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https://www.readbyqxmd.com/read/29165368/human-protoparvoviruses
#1
REVIEW
Elina Väisänen, Yu Fu, Klaus Hedman, Maria Söderlund-Venermo
Next-generation sequencing and metagenomics have revolutionized the discovery of novel viruses. In recent years, three novel protoparvoviruses have been discovered in fecal samples of humans: bufavirus (BuV) in 2012, tusavirus (TuV) in 2014, and cutavirus (CuV) in 2016. BuV has since been studied the most, disclosing three genotypes that also represent serotypes. Besides one nasal sample, BuV DNA has been found exclusively in diarrheal feces, but not in non-diarrheal feces, suggesting a causal relationship...
November 22, 2017: Viruses
https://www.readbyqxmd.com/read/29163505/il17escan-a-tool-for-the-identification-of-peptides-inducing-il-17-response
#2
Sudheer Gupta, Parul Mittal, Midhun K Madhu, Vineet K Sharma
IL-17 cytokines are pro-inflammatory cytokines and are crucial in host defense against various microbes. Induction of these cytokines by microbial antigens has been investigated in the case of ischemic brain injury, gingivitis, candidiasis, autoimmune myocarditis, etc. In this study, we have investigated the ability of amino acid sequence of antigens to induce IL-17 response using machine-learning approaches. A total of 338 IL-17-inducing and 984 IL-17 non-inducing peptides were retrieved from Immune Epitope Database...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29163444/progressive-colonization-of-bacteria-and-degradation-of-rice-straw-in-the-rumen-by-illumina-sequencing
#3
Yanfen Cheng, Ying Wang, Yuanfei Li, Yipeng Zhang, Tianyi Liu, Yu Wang, Thomas J Sharpton, Weiyun Zhu
The aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and the rice straw at 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 h were collected for analysis of the bacterial community and the degradation of the rice straw. The bacterial community and the carbohydrate-active enzymes in the rumen fluid were analyzed by metagenomics...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163423/microbial-community-composition-and-functional-capacity-in-a-terrestrial-ferruginous-sulfate-depleted-mud-volcano
#4
Tzu-Hsuan Tu, Li-Wei Wu, Yu-Shih Lin, Hiroyuki Imachi, Li-Hung Lin, Pei-Ling Wang
Terrestrial mud volcanoes (MVs) are an important natural source of methane emission. The role of microbial processes in methane cycling and organic transformation in such environments remains largely unexplored. In this study, we aim to uncover functional potentials and community assemblages across geochemical transitions in a ferruginous, sulfate-depleted MV of eastern Taiwan. Geochemical profiles combined with 16S rRNA gene abundances indicated that anaerobic oxidation of methane (AOM) mediated by ANME-2a group coincided with iron/manganese reduction by Desulfuromonadales at shallow depths deprived of sulfate...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163419/reconstruction-of-diverse-verrucomicrobial-genomes-from-metagenome-datasets-of-freshwater-reservoirs
#5
Pedro J Cabello-Yeves, Rohit Ghai, Maliheh Mehrshad, Antonio Picazo, Antonio Camacho, Francisco Rodriguez-Valera
The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163388/genomic-comparison-of-two-family-level-groups-of-the-uncultivated-nag1-archaeal-lineage-from-chemically-and-geographically-disparate-hot-springs
#6
Eric D Becraft, Jeremy A Dodsworth, Senthil K Murugapiran, Scott C Thomas, J Ingemar Ohlsson, Ramunas Stepanauskas, Brian P Hedlund, Wesley D Swingley
Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29161643/effect-of-vacuum-and-modified-atmosphere-packaging-on-the-microbiological-chemical-and-sensory-properties-of-tropical-red-drum-sciaenops-ocellatus-fillets-stored-at-4%C3%A2-c
#7
Adèle Silbande, Sandra Adenet, Christine Chopin, Josiane Cornet, Juliette Smith-Ravin, Katia Rochefort, Françoise Leroi
AIMS: The effect of vacuum (VP - 4°C) and CO2/N2-atmosphere (MAP - 4°C) packaging on the quality of red drum fillets compared with whole gutted iced fish was investigated. METHODS AND RESULTS: A metagenomic approach, bacterial enumeration and isolation, biochemical and sensory analyses were carried out. The organoleptic rejection of whole fish was observed at day 15 whereas VP and MAP fillets appeared unacceptable only after 29days. At these dates, total mesophilic counts reached 10(7)-10(8)CFU g(-1)...
