keyword
MENU ▼
Read by QxMD icon Read
search

Metatranscriptome

keyword
https://www.readbyqxmd.com/read/29339611/mechanism-of-1-4-dioxane-microbial-degradation-revealed-by-16s-rrna-and-metatranscriptomic-analyses
#1
Xiangyu Guan, Fei Liu, Jing Wang, Caoxiang Li, Xiaoxuan Zheng
1,4-Dioxane (dioxane), a probable human carcinogen, often exists in industrial wastewater and domestic sewage. In this study, we applied 16S rRNA and metatranscriptomic methods to analyze the dioxane biodegradation mechanism by activated sludge. Tetrahydrofuran (THF) was added as an essential co-metabolite to promote the degradation of dioxane. We found the dioxane removal ratio increased with increasing THF concentrations. When the THF concentration increased from 60.0 to 200.0 mg/L, the dioxane degradation rate was stable...
January 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/29335555/metatranscriptome-of-human-faecal-microbial-communities-in-a-cohort-of-adult-men
#2
Galeb S Abu-Ali, Raaj S Mehta, Jason Lloyd-Price, Himel Mallick, Tobyn Branck, Kerry L Ivey, David A Drew, Casey DuLong, Eric Rimm, Jacques Izard, Andrew T Chan, Curtis Huttenhower
The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29335554/stability-of-the-human-faecal-microbiome-in-a-cohort-of-adult-men
#3
Raaj S Mehta, Galeb S Abu-Ali, David A Drew, Jason Lloyd-Price, Ayshwarya Subramanian, Paul Lochhead, Amit D Joshi, Kerry L Ivey, Hamed Khalili, Gordon T Brown, Casey DuLong, Mingyang Song, Long H Nguyen, Himel Mallick, Eric B Rimm, Jacques Izard, Curtis Huttenhower, Andrew T Chan
Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29334812/anti-biofilm-effect-of-a-butenolide-polymer-coating-and-metatranscriptomic-analyses
#4
Wei Ding, Chunfeng Ma, Weipeng Zhang, Hoyin Chiang, Chunkit Tam, Ying Xu, Guangzhao Zhang, Pei-Yuan Qian
Butenolide is an environmentally friendly antifouling natural product, but its efficiency and mechanism in preventing biofilm formation have not been examined. Furthermore, controlling the release of butenolide from paints into seawater is technically challenging. A coating was developed by mixing butenolide with a biodegradable polymer, poly (ε-caprolactone)-based polyurethane, and a one-month in situ anti-biofilm test was conducted in a subtidal area. The constant release of butenolide from the surface suggested that its release was well controlled...
January 2018: Biofouling
https://www.readbyqxmd.com/read/29334654/phbv-polymer-supported-denitrification-system-efficiently-treated-high-nitrate-concentration-wastewater-denitrification-performance-microbial-community-structure-evolution-and-key-denitrifying-bacteria
#5
Zhongshuo Xu, Liyan Song, Xiaohu Dai, Xiaoli Chai
Biodegradable polymer supported denitrification (BPD) system shows good denitrification performance for the wastewater with low nitrate concentrations. In this study, a BPD system using Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) polymer as carbon source was developed to treat the wastewater with high nitrate concentrations. The denitrification performance, utilization ratio of PHBV polymers, and microbial community structure evolution and key denitrifying bacteria were comprehensively studied. Results indicated that an average nitrate removal efficiency of 99% could be achieved with an influent NO3--N concentration of 100 mg L-1 and a hydraulic retention time (HRT) of 7...
January 8, 2018: Chemosphere
https://www.readbyqxmd.com/read/29330533/soil-contamination-alters-the-willow-root-and-rhizosphere-metatranscriptome-and-the-root-rhizosphere-interactome
#6
Etienne Yergeau, Julien Tremblay, Simon Joly, Michel Labrecque, Christine Maynard, Frederic E Pitre, Marc St-Arnaud, Charles W Greer
Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29322917/identification-of-natural-antimicrobial-peptides-from-bacteria-through-metagenomic-and-metatranscriptomic-analysis-of-high-throughput-transcriptome-data-of-taiwanese-oolong-teas
#7
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29311644/dynamics-of-metatranscription-in-the-inflammatory-bowel-disease-gut-microbiome
#8
Melanie Schirmer, Eric A Franzosa, Jason Lloyd-Price, Lauren J McIver, Randall Schwager, Tiffany W Poon, Ashwin N Ananthakrishnan, Elizabeth Andrews, Gildardo Barron, Kathleen Lake, Mahadev Prasad, Jenny Sauk, Betsy Stevens, Robin G Wilson, Jonathan Braun, Lee A Denson, Subra Kugathasan, Dermot P B McGovern, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period...
