gene V3-V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere. A total of 1,931,252 quality checked reads were assembled into 204,818 contigs and were analysed using QIIME to reveal the abundance of Proteobacteria, Acidobacteria and Planctomycetes...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28932211/strain-level-streptococcus-colonization-patterns-during-the-first-year-of-life
#11
Meredith S Wright, Jamison McCorrison, Andres M Gomez, Erin Beck, Derek Harkins, Jyoti Shankar, Stephanie Mounaud, Edelwisa Segubre-Mercado, Aileen May R Mojica, Brian Bacay, Susan A Nzenze, Sheila Z M Kimaro, Peter Adrian, Keith P Klugman, Marilla G Lucero, Karen E Nelson, Shabir Madhi, Granger G Sutton, William C Nierman, Liliana Losada
Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28931373/improving-contig-binning-of-metagenomic-data-using-formula-see-text-oligonucleotide-frequency-dissimilarity
#12
Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun
BACKGROUND: Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development. RESULTS: According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes...
September 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28931073/bacterial-and-diazotrophic-diversities-of-endophytes-in-dendrobium-catenatum-determined-through-barcoded-pyrosequencing
#13
Ou Li, Rong Xiao, Lihua Sun, Chenglin Guan, Dedong Kong, Xiufang Hu
As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71...
2017: PloS One
https://www.readbyqxmd.com/read/28931053/identification-and-molecular-characterization-of-a-metagenome-derived-l-lysine-decarboxylase-gene-from-subtropical-soil-microorganisms
#14
Jie Deng, Hua Gao, Zhen Gao, Huaxian Zhao, Ying Yang, Qiaofen Wu, Bo Wu, Chengjian Jiang
L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs...
2017: PloS One
https://www.readbyqxmd.com/read/28930182/microbial-community-structure-and-functions-in-ethanol-fed-sulfate-removal-bioreactors-for-treatment-of-mine-water
#15
Malin Bomberg, Jarno Mäkinen, Marja Salo, Mona Arnold
Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L(-1) sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing...
September 20, 2017: Microorganisms
https://www.readbyqxmd.com/read/28930150/detection-of-bacterial-pathogens-from-broncho-alveolar-lavage-by-next-generation-sequencing
#16
Stefano Leo, Nadia Gaïa, Etienne Ruppé, Stephane Emonet, Myriam Girard, Vladimir Lazarevic, Jacques Schrenzel
The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells...
September 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28930022/diagnosis-of-fatal-human-case-of-st-louis-encephalitis-virus-infection-by-metagenomic-sequencing-california-2016
#17
Charles Y Chiu, Lark L Coffey, Jamie Murkey, Kelly Symmes, Hannah A Sample, Michael R Wilson, Samia N Naccache, Shaun Arevalo, Sneha Somasekar, Scot Federman, Doug Stryke, Paul Vespa, Gary Schiller, Sharon Messenger, Romney Humphries, Steve Miller, Jeffrey D Klausner
We used unbiased metagenomic next-generation sequencing to diagnose a fatal case of meningoencephalitis caused by St. Louis encephalitis virus in a patient from California in September 2016. This case is associated with the recent 2015-2016 reemergence of this virus in the southwestern United States.
October 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#18
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929212/an-insight-into-phage-diversity-at-environmental-habitats-using-comparative-metagenomics-approach
#19
Krupa Parmar, Nishant Dafale, Rajesh Pal, Hitesh Tikariha, Hemant Purohit
Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses...
September 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28928719/the-green-berry-consortia-of-the-sippewissett-salt-marsh-millimeter-sized-aggregates-of-diazotrophic-unicellular-cyanobacteria
#20
Elizabeth G Wilbanks, Verena Salman-Carvalho, Ulrike Jaekel, Parris T Humphrey, Jonathan A Eisen, Daniel H Buckley, Stephen H Zinder
Microbial interactions driving key biogeochemical fluxes often occur within multispecies consortia that form spatially heterogeneous microenvironments. Here, we describe the "green berry" consortia of the Sippewissett salt marsh (Falmouth, MA, United States): millimeter-sized aggregates dominated by an uncultured, diazotrophic unicellular cyanobacterium of the order Chroococcales (termed GB-CYN1). We show that GB-CYN1 is closely related to Crocosphaera watsonii (UCYN-B) and "Candidatus Atelocyanobacterium thalassa" (UCYN-A), two groups of unicellular diazotrophic cyanobacteria that play an important role in marine primary production...
2017: Frontiers in Microbiology
keyword
keyword
43010
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"