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https://www.readbyqxmd.com/read/28215046/genome-resolved-metagenomics-of-a-bioremediation-system-for-degradation-of-thiocyanate-in-mine-water-containing-suspended-solid-tailings
#1
Sumayah F Rahman, Rose S Kantor, Robert Huddy, Brian C Thomas, Andries W van Zyl, Susan T L Harrison, Jillian F Banfield
Thiocyanate (SCN(-) ) is a toxic compound that forms when cyanide (CN(-) ), used to recover gold, reacts with sulfur species. SCN(-) -degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory-based reactors operated without suspended solids...
February 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28213543/functional-characterization-of-a-28-kb-catabolic-island-from-pseudomonas-sp-m1-involved-in-biotransformation-of-%C3%AE-myrcene-and-related-plant-derived-volatiles
#2
Pedro Soares-Castro, Pedro Montenegro-Silva, Hermann J Heipieper, Pedro M Santos
Pseudomonas sp. M1 is able to mineralize highly hydrophobic and recalcitrant compounds such as benzene, phenol and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such spectrum of compounds as sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of M1 strain regarding β-myrcene catabolism was elucidated in this work, with focus on the biocatalytical potential of β-myrcene-associated core-code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213503/inhibition-of-inflammatory-gene-transcription-by-il-10-is-associated-with-rapid-suppression-of-lipopolysaccharide-induced-enhancer-activation
#3
Evan A Conaway, Dalila C de Oliveira, Christine M McInnis, Scott B Snapper, Bruce H Horwitz
IL-10 limits the magnitude of inflammatory gene expression following microbial stimuli and is essential to prevent inflammatory disease; however, the molecular basis for IL-10-mediated inhibition remains elusive. Using a genome-wide approach, we demonstrate that inhibition of transcription is the primary mechanism for IL-10-mediated suppression in LPS-stimulated macrophages and that inhibited genes can be divided into two clusters. Genes in the first cluster are inhibited only if IL-10 is included early in the course of LPS stimulation and is strongly enriched for IFN-inducible genes...
February 17, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28211847/syntrophic-linkage-between-predatory-carpediemonas-and-specific-prokaryotic-populations
#4
Emmo Hamann, Halina E Tegetmeyer, Dietmar Riedel, Sten Littmann, Soeren Ahmerkamp, Jianwei Chen, Philipp F Hach, Marc Strous
Most anoxic environments are populated by small (<10 μm) heterotrophic eukaryotes that prey on different microbial community members. How predatory eukaryotes engage in beneficial interactions with other microbes has rarely been investigated so far. Here, we studied an example of such an interaction by cultivating the anerobic marine flagellate, Carpediemonas frisia sp. nov. (supergroup Excavata), with parts of its naturally associated microbiome. This microbiome consisted of so far uncultivated members of the Deltaproteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia and Nanoarchaeota...
February 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28211844/a-tool-named-iris-for-versatile-high-throughput-phenotyping-in-microorganisms
#5
George Kritikos, Manuel Banzhaf, Lucia Herrera-Dominguez, Alexandra Koumoutsi, Morgane Wartel, Matylda Zietek, Athanasios Typas
Advances in our ability to systematically introduce and track controlled genetic variance in microorganisms have, in the past decade, fuelled high-throughput reverse genetics approaches. When coupled to quantitative readouts, such approaches are extremely powerful at elucidating gene function and providing insights into the underlying pathways and the overall cellular network organization. Yet, until now, all efforts to quantify microbial macroscopic phenotypes have been restricted to monitoring growth in a small number of model microorganisms...
February 17, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28211009/pneumococcal-predictive-proteins-selected-by-microbial-genomic-approach-are-serotype-cross-reactive-and-bind-to-host-extracellular-matrix-proteins
#6
Ana Paula Corrêa Argondizzo, Cláudio Marcos Rocha-de-Souza, Marta de Almeida Santiago, Ricardo Galler, Joice Neves Reis, Marco Alberto Medeiros
Streptococcus pneumoniae is a colonizer of the human nasopharynx, which accounts for most of the community-acquired pneumonia cases and can cause non-invasive and invasive diseases. Current available vaccines are serotype-specific and the use of recombinant proteins associated with virulence is an alternative to compose vaccines and to overcome these problems. In a previous work, we describe the identification of proteins in S. pneumoniae by reverse vaccinology and the genetic diversity of these proteins in clinical isolates...