January 8, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29304850/metabolic-capability-and-in-situ-activity-of-microorganisms-in-an-oil-reservoir
#9
Yi-Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S Zaramela, Ji-Dong Gu, Bo-Zhong Mu, Karsten Zengler
BACKGROUND: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. RESULTS: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach...
January 5, 2018: Microbiome
https://www.readbyqxmd.com/read/29284754/viral-discovery-and-diversity-in-trypanosomatid-protozoa-with-a-focus-on-relatives-of-the-human-parasite-leishmania
#10
Danyil Grybchuk, Natalia S Akopyants, Alexei Y Kostygov, Aleksandras Konovalovas, Lon-Fye Lye, Deborah E Dobson, Haroun Zangger, Nicolas Fasel, Anzhelika Butenko, Alexander O Frolov, Jan Votýpka, Claudia M d'Avila-Levy, Pavel Kulich, Jana Moravcová, Pavel Plevka, Igor B Rogozin, Saulius Serva, Julius Lukeš, Stephen M Beverley, Vyacheslav Yurchenko
Knowledge of viral diversity is expanding greatly, but many lineages remain underexplored. We surveyed RNA viruses in 52 cultured monoxenous relatives of the human parasite Leishmania (Crithidia and Leptomonas), as well as plant-infecting PhytomonasLeptomonas pyrrhocoris was a hotbed for viral discovery, carrying a virus (Leptomonas pyrrhocoris ostravirus 1) with a highly divergent RNA-dependent RNA polymerase missed by conventional BLAST searches, an emergent clade of tombus-like viruses, and an example of viral endogenization...
December 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29278751/correlation-between-gut-microbiota-and-personality-in-adults-a-cross-sectional-study
#11
Han-Na Kim, Yeojun Yun, Seungho Ryu, Yoosoo Chang, Min-Jung Kwon, Juhee Cho, Hocheol Shin, Hyung-Lae Kim
Personality affects fundamental behavior patterns and has been related with health outcomes and mental disorders. Recent evidence has emerged supporting a relationship between the microbiota and behavior, referred to as brain-gut relationships. Here, we first report correlations between personality traits and gut microbiota. This research was performed using the Revised NEO Personality Inventory and the sequencing data of the 16S rRNA gene in 672 adults. The diversity and the composition of the human gut microbiota exhibited significant difference when stratified by personality traits...
December 23, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/29274958/mining-metagenomic-and-metatranscriptomic-data-for-clues-about-microbial-metabolic-functions-in-ruminants
#12
Fuyong Li, Andre L A Neves, Bibaswan Ghoshal, Le Luo Guan
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29274424/biochemical-and-biophysical-characterization-of-novel-gh10-xylanase-prospected-from-a-sugar-cane-bagasse-compost-derived-microbial-consortia
#13
Danilo Elton Evangelista, Marco Antonio Seiki Kadowaki, Bruno Luan Mello, Igor Polikarpov
Environmental issues are promoting the development of innovative technologies for the production of renewable energy and "green products" from plant biomass residues. These technologies rely on the conversion of the plant cell wall (PCW) polysaccharides into simple sugars, which involve synergistic activities of different PCW degrading enzymes, including xylanases; these are widely applied in food and feed sectors, paper and textile industries, among others. We cloned, expressed and biochemically characterized a novel xylanase (Xyn10) from the GH10 identified in a metatranscriptome of compost-derived microbial consortia and determined its low-resolution SAXS molecular envelope in solution...
