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https://www.readbyqxmd.com/read/29678199/megan-lr-new-algorithms-allow-accurate-binning-and-easy-interactive-exploration-of-metagenomic-long-reads-and-contigs
#1
Daniel H Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic, Rohan B H Williams
BACKGROUND: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets...
April 20, 2018: Biology Direct
https://www.readbyqxmd.com/read/29676618/cancer-risk-from-paediatric-computed-tomography-scanning-implications-for-radiation-protection-in-medicine
#2
A Kesminiene, E Cardis
The use of computed tomography (CT) imaging is clearly beneficial for millions of patients. However, the potential adverse health effects, particularly cancer, of ionising radiation exposure from CT early in life are an issue of growing concern in the radiological protection, medical, and public health communities. Although efforts to quantify these effects have been conducted, the precision and accuracy of reported risks needs confirmation. EPI-CT, a European collaborative epidemiological study, was set up to quantify risks from paediatric CT to optimise paediatric diagnostic protocol...
January 1, 2018: Annals of the ICRP
https://www.readbyqxmd.com/read/29676472/the-first-taxus-rhizosphere-microbiome-revealed-by-shotgun-metagenomic-sequencing
#3
Da-Cheng Hao, Cai-Rong Zhang, Pei-Gen Xiao
In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539)...
April 20, 2018: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29675263/micro-ct-x-ray-imaging-exposes-structured-diffusion-barriers-within-biofilms
#4
Alona Keren-Paz, Vlad Brumfeld, Yaara Oppenheimer-Shaanan, Ilana Kolodkin-Gal
In nature, bacteria predominantly exist as highly structured biofilms, which are held together by extracellular polymeric substance and protect their residents from environmental insults, such as antibiotics. The mechanisms supporting this phenotypic resistance are poorly understood. Recently, we identified a new mechanism maintaining biofilms - an active production of calcite minerals. In this work, a high-resolution and robust µCT technique is used to study the mineralized areas within intact bacterial biofilms...
2018: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29672855/on-the-development-of-a-predictive-functional-trait-approach-for-studying-terrestrial-arthropods
#5
REVIEW
Pierre-Marc Brousseau, Dominique Gravel, I Tanya Handa
1.The characterization of ecological communities with functional traits allows to consider simultaneously the ability of a species to survive and reproduce in an environment, its interactions with other species, and its effects on the ecosystem. 2.Functional traits have been studied mainly by plant ecologists, but are increasingly common in the study of other taxa including arthropods. Arthropods represent a group for which a functional trait approach could be highly profitable because of their high diversity, abundance, ubiquity and role in many important ecological processes...
April 19, 2018: Journal of Animal Ecology
https://www.readbyqxmd.com/read/29672134/metabolism-and-biodegradation-of-spacecraft-cleaning-reagents-by-strains-of-spacecraft-associated-acinetobacter
#6
Rakesh Mogul, Gregory A Barding, Sidharth Lalla, Sooji Lee, Steve Madrid, Ryan Baki, Mahjabeen Ahmed, Hania Brasali, Ivonne Cepeda, Trevor Gornick, Shawn Gunadi, Nicole Hearn, Chirag Jain, Eun Jin Kim, Thi Nguyen, Vinh Bao Nguyen, Alex Oei, Nicole Perkins, Joseph Rodriguez, Veronica Rodriguez, Gautam Savla, Megan Schmitz, Nicholas Tedjakesuma, Jillian Walker
Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions...
April 19, 2018: Astrobiology
https://www.readbyqxmd.com/read/29666288/microbiota-and-metatranscriptome-changes-accompanying-the-onset-of-gingivitis
#7
Emily M Nowicki, Raghav Shroff, Jacqueline A Singleton, Diane E Renaud, Debra Wallace, Julie Drury, Jolene Zirnheld, Brock Colleti, Andrew D Ellington, Richard J Lamont, David A Scott, Marvin Whiteley
Over half of adults experience gingivitis, a mild yet treatable form of periodontal disease caused by the overgrowth of oral microbes. Left untreated, gingivitis can progress to a more severe and irreversible disease, most commonly chronic periodontitis. While periodontal diseases are associated with a shift in the oral microbiota composition, it remains unclear how this shift impacts microbiota function early in disease progression. Here, we analyzed the transition from health to gingivitis through both 16S v4-v5 rRNA amplicon and metatranscriptome sequencing of subgingival plaque samples from individuals undergoing an experimental gingivitis treatment...
