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https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#1
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28442658/predominant-but-previously-overlooked-prokaryotic-drivers-of-reductive-nitrogen-transformation-in-paddy-soils-revealed-by-metatranscriptomics
#2
Yoko Masuda, Hideomi Itoh, Yutaka Shiratori, Kazuo Isobe, Shigeto Otsuka, Keishi Senoo
Waterlogged paddy soils possess anoxic zones in which microbes actively induce reductive nitrogen transformation (RNT). In the present study, a shotgun RNA sequencing analysis (metatranscriptomics) of paddy soil samples revealed that most RNT gene transcripts in paddy soils were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter. Despite the frequent detection of the rRNA of these microbes in paddy soils, their RNT-associated genes have rarely been identified in previous PCR-based studies...
April 22, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28428832/a-meta-analysis-testing-eusocial-co-option-theories-in-termite-gut-physiology-and-symbiosis
#3
Michael E Scharf, Yunpeng Cai, Yijun Sun, Ruchira Sen, Rhitoban Raychoudhury, Drion G Boucias
The termite gut accomplishes key physiologic functions that underlie termite symbiosis and sociality. However, potential candidate functions of the host-symbiont holobiome have not yet been explored across seemingly divergent processes such as digestion, immunity, caste differentiation, and xenobiotic tolerance. This study took a meta-analysis approach for concurrently studying host and symbiont gut metatranscriptome responses of the lower termite Reticulitermes flavipes, which has ancestral characteristics and hosts a diverse mix of eukaryotic and bacterial symbionts...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28390722/factors-influencing-ruminal-bacterial-community-diversity-and-composition-and-microbial-fibrolytic-enzyme-abundance-in-lactating-dairy-cows-with-a-focus-on-the-role-of-active-dry-yeast
#4
Ousama AlZahal, Fuyong Li, Le Luo Guan, Nicola D Walker, Brian W McBride
The objective of the current study was to employ a DNA-based sequencing technology to study the effect of active dry yeast (ADY) supplementation, diet type, and sample location within the rumen on rumen bacterial community diversity and composition, and to use an RNA-based method to study the effect of ADY supplementation on rumen microbial metabolism during high-grain feeding (HG). Our previous report demonstrated that the supplementation of lactating dairy cows with ADY attenuated the effect of subacute ruminal acidosis...
April 5, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28389566/microbial-metabolites-in-health-and-disease-navigating-the-unknown-in-search-of-function
#5
Kristina B Martinez, Vanessa A Leone, Eugene B Chang
The gut microbiota has been implicated in the development of a number of chronic gastrointestinal and systemic diseases. These include inflammatory bowel diseases, irritable bowel syndrome, metabolic (i.e. obesity, non-alcoholic fatty liver disease, diabetes), and neurological diseases. The advanced understanding of host-microbe interactions has largely been due to new technologies such as 16S rRNA sequencing to identify previously unknown microbial communities and more importantly their functional characteristics through metagenomic sequencing, and other multi-omic technologies such as metatranscriptomics, metaproteomics, and metabolomics...
April 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28387773/expression-patterns-of-elemental-cycling-genes-in-the-amazon-river-plume
#6
Brandon M Satinsky, Christa B Smith, Shalabh Sharma, Marine Landa, Patricia M Medeiros, Victoria J Coles, Patricia L Yager, Byron C Crump, Mary Ann Moran
Metatranscriptomics and metagenomics data sets benchmarked with internal standards were used to characterize the expression patterns for biogeochemically relevant bacterial and archaeal genes mediating carbon, nitrogen, phosphorus and sulfur uptake and metabolism through the salinity gradient of the Amazon River Plume. The genes were identified in 48 metatranscriptomic and metagenomic data sets summing to >500 million quality-controlled reads from six locations in the plume ecosystem. The ratio of transcripts per gene copy (a direct measure of expression made possible by internal standard additions) showed that the free-living bacteria and archaea exhibited only small changes in the expression levels of biogeochemically relevant genes through the salinity and nutrient zones of the plume...
April 7, 2017: ISME Journal
https://www.readbyqxmd.com/read/28384412/second-era-of-omics-in-caries-research-moving-past-the-phase-of-disillusionment
#7
M M Nascimento, E Zaura, A Mira, N Takahashi, J M Ten Cate
Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing ( NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries...
April 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28382330/metatranscriptomics-supports-the-mechanism-for-biocathode-electroautotrophy-by-candidatus-tenderia-electrophaga
#8
Brian J Eddie, Zheng Wang, W Judson Hervey, Dagmar H Leary, Anthony P Malanoski, Leonard M Tender, Baochuan Lin, Sarah M Strycharz-Glaven
Biocathodes provide a stable electron source to drive reduction reactions in electrotrophic microbial electrochemical systems. Electroautotrophic biocathode communities may be more robust than monocultures in environmentally relevant settings, but some members are not easily cultivated outside the electrode environment. We previously used metagenomics and metaproteomics to propose a pathway for coupling extracellular electron transfer (EET) to carbon fixation in "Candidatus Tenderia electrophaga," an uncultivated but dominant member of an electroautotrophic biocathode community...
March 2017: MSystems
https://www.readbyqxmd.com/read/28369659/organophosphate-diazinon-altered-quorum-sensing-cell-motility-stress-response-and-carbohydrate-metabolism-of-gut-microbiome
#9
Bei Gao, Xiaoming Bian, Liang Chi, Pengcheng Tu, Hongyu Ru, Kun Lu
The gut microbiome plays a key role in energy production, immune system development, and host resistance against invading pathogens, etc. Disruption of gut bacterial homeostasis is associated with a number of human diseases. Several environmental chemicals have been reported to induce alterations of the gut microbiome. Diazinon, one of important organophosphate insecticides, has been widely used in agriculture. Diazinon and its metabolites are readily detected in different environmental settings and human urine...