February 17, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28211005/resequencing-and-annotation-of-the-nostoc-punctiforme-attc-29133-genome-facilitating-biofuel-and-high-value-chemical-production
#7
Luis E Moraes, Matthew J Blow, Erik R Hawley, Hailan Piao, Rita Kuo, Jennifer Chiniquy, Nicole Shapiro, Tanja Woyke, James G Fadel, Matthias Hess
Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28209833/metagenome-assembled-draft-genome-sequence-of-a-novel-microbial-stenotrophomonas-maltophilia-strain-isolated-from-caenorhabditisremanei-tissue
#8
Janna L Fierst, Duncan A Murdock, Chamali Thanthiriwatte, John H Willis, Patrick C Phillips
Stenotrophomonas maltophilia is a Gram-negative aerobic bacterium and emerging nosocomial pathogen. Here, we present a draft genome sequence for an S. maltophilia strain assembled from a metagenomic DNA extract isolated from a laboratory stock of the nematode worm Caenorhabditis remanei.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209150/penicillin-production-in-industrial-strain-penicillium-chrysogenum-p2niad18-is-not-dependent-on-the-copy-number-of-biosynthesis-genes
#9
Sandra Ziemons, Katerina Koutsantas, Kordula Becker, Tim Dahlmann, Ulrich Kück
BACKGROUND: Multi-copy gene integration into microbial genomes is a conventional tool for obtaining improved gene expression. For Penicillium chrysogenum, the fungal producer of the beta-lactam antibiotic penicillin, many production strains carry multiple copies of the penicillin biosynthesis gene cluster. This discovery led to the generally accepted view that high penicillin titers are the result of multiple copies of penicillin genes. Here we investigated strain P2niaD18, a production line that carries only two copies of the penicillin gene cluster...
February 16, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28205635/deciphering-the-distance-to-antibiotic-resistance-for-the-pneumococcus-using-genome-sequencing-data
#10
Fredrick M Mobegi, Amelieke J H Cremers, Marien I de Jonge, Stephen D Bentley, Sacha A F T van Hijum, Aldert Zomer
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203533/modification-of-extraction-method-for-community-dna-isolation-from-salt-affected-compact-wasteland-soil-samples
#11
Purvi Zaveri, Rushika Patel, Meghavi Patel, Devki Sarodia, Nasreen S Munshi
To overcome the issue of interferences by salt and compactness in release of bacterial cell required for lysis, method described by Yeates et al. (1998), was optimized for isolation of genomic material (Deoxyribo Nucleic Acid, DNA) from soil microbial community by addition of Al(NH4)SO4. Very low total viable count was observed in the samples tested and hence use of higher amount of soil is required primarily for DNA isolation from wasteland soils. The method proves itself efficient where commercially available bead beating and enzymatic lysis methods could not give isolation of any amount of community genomic DNA due to compact nature and salt concentrations present in soil...
2017: MethodsX
https://www.readbyqxmd.com/read/28202080/mentholation-affects-the-cigarette-microbiota-by-selecting-for-bacteria-resistant-to-harsh-environmental-conditions-and-selecting-against-potential-bacterial-pathogens
#12
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R Babik, Molly C Reid, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Amy R Sapkota, Emmanuel F Mongodin
BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product...
February 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28197141/metabolomic-and-metagenomic-analysis-of-two-crude-oil-production-pipelines-experiencing-differential-rates-of-corrosion
#13
Vincent Bonifay, Boris Wawrik, Jan Sunner, Emily C Snodgrass, Egemen Aydin, Kathleen E Duncan, Amy V Callaghan, Athenia Oldham, Turid Liengen, Iwona Beech
Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28196401/systematic-genetic-dissection-of-pts-in-vibrio-cholerae-uncovers-a-novel-glucose-transporter-and-a-limited-role-for-pts-during-infection-of-a-mammalian-host
#14
Chelsea A Hayes, Triana N Dalia, Ankur B Dalia
A common mechanism for high affinity carbohydrate uptake in microbial species is the phosphoenolpyruvate-dependent phosphotransferase system (PTS). This system consists of a shared component, EI, which is required for all PTS transport, and numerous carbohydrate uptake transporters. In V. cholerae, there are 13 distinct PTS transporters. Due to genetic redundancy within this system, the carbohydrate specificity of each of these transporters is not currently defined. Here, using multiplex genome editing by natural transformation (MuGENT), we systematically dissect PTS transport in V...