April 17, 2018: MBio
https://www.readbyqxmd.com/read/29665035/challenges-of-comprehensive-taxon-sampling-in-comparative-biology-wrestling-with-rosids
#8
Ryan A Folk, Miao Sun, Pamela S Soltis, Stephen A Smith, Douglas E Soltis, Robert P Guralnick
Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data-and doing this with rigor despite all the attendant challenges-is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems is hampered by a lingering series of theoretical and practical bottlenecks. The community is still wrestling with the challenges of how to develop species-level, comprehensively sampled phylogenies and associated geographic and phenotypic resources that enable global-scale analyses...
April 17, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29662224/the-spatial-scaling-of-species-interaction-networks
#9
REVIEW
Nuria Galiana, Miguel Lurgi, Bernat Claramunt-López, Marie-Josée Fortin, Shawn Leroux, Kevin Cazelles, Dominique Gravel, José M Montoya
Species-area relationships (SARs) are pivotal to understand the distribution of biodiversity across spatial scales. We know little, however, about how the network of biotic interactions in which biodiversity is embedded changes with spatial extent. Here we develop a new theoretical framework that enables us to explore how different assembly mechanisms and theoretical models affect multiple properties of ecological networks across space. We present a number of testable predictions on network-area relationships (NARs) for multi-trophic communities...
April 16, 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29661190/a-manually-annotated-actinidia-chinensis-var-chinensis-kiwifruit-genome-highlights-the-challenges-associated-with-draft-genomes-and-gene-prediction-in-plants
#10
Sarah M Pilkington, Ross Crowhurst, Elena Hilario, Simona Nardozza, Lena Fraser, Yongyan Peng, Kularajathevan Gunaseelan, Robert Simpson, Jibran Tahir, Simon C Deroles, Kerry Templeton, Zhiwei Luo, Marcus Davy, Canhong Cheng, Mark McNeilage, Davide Scaglione, Yifei Liu, Qiong Zhang, Paul Datson, Nihal De Silva, Susan E Gardiner, Heather Bassett, David Chagné, John McCallum, Helge Dzierzon, Cecilia Deng, Yen-Yi Wang, Lorna Barron, Kelvina Manako, Judith Bowen, Toshi M Foster, Zoe A Erridge, Heather Tiffin, Chethi N Waite, Kevin M Davies, Ella P Grierson, William A Laing, Rebecca Kirk, Xiuyin Chen, Marion Wood, Mirco Montefiori, David A Brummell, Kathy E Schwinn, Andrew Catanach, Christina Fullerton, Dawei Li, Sathiyamoorthy Meiyalaghan, Niels Nieuwenhuizen, Nicola Read, Roneel Prakash, Don Hunter, Huaibi Zhang, Marian McKenzie, Mareike Knäbel, Alastair Harris, Andrew C Allan, Andrew Gleave, Angela Chen, Bart J Janssen, Blue Plunkett, Charles Ampomah-Dwamena, Charlotte Voogd, Davin Leif, Declan Lafferty, Edwige J F Souleyre, Erika Varkonyi-Gasic, Francesco Gambi, Jenny Hanley, Jia-Long Yao, Joey Cheung, Karine M David, Ben Warren, Ken Marsh, Kimberley C Snowden, Kui Lin-Wang, Lara Brian, Marcela Martinez-Sanchez, Mindy Wang, Nadeesha Ileperuma, Nikolai Macnee, Robert Campin, Peter McAtee, Revel S M Drummond, Richard V Espley, Hilary S Ireland, Rongmei Wu, Ross G Atkinson, Sakuntala Karunairetnam, Sean Bulley, Shayhan Chunkath, Zac Hanley, Roy Storey, Amali H Thrimawithana, Susan Thomson, Charles David, Raffaele Testolin, Hongwen Huang, Roger P Hellens, Robert J Schaffer
BACKGROUND: Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. RESULTS: A second genome of an A...
April 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29657964/vive-la-persistence-engineering-human-microbiomes-in-the-21st-century
#11
Katrine L Whiteson
I imagine a future in which children grow up with healthy microbial communities. Engineering human microbiomes might actually be achievable in the near future, as we enter an era of hunting for human-adapted bacterial strains and phages. Furthermore, breath metabolites could allow us to track whether a probiotic colonizes persistently or a phage has knocked down a microbe of interest. Recent successes with probiotics, such as bifidobacteria that can break down human milk oligosaccharides, are making a future in which infants are intentionally colonized with health-promoting strains seem less unlikely...
