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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/29786876/temporal-and-long-term-gut-microbiota-variation-in-allergic-disease-a-prospective-study-from-infancy-to-school-age
#2
Kotryna Simonyté Sjödin, Marie-Louise Hammarström, Patrik Rydén, Andreas Sjödin, Olle Hernell, Lars Engstrand, Christina E West
BACKGROUND: Compositional changes of the early life gut microbiota have been implicated in IgE-associated allergic disease but there is lack of longitudinal studies. We examined gut microbiota development from infancy to school age in relation to onset of IgE-associated allergic diseases. At 8 years of age, we also examined the relationship between gut microbiota and T-cell regulation, estimated as responses to polyclonal T-cell activation. METHODS: Stool samples were collected from 93 children at 4, 6 and 13 months, and 8 years of age...
May 22, 2018: Allergy
https://www.readbyqxmd.com/read/29786847/assessment-of-antibiotic-susceptibility-within-lactic-acid-bacteria-and-coagulase-negative-staphylococci-isolated-from-hunan-smoked-pork-a-naturally-fermented-meat-product-in-china
#3
Jing Wang, Xinyuan Wei, Mingtao Fan
The aim of this study was to evaluate the antibiotic susceptibility of lactic acid bacteria (LAB) and coagulase-negative staphylococci (CNS) strains isolated from naturally fermented smoked pork produced in Hunan, China. A total of 48 strains were isolated by selective medium and identified at the species level by 16S rRNA gene sequencing as follows: Staphylococcus carnosus (23), Lactobacillus plantarum (12), Lactobacillus brevis (10), Lactobacillus sakei (1), Weissella confusa (1), and Weissella cibaria (1)...
May 22, 2018: Journal of Food Science
https://www.readbyqxmd.com/read/29786766/bacterial-dna-detected-on-pathologically-changed-heart-valves-using-16s-rrna-gene-amplification
#4
Miroslava Chalupova, Anna Skalova, Tomas Hajek, Lenka Geigerova, Dana Kralova, Pavel Liska, Hana Hecova, Jiri Molacek, Jaroslav Hrabak
Nowadays, dental diseases are one of the most common illnesses in the world. Some of them can lead to translocation of oral bacteria to the bloodstream causing intermittent bacteraemia. Therefore, a potential association between oral infection and cardiovascular diseases has been discussed in recent years as a result of adhesion of oral microbes to the heart valves. The aim of this study was to detect oral bacteria on pathologically changed heart valves not caused by infective endocarditis. In the study, patients with pathologically changed heart valves were involved...
May 22, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/29786497/massilia-armeniaca-sp-nov-isolated-from-desert-soil
#5
Mengnan Ren, Xiaoyan Li, Yueqi Zhang, Yu Jin, Siqi Li, Haidong Huang
A Gram-stain-negative, aerobic, motile and rod-shaped bacterium, strain ZMN-3T , was isolated from desert soil sample collected from Ongniod Qi, Inner Mongolia, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZMN-3T was affiliated with the genus Massilia and showed the highest similarity to Massilia humi THG S6-8T (98.9 %) and Massilia buxea A9T (98.2 %). In partial gyrB and lepA sequences, the highest similarity of strain ZMN-3T and M. humi THG S6-8T were 95.9 and 96.8 %, respectively...
May 22, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29786424/tuning-gene-activity-by-inducible-and-targeted-regulation-of-gene-expression-in-minimal-bacterial-cells
#6
Ana M Mariscal, Shigeyuki Kakizawa, Jonathan Y Hsu, Kazuki Tanaka, Luis González-González, Alicia Broto, Enrique Querol, Maria Lluch-Senar, Carlos Piñero-Lambea, Lijie Sun, Philip D Weyman, Kim S Wise, Chuck Merryman, Gavin Tse, Adam J Moore, Clyde A Hutchison, Hamilton O Smith, Masaru Tomita, J Craig Venter, John I Glass, Jaume Piñol, Yo Suzuki
Functional genomics studies in minimal mycoplasma cells enable unobstructed access to some of the most fundamental processes in biology. Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in mycoplasmas. Here we demonstrate systems for inducible repression of gene expression based on clustered regularly interspaced short palindromic repeats-mediated interference (CRISPRi) in Mycoplasma pneumoniae and synthetic Mycoplasma mycoides, two organisms with reduced genomes actively used in systems biology studies...
May 22, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29785674/assembly-of-a-complete-genome-sequence-for-gemmata-obscuriglobus-reveals-a-novel-prokaryotic-rrna-operon-gene-architecture
#7
Josef D Franke, Wilson R Blomberg, Robert T Todd, Robert W Thomas, Anna M Selmecki
Gemmata obscuriglobus is a Gram-negative bacterium with several intriguing biological features. Here, we present a complete, de novo whole genome assembly for G. obscuriglobus which consists of a single, circular 9 Mb chromosome, with no plasmids detected. The genome was annotated using the NCBI Prokaryotic Genome Annotation pipeline to generate common gene annotations. Analysis of the rRNA genes revealed three interesting features for a bacterium. First, linked G. obscuriglobus rrn operons have a unique gene order, 23S-5S-16S, compared to typical prokaryotic rrn operons (16S-23S-5S)...
May 21, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29785671/agarolytic-culturable-bacteria-associated-with-three-antarctic-subtidal-macroalgae
#8
Verónica Sánchez Hinojosa, Joel Asenjo, Sergio Leiva
Bacterial communities of Antarctic marine macroalgae remain largely underexplored in terms of diversity and biotechnological applications. In this study, three Antarctic subtidal macroalgae (Himantothallus grandifolius, Pantoneura plocamioides and Plocamium cartilagineum), two of them endemic of Antarctica, were investigated as a source for isolation of agar-degrading bacteria. A total of 21 epiphytic isolates showed agarolytic activity at low temperature on agar plates containing agar as the sole carbon source...