October 26, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29159825/modulation-of-the-intestinal-bile-acid-fxr-fgf15-axis-improves-alcoholic-liver-disease-in-mice
#8
Phillipp Hartmann, Katrin Hochrath, Angela Horvath, Peng Chen, Caroline T Seebauer, Cristina Llorente, Lirui Wang, Yazen Alnouti, Derrick E Fouts, Peter Stärkel, Rohit Loomba, Sally Coulter, Christopher Liddle, Ruth T Yu, Lei Ling, Stephen J Rossi, Alex M DePaoli, Michael Downes, Ronald M Evans, David A Brenner, Bernd Schnabl
Alcoholic liver disease is associated with changes in the intestinal microbiota. Functional consequences of alcohol-associated dysbiosis are largely unknown. The aim of this study was to identify a mechanism of how changes in the intestinal microbiota contribute to alcoholic liver disease. Metagenomic sequencing of intestinal contents demonstrated that chronic ethanol feeding in mice is associated with an overrepresentation of bacterial genomic DNA encoding choloylglycine hydrolase, which deconjugates bile acids in the intestine...
November 21, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29159590/nanovirus-alphasatellite-complex-identified-in-vicia-cracca-in-the-rh%C3%A3-ne-delta-region-of-france
#9
Romain Gallet, Simona Kraberger, Denis Filloux, Serge Galzi, Hugo Fontes, Darren P Martin, Arvind Varsani, Philippe Roumagnac
Nanoviruses are multi-component plant-infecting single-stranded DNA viruses. Using a viral metagenomics-informed approach, a new nanovirus and two associated alphasatellite molecules have been identified in an uncultivated asymptomatic Vicia cracca plant in the Rhône region of France. This novel nanovirus genome includes eight genomic components (named DNA-R, DNA-S, DNA-M, DNA-C, DNA-N, DNA-U1, DNA-U2 and DNA-U4) and, across all components, shares < 66% pairwise sequence identity with other nanovirus genomes...
November 20, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29159586/extensive-hydrolysis-of-raw-rice-starch-by-a-chimeric-%C3%AE-amylase-engineered-with-%C3%AE-amylase-amyp-and-a-starch-binding-domain-from-cryptococcus-sp-s-2
#10
Hui Peng, Rui Li, Fengling Li, Lu Zhai, Xiaohan Zhang, Yazhong Xiao, Yi Gao
Recombinant chimeric α-amylase (AmyP-Cr) was constructed by a catalytic core of α-amylase (AmyP) from a marine metagenomic library and a starch-binding domain (SBDCr) of α-amylase from Cryptococcus sp. S-2. The molecular fusion did not alter optimum pH, optimum temperature, hydrolysis products, and an ability of preferential and rapid degradation towards raw rice starch, but catalytic efficiency and thermostability were remarkably improved compared with those of the wild-type AmyP. AmyP-Cr achieved the final hydrolysis degree of 61...
November 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29159222/data-on-metagenomic-profiles-of-activated-sludge-from-a-full-scale-wastewater-treatment-plant
#11
Jianhua Guo, Bing-Jie Ni, Xiaoyu Han, Xueming Chen, Philip Bond, Yongzhen Peng, Zhiguo Yuan
The data in this article mainly present the sequences of activated sludge from a full-scale municipal wastewater treatment plant (WWTP) carrying out simultaneous nitrogen and phosphorous removal in Beijing, China. Data include the operational conditions and performance, dominant microbes and taxonomic analysis in this WWTP, and function annotation results based on SEED, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Sequencing data were generated by using Illumina HiSeq...
December 2017: Data in Brief
https://www.readbyqxmd.com/read/29158985/coral-associated-viral-communities-show-high-levels-of-diversity-and-host-auxiliary-functions
#12
Karen D Weynberg, Patrick W Laffy, Elisha M Wood-Charlson, Dmitrij Turaev, Thomas Rattei, Nicole S Webster, Madeleine J H van Oppen
Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent...
2017: PeerJ
https://www.readbyqxmd.com/read/29158944/comparative-metagenomic-analysis-of-electrogenic-microbial-communities-in-differentially-inoculated-swine-wastewater-fed-microbial-fuel-cells
#13
Irina V Khilyas, Anatoly A Sorokin, Larisa Kiseleva, David J W Simpson, V Fedorovich, Margarita R Sharipova, Mami Kainuma, Michael F Cohen, Igor Goryanin
Bioelectrochemical systems such as microbial fuel cells (MFCs) are promising new technologies for efficient removal of organic compounds from industrial wastewaters, including that generated from swine farming. We inoculated two pairs of laboratory-scale MFCs with sludge granules from a beer wastewater-treating anaerobic digester (IGBS) or from sludge taken from the bottom of a tank receiving swine wastewater (SS). The SS-inoculated MFC outperformed the IGBS-inoculated MFC with regard to COD and VFA removal and electricity production...
