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Microbial diversity

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https://www.readbyqxmd.com/read/29786880/metagenomic-study-of-bacterial-microbiota-in-persistent-endodontic-infections-using-next-generation-sequencing
#1
G Sánchez-Sanhueza, H Bello-Toledo, G González-Rocha, A T Gonçalves, V Valenzuela, C Gallardo-Escárate
AIM: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS). METHODOLOGY: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified...
May 22, 2018: International Endodontic Journal
https://www.readbyqxmd.com/read/29786168/variation-in-electrode-redox-potential-selects-for-different-microorganisms-under-cathodic-current-flow-from-electrodes-in-marine-sediments
#2
Bonita R Lam, Annette R Rowe, Kenneth H Nealson
Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favorable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods...
May 22, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#3
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/29785353/diet-breadth-and-exploitation-of-exotic-plants-shift-the-core-microbiome-of-cephaloleia-a-group-of-tropical-herbivorous-beetles
#4
Chelsea L Blankenchip, Dana E Michels, H Elizabeth Braker, Shana K Goffredi
The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter , Enterobacteriacea, Pseudomonas , Lactococcus, and Comamonas . The Acinetobacter and Enterobacteriacea together accounted for 35% of the total average 16S rRNA ribotypes recovered from all specimens...
2018: PeerJ
https://www.readbyqxmd.com/read/29785352/diversity-and-community-structure-of-marine-microbes-around-the-benham-rise-underwater-plateau-northeastern-philippines
#5
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/29785219/assessing-methanogenic-archaeal-community-in-full-scale-anaerobic-sludge-digester-systems-in-dubai-united-arab-emirates
#6
Munawwar A Khan, Poojabahen G Patel, Arpitha G Ganesh, Naushad Rais, Sultan M Faheem, Shams T Khan
Introduction: Anaerobic digestion for methane production comprises of an exceptionally diverse microbial consortium, a profound understanding about which is still constrained. In this study, the methanogenic archaeal communities in three full-scale anaerobic digesters of a Municipal Wastewater Treatment Plant were analyzed by Fluorescence in situ hybridization and quantitative real-time Polymerase Chain Reaction (qPCR) technique. Methods & Materials: Fluorescence in situ hybridization (FISH) was performed to detect and quantify the methanogenic Archaea in the sludge samples whereas qPCR was carried out to support the FISH analysis...
2018: Open Microbiology Journal
https://www.readbyqxmd.com/read/29784886/-legionella-pneumophila-is-directly-sensitive-to-2-deoxyglucose-phosphate-via-its-uhpc-transporter-but-is-indifferent-to-shifts-in-host-cell-glycolytic-metabolism
#7
Jordan V Price, Kallie Jiang, Abigail Galantowicz, Alana Freifeld, Russell E Vance
Toll-like receptor stimulation induces a pronounced shift to increased glycolytic metabolism in mammalian macrophages. We observed that bone marrow-derived macrophages (BMMs) increase glycolysis in response to infection with Legionella pneumophila ( L. pneumophila ), but the role of host macrophage glycolysis on intracellular L. pneumophila replication is not currently understood. Treatment with 2-deoxyglucose (2DG) blocks L. pneumophila replication in mammalian macrophages but has no effect on bacteria grown in broth...
May 21, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29783785/effects-of-pb-smelting-on-the-soil-bacterial-community-near-a-secondary-lead-plant
#8
Zhanbin Luo, Jing Ma, Fu Chen, Xiaoxiao Li, Shaoliang Zhang
Secondary lead smelting is a widespread industrial activity which has exacerbated Pb or Cd contamination of soil and water across the world. Soil physicochemical properties, soil enzyme activities, heavy metal concentrations, and bacterial diversity near a secondary lead plant in Xuzhou, China were examined in this study. The results showed that secondary lead smelting activities influenced nearby soils. Soil acidification decreased one order of magnitude, with a mean value of 7.3. Soil organic matter also showed a downward trend, while potassium and nitrogen appeared to accumulate...
May 20, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29783128/treatment-of-acidic-sulfate-containing-wastewater-using-revolving-algae-biofilm-reactors-sulfur-removal-performance-and-microbial-community-characterization
#9
Haoyuan Zhou, Yanqing Sheng, Xuefei Zhao, Martin Gross, Zhiyou Wen
Industries such as mining operations are facing challenges of treating sulfur-containing wastewater such as acid mine drainage (AMD) generated in their plant. The aim of this work is to evaluate the use of a revolving algal biofilm (RAB) reactor to treat AMD with low pH (3.5-4) and high sulfate content (1-4 g/L). The RAB reactors resulted in sulfate removal efficiency up to 46% and removal rate up to 0.56 g/L-day, much higher than those obtained in suspension algal culture. The high-throughput sequencing revealed that the RAB reactor contained diverse cyanobacteria, green algae, diatoms, and acid reducing bacteria that contribute the sulfate removal through various mechanisms...
