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"Microbial ecology"

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https://www.readbyqxmd.com/read/28524866/succession-in-the-petroleum-reservoir-microbiome-through-an-oil-field-production-lifecycle
#1
Adrien Vigneron, Eric B Alsop, Bartholomeus P Lomans, Nikos C Kyrpides, Ian M Head, Nicolas Tsesmetzis
Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28523076/metaproteomics-guided-selection-of-targeted-enzymes-for-bioprospecting-of-mixed-microbial-communities
#2
Jutta Speda, Bengt-Harald Jonsson, Uno Carlsson, Martin Karlsson
BACKGROUND: Hitherto, the main goal of metaproteomic analyses has been to characterize the functional role of particular microorganisms in the microbial ecology of various microbial communities. Recently, it has been suggested that metaproteomics could be used for bioprospecting microbial communities to query for the most active enzymes to improve the selection process of industrially relevant enzymes. In the present study, to reduce the complexity of metaproteomic samples for targeted bioprospecting of novel enzymes, a microbial community capable of producing cellulases was maintained on a chemically defined medium in an enzyme suppressed metabolic steady state...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28518116/the-wincf-model-an-inexpensive-and-tractable-microcosm-of-a-mucus-plugged-bronchiole-to-study-the-microbiology-of-lung-infections
#3
William J Comstock, Edwin Huh, Reiley Weekes, Connor Watson, Tianyang Xu, Pieter C Dorrestein, Robert A Quinn
Many chronic airway diseases result in mucus plugging of the airways. Lungs of an individual with cystic fibrosis are an exemplary case where their mucus-plugged bronchioles create a favorable habitat for microbial colonization. Various pathogens thrive in this environment interacting with each other and driving many of the symptoms associated with CF disease. Like any microbial community, the chemical conditions of their habitat have a significant impact on the community structure and dynamics. For example, different microorganisms thrive in differing levels of oxygen or other solute concentrations...
May 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28509909/experimental-evolution-and-the-dynamics-of-adaptation-and-genome-evolution-in-microbial-populations
#4
Richard E Lenski
Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection...
May 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28507535/bioreactor-scalability-laboratory-scale-bioreactor-design-influences-performance-ecology-and-community-physiology-in-expanded-granular-sludge-bed-bioreactors
#5
Stephanie Connelly, Seung G Shin, Robert J Dillon, Umer Z Ijaz, Christopher Quince, William T Sloan, Gavin Collins
Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB-a one-dimensional and a three- dimensional scale-down of a full-scale design-were built and operated in triplicate under near-identical conditions to a full-scale EGSB...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28506317/changes-in-microbial-ecology-after-fecal-microbiota-transplantation-for-recurrent-c-difficile-infection-affected-by-underlying-inflammatory-bowel-disease
#6
Sahil Khanna, Yoshiki Vazquez-Baeza, Antonio González, Sophie Weiss, Bradley Schmidt, David A Muñiz-Pedrogo, John F Rainey, Patricia Kammer, Heidi Nelson, Michael Sadowsky, Alexander Khoruts, Stefan L Farrugia, Rob Knight, Darrell S Pardi, Purna C Kashyap
BACKGROUND: Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance; consequently, it is now being investigated for its ability to improve inflammatory gut conditions such as IBD...
May 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28500319/airway-microbial-diversity-is-inversely-associated-with-mite-sensitized-rhinitis-and-asthma-in-early-childhood
#7
Chih-Yung Chiu, Yi-Ling Chan, Yu-Shuen Tsai, Ssu-An Chen, Chia-Jung Wang, Kuan-Fu Chen, I-Fang Chung
Microbiota plays an important role in regulating immune responses associated with atopic diseases. We sought to evaluate relationships among airway microbiota, serum IgE levels, allergic sensitization and their relevance to rhinitis and asthma. Microbial characterization was performed using Illumina-based 16S rRNA gene sequencing of 87 throat swabs collected from children with asthma (n = 32) and rhinitis (n = 23), and from healthy controls (n = 32). Data analysis was performed using QIIME (Quantitative Insights Into Microbial Ecology) v1...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28499076/single-cell-analysis-linking-ribosomal-r-dna-and-rrna-copy-numbers-to-cell-size-and-growth-rate-provides-insights-into-molecular-protistan-ecology
#8
Rao Fu, Jun Gong
Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)-based characteristics are linked with diversity, abundance and activity of protist populations and communities observed at organismal levels. Here, we applied a single-cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per-cell rDNA and rRNA CNs scaled with cell volume (CV) to 0...
