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Metagenomics

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https://www.readbyqxmd.com/read/28550779/pathways-in-bacterial-and-archaeal-communities-dictated-by-ammonium-stress-in-a-high-solid-anaerobic-digester-with-dewatered-sludge
#1
Ning Li, Jin He, Han Yan, Sisi Chen, Xiaohu Dai
Metagenomic comparisons of microbial profiles were conducted to investigate differences between the samples from steady (Day 42), ammonium-adjusting (Day 63), and ammonium-stressed (Day 102) periods during the 110-day operation of a high solid anaerobic digester of sewage sludge. Comparing to the steady period, biogas production was slightly inhibited after ammonium adjustment, during which the microbes showed higher abundance in 6 of the total 22 ammonium-related genes. In addition, among the 19 amino-acid-related genes, 9 genes involved in amino acid generation and utilization were reduced, which partially revealed the reason of deterioration of volatile solids (VSs) degradation following ammonium stress...
May 18, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28546829/vinasse-fertirrigation-alters-soil-resistome-dynamics-an-analysis-based-on-metagenomic-profiles
#2
Lucas P P Braga, Rafael F Alves, Marina T F Dellias, Acacio A Navarrete, Thiago O Basso, Siu M Tsai
Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database...
2017: BioData Mining
https://www.readbyqxmd.com/read/28546481/metagenomes-and-metatranscriptomes-of-activated-sludge-from-a-sewage-plant-with-or-without-aerobic-granule-enrichment
#3
Julien Crovadore, Vice Soljan, Gautier Calmin, Romain Chablais, Bastien Cochard, François Lefort
We report here the metagenomes and metatranscriptomes of activated sludge bioreactors, enriched or not enriched with aerobic granules, at an initial state and after 1 month of incubation. Data showed that the added granular biomass expressed higher levels of expression of genes involved in ammonia elimination.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28545131/major-changes-in-microbial-diversity-and-community-composition-across-gut-sections-of-a-juvenile-panchlora-cockroach
#4
Erin A Gontang, Frank O Aylward, Camila Carlos, Tijana Glavina Del Rio, Mansi Chovatia, Alison Fern, Chien-Chi Lo, Stephanie A Malfatti, Susannah G Tringe, Cameron R Currie, Roberto Kolter
Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica...
2017: PloS One
https://www.readbyqxmd.com/read/28544522/metagenomic-potential-for-and-diversity-of-n-cycle-driving-microorganisms-in-the-bothnian-sea-sediment
#5
Olivia Rasigraf, Julia Schmitt, Mike S M Jetten, Claudia Lüke
The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases...
May 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28544449/metagenomic-based-impact-study-of-transgenic-grapevine-rootstock-on-its-associated-virome-and-soil-bacteriome
#6
Jean-Michel Hily, Sandrine Demanèche, Nils Poulicard, Mélanie Tannières, Samia Djennane, Monique Beuve, Emmanuelle Vigne, Gérard Demangeat, Véronique Komar, Claude Gertz, Aurélie Marmonier, Caroline Hemmer, Sophie Vigneron, Armelle Marais, Thierry Candresse, Pascal Simonet, Olivier Lemaire
For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment...
May 25, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28543918/gut-microbiota-of-the-pine-weevil-degrades-conifer-diterpenes-and-increases-insect-fitness
#7
Aileen Berasategui, Hassan Salem, Christian Paetz, Maricel Santoro, Jonathan Gershenzon, Martin Kaltenpoth, Axel Schmdit
The pine weevil (Hylobius abietis), a major pest of conifer forests throughout Europe, feeds on the bark and cambium, tissues rich in terpenoid resins that are toxic to many insect herbivores. Here we report the ability of the pine weevil gut microbiota to degrade the diterpene acids of Norway spruce. The diterpene acid levels present in ingested bark were substantially reduced on passage through the pine weevil gut. This reduction was significantly less upon antibiotic treatment, and supplementing the diet with gut suspensions from untreated insects restored the ability to degrade diterpenes...
