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https://www.readbyqxmd.com/read/28813450/oral-microbial-community-assembly-under-the-influence-of-periodontitis
#1
Hongju Chen, Shuting Peng, Lin Dai, Quan Zou, Bin Yi, Xianghong Yang, Zhanshan Sam Ma
Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis...
2017: PloS One
https://www.readbyqxmd.com/read/28812643/a-submarine-volcanic-eruption-leads-to-a-novel-microbial-habitat
#2
Roberto Danovaro, Miquel Canals, Michael Tangherlini, Antonio Dell'Anno, Cristina Gambi, Galderic Lastras, David Amblas, Anna Sanchez-Vidal, Jaime Frigola, Antoni M Calafat, Rut Pedrosa-Pàmies, Jesus Rivera, Xavier Rayo, Cinzia Corinaldesi
Submarine volcanic eruptions are major catastrophic events that allow investigation of the colonization mechanisms of newly formed seabed. We explored the seafloor after the eruption of the Tagoro submarine volcano off El Hierro Island, Canary Archipelago. Near the summit of the volcanic cone, at about 130 m depth, we found massive mats of long, white filaments that we named Venus's hair. Microscopic and molecular analyses revealed that these filaments are made of bacterial trichomes enveloped within a sheath and colonized by epibiotic bacteria...
April 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811246/microbial-metagenomics-mock-scenario-based-sample-simulation-m3s3
#3
Yair Motro, Jacob Moran-Gilad
OBJECTIVES: Shotgun sequencing in increasingly applied in clinical microbiology for unbiased culture-independent diagnosis. While software solutions for metagenomics proliferate, integration of metagenomics in clinical care, requires method standardisation and validation. Virtual metagenomics samples could underpin validation by substituting real samples and thus we sought to develop a novel solution for simulation of metagenomics samples based on user-defined clinical scenarios. METHODS: We designed the Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3) workflow, which allows users to generate virtual samples from raw reads or assemblies...
August 12, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28811148/metagenomes-from-deep-baltic-sea-sediments-reveal-how-past-and-present-environmental-conditions-determine-microbial-community-composition
#4
Ian P G Marshall, Søren M Karst, Per H Nielsen, Bo Barker Jørgensen
Microbial communities that lived near the sediment surface in the past become slowly buried and are the source of deep subsurface communities thousands of years later. We used metagenomes to analyse how the composition of buried microbial communities may change to conform to altered environmental conditions at depth. Sediment samples were collected from down to 85m below sea floor during the Integrated Ocean Drilling Program Expedition 347, "Baltic Sea Paleoenvironment". The sediments vary in age, organic carbon content, porewater salinity, and other parameters that reflect the changing Baltic environment from the last ice age and throughout the Holocene...
August 12, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28810737/identification-of-the-colicin-v-bacteriocin-gene-cluster-by-functional-screening-of-a-human-microbiome-metagenomic-library
#5
Louis Cohen, Sun Han, Yun-Han Huang, Sean F Brady
The forces that shape human microbial ecology are complex. It is likely, that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli...
August 15, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28809851/grape-pomace-compost-harbors-organohalide-respiring-dehalogenimonas-species-with-novel-reductive-dehalogenase-genes
#6
Yi Yang, Steven A Higgins, Jun Yan, Burcu Şimşir, Karuna Chourey, Ramsunder Iyer, Robert L Hettich, Brett Baldwin, Dora M Ogles, Frank E Löffler
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28809429/dissection-of-the-module-network-implementation-lemontree-enhancements-towards-applications-in-metagenomics-and-translation-in-autoimmune-maladies
#7
Youtao Lu, Xiaoyuan Zhou, Christine Nardini
Under the current deluge of omics, module networks distinctively emerge as methods capable of not only identifying inherently coherent groups (modules), thus reducing dimensionality, but also hypothesizing cause-effect relationships between modules and their regulators. Module networks were first designed in the transcriptomic era and further exploited in the multi-omic context to assess (for example) miRNA regulation of gene expression. Despite a number of available implementations, expansion of module networks to other omics is constrained by a limited characterization of the solutions' (modules plus regulators) accuracy and stability - an immediate need for the better characterization of molecular biology complexity in silico...