May 21, 2018: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29785358/bacterial-community-changes-in-an-industrial-algae-production-system
#9
Scott P Fulbright, Adam Robbins-Pianka, Donna Berg-Lyons, Rob Knight, Kenneth F Reardon, Stephen T Chisholm
While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities...
April 2018: Algal Research
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
#10
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
#11
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/29784985/chronic-rhinosinusitis-with-nasal-polyps-is-characterized-by-dysbacteriosis-of-the-nasal-microbiota
#12
Thanit Chalermwatanachai, Ramiro Vilchez-Vargas, Gabriele Holtappels, Tim Lacoere, Ruy Jáuregui, Frederiek-Maarten Kerckhof, Dietmar H Pieper, Tom Van de Wiele, Mario Vaneechoutte, Thibaut Van Zele, Claus Bachert
Chronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP-A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A)...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29783658/quorum-sensing-versus-quenching-bacterial-isolates-obtained-from-mbr-plants-treating-leachates-from-municipal-solid-waste
#13
Albert Soler, Lucía Arregui, Miguel Arroyo, José Antonio Mendoza, Andrea Muras, Cristina Álvarez, Cristina García-Vera, Domingo Marquina, Antonio Santos, Susana Serrano
Quorum sensing (QS) is a mechanism dependent on bacterial density. This coordinated process is mediated by the synthesis and the secretion of signal molecules, called autoinducers (AIs). N -acyl-homoserine lactones (AHLs) are the most common AIs that are used by Gram-negative bacteria and are involved in biofilm formation. Quorum Quenching (QQ) is the interference of QS by producing hydrolyzing enzymes, among other strategies. The main objective of the present study was to identify QS and QQ strains from MBR wastewater treatment plants...
May 18, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29783165/preferential-feeding-in-naegleria-fowleri-intracellular-bacteria-isolated-from-amoebae-in-operational-drinking-water-distribution-systems
#14
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/29783055/characterization-and-coagulation-flocculation-performance-of-a-composite-flocculant-in-high-turbidity-drinking-water-treatment
#15
Xiang Xia, Shuhuan Lan, Xudong Li, Yifei Xie, Yajie Liang, Peihan Yan, Zhengyang Chen, Yunxiao Xing
Klebsiella variicola B16, a microbial bioflocculant (MBF-B16)-producing bacteria, was isolated and identified by its 16S rRNA sequence, biochemical properties, and physiological characteristics. The effects of culture conditions on MBF-B16 production, including carbon source, nitrogen source, C/N ratio, initial pH, and culture temperature, were investigated in this study. Results showed that 6.96 g of MBF-B16 could be extracted from a 1-L culture broth under optimized conditions. Chemical analysis showed that polysaccharide and protein were the main components...
April 30, 2018: Chemosphere
https://www.readbyqxmd.com/read/29783046/bacterial-community-of-industrial-raw-sausage-packaged-in-modified-atmosphere-throughout-the-shelf-life
#16
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/29782156/combining-high-throughput-sequencing-of-sedadna-and-traditional-palaeolimnological-techniques-to-infer-historical-trends-in-cyanobacterial-communities
#17
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/29782021/exploring-the-root-microbiome-extracting-bacterial-community-data-from-the-soil-rhizosphere-and-root-endosphere
#18
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/29781802/zobellella-maritima-sp-nov-a-polycyclic-aromatic-hydrocarbon-degrading-bacterium-isolated-from-beach-sediment
#19
Dong Wan Lee, Hanbyul Lee, Bong-Oh Kwon, Jong Seong Khim, Un Hyuk Yim, Hongjae Park, Byeonghyeok Park, In-Geol Choi, Beom Seok Kim, Jae-Jin Kim
A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain 102-Py4T , was isolated from Sinduri beach sediment in Taean, Republic of Korea. Cells were aerobic, oxidase-positive and catalase-positive. The isolate grew optimally with 1-3 % (w/v) NaCl, but NaCl is not an absolute requirement for growth. 16S rRNA gene sequence analysis revealed that strain 102-Py4T clustered together with Zobellella aerophila and fell within the clade formed by recognized species of the genus Zobellella. Its closest phylogenetic neighbours were Z...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29781801/methanonatronarchaeum-thermophilum-gen-nov-sp-nov-and-candidatus-methanohalarchaeum-thermophilum-extremely-halo-natrono-philic-methyl-reducing-methanogens-from-hypersaline-lakes-comprising-a-new-euryarchaeal-class-methanonatronarchaeia-classis-nov
#20
Dimitry Y Sorokin, Alexander Y Merkel, Ben Abbas, Kira S Makarova, W Irene C Rijpstra, M Koenen, Jaap S Sinninghe Damsté, Erwin A Galinski, Eugene V Koonin, Mark C M van Loosdrecht
Methanogenic enrichments from hypersaline lakes at moderate thermophilic conditions have resulted in the cultivation of an unknown deep lineage of euryarchaeota related to the class Halobacteria. Eleven soda lake isolates and three salt lake enrichment cultures were methyl-reducing methanogens that utilize C1 methylated compounds as electron acceptors and H2 or formate as electron donors, but they were unable to grow on either substrates alone or to form methane from acetate. They are extreme halophiles, growing optimally at 4 M total Na+ and the first representatives of methanogens employing the 'salt-in' osmoprotective mechanism...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
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