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https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#1
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28094312/unraveling-the-microbial-processes-of-black-band-disease-in-corals-through-integrated-genomics
#2
Yui Sato, Edmund Y S Ling, Dmitrij Turaev, Patrick Laffy, Karen D Weynberg, Thomas Rattei, Bette L Willis, David G Bourne
Coral disease outbreaks contribute to the ongoing degradation of reef ecosystems, however, microbial mechanisms underlying the onset and progression of most coral diseases are poorly understood. Black band disease (BBD) manifests as a cyanobacterial-dominated microbial mat that destroys coral tissues as it rapidly spreads over coral colonies. To elucidate BBD pathogenesis, we apply a comparative metagenomic and metatranscriptomic approach to identify taxonomic and functional changes within microbial lesions during in-situ development of BBD from a comparatively benign stage termed cyanobacterial patches...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#3
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28077143/pregnant-women-carrying-microcephaly-foetuses-and-zika-virus-contain-potentially-pathogenic-microbes-and-parasites-in-their-amniotic-fluid
#4
Diogo Antonio Tschoeke, Louisi Souza de Oliveira, Luciana Leomil, Amilcar Tanuri, Fabiano Lopes Thompson
BACKGROUND: Microcephaly has become a major public health problem in Brazil. The total number of newborns with microcephaly was reported to be >4000 in June 2016. Studies suggest that Zika Virus is a major cause of new microcephaly cases in Brazil. Inside the uterus, the foetus is surrounded by the Amniotic Fluid, a proximal fluid that contains foetal and maternal cells as well as microorganisms and where Zika Virus was already found. CASE PRESENTATION: A previous study reported the presence of the Zika Virus in the amniotic fluid (collected in the 28th gestational week) of two pregnant women carrying microcephaly foetuses in Brazil...
January 11, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28076288/transfer-rnas-with-novel-cloverleaf-structures
#5
Takahito Mukai, Oscar Vargas-Rodriguez, Markus Englert, H James Tripp, Natalia N Ivanova, Edward M Rubin, Nikos C Kyrpides, Dieter Söll
We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter T-stem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28063827/taxonomic-and-functional-diversity-of-a-coastal-planktonic-bacterial-community-in-a-river-influenced-marine-area
#6
Stefan Thiele, Michael Richter, Cecilia Balestra, Frank Oliver Glöckner, Raffaella Casotti
The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated and industrial areas. This paper reports on the diversity and community structure of the marine residential Bacteria and Archaea of the Gulf of Naples in an area close to the river Sarno plume and investigates their small-scale taxonomic diversity and expression patterns as a proxy of potential metabolic activity using metagenomics and metatranscriptomics...
January 4, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28061817/the-rumen-microbial-metaproteome-as-revealed-by-sds-page
#7
Timothy J Snelling, R John Wallace
BACKGROUND: Ruminal digestion is carried out by large numbers of bacteria, archaea, protozoa and fungi. Understanding the microbiota is important because ruminal fermentation dictates the efficiency of feed utilisation by the animal and is also responsible for major emissions of the greenhouse gas, methane. Recent metagenomic and metatranscriptomic studies have helped to elucidate many features of the composition and activity of the microbiota. The metaproteome provides complementary information to these other -omics technologies...
January 7, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28036141/expression-of-eukaryotic-like-protein-in-the-microbiome-of-sponges
#8
C Díez-Vives, L Moitinho-Silva, S Nielsen, D Reynolds, T Thomas
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host-microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28009005/low-abundance-of-archaeorhizomycetes-among-fungi-in-soil-metatranscriptomes
#9
Michal Choma, Jiří Bárta, Hana Šantrůčková, Tim Urich
The Archaeorhizomycetes are recently discovered fungi with poorly resolved ecology. Even their abundance in soil fungal communities is currently disputed. Here we applied a PCR-independent, RNA-based metatranscriptomic approach to determine their abundance among fungi in eleven different soils across Europe. Using small subunit (SSU) ribosomal RNA transcripts as marker, we detected Archaeorhizomycetes in 17 out of 28 soil metatranscriptomes. They had average relative SSU rRNA abundance of 2.0% with a maximum of 9...
December 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28007524/microbial-metatranscriptomes-from-the-thermally-stratified-gulf-of-aqaba-eilat-during-summer
#10
Dan R Miller, Ulrike Pfreundt, Hila Elifantz, Wolfgang R Hess, Ilana Berman-Frank
The water column in the oligotrophic Gulf of Aqaba/Eilat experiences distinct seasonal cycles with the cooling air and water temperatures of late fall and winter destabilizing the thermocline and forming mixed layer depths reaching 300 to 700m. As air temperatures warm thermal re-stratification results in a stable thermocline throughout the summer which physically separates a photic, nutrient-poor surface layer from an aphotic, nutrient-rich deep layer. Here we present the first metatranscriptome dataset, and its taxonomic assignments, sampled from three depths of the 700m deep Station A in the Gulf of Aqaba during the summer stratification (surface - 10m, deep chlorophyll maximum (DCM) - 85m, deep aphotic zone -500m)...
