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Shotgun metagenomics

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https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#1
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731470/a-genomic-perspective-on-stoichiometric-regulation-of-soil-carbon-cycling
#2
Wyatt H Hartman, Rongzhong Ye, William R Horwath, Susannah G Tringe
Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5-25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28730710/the-molecular-ecology-of-microcystis-sp-blooms-in-the-san-francisco-estuary-delta
#3
Timothy G Otten, Hans W Paerl, Theo W Dreher, Wim J Kimmerer, Alex E Parker
Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000's and their rise has coincided with substantial decreases in several important fish species. We sought to investigate direct and indirect effects Microcystis blooms may have on the Delta food web. The Microcystis population was tracked for two years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including six different microcystin-producing strains...
July 20, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28720679/potential-for-monitoring-gut-microbiota-for-diagnosing-infections-and-graft-versus-host-disease-in-cancer-and-stem-cell-transplant-patients
#4
Andrew Y Koh
BACKGROUND: Gut microbiota, the collective community of microorganisms inhabiting the intestine, have been shown to provide many beneficial functions for the host. Recent advances in next-generation sequencing and advanced molecular biology approaches have allowed researchers to identify gut microbiota signatures associated with disease processes and, in some cases, establish causality and elucidate underlying mechanisms. CONTENT: This report reviews 3 commonly used methods for studying the gut microbiota and microbiome (the collective genomes of the gut microorganisms): 16S rRNA gene sequencing, bacterial group or species-specific quantitative polymerase chain reaction (qPCR), and metagenomic shotgun sequencing (MSS)...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28719637/microbiome-overview-in-swine-lungs
#5
Franciele Maboni Siqueira, Esteban Pérez-Wohlfeil, Fabíola Marques Carvalho, Oswaldo Trelles, Irene Silveira Schrank, Ana Tereza Ribeiro Vasconcelos, Arnaldo Zaha
Mycoplasma hyopneumoniae is the etiologic agent of swine enzootic pneumonia. However other mycoplasma species and secondary bacteria are found as inhabitants of the swine respiratory tract, which can be also related to disease. In the present study we have performed a total DNA metagenomic analysis from the lungs of pigs kept in a field condition, with suggestive signals of enzootic pneumonia and without any infection signals to evaluate the bacteria variability of the lungs microbiota. Libraries from metagenomic DNA were prepared and sequenced using total DNA shotgun metagenomic pyrosequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28709472/potential-and-active-functions-in-the-gut-microbiota-of-a-healthy-human-cohort
#6
Alessandro Tanca, Marcello Abbondio, Antonio Palomba, Cristina Fraumene, Valeria Manghina, Francesco Cucca, Edoardo Fiorillo, Sergio Uzzau
BACKGROUND: The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28700218/response-of-soil-microbial-communities-to-elevated-antimony-and-arsenic-contamination-indicates-the-relationship-between-the-innate-microbiota-and-contaminant-fractions
#7
Weimin Sun, Enzong Xiao, Tangfu Xiao, Valdis Krumins, Qi Wang, Max M Haggblom, Yiran Dong, Song Tang, Min Hu, Baoqin Li, Bingqing Xia, Wei Liu
Mining of sulfide ore deposits containing metalloids, such as antimony and arsenic, has introduced serious soil contamination around the world, posing severe threats to food safety and human health. Hence, it is important to understand the behavior and composition of the microbial communities that control the mobilization or sequestration of these metal(loid)s. Here, we selected two sites in Southwest China with different levels of Sb and As contamination to study interactions among various Sb and As fractions and the soil microbiota, with a focus on the microbial response to metalloid contamination...
July 12, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28696003/relative-abundance-of-candidatus-tenderia-electrophaga-is-linked-to-cathodic-current-in-an-aerobic-biocathode-community
#8
Anthony P Malanoski, Baochuan Lin, Brian J Eddie, Zheng Wang, W Judson Hervey, Sarah M Glaven
Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28685163/sulfide-generation-by-dominant-halanaerobium-microorganisms-in-hydraulically-fractured-shales
#9
Anne E Booker, Mikayla A Borton, Rebecca A Daly, Susan A Welch, Carrie D Nicora, David W Hoyt, Travis Wilson, Samuel O Purvine, Richard A Wolfe, Shikha Sharma, Paula J Mouser, David R Cole, Mary S Lipton, Kelly C Wrighton, Michael J Wilkins
Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis...
July 2017: MSphere
https://www.readbyqxmd.com/read/28679656/staphylococcus-aureus-and-staphylococcus-epidermidis-strain-diversity-underlying-pediatric-atopic-dermatitis
#10
Allyson L Byrd, Clay Deming, Sara K B Cassidy, Oliver J Harrison, Weng-Ian Ng, Sean Conlan, Yasmine Belkaid, Julia A Segre, Heidi H Kong
The heterogeneous course, severity, and treatment responses among patients with atopic dermatitis (AD; eczema) highlight the complexity of this multifactorial disease. Prior studies have used traditional typing methods on cultivated isolates or sequenced a bacterial marker gene to study the skin microbial communities of AD patients. Shotgun metagenomic sequence analysis provides much greater resolution, elucidating multiple levels of microbial community assembly ranging from kingdom to species and strain-level diversification...
July 5, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28667104/response-of-microbial-community-function-to-fluctuating-geochemical-conditions-within-a-legacy-radioactive-waste-trench-environment
#11
Xabier Vázquez-Campos, Andrew S Kinsela, Mark W Bligh, Jennifer J Harrison, Timothy E Payne, T David Waite
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels impact upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry...