March 27, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28350876/mipe-a-metagenome-based-community-structure-explorer-and-ssu-primer-evaluation-tool
#10
Bin Zou, JieFu Li, Quan Zhou, Zhe-Xue Quan
An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers...
2017: PloS One
https://www.readbyqxmd.com/read/28348455/reflection-on-molecular-approaches-influencing-state-of-the-art-bioremediation-design-culturing-to-microbial-community-fingerprinting-to-omics
#11
Lauren M Czaplicki, Claudia K Gunsch
Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers...
October 2016: Journal of Environmental Engineering
https://www.readbyqxmd.com/read/28338677/integrated-metabolism-in-sponge-microbe-symbiosis-revealed-by-genome-centered-metatranscriptomics
#12
Lucas Moitinho-Silva, Cristina Díez-Vives, Giampiero Batani, Ana Is Esteves, Martin T Jahn, Torsten Thomas
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28320314/quorum-sensing-of-streptococcus-mutans-is-activated-by-aggregatibacter-actinomycetemcomitans-and-by-the-periodontal-microbiome
#13
Szymon P Szafrański, Zhi-Luo Deng, Jürgen Tomasch, Michael Jarek, Sabin Bhuju, Manfred Rohde, Helena Sztajer, Irene Wagner-Döbler
BACKGROUND: The oral cavity is inhabited by complex microbial communities forming biofilms that can cause caries and periodontitis. Cell-cell communication might play an important role in modulating the physiologies of individual species, but evidence so far is limited. RESULTS: Here we demonstrate that a pathogen of the oral cavity, Aggregatibacter actinomycetemcomitans (A. act.), triggers expression of the quorum sensing (QS) regulon of Streptococcus mutans, a well-studied model organism for cariogenic streptococci, in dual-species biofilms grown on artificial saliva...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28279485/discovering-protein-coding-genes-from-the-environment-time-for-the-eukaryotes
#14
REVIEW
Roland Marmeisse, Harald Kellner, Laurence Fraissinet-Tachet, Patricia Luis
Eukaryotic microorganisms from diverse environments encompass a large number of taxa, many of them still unknown to science. One strategy to mine these organisms for genes of biotechnological relevance is to use a pool of eukaryotic mRNA directly extracted from environmental samples. Recent reports demonstrate that the resulting metatranscriptomic cDNA libraries can be screened by expression in yeast for a wide range of genes and functions from many of the different eukaryotic taxa. In combination with novel emerging high-throughput technologies, we anticipate that this approach should contribute to exploring the functional diversity of the eukaryotic microbiota...
March 6, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28258137/metatranscriptomic-evidence-for-direct-interspecies-electron-transfer-between-geobacter-and-methanothrix-species-in-methanogenic-rice-paddy-soils
#15
Dawn E Holmes, Pravin M Shrestha, David J F Walker, Yan Dang, Kelly P Nevin, Trevor L Woodard, Derek R Lovley
The possibility that Methanothrix (formerly Methanosaeta) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries...
May 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28251799/diet-affects-arctic-ground-squirrel-gut-microbial-metatranscriptome-independent-of-community-structure
#16
Jasmine J Hatton, Timothy J Stevenson, C Loren Buck, Khrystyne N Duddleston
We examined the effect of diet on pre-hibernation fattening and the gut microbiota of captive arctic ground squirrels (Urocitellus parryii). We measured body composition across time and gut microbiota density, diversity and function prior to and after five-weeks on control, high-fat, low-fat (18%, 40% and 10% energy from fat, respectively), or restricted calorie (50% of control) diets. Squirrels fattened at the same rate and to the same degree on all diets. Additionally, we found no differences in gut microbiota diversity or short chain fatty acid production across time or with diet...
April 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28246035/functional-gene-profiling-through-metarnaseq-approach-reveals-diet-dependent-variation-in-rumen-microbiota-of-buffalo-bubalus-bubalis
#17
Ankit T Hinsu, Nidhi R Parmar, Neelam M Nathani, Ramesh J Pandit, Anand B Patel, Amrutlal K Patel, Chaitanya G Joshi
Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection...
April 2017: Anaerobe
https://www.readbyqxmd.com/read/28242596/research-progress-of-stoichiogenomics
#18
Lan Yang, Hu Jiangtao, Zhang Yujuan
Stoichiogenomics is a newly arisen research field, which concerns the element usage biases of biological macromolecules at genome, transcriptome, proteome, metabonome levels. Different biological macromolecules have different element compositions and contents. When the supply of some elements was constrained, natural selection might bias the usage of the monomers (amino acid or nucleotide) to reduce constrained element costs in the synthesis of biological macromolecules. This field is flourishing with the intensive applications of high throughput sequencing and assembly technologies, more and more available metagenomic and metatranscriptomic data, and the applications of new analysis strategies...
February 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28235871/metatranscriptomic-profiling-reveals-linkages-between-the-active-rumen-microbiome-and-feed-efficiency-in-beef-cattle
#19
Fuyong Li, Le Luo Guan
Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets...
May 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28218463/closed-reference-metatranscriptomics-enables-in-planta-profiling-of-putative-virulence-activities-in-the-grapevine-trunk-disease-complex
#20
Abraham Morales-Cruz, Gabrielle Allenbeck, Rosa Figueroa-Balderas, Vanessa E Ashworth, Daniel P Lawrence, Renaud Travadon, Rhonda J Smith, Kendra Baumgartner, Philippe E Rolshausen, Dario Cantu
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i...
February 20, 2017: Molecular Plant Pathology
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