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David Hibbett, Kessy Abarenkov, Urmas Koljalg, Maarja Opik, Benli Chai, James R Cole, Qiong Wang, Pedro W Crous, Vincent A R G Robert, Thorunn Helgason, Josh Herr, Paul Kirk, Shiloh Lueschow, Kerry O'Donnell, Henrik Nilsson, Ryoko Oono, Conrad L Schoch, Christopher Smyth, Donny Walker, Andrea Porras-Alfaro, John W Taylor, David M Geiser
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes...
October 19, 2016: Mycologia
Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H Janssen, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts...
October 19, 2016: Microbiome
Shengwei Hou, Ulrike Pfreundt, Dan Miller, Ilana Berman-Frank, Wolfgang R Hess
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5' ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities...
October 19, 2016: Scientific Reports
Lars Grossmann, Daniela Beisser, Christina Bock, Antonis Chatzinotas, Manfred Jensen, Angelika Preisfeld, Roland Psenner, Sven Rahmann, Sabina Wodniok, Jens Boenigk
Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater dataset which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a...
October 16, 2016: Molecular Ecology
Hui-Ling Liao, Yuan Chen, Rytas Vilgalys
Ectomycorrhizal fungi (EMF) represent one of the major guilds of symbiotic fungi associated with roots of forest trees, where they function to improve plant nutrition and fitness in exchange for plant carbon. Many groups of EMF exhibit preference or specificity for different plant host genera; a good example is the genus Suillus, which grows in association with the conifer family Pinaceae. We investigated genetics of EMF host-specificity by cross-inoculating basidiospores of five species of Suillus onto ten species of Pinus, and screened them for their ability to form ectomycorrhizae...
October 2016: PLoS Genetics
Joshua M A Stough, Stephen P Dearth, Joshua E Denny, Gary R LeCleir, Nathan W Schmidt, Shawn R Campagna, Steven W Wilhelm
C57BL/6 mice are widely used for in vivo studies of immune function and metabolism in mammals. In a previous study, it was observed that when C57BL/6 mice purchased from different vendors were infected with Plasmodium yoelii, a causative agent of murine malaria, they exhibited both differential immune responses and significantly different parasite burdens: these patterns were reproducible when gut contents were transplanted into gnotobiotic mice. To gain insight into the mechanism of resistance, we removed whole ceca from mice purchased from two vendors, Taconic Biosciences (low parasitemia) and Charles River Laboratories (high parasitemia), to determine the combined host and microflora metabolome and metatranscriptome...
2016: Frontiers in Microbiology
Jiwoong Kim, Min Soo Kim, Andrew Y Koh, Yang Xie, Xiaowei Zhan
BACKGROUND: Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. RESULTS: Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline)...
October 10, 2016: BMC Bioinformatics
Anna Heintz-Buschart, Patrick May, Cédric C Laczny, Laura A Lebrun, Camille Bellora, Abhimanyu Krishna, Linda Wampach, Jochen G Schneider, Angela Hogan, Carine de Beaufort, Paul Wilmes
The gastrointestinal microbiome is a complex ecosystem with functions that shape human health. Studying the relationship between taxonomic alterations and functional repercussions linked to disease remains challenging. Here, we present an integrative approach to resolve the taxonomic and functional attributes of gastrointestinal microbiota at the metagenomic, metatranscriptomic and metaproteomic levels. We apply our methods to samples from four families with multiple cases of type 1 diabetes mellitus (T1DM)...
October 10, 2016: Nature Microbiology
Brittany F Peterson, Michael E Scharf
BACKGROUND: Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitation, fitness advantages, and even speciation events. These phenomena include expansions in host diet, detoxification of insecticides and toxins, and increased defense against pathogens. However, dissecting the contributions of individual groups of symbionts at the molecular level is often underexplored due to methodological and analytical limitations...
October 1, 2016: BMC Genomics
Francesca De Filippis, Eugenio Parente, Danilo Ercolini
This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High-throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia...
October 6, 2016: Microbial Biotechnology
Samuel T Westreich, Ian Korf, David A Mills, Danielle G Lemay
BACKGROUND: Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated computing cluster, or metagenome-based approaches that have not been fully evaluated for processing metatranscriptomic datasets. We created a new bioinformatics pipeline, designed specifically for metatranscriptome dataset analysis, which runs in conjunction with Metagenome-RAST (MG-RAST) servers...
September 29, 2016: BMC Bioinformatics
William H DePas, Ruth Starwalt-Lee, Lindsey Van Sambeek, Sripriya Ravindra Kumar, Viviana Gradinaru, Dianne K Newman
: Physiological resistance to antibiotics confounds the treatment of many chronic bacterial infections, motivating researchers to identify novel therapeutic approaches. To do this effectively, an understanding of how microbes survive in vivo is needed. Though much can be inferred from bulk approaches to characterizing complex environments, essential information can be lost if spatial organization is not preserved. Here, we introduce a tissue-clearing technique, termed MiPACT, designed to retain and visualize bacteria with associated proteins and nucleic acids in situ on various spatial scales...