June 30, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28663745/viromes-as-genetic-reservoir-for-the-microbial-communities-in-aquatic-environments-a-focus-on-antimicrobial-resistance-genes
#12
Stefano Colombo, Stefania Arioli, Eros Neri, Giulia Della Scala, Giorgio Gargari, Diego Mora
Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28662396/stormwater-loadings-of-antibiotic-resistance-genes-in-an-urban-stream
#13
Emily Garner, Romina Benitez, Emily von Wagoner, Richard Sawyer, Erin Schaberg, W Cully Hession, Leigh-Anne H Krometis, Brian D Badgley, Amy Pruden
Antibiotic resistance presents a critical public health challenge and the transmission of antibiotic resistance via environmental pathways continues to gain attention. Factors driving the spread of antibiotic resistance genes (ARGs) in surface water and sources of ARGs in urban stormwater have not been well-characterized. In this study, five ARGs (sul1, sul2, tet(O), tet(W), and erm(F)) were quantified throughout the duration of three storm runoff events in an urban inland stream. Storm loads of all five ARGs were significantly greater than during equivalent background periods...
June 19, 2017: Water Research
https://www.readbyqxmd.com/read/28655159/two-distinct-metacommunities-characterize-the-gut-microbiota-in-crohn-s-disease-patients
#14
Qing He, Yuan Gao, Zhuye Jie, Xinlei Yu, Janne Marie Laursen, Liang Xiao, Ying Li, Lingling Li, Faming Zhang, Qiang Feng, Xiaoping Li, Jinghong Yu, Chuan Liu, Ping Lan, Ting Yan, Xin Liu, Xun Xu, Huanming Yang, Jian Wang, Lise Madsen, Susanne Brix, Jianping Wang, Karsten Kristiansen, Huijue Jia
Background: The inflammatory intestinal disorder Crohn's disease (CD) has become a health challenge worldwide. The gut microbiota closely interacts with the host immune system, but its functional impact in CD is unclear. Except for studies on a small number of CD patients, analyses of the gut microbiota in CD have used 16S rDNA amplicon sequencing. Here we employed metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of the CD microbiota, comprising also unannotated bacteria, and investigated its modulation by exclusive enteral nutrition (EEN)...
June 26, 2017: GigaScience
https://www.readbyqxmd.com/read/28649415/unexplored-diversity-and-strain-level-structure-of-the-skin-microbiome-associated-with-psoriasis
#15
Adrian Tett, Edoardo Pasolli, Stefania Farina, Duy Tin Truong, Francesco Asnicar, Moreno Zolfo, Francesco Beghini, Federica Armanini, Olivier Jousson, Veronica De Sanctis, Roberto Bertorelli, Giampiero Girolomoni, Mario Cristofolini, Nicola Segata
Psoriasis is an immune-mediated inflammatory skin disease that has been associated with cutaneous microbial dysbiosis by culture-dependent investigations and rRNA community profiling. We applied, for the first time, high-resolution shotgun metagenomics to characterise the microbiome of psoriatic and unaffected skin from 28 individuals. We demonstrate psoriatic ear sites have a decreased diversity and psoriasis is associated with an increase in Staphylococcus, but overall the microbiomes of psoriatic and unaffected sites display few discriminative features at the species level...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28642744/unexpected-dominance-of-elusive-acidobacteria-in-early-industrial-soft-coal-slags
#16
Carl-Eric Wegner, Werner Liesack
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28631400/effects-of-uranium-concentration-on-microbial-community-structure-and-functional-potential
#17
Brodie Sutcliffe, Anthony A Chariton, Andrew J Harford, Grant C Hose, Greenfield Paul, Liam D H Elbourne, Yalchin Oytam, Sarah Stephenson, David J Midgley, Ian T Paulsen
Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0 - 4,000 mg U/kg), with the study design maximising the advantages of both field surveys and laboratory manipulative studies...
June 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28625983/strain-level-metagenomic-analysis-of-the-fermented-dairy-beverage-nunu-highlights-potential-food-safety-risks
#18
Aaron M Walsh, Fiona Crispie, Kareem Daari, Orla O'Sullivan, Jennifer C Martin, Cornelius T Arthur, Marcus J Claesson, Karen P Scott, Paul D Cotter
The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole metagenome assembly, which is a computationally demanding process. Here, we demonstrate that three short read alignment-based methods, MetaMLST, PanPhlAn, and StrainPhlAn, can accurately, and rapidly, identify pathogenic strains in spinach metagenomes which were intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28618206/grazing-of-leaf-associated-cercomonads-protists-rhizaria-cercozoa-structures-bacterial-community-composition-and-function
#19
Sebastian Flues, David Bass, Michael Bonkowski
Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation upon bacteria...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28606169/profound-perturbation-induced-by-triclosan-exposure-in-mouse-gut-microbiome-a-less-resilient-microbial-community-with-elevated-antibiotic-and-metal-resistomes
#20
Bei Gao, Pengcheng Tu, Xiaoming Bian, Liang Chi, Hongyu Ru, Kun Lu
BACKGROUND: Environmental chemical-induced perturbations of gut microbiome are associated with a series of adverse health outcomes. The effects of triclosan on human health have been controversial in recent years. The purpose of this study is to investigate the functional impact of triclosan on the mouse gut microbiome and the link between triclosan exposure and resistomes in gut bacteria. METHODS: We combined 16S rRNA gene sequencing and shotgun metagenomics sequencing to examine the compositional and functional impact of triclosan exposure on the gut microbiota of C57BL/6 mice...
June 12, 2017: BMC Pharmacology & Toxicology
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