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Metagenomics

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https://www.readbyqxmd.com/read/28319100/metagenomic-discovery-of-polybrominated-diphenyl-ether-biosynthesis-by-marine-sponges
#1
Vinayak Agarwal, Jessica M Blanton, Sheila Podell, Arnaud Taton, Michelle A Schorn, Julia Busch, Zhenjian Lin, Eric W Schmidt, Paul R Jensen, Valerie J Paul, Jason S Biggs, James W Golden, Eric E Allen, Bradley S Moore
Naturally produced polybrominated diphenyl ethers (PBDEs) pervade the marine environment and structurally resemble toxic man-made brominated flame retardants. PBDEs bioaccumulate in marine animals and are likely transferred to the human food chain. However, the biogenic basis for PBDE production in one of their most prolific sources, marine sponges of the order Dysideidae, remains unidentified. Here, we report the discovery of PBDE biosynthetic gene clusters within sponge-microbiome-associated cyanobacterial endosymbionts through the use of an unbiased metagenome-mining approach...
March 20, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28318115/microbial-players-and-processes-involved-in-phytoplankton-bloom-utilization-in-the-water-column-of-a-fast-flowing-river-dominated-estuary
#2
Maria W Smith, Lydie Herfort, Caroline S Fortunato, Byron C Crump, Holly M Simon
Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3-μm prefilter and 0...
March 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28314726/global-distribution-patterns-and-pangenomic-diversity-of-the-candidate-phylum-latescibacteria-ws3
#3
Ibrahim F Farag, Noha H Youssef, Mostafa S Elshahed
We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic datasets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene datasets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic datasets comprising 73,079 proteins...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28306234/whole-community-metagenomics-in-two-different-anammox-configurations-process-performance-and-community-structure
#4
Ananda S Bhattacharjee, Sha Wu, Christopher E Lawson, Mike S M Jetten, Vikram Kapoor, Jorge W Santo Domingo, Katherine D McMahon, Daniel R Noguera, Ramesh Goel
Anaerobic-ammonia-oxidation (anammox) combined with partial-nitritation (PN) is an innovative treatment process for energy-efficient nitrogen removal from wastewater. In this study, we used genome-based metagenomics to investigate the overall community structure and anammox species enriched in suspended growth (SGR) and attached growth packed bed (AGR) anammox reactors after 220 days of operation. Both reactors removed more than 85% of the total inorganic nitrogen. Metagenomic binning and phylogenetic analysis revealed that two anammox population genomes, affiliated with the genus 'Candidatus Brocadia', were differentially abundant between the SGR and AGR...
March 17, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28304370/identification-of-dimethylamine-monooxygenase-in-marine-bacteria-reveals-a-metabolic-bottleneck-in-the-methylated-amine-degradation-pathway
#5
Ian Lidbury, Michaela A Mausz, David J Scanlan, Yin Chen
Methylated amines (MAs) are ubiquitous in the marine environment and their subsequent flux into the atmosphere can result in the formation of aerosols and ultimately cloud condensation nuclei. Therefore, these compounds have a potentially important role in climate regulation. Using Ruegeria pomeroyi as a model, we identified the genes encoding dimethylamine (DMA) monooxygenase (dmmABC) and demonstrate that this enzyme degrades DMA to monomethylamine (MMA). Although only dmmABC are required for enzyme activity in recombinant Escherichia coli, we found that an additional gene, dmmD, was required for the growth of R...
March 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28304358/a-pelagic-microbiome-viruses-to-protists-from-a-small-cup-of-seawater
#6
Flavia Flaviani, Declan C Schroeder, Cecilia Balestreri, Joanna L Schroeder, Karen Moore, Konrad Paszkiewicz, Maya C Pfaff, Edward P Rybicki
The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment...
