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"Microbial ecology"

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https://www.readbyqxmd.com/read/28339946/pasture-flock-chicken-cecal-microbiome-responses-to-prebiotics-and-plum-fiber-feed-amendments
#1
S H Park, A Perrotta, I Hanning, S Diaz-Sanchez, S Pendleton, E Alm, S C Ricke
When prebiotics and other fermentation substrates are delivered to animals as feed supplements, the typical goal is to improve weight gain and feed conversion. In this work, we examined pasture flock chicken cecal contents using next generation sequencing (NGS) to identify and understand the composition of the microbiome when prebiotics and fermentation substrates were supplemented. We generated 16S rRNA sequencing data for 120 separate cecal samples from groups of chickens receiving one of 3 prebiotics or fiber feed additives...
March 3, 2017: Poultry Science
https://www.readbyqxmd.com/read/28334218/reconciliation-between-operational-taxonomic-units-and-species-boundaries
#2
Mohamed Mysara, Peter Vandamme, Ruben Props, Frederiek-Maarten Kerckhof, Natalie Leys, Nico Boon, Jeroen Raes, Pieter Monsieurs
The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into Operational Taxonomic Units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for a bacterial species. Our results show that the robustness of such a generalized cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene...
March 10, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28317257/top-down-control-of-carbon-sequestration-grazing-affects-microbial-structure-and-function-in-salt-marsh-soils
#3
Peter Mueller, Dirk Granse, Stefanie Nolte, Hai Thi Do, Magdalena Weingartner, Stefan Hoth, Kai Jensen
Tidal wetlands have been increasingly recognized as long-term carbon sinks in recent years. Work on carbon sequestration and decomposition processes in tidal wetlands focused so far mainly on effects of global-change factors such as sea-level rise and increasing temperatures. However, little is known about effects of land use, such as livestock grazing, on organic matter decomposition and ultimately carbon sequestration. The present work aims at understanding the mechanisms by which large herbivores can affect organic matter decomposition in tidal wetlands...
March 20, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28292322/revealing-large-metagenomic-regions-through-long-dna-fragment-hybridization-capture
#4
Cyrielle Gasc, Pierre Peyret
BACKGROUND: High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies...
March 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28289787/changes-in-bacterial-diversity-associated-with-bioremediation-of-used-lubricating-oil-in-tropical-soils
#5
Naruemon Meeboon, Mary-Cathrine Leewis, Sireewan Kaewsuwan, Suppasil Maneerat, Mary Beth Leigh
Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C)...
March 13, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28282040/impact-of-water-heater-temperature-setting-and-water-use-frequency-on-the-building-plumbing-microbiome
#6
Pan Ji, William J Rhoads, Marc A Edwards, Amy Pruden
Hot water plumbing is an important conduit of microbes into the indoor environment and can increase risk of opportunistic pathogens (for example, Legionella pneumophila). We examined the combined effects of water heater temperature (39, 42, 48, 51 and 58 °C), pipe orientation (upward/downward), and water use frequency (21, 3 and 1 flush per week) on the microbial composition at the tap using a pilot-scale pipe rig. 16S rRNA gene amplicon sequencing indicated that bulk water and corresponding biofilm typically had distinct taxonomic compositions (R(2)Adonis=0...
March 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28281565/changes-in-land-use-driven-by-urbanization-impact-nitrogen-cycling-and-the-microbial-community-composition-in-soils
#7
Haitao Wang, Christopher W Marshall, Minying Cheng, Huijuan Xu, Hu Li, Xiaoru Yang, Tianling Zheng
Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28280926/enhanced-detoxification-of-arsenic-under-carbon-starvation-a-new-insight-into-microbial-arsenic-physiology
#8
Vinod S Nandre, Sachin P Bachate, Rahul C Salunkhe, Aditi V Bagade, Yogesh S Shouche, Kisan M Kodam
Nutrient availability in nature influenced the microbial ecology and behavior present in existing environment. In this study, we have focused on isolation of arsenic-oxidizing cultures from arsenic devoid environment and studied effect of carbon starvation on rate of arsenite oxidation. In spite of the absence of arsenic, a total of 40 heterotrophic, aerobic, arsenic-transforming bacterial strains representing 18 different genera were identified. Nineteen bacterial species were isolated from tannery effluent and twenty-one from tannery soil...
March 10, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28278266/model-based-quantification-of-metabolic-interactions-from-dynamic-microbial-community-data
#9
Mark Hanemaaijer, Brett G Olivier, Wilfred F M Röling, Frank J Bruggeman, Bas Teusink
An important challenge in microbial ecology is to infer metabolic-exchange fluxes between growing microbial species from community-level data, concerning species abundances and metabolite concentrations. Here we apply a model-based approach to integrate such experimental data and thereby infer metabolic-exchange fluxes. We designed a synthetic anaerobic co-culture of Clostridium acetobutylicum and Wolinella succinogenes that interact via interspecies hydrogen transfer and applied different environmental conditions for which we expected the metabolic-exchange rates to change...
2017: PloS One
https://www.readbyqxmd.com/read/28276199/new-insights-into-a-hot-environment-for-early-life
#10
REVIEW
Jianghong Dai
Investigating the physical-chemical setting of early life is a challenging task. In this contribution, I attempt to introduce a provocative concept from cosmology-cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe-to the field. For this purpose, I revisit a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB...