December 19, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27986083/imp-a-pipeline-for%C3%A2-reproducible-reference-independent-integrated-metagenomic-and-metatranscriptomic-analyses
#11
Shaman Narayanasamy, Yohan Jarosz, Emilie E L Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C Laczny, Nicolás Pinel, Patrick May, Paul Wilmes
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases...
December 16, 2016: Genome Biology
https://www.readbyqxmd.com/read/27981239/ionic-liquids-impact-the-bioenergy-feedstock-degrading-microbiome-and-transcription-of-enzymes-relevant-to-polysaccharide-hydrolysis
#12
Yu-Wei Wu, Brendan Higgins, Chaowei Yu, Amitha P Reddy, Shannon Ceballos, Lawrence D Joh, Blake A Simmons, Steven W Singer, Jean S VanderGheynst
Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified...
November 2016: MSystems
https://www.readbyqxmd.com/read/27941956/microbial-community-structure-and-dynamics-in-thermophilic-composting-viewed-through-metagenomics-and-metatranscriptomics
#13
Luciana Principal Antunes, Layla Farage Martins, Roberta Verciano Pereira, Andrew Maltez Thomas, Deibs Barbosa, Leandro Nascimento Lemos, Gianluca Major Machado Silva, Livia Maria Silva Moura, George Willian Condomitti Epamino, Luciano Antonio Digiampietri, Karen Cristina Lombardi, Patricia Locosque Ramos, Ronaldo Bento Quaggio, Julio Cezar Franco de Oliveira, Renata Castiglioni Pascon, João Batista da Cruz, Aline Maria da Silva, João Carlos Setubal
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem...
December 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27935592/molecular-insights-into-a-dinoflagellate-bloom
#14
Weida Gong, Jamie Browne, Nathan Hall, David Schruth, Hans Paerl, Adrian Marchetti
In coastal waters worldwide, an increase in frequency and intensity of algal blooms has been attributed to eutrophication, with further increases predicted because of climate change. Yet, the cellular-level changes that occur in blooming algae remain largely unknown. Comparative metatranscriptomics was used to investigate the underlying molecular mechanisms associated with a dinoflagellate bloom in a eutrophied estuary. Here we show that under bloom conditions, there is increased expression of metabolic pathways indicative of rapidly growing cells, including energy production, carbon metabolism, transporters and synthesis of cellular membrane components...
December 9, 2016: ISME Journal
https://www.readbyqxmd.com/read/27918579/a-graph-centric-approach-for-metagenome-guided-peptide-and-protein-identification-in-metaproteomics
#15
Haixu Tang, Sujun Li, Yuzhen Ye
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27901108/survey-of-the-green-picoalga-bathycoccus-genomes-in-the-global-ocean
#16
Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Eric Pelletier, Jean-Marc Aury, Colomban de Vargas, Michael Sieracki, Daniele Iudicone, Daniel Vaulot, Patrick Wincker, Olivier Jaillon
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#17
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895636/genomic-and-transcriptomic-evidence-for-carbohydrate-consumption-among-microorganisms-in-a-cold-seep-brine-pool
#18
Weipeng Zhang, Wei Ding, Bo Yang, Renmao Tian, Shuo Gu, Haiwei Luo, Pei-Yuan Qian
The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27886631/metagenomics-analysis-reveals-a-new-metallothionein-family-sequence-and-metal-binding-features-of-new-environmental-cysteine-rich-proteins
#19
Antoine Ziller, Rajiv Kumar Yadav, Mercè Capdevila, Mondem Sudhakara Reddy, Laurent Vallon, Roland Marmeisse, Silvia Atrian, Òscar Palacios, Laurence Fraissinet-Tachet
Metallothioneins are cysteine-rich proteins, which function as (i) metal carriers in basal cell metabolism and (ii) protective metal chelators in conditions of metal excess. Metallothioneins have been characterized from different eukaryotic model and cultivable species. Presently, they are categorized in 15 families but evolutionary relationships between these metallothionein families remain unresolved. Several cysteine-rich protein encoding genes that conferred Cd-tolerance in Cd-sensitive yeast mutants have previously been isolated from soil eukaryotic metatranscriptomes...
February 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/27876823/alignment-free-transcriptomic-and-metatranscriptomic-comparison-using-sequencing-signatures-with-variable-length-markov-chains
#20
Weinan Liao, Jie Ren, Kun Wang, Shun Wang, Feng Zeng, Ying Wang, Fengzhu Sun
The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC)...
November 23, 2016: Scientific Reports
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