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microbial ecology

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https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#1
Umay Kulsum, Arti Kapil, Harpreet Singh, Punit Kaur
Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29785352/diversity-and-community-structure-of-marine-microbes-around-the-benham-rise-underwater-plateau-northeastern-philippines
#2
Andrian P Gajigan, Aletta T Yñiguez, Cesar L Villanoy, Maria Lourdes San Diego-McGlone, Gil S Jacinto, Cecilia Conaco
Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing...
2018: PeerJ
https://www.readbyqxmd.com/read/29783165/preferential-feeding-in-naegleria-fowleri-intracellular-bacteria-isolated-from-amoebae-in-operational-drinking-water-distribution-systems
#3
Haylea C Miller, Matthew J Morgan, Tom Walsh, Jason T Wylie, Anna H Kaksonen, Geoffrey J Puzon
The amoeba Naegleria fowleri is the causative agent of the highly fatal disease, primary amoebic meningoencephalitis, and estimated to cause 16 deaths per year in the United States alone. Colonisation of drinking water distribution systems (DWDSs) by the N. fowleri is a significant public health issue. Understanding the factors which enable this pathogen to colonise and thrive in DWDSs is critical for proper management. The microbial ecology within DWDSs may influence the ability of N. fowleri to colonise DWDSs by facilitating the availability of an appropriate food source...
May 6, 2018: Water Research
https://www.readbyqxmd.com/read/29782923/clinical-applications-of-gut-microbiota-in-cancer-biology
#4
REVIEW
Sunny H Wong, Thomas N Y Kwong, Chun-Ying Wu, Jun Yu
The involvement of microorganisms in cancer has been increasing recognized. Collectively, microorganisms have been estimated to account for ~20% of all cancers worldwide. Recent advances in metagenomics and bioinformatics have provided new insights on the microbial ecology in different tumors, pinpointing the roles of microorganisms in cancer formation, development and response to treatments. Furthermore, studies have emphasized the importance of host-microbial and inter-microbial interactions in the cancer microbiota...
May 18, 2018: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29774049/bioreactor-microbial-ecosystems-with-differentiated-methanogenic-phenol-biodegradation-and-competitive-metabolic-pathways-unraveled-with-genome-resolved-metagenomics
#5
Feng Ju, Yubo Wang, Tong Zhang
Background: Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information. Results: Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29774016/taxon-function-decoupling-as-an-adaptive-signature-of-lake-microbial-metacommunities-under-a-chronic-polymetallic-pollution-gradient
#6
Bachar Cheaib, Malo Le Boulch, Pierre-Luc Mercier, Nicolas Derome
Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29769279/microbial-interactions-in-the-cystic-fibrosis-airway
#7
Ann M Granchelli, Frederick R Adler, Ruth H Keogh, Christiana Kartsonaki, David R Cox, Theodore G Liou
Interactions in the airway ecology of cystic fibrosis may alter organism persistence and clinical outcomes. Better understanding of such interactions could guide clinical decisions. We fitted logistic regression models using generalized estimating equations to longitudinal two-year patient cohorts in the Cystic Fibrosis Foundation Patient Registry, 2003-2011 to study associations between airway organisms present in each calendar year and their presence in the subsequent year. Models were adjusted for clinical characteristics and multiple observations per patient and tested for sensitivity to cystic fibrosis-specific treatments...
May 16, 2018: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29768432/the-ecology-of-the-drosophila-yeast-mutualism-in-wineries
#8
Allison S Quan, Michael B Eisen
The fruit fly, Drosophila melanogaster, is preferentially found on fermenting fruits. The yeasts that dominate the microbial communities of these substrates are the primary food source for developing D. melanogaster larvae, and adult flies manifest a strong olfactory system-mediated attraction for the volatile compounds produced by these yeasts during fermentation. Although most work on this interaction has focused on the standard laboratory yeast Saccharomyces cerevisiae, a wide variety of other yeasts naturally ferment fallen fruit...