May 18, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29783110/temporal-and-spatial-variation-in-the-mechanisms-used-by-microorganisms-to-form-methylmercury-in-the-water-column-of-changshou-lake
#10
Zhilin Xing, Tiantao Zhao, Weiyang Bai, Xu Yang, Shuai Liu, Lijie Zhang
The microbiome in artificial lake water and its impact on mercury (Hg) methylation remain largely unknown. We selected the largest artificial lake in southeastern china, Changshou Lake (CSL), which has high background levels of Hg, for our investigation of Hg transformation microorganisms. Five different sections of the water column of CSL were sampled during four seasons. The water samples were subjected to analysis of geochemical parameters, various Hg species and microbiome information. High concentrations of total mercury (THg) were detected in CSL in comparison with those found in natural lakes...
May 18, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29783046/bacterial-community-of-industrial-raw-sausage-packaged-in-modified-atmosphere-throughout-the-shelf-life
#11
Stefano Raimondi, Maria Rosaria Nappi, Tiziana Maria Sirangelo, Alan Leonardi, Alberto Amaretti, Alessandro Ulrici, Rudy Magnani, Chiara Montanari, Giulia Tabanelli, Fausto Gardini, Maddalena Rossi
Ten lots of industrial raw sausages in modified atmosphere (CO2 30%, O2 70%), produced in the same plant over 7 months, were analyzed at the day after production (S samples) and at the end of shelf life (E samples), after 12 days storage at 7 °C to simulate thermal abuse. Quality of the products was generally compromised by storage at 7 °C, with only 3 E samples without alterations. During the shelf life, the pH decreased for the accumulation of acetic and lactic acids. A few biogenic amines accumulated, remaining below acceptable limits...
April 28, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29782468/potential-role-of-gut-microbiota-in-als-pathogenesis-and-possible-novel-therapeutic-strategies
#12
Letizia Mazzini, Luca Mogna, Fabiola De Marchi, Angela Amoruso, Marco Pane, Irene Aloisio, Nicole Bozzi Cionci, Francesca Gaggìa, Ausiliatrice Lucenti, Enrica Bersano, Roberto Cantello, Diana Di Gioia, Giovanni Mogna
BACKGROUND: Recent preclinical studies suggest that dysfunction of gastrointestinal tract may play a role in amyotrophic lateral sclerosis (ALS) pathogenesis through a modification of the gut microbiota brain axis. Our study is the first focused on microbiota analysis in ALS patients. AIM: Our aim was to study the main human gut microbial groups and the overall microbial diversity in ALS and healthy subjects. Moreover we have examined the influence of a treatment with a specific bacteriotherapy composed of Lactobacillus strains (Lactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus salivarius) acting on the gastrointestinal barrier...
May 18, 2018: Journal of Clinical Gastroenterology
https://www.readbyqxmd.com/read/29782156/combining-high-throughput-sequencing-of-sedadna-and-traditional-palaeolimnological-techniques-to-infer-historical-trends-in-cyanobacterial-communities
#13
Timothy J Tse, Lorne E Doig, Song Tang, Xiaohui Zhang, Weimin Sun, Steve B Wiseman, Cindy Xin Feng, Hongling Liu, John P Giesy, Markus Hecker, Paul D Jones
Freshwaters worldwide are under increasing pressure from anthropogenic activities and changing climate. Unfortunately, many inland waters lack sufficient long-term monitoring to assess environmental trends. Analysis of sedimentary ancient DNA (sedaDNA) is emerging as a means to reconstruct the past occurrence of microbial communities of inland waters. The purpose of this study was to assess a combination of high-throughput sequencing (16S rRNA) of sedaDNA and traditional palaeolimnological analyses to explore multidecadal relationships among cyanobacterial community composition, the potential for cyanotoxin production and palaeoenvironmental proxies...
May 21, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29782032/leaf-associated-bacterial-microbiota-of-coffee-and-its-correlation-with-manganese-and-calcium-levels-on-leaves
#14
Leandro Pio de de Sousa, Marcio José da da Silva, Jorge Maurício Mondego
Coffee is one of the most valuable agricultural commodities and the plants' leaves are the primary site of infection for most coffee diseases, such as the devastating coffee leaf rust. Therefore, the use of bacterial microbiota that inhabits coffee leaves to fight infections could be an alternative agricultural method to protect against coffee diseases. Here, we report the leaf-associated bacteria in three coffee genotypes over the course of a year, with the aim to determine the diversity of bacterial microbiota...