December 20, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29259591/natural-selection-in-synthetic-communities-highlights-the-roles-of-methylococcaceae-and-methylophilaceae-and-suggests-differential-roles-for-alternative-methanol-dehydrogenases-in-methane-consumption
#14
Zheng Yu, David A C Beck, Ludmila Chistoserdova
We describe experiments that follow species dynamics and gene expression patterns in synthetic bacterial communities including species that compete for the single carbon substrate supplied, methane, and species unable to consume methane, which could only succeed through cooperative interactions. We demonstrate that these communities mostly select for two functional guilds, methanotrophs of the family Methylococcaceae and non-methanotrophic methylotrophs of the family Methylophilaceae, these taxonomic guilds outcompeting all other species included in the synthetic mix...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29232952/ethyl-carbamate-formation-regulated-by-lactic-acid-bacteria-and-nonconventional-yeasts-in-solid-state-fermentation-of-chinese-moutai-flavor-liquor
#15
Hai Du, Zhewei Song, Yan Xu
This study aimed to identify specific microorganisms related to the formation of precursors of ethyl carbamate (EC) in the solid-state fermentation of a Chinese Moutai-flavor liquor. The EC content was significantly correlated with the urea content during the fermentation process (R2 = 0.772, P < 0.01). Differences in urea production and degradation were found between members of the microbiota in the fermentation (at both species and functional gene levels) by metatranscriptomic sequencing and culture-dependent analysis...
December 13, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29209303/ph-stress-induced-cooperation-between-rhodococcus-ruber-yyl-and-bacillus-cereus-mly1-in-biodegradation-of-tetrahydrofuran
#16
Zubi Liu, Zhixing He, Hui Huang, Xuebin Ran, Adebanjo O Oluwafunmilayo, Zhenmei Lu
Microbial consortia consisting of cooperational strains exhibit biodegradation performance superior to that of single microbial strains and improved remediation efficiency by relieving the environmental stress. Tetrahydrofuran (THF), a universal solvent widely used in chemical and pharmaceutical synthesis, significantly affects the environment. As a refractory pollutant, THF can be degraded by some microbial strains under suitable conditions. There are often a variety of stresses, especially pH stress, that inhibit the THF-degradation efficiency of microbial consortia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29205917/targeted-in%C3%A2-situ-metatranscriptomics-for-selected-taxa-from-mesophilic-and-thermophilic-biogas-plants
#17
Yvonne Stolze, Andreas Bremges, Irena Maus, Alfred Pühler, Alexander Sczyrba, Andreas Schlüter
Biogas production is performed anaerobically by complex microbial communities with key species driving the process. Hence, analyses of their in situ activities are crucial to understand the process. In a previous study, metagenome sequencing and subsequent genome binning for different production-scale biogas plants (BGPs) resulted in four genome bins of special interest, assigned to the phyla Thermotogae, Fusobacteria, Spirochaetes and Cloacimonetes, respectively, that were genetically analysed. In this study, metatranscriptome sequencing of the same BGP samples was conducted, enabling in situ transcriptional activity determination of these genome bins...
December 4, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29205750/spatially-distinct-temporally-stable-microbial-populations-mediate-biogeochemical-cycling-at-and-below-the-seafloor-in-hydrothermal-vent-fluids
#18
Caroline S Fortunato, Benjamin Larson, David A Butterfield, Julie A Huber
At deep-sea hydrothermal vents, microbial communities thrive across geochemical gradients above, at, and below the seafloor. In this study, we determined the gene content and transcription patterns of microbial communities and specific populations to understand the taxonomy and metabolism both spatially and temporally across geochemically different diffuse fluid hydrothermal vents. Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and geochemical analyses from Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge in the NE Pacific Ocean, from 2013-2015 at three different vents: Anemone, Marker 33, and Marker 113...
December 4, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29198031/metatranscriptomics-analysis-of-cyanobacterial-aggregates-during-cyanobacterial-bloom-period-in-lake-taihu-china
#19
Zhenzhu Chen, Junyi Zhang, Rui Li, Fei Tian, Yanting Shen, Xueying Xie, Qinyu Ge, Zuhong Lu
Molecular mechanism of interaction between the bloom-forming cyanobacterial species and attached microbios within cyanobacterial aggregates has not been elucidated yet and understanding of which would help to unravel the cyanobacteria bloom-forming mechanism. In this study, we profiled the metabolically active community by high-throughput metatranscriptome sequencing from cyanobacterial aggregates during cyanobacterial bloom period in Lake Taihu, China. A total of 308 million sequences were obtained using the HiSeq 2500 sequencing platform, which provided a great sequence coverage to carry out the in-depth taxonomic classification, functional classification, and metabolic pathway analysis of the cyanobacterial aggregates...
December 3, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29191900/ocean-biogeochemistry-modeled-with-emergent-trait-based-genomics
#20
V J Coles, M R Stukel, M T Brooks, A Burd, B C Crump, M A Moran, J H Paul, B M Satinsky, P L Yager, B L Zielinski, R R Hood
Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes...
December 1, 2017: Science
keyword
keyword
66490
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"