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https://www.readbyqxmd.com/read/29684641/methodological-considerations-for-the-identification-of-choline-and-carnitine-degrading-bacteria-in-the-gut
#1
REVIEW
Eleanor Jameson, Mussa Quareshy, Yin Chen
The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut...
April 19, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29683411/microbial-community-composition-and-methanogens-biodiversity-during-a-temperature-shift-in-a-methane-fermentation-chamber
#2
Anna Banach, Slawomir Ciesielski, Tomasz Bacza, Marek Pieczykolan, Aleksandra Ziembińska-Buczyńska
More information on the connection between anaerobic digestion parameters and composition of the microbial community involved in the anaerobic digestion process is required to gain a better understanding of how a bioreactor functions. The aim of this study was to analyse the composition of microbial communities and the dynamics of methanogens' biodiversity changes during the shift from mesophilic (38 °C) to thermophilic (55 °C) conditions during biogas production. The total microbial composition was examined via the metagenomic approach based on 16S rRNA gene sequencing, whereas the methanogen communities were analysed using PCR-DGGE (Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis) of mcrA...
April 23, 2018: Environmental Technology
https://www.readbyqxmd.com/read/29682427/natural-history-bycatch-a-pipeline-for-identifying-metagenomic-sequences-in-radseq-data
#3
Iris Holmes, Alison R Davis Rabosky
Background: Reduced representation genomic datasets are increasingly becoming available from a variety of organisms. These datasets do not target specific genes, and so may contain sequences from parasites and other organisms present in the target tissue sample. In this paper, we demonstrate that (1) RADseq datasets can be used for exploratory analysis of tissue-specific metagenomes, and (2) tissue collections house complete metagenomic communities, which can be investigated and quantified by a variety of techniques...
2018: PeerJ
https://www.readbyqxmd.com/read/29680562/microbial-community-and-metagenome-dynamics-during-biodegradation-of-dispersed-oil-reveals-potential-key-players-in-cold-norwegian-seawater
#4
Deni Ribicic, Roman Netzer, Terry C Hazen, Stephen M Techtmann, Finn Drabløs, Odd Gunnar Brakstad
Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation...
April 2018: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/29679832/natural-revegetation-of-a-semiarid-habitat-alters-taxonomic-and-functional-diversity-of-soil-microbial-communities
#5
Yanqing Guo, Xiaotian Chen, Yuanyuan Wu, Lu Zhang, Jimin Cheng, Gehong Wei, Yanbing Lin
Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China...
April 18, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29679417/a-probiotic-modulates-the-microbiome-and-immunity-in-multiple-sclerosis
#6
Stephanie K Tankou, Keren Regev, Brian C Healy, Emily Tjon, Luca Laghi, Laura M Cox, Pia Kivisäkk, Isabelle V Pierre, Hrishikesh Lokhande, Roopali Gandhi, Sandra Cook, Bonnie Glanz, James Stankiewicz, Howard L Weiner
OBJECTIVE: Effect of a probiotic on the gut microbiome and peripheral immune function in healthy controls and relapsing-remitting multiple sclerosis (RRMS) patients. METHODS: MS patients (N=9) and controls (N=13) were orally administered a probiotic containing Lactobacillus, Bifidobacterium and Streptococcus twice daily for two months. Blood and stool specimens were collected at baseline, after completion of the 2-month treatment, and 3 months after discontinuation of therapy...
April 20, 2018: Annals of Neurology
https://www.readbyqxmd.com/read/29678199/megan-lr-new-algorithms-allow-accurate-binning-and-easy-interactive-exploration-of-metagenomic-long-reads-and-contigs
#7
Daniel H Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic, Rohan B H Williams
BACKGROUND: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets...