May 12, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28497651/harnessing-the-power-of-digital-droplet-pcr-to-conduct-real-world-microbial-competitions
#9
Helen A Murphy
The budding yeast, Saccharomyces cerevisiae, has a long and storied history as a model organism for genetic, cellular and molecular biological research. More recently, researchers have sought to understand the ecology and evolution of its sister species, Saccharomyces paradoxus, in part to put our vast knowledge of the model yeast into its natural context (Replansky et al. ). However, the research tools have been limited, and most investigations into natural populations have either been descriptions of patterns of biogeography or taken the organism back into the laboratory for mating, growth and competition assays (Kuehne et al...
May 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28495244/rumen-prokaryotic-communities-of-ruminants-under-different-feeding-paradigms-on-the-qinghai-tibetan-plateau
#10
Dan Xue, Huai Chen, Xinquan Zhao, Shixiao Xu, Linyong Hu, Tianwei Xu, Lin Jiang, Wei Zhan
Yak and Tibetan sheep are the major indigenous ruminants on the Qinghai-Tibetan Plateau in China. The aim of this work was to study the differences in ruminal fermentation parameters and rumen prokaryotic community composition between hosts and feeding paradigms. The 16S rRNA genes targeting bacteria and archaea were sequenced using the MiSeq platform. The results showed that the prokaryotic community structure between yak and Tibetan sheep was significantly different (P<0.01). A significant difference in structure was also found between groups of yaks barn fed with a total mixed ration (TMR) and those naturally grazing (NG) (P=0...
April 18, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28488787/nitrotoga-is-selected-over-nitrospira-in-newly-assembled-biofilm-communities-from-a-tap-water-source-community-at-increased-nitrite-loading
#11
Marta Kinnunen, Arda Gülay, Hans-Jørgen Albrechtsen, Arnaud Dechesne, Barth F Smets
Community assembly is a central topic in microbial ecology: how do assembly processes interact and what is the relative contribution of stochasticity and determinism? Here, we exposed replicate flow-through biofilm systems, fed with nitrite-supplemented tap water, to continuous immigration from a source community, present in the tap water, to determine the extent of selection and neutral processes in newly assembled biofilm communities at both the community and the functional guild (of nitrite-oxidizing bacteria, NOB) levels...
May 10, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28484431/exploring-the-ecological-coherence-between-the-spatial-and-temporal-patterns-of-bacterioplankton-in-boreal-lakes
#12
Juan Pablo Niño-García, Clara Ruiz-González, Paul A Del Giorgio
One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs) within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada), and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28477379/tolyporphin-an-unusual-green-chlorin-like-dioxobacteriochlorin
#13
Christian Brückner
The tolyporphins, a family of green tetrapyrrolic pigments isolated from a cyanobacterium-microbial ecological unit, possess unique carbohydrate-derivatized dioxobacteriochlorin frameworks. A brief overview over the history, synthesis, chemistry, and biological properties of the tolyporphins form the backdrop for highlighting the contribution by Hood et al. [Hood, D., D. M. Niedzwiedzki, R. Zhang, Y. Zhang, J. Dai, E. S. Miller, D. F. Bocian, P. G. Williams, J. S. Lindsey and D. Holten (2017) Photochem. Photobiol...