2018: PloS One
https://www.readbyqxmd.com/read/29767159/niacin-alters-the-ruminal-microbial-composition-of-cattle-under-high-concentrate-condition
#9
Dan Luo, Yufei Gao, Youyou Lu, Mingren Qu, Xiaowen Xiong, Lanjiao Xu, Xianghui Zhao, Ke Pan, Kehui Ouyang
To understand the effects of niacin on the ruminal microbial ecology of cattle under high-concentrate diet condition, Illumina MiSeq sequencing technology was used. Three cattle with rumen cannula were used in a 3 × 3 Latin-square design trial. Three diets were fed to these cattle during 3 periods for 3 days, respectively: high-forage diet (HF; forage-to-concentrate ratio = 80:20), high-concentrate diet (HC; forage-to-concentrate ratio = 20:80), and HC supplemented with 800 mg/kg niacin (HCN). Ruminal pH was measured before feeding and every 2 h after initiating feeding...
June 2017: Animal nutrition
https://www.readbyqxmd.com/read/29766233/environmental-drivers-controlling-bacterial-and-archaeal-abundance-in-the-sediments-of-a-mediterranean-lagoon-ecosystem
#10
Claudia Pala, Massimiliano Molari, Daniele Nizzoli, Marco Bartoli, Pierluigi Viaroli, Elena Manini
The environmental factors controlling the abundance of Bacteria and Archaea in lagoon ecosystems are poorly understood. Here, an integrated physico-chemical, biogeochemical, and microbiological survey was applied in the Sacca di Goro lagoon (Po River Delta, Italy) to investigate the variation of bacterial and archaeal abundance, as assessed by Fluorescence In Situ Hybridization, along winter and summer environmental gradients. We hypothesised that bacterial and archaeal cells respond differentially to physico-chemical parameters of the sediment, which can be manifested in variations of total cells number...
May 15, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29765359/comparing-microbiome-sampling-methods-in-a-wild-mammal-fecal-and-intestinal-samples-record-different-signals-of-host-ecology-evolution
#11
Melissa R Ingala, Nancy B Simmons, Claudia Wultsch, Konstantinos Krampis, Kelly A Speer, Susan L Perkins
The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29764656/rapid-evolution-of-aphid-pests-in-agricultural-environments
#12
REVIEW
Jean-Christophe Simon, Jean Peccoud
Aphids constitute a major group of crop pests that inflict serious damages to plants, both directly by ingesting phloem and indirectly as vectors of numerous diseases. In response to intense and repeated human-induced pressures, such as insecticide treatments, the use of resistant plants and biological agents, aphids have developed a series of evolutionary responses relying on adaptation and phenotypic plasticity. In this review, we highlight some remarkable evolutionary responses to anthropogenic pressures in agroecosystems and discuss the mechanisms underlying the ecological and evolutionary success of aphids...
April 2018: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/29764649/the-biology-and-prevalence-of-fungal-diseases-in-managed-and-wild-bees
#13
REVIEW
Sophie Ef Evison, Annette B Jensen
Managed and wild bees, whether solitary or social have a plethora of microbial associations that vary in their influence on the health of the bees. In this review, we summarise our current knowledge of aspects of the biology and ecology of bee associated fungi. The biology of bees that fungi are associated with are described, and the likely influences on fungal transmission are discussed. There is a clear disparity in research on fungi associated with managed compared to wild bees, leaving gaps in our understanding of fungal pathogen epidemiology...
April 2018: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/29762899/metagenomics-analysis-of-gut-microbiota-in-a-high-fat-diet-induced-obesity-mouse-model-fed-with-epigallocatechin-3-o-3-o-methyl-gallate-egcg3-me
#14
Xin Zhang, Yuhui Chen, Jieyu Zhu, Man Zhang, Chi-Tang Ho, Qingrong Huang, Jinxuan Cao
SCOPE: (-)-Epigallocatechin 3-O-(3-O-methyl) gallate (EGCG3''Me) has been shown to have a modulatory effect on human intestinal microbiota, and the relationship between intestinal flora and obesity has attracted more and more attention recently. Here, we investigated the potential link between EGCG3''Me and gut microbiota composition, as well as the underlying mechanisms of the anti-obesity activity of EGCG3''Me. METHODS AND RESULTS: EGCG3''Me was prepared from oolong tea by column chromatography, and the influence of EGCG3''Me on intestinal microbiota was analysed using a human flora-associated high fat diet (HFD)-induced obesity mouse model by metagenomics...