May 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28543439/metagenomic-profiling-of-the-microbial-freshwater-communities-in-two-bulgarian-reservoirs
#8
Ivan Iliev, Galina Yahubyan, Mariana Marhova, Elena Apostolova, Mariyana Gozmanova, Gana Gecheva, Sonya Kostadinova, Angelina Ivanova, Vesselin Baev
Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA)...
May 22, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28542523/impact-of-maintenance-immunosuppressive-therapy-on-the-fecal-microbiome-of-renal-transplant-recipients-comparison-between-an-everolimus-and-a-standard-tacrolimus-based-regimen
#9
Gianluigi Zaza, Alessandra Dalla Gassa, Giovanna Felis, Simona Granata, Sandra Torriani, Antonio Lupo
BACKGROUND: The gut microbiome is the full set of microbes living in the gastrointestinal tract and is emerging as an important dynamic/fluid system that, if altered by environmental, dietetic or pharmacological factors, could considerably influence drug response. However, the immunosuppressive drug-induced modifications of this system are still poorly defined. METHODS: We employed an innovative bioinformatics approach to assess differences in the whole-gut microbial metagenomic profile of 20 renal transplant recipients undergoing maintenance treatment with two different immunosuppressive protocols...
2017: PloS One
https://www.readbyqxmd.com/read/28542458/a-pilot-study-using-metagenomic-sequencing-of-the-sputum-microbiome-suggests-potential-bacterial-biomarkers-for-lung-cancer
#10
Simon J S Cameron, Keir E Lewis, Sharon A Huws, Matthew J Hegarty, Paul D Lewis, Justin A Pachebat, Luis A J Mur
Lung cancer (LC) is the most prevalent cancer worldwide, and responsible for over 1.3 million deaths each year. Currently, LC has a low five year survival rates relative to other cancers, and thus, novel methods to screen for and diagnose malignancies are necessary to improve patient outcomes. Here, we report on a pilot-sized study to evaluate the potential of the sputum microbiome as a source of non-invasive bacterial biomarkers for lung cancer status and stage. Spontaneous sputum samples were collected from ten patients referred with possible LC, of which four were eventually diagnosed with LC (LC+), and six had no LC after one year (LC-)...
2017: PloS One
https://www.readbyqxmd.com/read/28542207/metagenomic-sequencing-complements-routine-diagnostics-in-identifying-viral-pathogens-in-lung-transplant-recipients-with-unknown-etiology-of-respiratory-infection
#11
Dagmara W Lewandowska, Peter W Schreiber, Macé M Schuurmans, Bettina Ruehe, Osvaldo Zagordi, Cornelia Bayard, Michael Greiner, Fabienne D Geissberger, Riccarda Capaul, Andrea Zbinden, Jürg Böni, Christian Benden, Nicolas J Mueller, Alexandra Trkola, Michael Huber
BACKGROUND: Lung transplant patients are a vulnerable group of immunosuppressed patients that are prone to frequent respiratory infections. We studied 60 episodes of respiratory symptoms in 71 lung transplant patients. Almost half of these episodes were of unknown infectious etiology despite extensive routine diagnostic testing. METHODS: We re-analyzed respiratory samples of all episodes with undetermined etiology in order to detect potential viral pathogens missed/not accounted for in routine diagnostics...
2017: PloS One
https://www.readbyqxmd.com/read/28541905/inferring-gene-species-assignments-in-the-presence-of-horizontal-gene-transfer
#12
Agnieszka Mykowiecka, Pawel Szczesny, Pawel Gorecki
BACKGROUND: Microbial communities from environmental samples show great diversity as bacteria quickly response to changes in their ecosystems. To assess the scenario of the actual changes, metagenomics experiments aimed at sequencing genomic DNA from such samples are performed. These new obtained sequences together with already known are used to infer phylogenetic trees assessing the taxonomic groups the species with these genes belong to. Here we propose the first approach to the gene-species assignment problem by using reconciliation with horizontal gene transfer...