May 6, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28473000/tracking-microbial-colonization-in-fecal-microbiota-transplantation-experiments-via-genome-resolved-metagenomics
#14
Sonny T M Lee, Stacy A Kahn, Tom O Delmont, Alon Shaiber, Özcan C Esen, Nathaniel A Hubert, Hilary G Morrison, Dionysios A Antonopoulos, David T Rubin, A Murat Eren
BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits...
May 4, 2017: Microbiome
https://www.readbyqxmd.com/read/28472072/dbotu3-a-new-implementation-of-distribution-based-otu-calling
#15
Scott W Olesen, Claire Duvallet, Eric J Alm
Distribution-based operational taxonomic unit-calling (dbOTU) improves on other approaches by incorporating information about the input sequences' distribution across samples. Previous implementations of dbOTU presented challenges for users. Here we introduce and evaluate a new implementation of dbOTU that is faster and more user-friendly. We show that this new implementation has theoretical and practical improvements over previous implementations of dbOTU, making the algorithm more accessible to microbial ecology and biomedical researchers...
2017: PloS One
https://www.readbyqxmd.com/read/28468277/sampling-terrestrial-environments-for-bacterial-polyketides
#16
REVIEW
Patrick Hill, Graham W Heberlig, Christopher N Boddy
Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment...
April 29, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28466638/toward-quantitative-understanding-of-the-bioavailability-of-dissolved-organic-matter-in-freshwater-lake-during-cyanobacteria-blooming
#17
Leilei Bai, Chicheng Cao, Changhui Wang, Huacheng Xu, Hui Zhang, Vera I Slaveykova, Helong Jiang
Occurrence of cyanobacterial harmful algal blooms (CyanoHAB) can induce considerable patchiness in the concentration and bioavailability of dissolved organic matter (DOM), which could influence biogeochemical processes and fuel microbial metabolism. In the present study, a laboratory 4-stage plug-flow bioreactor was used to successfully separate the CyanoHAB-derived DOM isolated from the eutrophic Lake Taihu (China) into continuum classes of bioavailable compounds. A combination of new state-of-the-art tools borrowed from analytical chemistry and microbial ecology were used to characterize quantitatively the temporary evolution of DOM and to get deeper insights into its bioavailability...
May 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28464950/illumina-miseq-16s-amplicon-sequence-analysis-of-bovine-respiratory-disease-associated-bacteria-in-lung-and-mediastinal-lymph-node-tissue
#18
Dayle Johnston, Bernadette Earley, Paul Cormican, Gerard Murray, David Anthony Kenny, Sinead Mary Waters, Mark McGee, Alan Kieran Kelly, Matthew Sean McCabe
BACKGROUND: Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract...
May 2, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28459886/bacterial-microbiome-of-the-nose-of-healthy-dogs-and-dogs-with-nasal-disease
#19
Barbara Tress, Elisabeth S Dorn, Jan S Suchodolski, Tariq Nisar, Prajesh Ravindran, Karin Weber, Katrin Hartmann, Bianka S Schulz
The role of bacterial communities in canine nasal disease has not been studied so far using next generation sequencing methods. Sequencing of bacterial 16S rRNA genes has revealed that the canine upper respiratory tract harbors a diverse microbial community; however, changes in the composition of nasal bacterial communities in dogs with nasal disease have not been described so far. Aim of the study was to characterize the nasal microbiome of healthy dogs and compare it to that of dogs with histologically confirmed nasal neoplasia and chronic rhinitis...
2017: PloS One
https://www.readbyqxmd.com/read/28453559/evaluation-of-the-reproducibility-of-amplicon-sequencing-with-illumina-miseq-platform
#20
Chongqing Wen, Liyou Wu, Yujia Qin, Joy D Van Nostrand, Daliang Ning, Bo Sun, Kai Xue, Feifei Liu, Ye Deng, Yuting Liang, Jizhong Zhou
Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33...
2017: PloS One
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