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https://www.readbyqxmd.com/read/28230768/bioinformatic-analysis-reveals-archaeal-trna-tyr-and-trna-trp-identities-in-bacteria
#1
Takahito Mukai, Noah M Reynolds, Ana Crnković, Dieter Söll
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins...
February 21, 2017: Life
https://www.readbyqxmd.com/read/28230723/bifidobacterium-adolescentis-exerts-strain-specific-effects-on-constipation-induced-by-loperamide-in-balb-c-mice
#2
Linlin Wang, Lujun Hu, Qi Xu, Boxing Yin, Dongsheng Fang, Gang Wang, Jianxin Zhao, Hao Zhang, Wei Chen
Constipation is one of the most common gastrointestinal complaints worldwide. This study was performed to determine whether Bifidobacterium adolescentis exerts inter-strain differences in alleviating constipation induced by loperamide in BALB/c mice and to analyze the main reasons for these differences. BALB/c mice underwent gavage with B. adolescentis (CCFM 626, 667, and 669) once per day for 17 days. The primary outcome measures included related constipation indicators, and the secondary outcome measures were the basic biological characteristics of the strains, the concentration changes of short-chain fatty acids in feces, and the changes in the fecal flora...
February 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28229558/microbial-diversity-of-a-full-scale-uasb-reactor-applied-to-poultry-slaughterhouse-wastewater-treatment-integration-of-16s-rrna-gene-amplicon-and-shotgun-metagenomic-sequencing
#3
Tiago Palladino Delforno, Gileno Vieira Lacerda Júnior, Melline F Noronha, Isabel K Sakamoto, Maria Bernadete A Varesche, Valéria M Oliveira
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset...
February 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28229543/developmental-trajectories-of-amphibian-microbiota-response-to-bacterial-therapy-depends-on-initial-community-structure
#4
Leyla R Davis, Laurent Bigler, Douglas C Woodhams
Improving host health through microbial manipulation requires untangling factors that shape the microbiome. There is currently little understanding of how initial community structure may drive the microbiota trajectory across host development or influence bacterial therapy. Probiotic baths of surface symbionts, Pseudomonas fluorescens and Flavobacterium johnsoniae were administered to 240 tadpoles of the midwife toad, Alytes obstetricans in semi-natural outdoor mesocosms originating from geographically and genetically distinct populations in Switzerland...
February 22, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28229521/microbial-potential-for-carbon-and-nutrient-cycling-in-a-geogenic-supercritical-carbon-dioxide-reservoir
#5
Adam J E Freedman, BoonFei Tan, Janelle R Thompson
Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a "deep carbonated biosphere" with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content...
February 22, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28224712/a-novel-astrovirus-associated-with-encephalitis-and-ganglionitis-in-domestic-sheep
#6
F Pfaff, K Schlottau, S Scholes, A Courtenay, B Hoffmann, D Höper, M Beer
In June 2013, a 4-year-old Welsh Mountain ewe and in March 2014 a 10-day-old lamb of the same breed and the same flock presented progressive neurological signs including depressed sensorium, tremor, and unusual behaviour. Neuropathological examination of the brain and spinal cord detected non-suppurative polioencephalomyelitis and dorsal root ganglionitis, characteristic of a neurotropic viral agent in both sheep. Metagenomic analysis of different tissue samples from both animals identified a novel Ovine Astrovirus (OvAstV)...
February 22, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28223973/a-perspective-study-of-koumiss-microbiome-by-metagenomics-analysis-based-on-single-cell-amplification-technique
#7
Guoqiang Yao, Jie Yu, Qiangchuan Hou, Wenyan Hui, Wenjun Liu, Lai-Yu Kwok, Bilige Menghe, Tiansong Sun, Heping Zhang, Wenyi Zhang
Koumiss is a traditional fermented dairy product and a good source for isolating novel bacteria with biotechnology potential. In the present study, we applied the single-cell amplification technique in the metagenomics analysis of koumiss. This approach aimed at detecting the low-abundant bacteria in the koumiss. Briefly, each sample was first serially diluted until reaching the level of approximately 100 cells. Then, three diluted bacterial suspensions were randomly picked for further study. By analyzing 30 diluted koumiss suspensions, a total of 24 bacterial species were identified...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28223457/the-source-and-evolutionary-history-of-a-microbial-contaminant-identified-through-soil-metagenomic-analysis
#8
Matthew R Olm, Cristina N Butterfield, Alex Copeland, T Christian Boles, Brian C Thomas, Jillian F Banfield
In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223214/expression-studies-of-bacillus-licheniformis-chitin-deacetylase-in-e-coli-rosetta-cells
#9
Ritu Raval, Simsa Robin, Keyur Raval
Chitin, the biopolymer of the N-acetylglucosamine, is the most abundant biopolymer on the planet after cellulose. However owing to its crystalline nature, its deacetylated derivative; chitosan is industrially more potent. This conversion on an enzymatic scale can be made using chitin deacetylase. The metagenomics library constructed from the soil exposed to chitin and chitosan yielded chitin modifying enzymes, one of them being chitin deacetylase (CDA) utilized for the present study. The gene was amplified and expressed using the pET 22b vector in E...