March 17, 2017: Viruses
https://www.readbyqxmd.com/read/28303907/crystal-structure-of-a-raw-starch-degrading-bacterial-%C3%AE-amylase-belonging-to-subfamily-37-of-the-glycoside-hydrolase-family-gh13
#7
Yanhong Liu, Jigang Yu, Fudong Li, Hui Peng, Xuecheng Zhang, Yazhong Xiao, Chao He
Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302791/genomic-characterization-of-three-melon-necrotic-spot-viruses-detected-in-human-stool-specimens
#8
Rachel Marine, Christina Castro, Laura Magaña, Terry Fei Fan Ng, Kshama Aswath, Nikail Collins, Geun Woo Park, Jan Vinjé, M Steven Oberste
The complete coding sequences of three melon necrotic spot viruses (MNSVs) were obtained from viral metagenomics of stool samples from patients with acute gastroenteritis. These genomes were most similar to Spanish strains sequenced in 2003 and a novel MNSV watermelon strain in 2014.
March 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28302781/genome-sequence-of-cauliflower-mosaic-virus-identified-in-earwigs-doru-luteipes-through-a-metagenomic-approach
#9
Márcio Tadeu Godinho, Débora Pires Paula, Arvind Varsani, Simone Graça Ribeiro
Here we report the first complete genome sequence of a cauliflower mosaic virus from Brazil, obtained from the gut content of the predator earwig (Doru luteipes). This virus has a genome of 8,030 nucleotides (nt) and shares 97% genome-wide identity with an isolate from Argentina.
March 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28302780/draft-genome-sequence-of-pseudomonas-sp-bdal1-reconstructed-from-a-bakken-shale-hydraulic-fracturing-produced-water-storage-tank-metagenome
#10
Daniel Lipus, Daniel Ross, Kyle Bibby, Djuna Gulliver
We report the 5,425,832 bp draft genome of Pseudomonas sp. strain BDAL1, recovered from a Bakken shale hydraulic fracturing-produced water tank metagenome. Genome annotation revealed several key biofilm formation genes and osmotic stress response mechanisms necessary for survival in hydraulic fracturing-produced water.
March 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28298908/serpentinization-influenced-groundwater-harbors-extremely-low-diversity-microbial-communities-adapted-to-high-ph
#11
Katrina I Twing, William J Brazelton, Michael D Y Kubo, Alex J Hyer, Dawn Cardace, Tori M Hoehler, Tom M McCollom, Matthew O Schrenk
Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28298430/metaspades-a-new-versatile-metagenomic-assembler
#12
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, as-sembly of metagenomic data remains challenging thus stifling biological discoveries. Moreover, re-cent studies revealed that complex bacterial populations may be composed from dozens of related strains thus further amplifying the challenge metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes...
March 15, 2017: Genome Research
https://www.readbyqxmd.com/read/28293553/pcr-primer-design-for-16s-rrnas-for-experimental-horizontal-gene-transfer-test-in-escherichia-coli
#13
Kentaro Miyazaki, Mitsuharu Sato, Miyuki Tsukuda
We recently demonstrated that the Escherichia coli ribosome is robust enough to accommodate foreign 16S rRNAs from diverse gamma- and betaproteobacteria bacteria (Kitahara et al., 2012). Therein, we used the common universal primers Bac8f and UN1541r to obtain a nearly full-length gene. However, we noticed that these primers overlap variable sites at 19[A/C] and 1527[U/C] in Bac8f and UN1541r, respectively, and thus, the amplicon could contain mutations. This is problematic, particularly for the former site, because the 19th nucleotide pairs with the 916th nucleotide, which is a part of the "central pseudoknot" and is critical for function...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/28292322/revealing-large-metagenomic-regions-through-long-dna-fragment-hybridization-capture
#14
Cyrielle Gasc, Pierre Peyret
BACKGROUND: High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies...
