keyword
MENU ▼
Read by QxMD icon Read
search

Shotgun metagenomics

keyword
https://www.readbyqxmd.com/read/28631400/effects-of-uranium-concentration-on-microbial-community-structure-and-functional-potential
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28595639/diet-shifts-provoke-complex-and-variable-changes-in-the-metabolic-networks-of-the-ruminal-microbiome
#5
Sara M Wolff, Melinda J Ellison, Yue Hao, Rebecca R Cockrum, Kathy J Austin, Michael Baraboo, Katherine Burch, Hyuk Jin Lee, Taylor Maurer, Rocky Patil, Andrea Ravelo, Tasia M Taxis, Huan Truong, William R Lamberson, Kristi M Cammack, Gavin C Conant
BACKGROUND: Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal's diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data. RESULTS: Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host...
June 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28595314/a-combined-meta-barcoding-and-shotgun-metagenomic-analysis-of-spontaneous-wine-fermentation
#6
Peter R Sternes, Danna Lee, Dariusz R Kutyna, Anthony R Borneman
Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. Commercially, there is now a growing trend away from using wine yeast ( Saccharomyces ) starter cultures, towards the historic practice of uninoculated or "wild" fermentation, where the yeasts and bacteria associated with the grapes and/or winery perform the fermentation. It is the varied metabolic contributions of these numerous non- Saccharomyces species that are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts...
June 8, 2017: GigaScience
https://www.readbyqxmd.com/read/28591831/the-gut-metagenome-changes-in-parallel-to-waist-circumference-brain-iron-deposition-and-cognitive-function
#7
Gerard Blasco, José Maria Moreno-Navarrete, Mireia Rivero, Vicente Pérez-Brocal, Josep Garre-Olmo, Josep Puig, Pepus Daunis-I-Estadella, Carles Biarnés, Jordi Gich, Fernando Fernández-Aranda, Ángel Alberich-Bayarri, Andrés Moya, Salvador Pedraza, Wifredo Ricart, Miguel López, Manuel Portero-Otin, José-Manuel Fernandez-Real
Context: Microbiota perturbations seem to exert modulatory effects on emotional behavior, stress- and pain-modulation systems in adult animals; however, limited information is available in humans. Objective: To study potential relationships among the gut metagenome, brain microstructure and cognitive performance in middle-aged, apparently healthy, obese and nonobese subjects, after weight changes. Design: This is a longitudinal study over a 2-year period...
June 7, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28585356/decreased-plant-productivity-resulting-from-plant-group-removal-experiment-constrains-soil-microbial-functional-diversity
#8
Ximei Zhang, Eric R Johnston, Albert Barberán, Yi Ren, Xiaotao Lü, Xingguo Han
Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing...
June 6, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28570584/characterisation-of-the-canine-faecal-virome-in-healthy-dogs-and-dogs-with-acute-diarrhoea-using-shotgun-metagenomics
#9
Paloma S Moreno, Josef Wagner, Caroline S Mansfield, Matthew Stevens, James R Gilkerson, Carl D Kirkwood
The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented...
2017: PloS One
https://www.readbyqxmd.com/read/28536449/effect-of-experimental-soil-disturbance-and-recovery-on-structure-and-function-of-soil-community-a-metagenomic-and-metagenetic-approach
#10
Soobeom Choi, Hokyung Song, Binu M Tripathi, Dorsaf Kerfahi, Hyoki Kim, Jonathan M Adams
There has been little study of effects of disturbance on soil biota combining closely controlled experimental conditions and DNA-based methods. We sampled pots of soil at varying times following an initial simulated mass mortality event. Soil DNA was extracted at intervals up to 24 weeks after the event, and shotgun metagenomes sequenced using NextSeq. Compared to initial conditions, we found: consistent, sequential changes in functional metagenome and community structure over time, indicating successional niche differentiation amongst soil biota...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28530140/associations-of-nasopharyngeal-metabolome-and-microbiome-with-severity-among-infants-with-bronchiolitis-a-multi-omic-analysis
#11
Christopher J Stewart, Jonathan M Mansbach, Matthew C Wong, Nadim J Ajami, Joseph F Petrosino, Carlos A Camargo, Kohei Hasegawa
RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, while emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis...