May 17, 2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29782021/exploring-the-root-microbiome-extracting-bacterial-community-data-from-the-soil-rhizosphere-and-root-endosphere
#15
Tuesday Simmons, Daniel F Caddell, Siwen Deng, Devin Coleman-Derr
The intimate interaction between plant host and associated microorganisms is crucial in determining plant fitness, and can foster improved tolerance to abiotic stresses and diseases. As the plant microbiome can be highly complex, low-cost, high-throughput methods such as amplicon-based sequencing of the 16S rRNA gene are often preferred for characterizing its microbial composition and diversity. However, the selection of appropriate methodology when conducting such experiments is critical for reducing biases that can make analysis and comparisons between samples and studies difficult...
May 2, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29780391/concepts-collide-genomic-immune-and-microbial-influences-on-the-tumor-microenvironment-and-response-to-cancer-therapy
#16
REVIEW
Miles C Andrews, Alexandre Reuben, Vancheswaran Gopalakrishnan, Jennifer A Wargo
Cancer research has seen unprecedented advances over the past several years, with tremendous insights gained into mechanisms of response and resistance to cancer therapy. Central to this has been our understanding of crosstalk between the tumor and the microenvironment, with the recognition that complex interactions exist between tumor cells, stromal cells, overall host immunity, and the environment surrounding the host. This is perhaps best exemplified in cancer immunotherapy, where numerous studies across cancer types have illuminated our understanding of the genomic and immune factors that shape responses to therapy...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29779667/terminal-alkyne-biosynthesis-in-marine-microbes
#17
Xuejun Zhu, Wenjun Zhang
The terminal alkyne is a readily derivatized functionality valued for its diverse applications in material synthesis, pharmaceutical science, and chemical biology. The synthetic biology routes to terminal alkynes are highly desired and yet underexplored. Some marine natural products contain a terminal alkyne functionality, and the discovery of the biosynthetic gene clusters for jamaicamide B and carmabin A marked the beginning of a new era in the understanding and engineering of terminal alkyne biosynthesis...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29779655/cobalamin-dependent-c-methyltransferases-from-marine-microbes-accessibility-via-rhizobia-expression
#18
Michael F Freeman
Cobalamin-dependent radical S-adenosylmethionine (rSAM) methyltransferases catalyze chemically challenging methylation reactions on diverse natural products at unactivated carbon centers. In vivo reconstitution and biosynthetic studies of natural product gene clusters encoding these enzymes are often severely limited by ineffective heterologous expression hosts, including the otherwise versatile Escherichia coli. In this chapter, we describe the use of rhizobia bacteria as effective expression hosts for cobalamin-dependent rSAM C-methyltransferases...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29779275/-salivary-microbial-communities-associated-with-severe-early-childhood-caries
#19
Tong-Zheng Sun, Fei Teng, Song-Bo Jia, Yong-Ping Tang, Ming Jiang, Shi Huang, Xiao Yuan, Xiao-Lan Li, Fang Yang
OBJECTIVE: To compare the salivary microbial profiles of healthy subjects and those with severe early childhood caries (S-ECC) by using high-throughput sequencing. METHODS: Salivary samples were obtained from children with S-ECC (group C, n=24) and healthy children (group H, n=24). Total metagenomic DNA was extracted, and DNA amplicons of the V1-V3 hypervariable region of the 16S rRNA gene were generated and subjected to 454 sequencing. The characteristics of oral microbial communities from the two groups were compared based on microbial diversity and taxonomy assignment...
April 1, 2018: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/29778217/the-inflammasome-regulation-of-nitric-oxide-and-antimicrobial-host-defence
#20
Rajalaksmy A Ramachandran, Christopher Lupfer, Hasan Zaki
Nitric oxide (NO) is a gaseous signalling molecule that plays diverse physiological functions including antimicrobial host defence. During microbial infection, NO is synthesized by inducible NO synthase (iNOS), which is expressed by host immune cells through the recognition of microbial pattern molecules. Therefore, sensing pathogens or their pattern molecules by pattern recognition receptors (PRRs), which are located at the cell surface, endosomal and phagosomal compartment, or in the cytosol, is key in inducing iNOS and eliciting antimicrobial host defence...
2018: Advances in Microbial Physiology
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