April 20, 2018: Biology Direct
https://www.readbyqxmd.com/read/29678163/comparison-of-normalization-methods-for-the-analysis-of-metagenomic-gene-abundance-data
#8
Mariana Buongermino Pereira, Mikael Wallroth, Viktor Jonsson, Erik Kristiansson
BACKGROUND: In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional differences between the communities can be identified. However, gene abundance data is affected by high levels of systematic variability, which can greatly reduce the statistical power and introduce false positives. Normalization, which is the process where systematic variability is identified and removed, is therefore a vital part of the data analysis...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29677111/genome-characterization-of-a-pathogenic-porcine-rotavirus-b-strain-identified-in-buryat-republic-russia-in-2015
#9
Konstantin P Alekseev, Aleksey A Penin, Alexey N Mukhin, Kizkhalum M Khametova, Tatyana V Grebennikova, Anton G Yuzhakov, Anna S Moskvina, Maria I Musienko, Sergey A Raev, Alexandr M Mishin, Alexandr P Kotelnikov, Oleg A Verkhovsky, Taras I Aliper, Eugeny A Nepoklonov, Diana M Herrera-Ibata, Frances K Shepherd, Douglas G Marthaler
An outbreak of enteric disease of unknown etiology with 60% morbidity and 8% mortality in weaning piglets occurred in November 2015 on a farm in Buryat Republic, Russia. Metagenomic sequencing revealed the presence of rotavirus B in feces from diseased piglets while no other pathogens were identified. Clinical disease was reproduced in experimentally infected piglets, yielding the 11 RVB gene segments for strain Buryat15, with an RVB genotype constellation of G12-P[4]-I13-R4-C4-M4-A8-N10-T4-E4-H7. This genotype constellation has also been identified in the United States...
April 20, 2018: Pathogens
https://www.readbyqxmd.com/read/29676472/the-first-taxus-rhizosphere-microbiome-revealed-by-shotgun-metagenomic-sequencing
#10
Da-Cheng Hao, Cai-Rong Zhang, Pei-Gen Xiao
In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539)...
April 20, 2018: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29675014/the-resistome-of-low-impacted-marine-environments-is-composed-by-distant-metallo-%C3%AE-lactamases-homologs
#11
Erica L Fonseca, Bruno G N Andrade, Ana C P Vicente
The worldwide dispersion and sudden emergence of new antibiotic resistance genes (ARGs) determined the need in uncovering which environment participate most as their source and reservoir. ARGs closely related to those currently found in human pathogens occur in the resistome of anthropogenic impacted environments. However, the role of pristine environment as the origin and source of ARGs remains underexplored and controversy, particularly, the marine environments represented by the oceans. Here, due to the ocean nature, we hypothesized that the resistome of this pristine/low-impacted marine environment is represented by distant ARG homologs...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29674608/culturing-of-female-bladder-bacteria-reveals-an-interconnected-urogenital-microbiota
#12
Krystal Thomas-White, Samuel C Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D Stares, Evann E Hilt, Travis K Price, Alan J Wolfe, Trevor D Lawley
Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota...
April 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29673787/optimisation-of-protocol-for-effective-detachment-and-selective-recovery-of-the-representative-bacteria-for-extraction-of-metagenomic-dna-from-eucalyptus-spp-woodchips
#13
Chika F Nnadozie, Johnson Lin, Roshini Govinden
For some environments such as planktonic/aqueous environments, the separation of bacteria cells from eukaryotic cells prior to DNA extraction using filtration is relatively straightforward. However, for woodchips, the bacteria are attached/embedded within the wood matrix, which prevents easy removal of bacterial cells. In this study, a method for the selective extraction of DNA from bacteria inhabiting Eucalyptus spp. woodchips has been developed. The objective was to compare milled and unmilled woodchips processed via three detachment methods, viz...