May 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28473000/tracking-microbial-colonization-in-fecal-microbiota-transplantation-experiments-via-genome-resolved-metagenomics
#12
Sonny T M Lee, Stacy A Kahn, Tom O Delmont, Alon Shaiber, Özcan C Esen, Nathaniel A Hubert, Hilary G Morrison, Dionysios A Antonopoulos, David T Rubin, A Murat Eren
BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits...
May 4, 2017: Microbiome
https://www.readbyqxmd.com/read/28472388/cafe-accelerated-alignment-free-sequence-analysis
#13
Yang Young Lu, Kujin Tang, Jie Ren, Jed A Fuhrman, Michael S Waterman, Fengzhu Sun
Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures...
May 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28472118/effect-of-dietary-supplementation-with-lactobacillus-acidophilus-d2-csl-cect-4529-on-caecum-microbioma-and-productive-performance-in-broiler-chickens
#14
Alessandra De Cesare, Federico Sirri, Gerardo Manfreda, Paola Moniaci, Alberto Giardini, Marco Zampiga, Adele Meluzzi
This study examines the effects of the dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) (LA) on productive performances, incidence of foot pad dermatitis and caecum microbioma in broiler chickens. A total of 1,100 one-day old male Ross 308 chicks were divided into 2 groups of 16 replicates with 25 birds each and reared from 1-41 d. One group was fed a basal diet (CON) and the other group the same diet supplemented with LA. Caecum contents were collected from 4 selected birds at day one and 5 selected birds at the end of the rearing period...
2017: PloS One
https://www.readbyqxmd.com/read/28469608/genome-centric-analysis-of-a-thermophilic-and-cellulolytic-bacterial-consortium-derived-from-composting
#15
Leandro N Lemos, Roberta V Pereira, Ronaldo B Quaggio, Layla F Martins, Livia M S Moura, Amanda R da Silva, Luciana P Antunes, Aline M da Silva, João C Setubal
Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28467925/gut-microbiome-based-metagenomic-signature-for-non-invasive-detection-of-advanced-fibrosis-in-human-nonalcoholic-fatty-liver-disease
#16
Rohit Loomba, Victor Seguritan, Weizhong Li, Tao Long, Niels Klitgord, Archana Bhatt, Parambir Singh Dulai, Cyrielle Caussy, Richele Bettencourt, Sarah K Highlander, Marcus B Jones, Claude B Sirlin, Bernd Schnabl, Lauren Brinkac, Nicholas Schork, Chi-Hua Chen, David A Brenner, William Biggs, Shibu Yooseph, J Craig Venter, Karen E Nelson
The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis)...
May 2, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28453677/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#17
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28452176/microbial-acceleration-of-aerobic-pyrite-oxidation-at-circumneutral-ph
#18
E Percak-Dennett, S He, B Converse, H Konishi, H Xu, A Corcoran, D Noguera, C Chan, A Bhayyacharyya, T Borch, E Boyd, E E Roden
Pyrite (FeS2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH...
April 27, 2017: Geobiology
https://www.readbyqxmd.com/read/28451970/an-agile-functional-analysis-of-metagenomic-data-using-super-focus
#19
Genivaldo Gueiros Z Silva, Fabyano A C Lopes, Robert A Edwards
One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, "What can the organisms in the sample do?" Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28451968/ghostx-a-fast-sequence-homology-search-tool-for-functional-annotation-of-metagenomic-data
#20
Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, Yutaka Akiyama
Metagenomic analysis based on whole genome shotgun sequencing data requires fast protein sequence homology searches for predicting the function of proteins coded on metagenome short reads. However, huge amounts of sequence data cause even general homology search analyses using BLASTX to become difficult in terms of computational cost. GHOSTX is a sequence homology search tool specifically developed for functional annotation of metagenome sequences. The tool is more than 160 times faster than BLASTX and has sufficient search sensitivity for metagenomic analysis...
2017: Methods in Molecular Biology
keyword
keyword
72454
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"