2017: Scientifica
https://www.readbyqxmd.com/read/29158776/genomics-and-prevalence-of-bacterial-and-archaeal-isolates-from-biogas-producing-microbiomes
#14
Irena Maus, Andreas Bremges, Yvonne Stolze, Sarah Hahnke, Katharina G Cibis, Daniela E Koeck, Yong S Kim, Jana Kreubel, Julia Hassa, Daniel Wibberg, Aaron Weimann, Sandra Off, Robbin Stantscheff, Vladimir V Zverlov, Wolfgang H Schwarz, Helmut König, Wolfgang Liebl, Paul Scherer, Alice C McHardy, Alexander Sczyrba, Michael Klocke, Alfred Pühler, Andreas Schlüter
Background: To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. Results: Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29157743/next-generation-microbiological-risk-assessment-meta-omics-the-next-need-for-integration
#15
Luca Cocolin, Marios Mataragas, Francois Bourdichon, Agapi Doulgeraki, Marie-France Pilet, Balamurugan Jagadeesan, Kalliopi Rantsiou, Trevor Phister
The development of a multi-omics approach has provided a new approach to the investigation of microbial communities allowing an integration of data, which can be used to better understand the behaviour of and interactions between community members. Metagenomics, metatranscriptomics, metaproteomics and metabolomics have the potential of producing a large amount of data in a very short time, however an important challenge is how to exploit and interpret these data to assist risk managers in food safety and quality decisions...
November 13, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29156625/gene-based-pathogen-detection-can-we-use-qpcr-to-predict-the-outcome-of-diagnostic-metagenomics
#16
Sandra Christine Andersen, Mette Sofie Rousing Fachmann, Kristoffer Kiil, Eva Møller Nielsen, Jeffrey Hoorfar
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through screening of methods, whether qPCR can be used as an indicator for the optimization of sample preparation for NGS-based shotgun metagenomics with a diagnostic focus...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29156552/diversity-of-dsdna-viruses-in-a-south-african-hot-spring-assessed-by-metagenomics-and-microscopy
#17
Olivier Zablocki, Leonardo Joaquim van Zyl, Bronwyn Kirby, Marla Trindade
The current view of virus diversity in terrestrial hot springs is limited to a few sampling sites. To expand our current understanding of hot spring viral community diversity, this study aimed to investigate the first African hot spring (Brandvlei hot spring; 60 °C, pH 5.7) by means of electron microscopy and sequencing of the virus fraction. Microscopy analysis revealed a mixture of regular- and 'jumbo'-sized tailed morphotypes (Caudovirales), lemon-shaped virions (Fuselloviridae-like; salterprovirus-like) and pleiomorphic virus-like particles...
November 18, 2017: Viruses
https://www.readbyqxmd.com/read/29156542/computational-approaches-for-integrative-analysis-of-the-metabolome-and-microbiome
#18
REVIEW
Jasmine Chong, Jianguo Xia
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies...
November 18, 2017: Metabolites
https://www.readbyqxmd.com/read/29156487/evolution-and-molecular-mechanism-of-four-electron-reducing-ferredoxin-dependent-bilin-reductases-from-oceanic-phages
#19
Benjamin Ledermann, Meike Schwan, Johannes A Sommerkamp, Eckhard Hofmann, Oded Béjà, Nicole Frankenberg-Dinkel
Ferredoxin-dependent bilin reductases (FDBRs) are a class of enzymes reducing the heme metabolite biliverdin IXα (BV) to form open-chain tetrapyrroles used for light-perception and light-harvesting in photosynthetic organisms. Thus far, seven FDBR families have been identified, each catalyzing a distinct reaction and either transferring two or four electrons from ferredoxin onto the substrate. The newest addition to the family is PcyX, originally identified from metagenomics data derived from phage. Phylogenetically, PcyA is the closest relative catalyzing the reduction of BV to phycocyanobilin...
November 20, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29156289/the-extracellular-metaproteome-of-soils-under-semiarid-climate-a-methodological-comparison-of-extraction-buffers
#20
F Bastida, N Jehmlich, I F Torres, C García
We compare the protein extraction efficiencies, as well as the phylogenetic and functional information provided, of two extraction protocols in soils that differ mainly in their organic matter and clay contents, the main factors limiting protein extraction in semiarid soils. These protocols utilise extractants commonly used for the assay of extracellular enzyme activities. The first method was based on the utilisation of the modified universal buffer (MUB). The second was based on the extraction of humic substances with sodium pyrophosphate...
November 17, 2017: Science of the Total Environment
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