March 9, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28273592/distribution-of-picoplankton-in-the-northeastern-south-china-sea-with-special-reference-to-the-effects-of-the-kuroshio-intrusion-and-the-associated-mesoscale-eddies
#11
Jiajun Li, Xin Jiang, Gang Li, Zhiyou Jing, Linbin Zhou, Zhixin Ke, Yehui Tan
We investigated picoplankton distribution patterns and environmental variables along an east-to-west transect in the northeastern South China Sea (SCS) during late winter 2016, giving us the opportunity to examine the impacts of the Kuroshio intrusion and the associated eddies. The results indicated that the subsurface (50-75m) phytoplankton biomass chlorophyll (Chl a) maximum (SCM) disappeared and was replaced by higher Chl a in the middle part of the transect due to the impacts of the Kuroshio intrusion and mesoscale eddies...
March 3, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28273164/mi-sim-a-matlab-package-for-the-numerical-analysis-of-microbial-ecological-interactions
#12
Matthew J Wade, Jordan Oakley, Sophie Harbisher, Nicholas G Parker, Jan Dolfing
Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties...
2017: PloS One
https://www.readbyqxmd.com/read/28266111/dental-biofilm-ecological-interactions-in-health-and-disease
#13
P D Marsh, Egija Zaura
BACKGROUND: The oral microbiome is diverse and exists as multispecies microbial communities on oral surfaces in structurally and functionally organized biofilms. AIM: To describe the network of microbial interactions (both synergistic and antagonistic) occurring within these biofilms and assess their role in oral health and dental disease. METHODS: PubMed database was searched for studies on microbial ecological interactions in dental biofilms...
March 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/28255684/defining-disturbance-for-microbial-ecology
#14
Craig J Plante
Disturbance can profoundly modify the structure of natural communities. However, microbial ecologists' concept of "disturbance" has often deviated from conventional practice. Definitions (or implicit usage) have frequently included climate change and other forms of chronic environmental stress, which contradict the macrobiologist's notion of disturbance as a discrete event that removes biomass. Physical constraints and disparate biological characteristics were compared to ask whether disturbances fundamentally differ in microbial and macroorganismal communities...
March 2, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28253864/bacterial-and-fungal-core-microbiomes-associated-with-small-grain-silages-during-ensiling-and-aerobic-spoilage
#15
Lysiane Duniere, Shanwei Xu, Jin Long, Chijioke Elekwachi, Yuxi Wang, Kelly Turkington, Robert Forster, Tim A McAllister
BACKGROUND: Describing the microbial populations present in small grain silage and understanding their changes during ensiling is of interest for improving the nutrient value of these important forage crops. Barley, oat and triticale forages as well as an intercropped mixture of the 3 crops were harvested and ensiled in mini silos for a period of 90 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages and bacterial and fungal communities during ensiling and aerobic exposure were described using 16S and 18S rDNA sequencing, respectively...
March 3, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28251186/uncovering-the-horseshoe-effect-in-microbial-analyses
#16
James T Morton, Liam Toran, Anna Edlund, Jessica L Metcalf, Christian Lauber, Rob Knight
The horseshoe effect is a phenomenon that has long intrigued ecologists. The effect was commonly thought to be an artifact of dimensionality reduction, and multiple techniques were developed to unravel this phenomenon and simplify interpretation. Here, we provide evidence that horseshoes arise as a consequence of distance metrics that saturate-a familiar concept in other fields but new to microbial ecology. This saturation property loses information about community dissimilarity, simply because it cannot discriminate between samples that do not share any common features...
January 2017: MSystems
https://www.readbyqxmd.com/read/28242419/sourdough-type-propagation-of-faba-bean-flour-dynamics-of-microbial-consortia-and-biochemical-implications
#17
Rossana Coda, Maryam Kianjam, Erica Pontonio, Michela Verni, Raffaella Di Cagno, Kati Katina, Carlo Giuseppe Rizzello, Marco Gobbetti
The microbial ecology of faba bean sourdoughs obtained from an Italian (Ita) and a Finnish (Fi) cultivar, belonging respectively to Vicia faba major and V. faba minor groups, was described by 16S rRNA gene pyrosequencing and culture-dependent analysis. The sourdoughs were propagated with traditional backslopping procedure throughout 14days. Higher microbial diversity was found in the sourdough deriving from V. faba minor (Fi), still containing residual hulls after the milling procedure. After 2days of propagation, the microbial profile of Ita sourdough was characterized by the dominance of the genera Pediococcus, Leuconostoc and Weissella, while the genera Lactococcus, Lactobacillus and Escherichia, as well as Enterobacteriaceae were present in Fi sourdoughs...
February 20, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28223257/the-fecal-microbiome-of-dogs-with-exocrine-pancreatic-insufficiency
#18
Anitha Isaiah, Joseph Cyrus Parambeth, Jörg M Steiner, Jonathan A Lidbury, Jan S Suchodolski
Exocrine pancreatic insufficiency (EPI) in dogs is a syndrome of inadequate synthesis and secretion of pancreatic enzymes. Small intestinal bacterial dysbiosis occurs in dogs with EPI, and is reversed with pancreatic enzyme therapy. However, there are no studies evaluating the fecal microbiome of dogs with EPI. The objective of this study was to evaluate the fecal microbiome of dogs with EPI. Three day pooled fecal samples were collected from healthy dogs (n = 18), untreated (n = 7) dogs with EPI, and dogs with EPI treated with enzyme replacement therapy (n = 19)...
February 18, 2017: Anaerobe
https://www.readbyqxmd.com/read/28213337/effect-of-advanced-oxidation-on-n-nitrosodimethylamine-ndma-formation-and-microbial-ecology-during-pilot-scale-biological-activated-carbon-filtration
#19
Dong Li, Ben Stanford, Eric Dickenson, Wendell O Khunjar, Carissa L Homme, Erik J Rosenfeldt, Jonathan O Sharp
Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H2O2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H2O2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated...
April 15, 2017: Water Research
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
#20
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
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