February 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28195220/induction-of-invertebrate-larval-settlement-different-bacteria-different-mechanisms
#15
Marnie L Freckelton, Brian T Nedved, Michael G Hadfield
Recruitment via settlement of pelagic larvae is critical for the persistence of benthic marine populations. For many benthic invertebrates, larval settlement occurs in response to surface microbial films. Larvae of the serpulid polychaete Hydroides elegans can be induced to settle by single bacterial species. Until now, only Pseudoalteromonas luteoviolacea had been subjected to detailed genetic and mechanistic studies. To determine if the complex structures, termed tailocins, derived from phage-tail gene assemblies and hypothesized to be the settlement cue in P...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194258/complete-genome-sequence-of-pseudomonas-stutzeri-strain-rch2-isolated-from-a-hexavalent-chromium-cr-vi-contaminated-site
#16
Romy Chakraborty, Hannah Woo, Paramvir Dehal, Robert Walker, Marcin Zemla, Manfred Auer, Lynne A Goodwin, Alexey Kazakov, Pavel Novichkov, Adam P Arkin, Terry C Hazen
Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28194142/respiratory-ammonification-of-nitrate-coupled-to-anaerobic-oxidation-of-elemental-sulfur-in-deep-sea-autotrophic-thermophilic-bacteria
#17
Galina B Slobodkina, Andrey V Mardanov, Nikolai V Ravin, Anastasia A Frolova, Nikolay A Chernyh, Elizaveta A Bonch-Osmolovskaya, Alexander I Slobodkin
Respiratory ammonification of nitrate is the microbial process that determines the retention of nitrogen in an ecosystem. To date, sulfur-dependent dissimilatory nitrate reduction to ammonium has been demonstrated only with sulfide as an electron donor. We detected a novel pathway that couples the sulfur and nitrogen cycles. Thermophilic anaerobic bacteria Thermosulfurimonas dismutans and Dissulfuribacter thermophilus, isolated from deep-sea hydrothermal vents, grew autotrophically with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28188205/metagenomic-and-metatranscriptomic-analyses-reveal-structure-and-dynamics-of-a-dechlorinating-community-containing-dehalococcoides-mccartyi-and-corrinoid-providing-microorganisms-under-cobalamin-limited-condition
#18
Yujie Men, Ke Yu, Jacob Bælum, Ying Gao, Julien Tremblay, Emmanuel Prestat, Ben Stenuit, Susannah G Tringe, Janet Jansson, Tong Zhang, Lisa Alvarez-Cohen
The aim of this study is to obtain a systems level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities and dynamics in trichloroethene (TCE) - dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 d), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment with exogenous cobalamin compared to the one without cobalamin addition...
February 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28187782/sputum-dna-sequencing-in-cystic-fibrosis-non-invasive-access-to-the-lung-microbiome-and-to-pathogen-details
#19
Rounak Feigelman, Christian R Kahlert, Florent Baty, Frank Rassouli, Rebekka L Kleiner, Philipp Kohler, Martin H Brutsche, Christian von Mering
BACKGROUND: Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution...
February 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28187704/the-nucleotide-composition-of-microbial-genomes-indicates-differential-patterns-of-selection-on-core-and-accessory-genomes
#20
Jon Bohlin, Vegard Eldholm, John H O Pettersson, Ola Brynildsrud, Lars Snipen
BACKGROUND: The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding accessory genomes in 36 species, represented by the genomes of 731 bacterial strains, to assess the impact of selective forces on base composition in microbes...
February 10, 2017: BMC Genomics
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