February 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28222236/differential-sharing-and-distinct-co-occurrence-networks-among-spatially-close-bacterial-microbiota-of-bark-mosses-and-lichens%C3%A2-%C3%A2
#10
Ines Aline Aschenbrenner, Tomislav Cernava, Armin Erlacher, Gabriele Berg, Martin Grube
Knowledge of bacterial community host-specificity has increased greatly in recent years. However, the inter-microbiome relationships of unrelated but spatially close organisms remain little understood. Trunks of trees covered by epiphytes represent complex habitats with a mosaic of ecological niches. In this context, we investigated the structure, diversity and interactions of microbiota associated with lichens, mosses and the bare tree bark. Comparative analysis revealed significant differences in the habitat-associated community structures...
February 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28222161/the-distinct-features-of-microbial-dysbiosis-of-crohn-s-disease-do-not-occur-to-the-same-extent-in-their-unaffected-genetically-linked-kindred
#11
Umer Zeeshan Ijaz, Christopher Quince, Laura Hanske, Nick Loman, Szymon T Calus, Martin Bertz, Christine A Edwards, Daniel R Gaya, Richard Hansen, Paraic McGrogan, Richard K Russell, Konstantinos Gerasimidis
BACKGROUND/AIMS: Studying the gut microbiota in unaffected relatives of people with Crohn's disease (CD) may advance our understanding of the role of bacteria in disease aetiology. METHODS: Faecal microbiota composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared in unaffected adult relatives of CD children (CDR, n = 17) and adult healthy controls, unrelated to CD patients (HUC, n = 14)...
2017: PloS One
https://www.readbyqxmd.com/read/28220773/new-crispr-cas-systems-discovered
#12
Hui Yang, Dinshaw J Patel
In bacteria and archaea, CRISPR-Cas adaptive immune systems utilize RNA-guided endonucleases to defend against invasion by foreign nucleic acids of bacteriophage, virus and plasmid origin. In a recent paper published in Nature, Burstein et al. identified the first Cas9 protein in uncultivated archaea and two novel CRISPR-CasX and CRISPR-CasY systems in uncultivated bacteria by capitalizing on analysis of terabase-scale metagenomic datasets from natural uncultivated organisms.
February 21, 2017: Cell Research
https://www.readbyqxmd.com/read/28219787/a-novel-archaeal-species-belonging-to-methanoculleus-genus-identified-via-de-novo-assembly-and-metagenomic-binning-process-in-biogas-reactors
#13
Panagiotis G Kougias, Stefano Campanaro, Laura Treu, Xinyu Zhu, Irini Angelidaki
Recently, a first comprehensive catalogue of microbial genomes populating biogas reactors treating manure and agro-industrial residues was determined by sequencing samples collected from 22 biogas reactors including laboratory and full scale. Among the archaeal community, one of the most abundant methanogens belongs to Methanoculleus genus and for this reason it was provisionally named Methanoculleus sp. DTU006. Its full length 16S rRNA sequence is 97% similar to Methanoculleus marisnigri JR1 and to Methanoculleus palmolei DSM 4273...
February 17, 2017: Anaerobe
https://www.readbyqxmd.com/read/28218463/closed-reference-metatranscriptomics-enables-in-planta-profiling-of-putative-virulence-activities-in-the-grapevine-trunk-disease-complex
#14
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
https://www.readbyqxmd.com/read/28217901/the-choice-of-the-dna-extraction-method-may-influence-the-outcome-of-the-soil-microbial-community-structure-analysis
#15
Sylwia Zielińska, Piotr Radkowski, Aleksandra Blendowska, Agnieszka Ludwig-Gałęzowska, Joanna M Łoś, Marcin Łoś
Metagenomics approaches and recent improvements in the next-generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28217745/the-baltic-sea-virome-diversity-and-transcriptional-activity-of-dna-and-rna-viruses
#16
Lisa Zeigler Allen, John P McCrow, Karolina Ininbergs, Christopher L Dupont, Jonathan H Badger, Jeffery M Hoffman, Martin Ekman, Andrew E Allen, Birgitta Bergman, J Craig Venter
Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae...
January 2017: MSystems
https://www.readbyqxmd.com/read/28217111/integration-of-metagenomic-and-stable-carbon-isotope-evidence-reveals-the-extent-and-mechanisms-of-carbon-dioxide-fixation-in-high-temperature-microbial-communities
#17
Ryan de Montmollin Jennings, James J Moran, Zackary J Jay, Jacob P Beam, Laura M Whitmore, Mark A Kozubal, Helen W Kreuzer, William P Inskeep
Although the biological fixation of CO2 by chemolithoautotrophs provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs as a carbon and energy source, the relative amounts of autotrophic C in chemotrophic microbial communities are not well-established. The extent and mechanisms of CO2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable (13)C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous "streamer" communities) were investigated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28215046/genome-resolved-metagenomics-of-a-bioremediation-system-for-degradation-of-thiocyanate-in-mine-water-containing-suspended-solid-tailings
#18
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/28214713/comparative-analysis-of-metagenomes-of-italian-top-soil-improvers
#19
Federica Gigliucci, Gianfranco Brambilla, Rosangela Tozzoli, Valeria Michelacci, Stefano Morabito
Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E...
February 16, 2017: Environmental Research
https://www.readbyqxmd.com/read/28209840/genome-sequences-of-three-novel-bunyaviruses-two-novel-rhabdoviruses-and-one-novel-nyamivirus-from-washington-state-moths
#20
Negar Makhsous, Ryan C Shean, David Droppers, Jonathan Guan, Keith R Jerome, Alexander L Greninger
We report draft genome sequences of three novel bunyaviruses, two novel rhabdoviruses, and one novel nyamivirus identified metagenomically from 10 moths in Washington state.
February 16, 2017: Genome Announcements
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