March 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28290701/identification-of-pyridinium-with-three-indole-moieties-as-an-antimicrobial-agent
#15
Masahiro Okada, Tomotoshi Sugita, Chin Piow Wong, Toshiyuki Wakimoto, Ikuro Abe
A novel pyridinium with three indole moieties, tricepyridinium, was obtained from the culture of an Escherichia coli clone incorporating metagenomic libraries from the marine sponge Discodermia calyx. For the important structural elements of tricepyridinium to be investigated for antibacterial activity, tricepyridinium and its analogues were chemically synthesized. Tricepyridinium had antimicrobial activity, but not against E. coli, and cytotoxicity against P388 cells. Additional bioassays with its synthetic analogues revealed that the intriguing combination of the indole moieties, most likely derived from three tryptamines, as well as the pyridinium moiety were chiefly responsible for its potent biological activities...
March 14, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28289604/metagenome-analysis-of-the-root-endophytic-microbial-community-of-indian-rice-o-sativa-l
#16
Subhadipa Sengupta, Sayak Ganguli, Pankaj K Singh
This study reports the root endophytic microbial community profile in rice (Oryza sativa L.), the largest food crop of Asia, using 16S rRNA gene amplicon sequencing. Metagenome of OS01 and OS04 consisted of 11,17,900 sequences with 300 Mbp size and average 55.6% G + C content. Data of this study are available at NCBI Bioproject (PRJNA360379). The taxonomic analysis of 843 OTU's showed that the sequences belonged to four major phyla revealing dominance of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28289564/binsanity-unsupervised-clustering-of-environmental-microbial-assemblies-using-coverage-and-affinity-propagation
#17
Elaina D Graham, John F Heidelberg, Benjamin J Tully
Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of 'binning' contigs into phylogenetically related units or putative genomes...
2017: PeerJ
https://www.readbyqxmd.com/read/28288568/deep-sequencing-of-hpv-e6-e7-genes-reveals-loss-of-genotypic-diversity-and-gain-of-clonal-dominance-in-high-grade-intraepithelial-lesions-of-the-cervix
#18
Jane Shen-Gunther, Yufeng Wang, Zhao Lai, Graham M Poage, Luis Perez, Tim H M Huang
BACKGROUND: Human papillomavirus (HPV) is the carcinogen of almost all invasive cervical cancer and a major cause of oral and other anogenital malignancies. HPV genotyping by dideoxy (Sanger) sequencing is currently the reference method of choice for clinical diagnostics. However, for samples with multiple HPV infections, genotype identification is singular and occasionally imprecise or indeterminable due to overlapping chromatograms. Our aim was to explore and compare HPV metagenomes in abnormal cervical cytology by deep sequencing for correlation with disease states...
March 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28287094/enlightening-discriminative-network-functional-modules-behind-principal-component-analysis-separation-in-differential-omic-science-studies
#19
Sara Ciucci, Yan Ge, Claudio Durán, Alessandra Palladini, Víctor Jiménez-Jiménez, Luisa María Martínez-Sánchez, Yuting Wang, Susanne Sales, Andrej Shevchenko, Steven W Poser, Maik Herbig, Oliver Otto, Andreas Androutsellis-Theotokis, Jochen Guck, Mathias J Gerl, Carlo Vittorio Cannistraci
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28285599/microbiome-and-metabolome-modifying-effects-of-several-cardiovascular-disease-interventions-in-apo-e-mice
#20
Paul M Ryan, Lis E E London, Trent C Bjorndahl, Rupasri Mandal, Kiera Murphy, Gerald F Fitzgerald, Fergus Shanahan, R Paul Ross, David S Wishart, Noel M Caplice, Catherine Stanton
BACKGROUND: There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositional and functional effects of several nutritional, neutraceutical, and pharmaceutical cardiovascular disease interventions on the gut microbiome, through metagenomic and metabolomic approaches. Apolipoprotein-E-deficient mice were fed for 24 weeks either high-fat/cholesterol diet alone (control, HFC) or high-fat/cholesterol in conjunction with one of three dietary interventions, as follows: plant sterol ester (PSE), oat β-glucan (OBG) and bile salt hydrolase-active Lactobacillus reuteri APC 2587 (BSH), or the drug atorvastatin (STAT)...
March 13, 2017: Microbiome
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