March 2018: MSystems
https://www.readbyqxmd.com/read/29657133/development-of-a-prototype-system-for-archiving-integrative-hybrid-structure-models-of-biological-macromolecules
#12
Brinda Vallat, Benjamin Webb, John D Westbrook, Andrej Sali, Helen M Berman
Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms...
April 9, 2018: Structure
https://www.readbyqxmd.com/read/29655918/embracing-community-ecology-in-plant-microbiome-research
#13
Francisco Dini-Andreote, Jos M Raaijmakers
Community assembly is mediated by selection, dispersal, drift, and speciation. Environmental selection is mostly used to date to explain patterns in plant microbiome assembly, whereas the influence of the other processes remains largely elusive. Recent studies highlight that adopting community ecology concepts provides a mechanistic framework for plant microbiome research.
April 11, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29655761/the-relationship-between-culinary-skills-and-eating-behaviors-challenges-and-opportunities-for-parents-and-families
#14
Jessica Jarick Metcalfe, Darin Leonard
Unhealthy dietary intake among American children and adults is of great concern to public health practitioners, nutritional scientists, and child development experts. Cooking skills are related to healthier dietary intake among Americans of all ages, but remain a substantial barrier for many parents who want to serve healthy meals for their families at home. Culinary education interventions are effective solutions for many parents who do not know how to cook, but issues with participation bias mean that these programs are not effective solutions for all individuals...
April 12, 2018: Physiology & Behavior
https://www.readbyqxmd.com/read/29651160/structure-and-co-occurrence-patterns-in-microbial-communities-under-acute-environmental-stress-reveal-ecological-factors-fostering-resilience
#15
Dinka Mandakovic, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, Erwan Delage, Audrey Bihouée, Géraldine Jean, Francisca P Díaz, Beatriz Fernández-Gómez, Pablo Cabrera, Alexis Gaete, Claudio Latorre, Rodrigo A Gutiérrez, Alejandro Maass, Verónica Cambiazo, Sergio A Navarrete, Damien Eveillard, Mauricio González
Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29645089/nitrogen-enrichment-suppresses-other-environmental-drivers-and-homogenizes-salt-marsh-leaf-microbiome
#16
Pedro Daleo, Juan Alberti, Ari Jumpponen, Allison Veach, Florencia Ialonardi, Oscar Iribarne, Brian Silliman
Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities...
April 12, 2018: Ecology
https://www.readbyqxmd.com/read/29643938/a-hybrid-reference-guided-de-novo-assembly-approach-for-generating-cyclospora-mitochondrion-genomes
#17
G R Gopinath, H N Cinar, H R Murphy, M Durigan, M Almeria, B D Tall, A J DaSilva
Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations...
2018: Gut Pathogens
https://www.readbyqxmd.com/read/29629415/toward-personalized-control-of-human-gut-bacterial-communities
#18
Lawrence A David
A key challenge in microbiology will be developing tools for manipulating human gut bacterial communities. Our ability to predict and control the dynamics of these communities is now in its infancy. To manage human gut microbiota, I am developing methods in three research domains. First, I am refining in vitro tools to experimentally study gut microbes at high throughput and in controlled settings. Second, I am adapting "big data" techniques to overcome statistical challenges confronting microbiota modeling...
March 2018: MSystems
https://www.readbyqxmd.com/read/29629414/using-cultivated-microbial-communities-to-dissect-microbiome-assembly-challenges-limitations-and-the-path-ahead
#19
Benjamin E Wolfe
As troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems provide opportunities to identify drivers of microbiome assembly, but key challenges and limitations need to be carefully considered in their development, implementation, and interpretation. How well do model microbial communities mimic in vitro communities in terms of taxonomic diversity, trophic levels, intraspecific diversity, and the abiotic environment? What are the best ways to manipulate and measure inputs and outputs in model community experiments? In this perspective, I briefly address some of these challenges on the basis of our experience developing fermented food model communities...
March 2018: MSystems
https://www.readbyqxmd.com/read/29628800/modelling-understorey-dynamics-in-temperate-forests-under-global-change-challenges-and-perspectives
#20
D Landuyt, M P Perring, R Seidl, F Taubert, H Verbeeck, K Verheyen
The understorey harbours a substantial part of vascular plant diversity in temperate forests and plays an important functional role, affecting ecosystem processes such as nutrient cycling and overstorey regeneration. Global change, however, is putting these understorey communities on trajectories of change, potentially altering and reducing their functioning in the future. Developing mitigation strategies to safeguard the diversity and functioning of temperate forests in the future is challenging and requires improved predictive capacity...
April 2018: Perspectives in Plant Ecology, Evolution and Systematics
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