August 15, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28808691/fluoride-depletes-acidogenic-taxa-in-oral-but-not-gut-microbial-communities-in-mice
#8
Koji Yasuda, Tiffany Hsu, Carey A Gallini, Lauren J Mclver, Emma Schwager, Andy Shi, Casey R DuLong, Randall N Schwager, Galeb S Abu-Ali, Eric A Franzosa, Wendy S Garrett, Curtis Huttenhower, Xochitl C Morgan
Fluoridation of drinking water and dental products prevents dental caries primarily by inhibiting energy harvest in oral cariogenic bacteria (such as Streptococcus mutans and Streptococcus sanguinis), thus leading to their depletion. However, the extent to which oral and gut microbial communities are affected by host fluoride exposure has been underexplored. In this study, we modeled human fluoride exposures to municipal water and dental products by treating mice with low or high levels of fluoride over a 12-week period...
July 2017: MSystems
https://www.readbyqxmd.com/read/28808230/environmental-drivers-of-a-microbial-genomic-transition-zone-in-the-ocean-s-interior
#9
Daniel R Mende, Jessica A Bryant, Frank O Aylward, John M Eppley, Torben Nielsen, David M Karl, Edward F DeLong
The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea (1,2) . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain (3-7) . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift...
August 14, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28807044/metameta-integrating-metagenome-analysis-tools-to-improve-taxonomic-profiling
#10
Vitor C Piro, Marcel Matschkowski, Bernhard Y Renard
BACKGROUND: Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28806689/fungal-diversity-of-tomme-d-orchies-cheese-during-the-ripening-process-as-revealed-by-a-metagenomic-study
#11
Alexandre Ceugniez, Bernard Taminiau, Françoise Coucheney, Philippe Jacques, Véronique Delcenserie, Georges Daube, Djamel Drider
Tomme d'Orchies is an artisanal pressed and uncooked cheese produced and marketed in the north of France. This study aimed at showing the fungal microbiota evolution of this cheese using a metagenetic based Illumina technology targeting the ITS2 domain of 5.8S fungal rDNAs. To this end, samples were taken from the rind and the core of different cheeses, after 0, 1, 3, 7, 14 and 21days of ripening. The data underpinned the prevalence of Yarrowia lipolytica and Galactomyces geotrichum for both microbiotas. Unusual species including Clavispora lusitaniae, Kazachstania unispora and Cladosporium cladosporioides were also detected, but their origins remain to be ascertained...
July 25, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28804942/metagenomic-alkaline-protease-from-mangrove-sediment
#12
Tharcilla B A Pessoa, Rachel P Rezende, Eric de Lima Silva Marques, Carlos P Pirovani, Thalis F Dos Santos, Ana C Dos Santos Gonçalves, Carla C Romano, Natielle C Dotivo, Ana C O Freitas, Luiz C Salay, João C T Dias
Functional screening of metagenomic libraries is an important tool for the discovery of new molecules. The metabolic diversity of microorganisms enables survival in harsh environments and is related to the production of enzymes. In this study, we identified a protease-producing clone from a metagenomic library derived from mangrove sediment. The protease was purified by ammonium sulphate precipitation and gel filtration chromatography, with a yield of 77.27% and a specific activity of 8.57 U μg(-1) . It had a molecular weight of approximately 70 kDa...
