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Metagenomics

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/29155880/molecular-characterization-of-novel-mosquito-borne-rickettsia-spp-from-mosquitoes-collected-at-the-demilitarized-zone-of-the-republic-of-korea
#15
Alice N Maina, Terry A Klein, Heung-Chul Kim, Sung-Tae Chong, Yu Yang, Kristin Mullins, Ju Jiang, Heidi St John, Richard G Jarman, Jun Hang, Allen L Richards
Rickettsiae are associated with a diverse range of invertebrate hosts. Of these, mosquitoes could emerge as one of the most important vectors because of their ability to transmit significant numbers of pathogens and parasites throughout the world. Recent studies have implicated Anopheles gambiae as a potential vector of Rickettsia felis. Herein we report that a metagenome sequencing study identified rickettsial sequence reads in culicine mosquitoes from the Republic of Korea. The detected rickettsiae were characterized by a genus-specific quantitative real-time PCR assay and sequencing of rrs, gltA, 17kDa, ompB, and sca4 genes...
2017: PloS One
https://www.readbyqxmd.com/read/29155322/digestive-tract-colonization-by-multidrug-resistant-enterobacteriaceae-in-travellers-an-update
#16
REVIEW
Etienne Ruppé, Antoine Andremont, Laurence Armand-Lefèvre
BACKGROUND: Enterobacteriaceae have become increasingly resistant, especially due to the acquisition and spread of extended-spectrum beta-lactamases (ESBLs), which confer resistance to the majority of beta-lactams. Multi-resistant Enterobacteriaceae (MRE) were first isolated in hospitals, but now they are disseminating in the community setting, mostly in low and middle income countries. Consequently, the increasing number of international travels leads to the importation of MRE from high-prevalence to low-prevalence countries...
November 16, 2017: Travel Medicine and Infectious Disease
https://www.readbyqxmd.com/read/29155257/contrasting-the-microbiomes-from-forest-rhizosphere-and-deeper-bulk-soil-from-an-amazon-rainforest-reserve
#17
Jose Pedro Fonseca, Luisa Hoffmann, Bianca Catarina Azeredo Cabral, Victor Hugo Giordano Dias, Marcio Rodrigues Miranda, Allan Cezar de Azevedo Martins, Clarissa Boschiero, Wanderley Rodrigues Bastos, Rosane Silva
Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach...
November 15, 2017: Gene
https://www.readbyqxmd.com/read/29154906/increase-in-taxonomic-assignment-efficiency-of-viral-reads-in-metagenomic-studies
#18
S François, D Filloux, M Frayssinet, P Roumagnac, D P Martin, M Ogliastro, R Froissart
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms...
November 14, 2017: Virus Research
https://www.readbyqxmd.com/read/29153320/novel-microbial-diversity-and-functional-potential-in-the-marine-mammal-oral-microbiome
#19
Natasha K Dudek, Christine L Sun, David Burstein, Rose S Kantor, Daniela S Aliaga Goltsman, Elisabeth M Bik, Brian C Thomas, Jillian F Banfield, David A Relman
The vast majority of bacterial diversity lies within phylum-level lineages called "candidate phyla," which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum...
November 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29152585/total-lipopolysaccharide-from-the-human-gut-microbiome-silences-toll-like-receptor-signaling
#20
Eva d'Hennezel, Sahar Abubucker, Leon O Murphy, Thomas W Cullen
Cohabitation of microbial communities with the host enables the formation of a symbiotic relationship that maintains homeostasis in the gut and beyond. One prevailing model suggests that this relationship relies on the capacity of host cells and tissues to remain tolerant to the strong immune stimulation generated by the microbiota such as the activation of Toll-like receptor 4 (TLR4) pathways by lipopolysaccharide (LPS). Indeed, gut microbial LPS is thought to be one of the most potent activators of innate immune signaling and an important mediator of the microbiome's influence on host physiology...
November 2017: MSystems
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