May 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28540714/arbitrarily-primed-pcr-for-comparison-of-meta-genomes-and-extracting-useful-loci-from-them
#13
Leigh Burgoyne, Lin Y Koh, David Catcheside
A method is described that uses arbitrarily primed PCR followed by many cycles of amplification under stringent conditions and selection by computational means to obtain a set of sequence tags that can be used for the comparison of metagenomes. Relative to unselective shot-gun sequencing, the results are small data sets that can be csompared electronically or plotted as scattergrams that are simple to interpret. The method can be used to compare groups of samples of any size to build in-house databases from which, for example, the provenance of trace soil samples may be inferred...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540713/pcr-in-metagenomics
#14
Tina Kollannoor Johny, Sarita Ganapathy Bhat
Metagenomics approach involves direct genetic analysis of environmental samples, evading the tedious culturing process. Polymerase chain reaction is one invaluable tool used for such analyses. Here, we describe one protocol for metagenomic DNA isolation that gives inhibitor-free DNA suitable for PCR and other genetic manipulations. Subsequently, the chapter describes the use of PCR as an indicator of quality of DNA and to amplify a marker of phylogeny. Further, the application of PCR for detection of specific genes and screening of metagenomic libraries is outlined...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28539477/bacterial-colonization-and-succession-in-a-newly-opened-hospital
#15
Simon Lax, Naseer Sangwan, Daniel Smith, Peter Larsen, Kim M Handley, Miles Richardson, Kristina Guyton, Monika Krezalek, Benjamin D Shogan, Jennifer Defazio, Irma Flemming, Baddr Shakhsheer, Stephen Weber, Emily Landon, Sylvia Garcia-Houchins, Jeffrey Siegel, John Alverdy, Rob Knight, Brent Stephens, Jack A Gilbert
The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room...
May 24, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28539351/bacteriophage-transfer-during-faecal-microbiota-transplantation-in-clostridium-difficile-infection-is-associated-with-treatment-outcome
#16
Tao Zuo, Sunny H Wong, Kelvin Lam, Rashid Lui, Kitty Cheung, Whitney Tang, Jessica Y L Ching, Paul K S Chan, Martin C W Chan, Justin C Y Wu, Francis K L Chan, Jun Yu, Joseph J Y Sung, Siew C Ng
OBJECTIVE: Faecal microbiota transplantation (FMT) is effective for the treatment of recurrent Clostridium difficile infection (CDI). Studies have shown bacterial colonisation after FMT, but data on viral alterations in CDI are scarce. We investigated enteric virome alterations in CDI and the association between viral transfer and clinical outcome in patients with CDI. DESIGN: Ultra-deep metagenomic sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on stool samples from 24 subjects with CDI and 20 healthy controls...
May 24, 2017: Gut
https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#17
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28538703/metagenomic-approaches-to-assess-bacteriophages-in-various-environmental-niches
#18
REVIEW
Stephen Hayes, Jennifer Mahony, Arjen Nauta, Douwe van Sinderen
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral 'dark matter' of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research...
May 24, 2017: Viruses
https://www.readbyqxmd.com/read/28536564/a-metagenomic-approach-to-cyanobacterial-genomics
#19
REVIEW
Danillo O Alvarenga, Marli F Fiore, Alessandro M Varani
Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28536561/differences-in-microbiota-membership-along-the-gastrointestinal-tract-of-piglets-and-their-differential-alterations-following-an-early-life-antibiotic-intervention
#20
Chunlong Mu, Yuxiang Yang, Yong Su, Erwin G Zoetendal, Weiyun Zhu
Early-life antibiotic interventions can change the predisposition to disease by disturbing the gut microbiota. However, the impact of antibiotics on gut microbiota in the gastrointestinal tract is not completely understood, although antibiotic-induced alterations in the distal gut have been reported. Here, employing a piglet model, the microbial composition was analyzed by high-throughput 16S rRNA gene sequencing and PICRUSt predictions of metagenome function. The present study showed clear spatial variation of microbial communities in the stomach and intestine, and found that the administration of antibiotics (a mixture of olaquindox, oxytetracycline calcium, kitasamycin) in early life caused markedly differential alterations in the compartmentalized microbiota, with major alterations in their spatial variation in the lumen of the stomach and small intestine...
2017: Frontiers in Microbiology
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