May 15, 2018: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/29761037/uncovering-the-hidden-players-in-lepidoptera-biology-the-heritable-microbial-endosymbionts
#15
Anne Duplouy, Emily A Hornett
The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host's body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse...
2018: PeerJ
https://www.readbyqxmd.com/read/29760689/-trichoderma-biofertilizer-links-to-altered-soil-chemistry-altered-microbial-communities-and-improved-grassland-biomass
#16
Fengge Zhang, Yunqian Huo, Adam B Cobb, Gongwen Luo, Jiqiong Zhou, Gaowen Yang, Gail W T Wilson, Yingjun Zhang
In grasslands, forage and livestock production results in soil nutrient deficits as grasslands typically receive no nutrient inputs, leading to a loss of grassland biomass. The application of mature compost has been shown to effectively increase grassland nutrient availability. However, research on fertilization regime influence and potential microbial ecological regulation mechanisms are rarely conducted in grassland soil. We conducted a two-year experiment in meadow steppe grasslands, focusing on above- and belowground consequences of organic or Trichoderma biofertilizer applications and potential soil microbial ecological mechanisms underlying soil chemistry and microbial community responses...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29759899/integrated-diversity-analysis-of-the-microbial-community-in-a-reverse-osmosis-system-from-a-brazilian-oil-refinery
#17
Daiane R B Belgini, Virgínia M Siqueira, Douglas M Oliveira, Samantha G Fonseca, Viviane Piccin-Santos, Roberto S Dias, Larissa Quartaroli, Rodrigo S Souza, Ana Paula R Torres, Maíra P Sousa, Cláudio M Silva, Cynthia C Silva, Sérgio O De Paula, Valéria M Oliveira
Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality...
April 13, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29758429/microbial-ecology-of-two-hot-springs-of-sikkim-predominate-population-and-geochemistry
#18
Ishfaq Nabi Najar, Mingma Thundu Sherpa, Sayak Das, Saurav Das, Nagendra Thakur
Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches...
May 11, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29754736/unrevealing-variation-of-microbial-communities-and-correlation-with-environmental-variables-in-a-full-culture-cycle-of-undaria-pinnatifida
#19
Zelong Zhao, Yongjia Pan, Jingwei Jiang, Shan Gao, Hongjuan Sun, Ying Dong, Pihai Sun, Xiaoyan Guan, Zunchun Zhou
Bacteria are the most abundant organisms in natural environment and dominant drivers of multiple geochemical functions. Drawing a global picture of microbial community structure and understanding their ecological status remain a grand challenge. As a typical artificial process, aquaculture provides a large amount of foods and creates great economic benefits for human beings. However, few studies are aimed at the microbial community in the aquaculture environment of aquatic plants. We analyzed microbial communities from 21 water samples in a coastal aquaculture area during the whole cultural process of Undaria pinnatifida by using high-throughout sequencing of 16S rRNA gene...
May 8, 2018: Marine Environmental Research
https://www.readbyqxmd.com/read/29754084/the-samarco-mine-tailing-disaster-a-possible-time-bomb-for-heavy-metals-contamination
#20
Hermano M Queiroz, Gabriel N Nóbrega, Tiago O Ferreira, Leandro S Almeida, Thais B Romero, Sandra T Santaella, Angelo F Bernardino, Xosé L Otero
In November 2015, the largest socio-environmental disaster in the history of Brazil occurred when approximately 50 million m3 of mine tailings were released into the Doce River (SE Brazil), during the greatest failure of a tailings dam worldwide. The mine tailings passed through the Doce River basin, reaching the ecologically important estuary 17 days later. On the arrival of the mine wastes to the coastal area, contamination levels in the estuarine soils were measured to determine the baseline level of contamination and to enable an environmental risk assessment...
May 10, 2018: Science of the Total Environment
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