April 16, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29672704/homologous-recombination-and-transposon-propagation-shape-the-population-structure-of-an-organism-from-the-deep-subsurface-with-minimal-metabolism
#14
Alexander J Probst, Jillian F Banfield
DPANN archaea are primarily known based on genomes from metagenomes and single cells. We reconstructed a complete population genome for Candidatus "Forterrea," a Diapherotrite with a predicted symbiotic lifestyle probably centered around nucleotide metabolism and RuBisCO. Genome-wide analysis of sequence variation provided insights into the processes that shape its population structure in the deep subsurface. The genome contains many transposons, yet reconstruction of a complete genome from a short-read insert data set was possible because most occurred only in some individuals...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29672703/phylogenomic-analysis-of-%C3%AE-lactamase-in-archaea-and-bacteria-enables-the-identification-of-putative-new-members
#15
Vivek Keshri, Arup Panda, Anthony Levasseur, Jean-Marc Rolain, Pierre Pontarotti, Didier Raoult
β-lactamases are enzymes which are commonly produced by bacteria and which degrade the β-lactam ring of β-lactam antibiotics, namely penicillins, cephalosporins, carbapenems, and monobactams, and inactivate these antibiotics. We performed a rational and comprehensive investigation of β-lactamases in different biological databases. In this study, we constructed hidden Markov model profiles as well as the ancestral sequence of four classes of β-lactamases (A, B, C, and D), which were used to identify potential β-lactamases from environmental metagenomic (1206), human microbiome metagenomic (6417), human microbiome reference genome (1310), and NCBI's nonredundant databases (44101)...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29672169/functional-bla-kpc-2-sequences-are-present-in-u-s-beef-cattle-feces-regardless-of-antibiotic-use
#16
Amit Vikram, John W Schmidt
Carbapenems are classified as critically important antibiotics since they are employed when resistant Gram-negative bacterial infections fail to respond to other antibiotic therapies. Carbapenem-resistant bacteria (CRB) were traditionally understood to be rare in the U.S. food-producing animals. Recently, using quantitative polymerase chain reaction (qPCR), our group detected blaKPC-2 in all 72 metagenomic DNA (mgDNA) samples prepared from the feces of 36 lots of beef cattle "raised without antibiotics" (RWA) and 36 lots raised "conventionally" (CONV)...
April 19, 2018: Foodborne Pathogens and Disease
https://www.readbyqxmd.com/read/29670596/metagenomic-insights-into-the-microbial-community-and-nutrient-cycling-in-the-western-subarctic-pacific-ocean
#17
Yingdong Li, Hongmei Jing, Xiaomin Xia, Shunyan Cheung, Koji Suzuki, Hongbin Liu
The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales , and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29670191/fecal-microbiota-transplantation-reverses-antibiotic-and-chemotherapy-induced-gut-dysbiosis-in-mice
#18
Quentin Le Bastard, Tonya Ward, Dimitri Sidiropoulos, Benjamin M Hillmann, Chan Lan Chun, Michael J Sadowsky, Dan Knights, Emmanuel Montassier
Fecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection, but has been less studied as a means to restore microbiome diversity and composition following antibiotic or chemotherapy treatments. The purpose of our study was to assess the efficacy of FMT to reverse antibiotic- and chemotherapy-induced gut dysbiosis in a mouse model. C57BL/6J mice were treated with ampicillin for 1 week and/or received a single intraperitoneal injection of 5-Fluorouracil. Fresh stool was collected and analyzed using shotgun metagenomics and the Illumina sequencing platform...
April 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29669589/similarity-of-the-dog-and-human-gut-microbiomes-in-gene-content-and-response-to-diet
#19
Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Robert Hayward, Sofia K Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R Jackson, Qinghong Li, Peer Bork
BACKGROUND: Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs. RESULTS: We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data)...
April 19, 2018: Microbiome
https://www.readbyqxmd.com/read/29669298/bioproduction-and-characterization-of-extracellular-melanin-like-pigment-from-industrially-polluted-metagenomic-library-equipped-escherichia-coli
#20
Shivani Amin, Rajesh P Rastogi, Ravi R Sonani, Arabinda Ray, Rakesh Sharma, Datta Madamwar
To explore the potential genes from the industrially polluted Amlakhadi canal, located in Ankleshwar, Gujarat, India, its community genome was extracted and cloned into E. coli EPI300™-T1R using a fosmid vector (pCC2 FOS™) generating a library of 3,92,000 clones with average size of 40kb of DNA-insert. From this library, the clone DM1 producing brown colored melanin-like pigment was isolated and characterized. For over expression of the pigment, further sub-cloning of the clone DM1 was done. Sub-clone containing 10kb of the insert was sequenced for gene identification...
April 15, 2018: Science of the Total Environment
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