September 27, 2016: MBio
Diego Chaves-Moreno, Melissa L Wos-Oxley, Ruy Jáuregui, Eva Medina, Andrew Pa Oxley, Dietmar H Pieper
Staphylococcus aureus is an important human pathogen and commensal, where the human nose is the predominant reservoir. To better understand its behavior in this environmental niche, RNA was extracted from the anterior nares of three documented S. aureus carriers and the metatranscriptome analyzed by RNAseq. In addition, the in vivo transcriptomes were compared to previously published transcriptomes of two in vitro grown S. aureus strains. None of the in vitro conditions, even growth in medium resembling the anterior nares environment, mimicked in vivo conditions...
2016: Scientific Reports
Ying Wang, Haiyan Hu, Xiaoman Li
Metatranscriptomics studies the transcriptome of all microbial species in a habitat. Removing ribosomal RNA (rRNA) reads in metatranscriptomic data is essential for the study of microbial gene expression. Although several methods are developed, all of them rely on rRNA databases that contain a limited number of known rRNA sequences and cannot work well on rRNA reads from unknown rRNA sequences. To address this problem, we have developed a novel approach called rRNAFilter. Our method can accurately and rapidly remove rRNA reads from metatranscriptomes without any prior knowledge of known rRNA sequences...
September 9, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Brian L Zielinski, Andrew E Allen, Edward J Carpenter, Victoria J Coles, Byron C Crump, Mary Doherty, Rachel A Foster, Joaquim I Goes, Helga R Gomes, Raleigh R Hood, John P McCrow, Joseph P Montoya, Ahmed Moustafa, Brandon M Satinsky, Shalabh Sharma, Christa B Smith, Patricia L Yager, John H Paul
The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes...
2016: PloS One
Ian J Miller, Niti Vanee, Stephen S Fong, Grace E Lim-Fong, Jason C Kwan
: The uncultured bacterial symbiont "Candidatus Endobugula sertula" is known to produce cytotoxic compounds called bryostatins, which protect the larvae of its host, Bugula neritina The symbiont has never been successfully cultured and it was thought that its genome might be significantly reduced. Here, we took a shotgun metagenomics and metatranscriptomics approach to assemble and characterize the genome of "Ca. E. sertula". We found that it had specific metabolic deficiencies in the biosynthesis of certain amino acids, but few other signs of genome degradation such as small size, abundant pseudogenes or low coding density...
September 2, 2016: Applied and Environmental Microbiology
Sara Billerbeck, Bernd Wemheuer, Sonja Voget, Anja Poehlein, Helge-Ansgar Giebel, Thorsten Brinkhoff, Lone Gram, Wade H Jeffrey, Rolf Daniel, Meinhard Simon
The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up to 22% of the active North Sea bacterioplankton in the summer...
2016: Nature Microbiology
Damian Rafal Plichta, Agnieszka Sierakowska Juncker, Marcelo Bertalan, Elizabeth Rettedal, Laurent Gautier, Encarna Varela, Chaysavanh Manichanh, Charlène Fouqueray, Florence Levenez, Trine Nielsen, Joël Doré, Ana Manuel Dantas Machado, Mari Cristina Rodriguez de Evgrafov, Torben Hansen, Torben Jørgensen, Peer Bork, Francisco Guarner, Oluf Pedersen, Morten O A Sommer, S Dusko Ehrlich, Thomas Sicheritz-Pontén, Søren Brunak, H Bjørn Nielsen
The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species(1). Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species(2,3). To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from Europeans...
2016: Nature Microbiology
Regenia B Phillips Campbell, Michelle M Duffourc, Robert V Schoborg, Yanji Xu, Xinyi Liu, Bruce H KenKnight, Eric Beaumont
Altered gut microbial diversity has been associated with several chronic disease states, including heart failure. Stimulation of the vagus nerve, which innervates the heart and abdominal organs, is proving to be an effective therapeutic in heart failure. We hypothesized that cervical vagus nerve stimulation (VNS) could alter fecal flora and prevent aberrations observed in fecal samples from heart failure animals. To determine if microbial abundances were altered by pressure overload (PO) leading to heart failure and VNS therapy, a VNS pulse generator was implanted with a stimulus lead on either the left or right vagus nerve prior to creation of PO by aortic constriction...
August 25, 2016: American Journal of Physiology. Gastrointestinal and Liver Physiology
Anastasia A Ivanova, Carl-Eric Wegner, Yongkyu Kim, Werner Liesack, Svetlana N Dedysh
Northern peatlands play a crucial role in the global carbon balance, serving as a persistent sink for atmospheric CO2 and a global carbon store. Their most extensive type, Sphagnum-dominated acidic peatlands, is inhabited by microorganisms with poorly understood degradation capabilities. Here, we applied a combination of barcoded pyrosequencing of SSU rRNA genes and Illumina RNA-Seq of total RNA (metatranscriptomics) to identify microbial populations and enzymes involved in degrading the major components of Sphagnum-derived litter and exoskeletons of peat-inhabiting arthropods: cellulose, xylan, pectin and chitin...
October 2016: Molecular Ecology
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