August 14, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28804480/microbial-community-structure-and-the-persistence-of-cyanobacterial-populations-in-salt-crusts-of-the-hyperarid-atacama-desert-from-genome-resolved-metagenomics
#13
Kari M Finstad, Alexander J Probst, Brian C Thomas, Gary L Andersen, Cecilia Demergasso, Alex Echeverría, Ronald G Amundson, Jillian F Banfield
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28803266/a-degradome-based-polymerase-chain-reaction-to-resolve-the-potential-of-environmental-samples-for-2-4-dichlorophenol-biodegradation
#14
Eslam S Ibrahim, Mona T Kashef, Tamer M Essam, Mohammed A Ramadan
A clean way to overcome environmental pollution is biodegradation. In this perspective, at the intersection of biodegradation and metagenomics, the degradome is defined as the totality of genes related to the biodegradation of a certain compound. It includes the genetic elements from both culturable and uncultured microorganisms. The possibility of assessing the biodegradation potential of an environmental samples, using a degradome-based polymerase chain reaction, was explored. 2,4-Dichlorophenol (2,4-DCP) was chosen as a model and the use of tfdB gene as a biodegradation marker was confirmed by bioinformatics study of TfdB protein...
August 12, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28803067/ppargc1a-is-upregulated-and-facilitates-lung-cancer-metastasis
#15
Jin-Dong Li, Qing-Chuan Feng, Yu Qi, Guanghui Cui, Song Zhao
Lung cancer remains a leading cause of cancer-related mortality, with metastatic progression remaining the single largest cause of lung cancer mortality. Hence it is imperative to determine reliable biomarkers for lung cancer prognosis. We performed quantitative real-time PCR (qRT-PCR) analysis to explore epithelial-mesenchymal transition (EMT) inducers that regulate EMT process in three patients with advanced lung cancer disease. Peroxisome proliferator-activated receptor gamma (PPARGC1A) was uniformly the topmost overexpressed gene in all three human non-small cell lung cancer (NSCLC) patient samples...
August 9, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28802203/disentangling-the-origins-of-virophages-and-polintons
#16
REVIEW
Samuel Campbell, Amr Aswad, Aris Katzourakis
Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts...
August 9, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28801990/degradation-of-euptox-a-by-tannase-producing-rumen-bacteria-from-migratory-goats
#17
D Sharma, G Mal, A Kannan, R Bhar, R Sharma, B Singh
AIMS: The gut microbiota capable of degrading plant biomass and anti-nutritional phytometabolites are of immense importance. This study reports isolation and characterization of tannase-producing rumen bacteria that could also degrade euptox A (9-oxo-10,11-dehydroageraphorone) present in Eupatorium adenophorum (Spreng). METHODS AND RESULTS: Migratory Gaddi goats were selected as source of inoculums for isolating rumen bacteria with ability to produce tannase which catalyzes degradation of hydrolysable tannins (HTs)...
August 12, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28800138/phylogenetically-conserved-resource-partitioning-in-the-coastal-microbial-loop
#18
Samuel Bryson, Zhou Li, Francisco Chavez, Peter K Weber, Jennifer Pett-Ridge, Robert L Hettich, Chongle Pan, Xavier Mayali, Ryan S Mueller
Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six (13)C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800137/chemical-dispersants-enhance-the-activity-of-oil-and-gas-condensate-degrading-marine-bacteria
#19
Julien Tremblay, Etienne Yergeau, Nathalie Fortin, Susan Cobanli, Miria Elias, Thomas L King, Kenneth Lee, Charles W Greer
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28799297/exploring-the-microbial-diversity-in-jordanian-hot-springs-by-comparative-metagenomic-analysis
#20
Emad I Hussein, Jacob H Jacob, Muhamad Ali K Shakhatreh, Mutaz A Abd Al-Razaq, Abdul-Salam F Juhmani, Christopher T Cornelison
A culture-independent approach was utilized in this study to reveal the microbial diversity in Jordanian hot springs represented by Ma'in and Afra hot springs. Water samples from Ma'in and Afra hot springs were collected in June 2015. The in situ temperature of water samples range was 38-59°C and the pH range was 7.4-8.4. The metagenome was extracted and analyzed using the next generation technology (bTEFAP(®) ). A total of 314,310 sequences were parsed and 288,452 were then clustered. The sequences were predominated by bacteria (>84%) and the relative abundance of archaea in each sample was <1%...
August 10, 2017: MicrobiologyOpen
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