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MicrobiologyOpen

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https://www.readbyqxmd.com/read/28332311/characterization-of-blue-light-irradiation-effects-on-pathogenic-and-nonpathogenic-escherichia-coli
#1
Courtney M Abana, John R Brannon, Rebecca A Ebbott, Taryn L Dunigan, Kirsten R Guckes, Hubaida Fuseini, Jennifer Powers, Bridget R Rogers, Maria Hadjifrangiskou
Blue light irradiation (BLI) is an FDA-approved method for treating certain types of infections, like acne, and is becoming increasingly attractive as an antimicrobial strategy as the prevalence of antibiotic-resistant "superbugs" rises. However, no study has delineated the effectiveness of BLI throughout different bacterial growth phases, especially in more BLI-tolerant organisms such as Escherichia coli. While the vast majority of E. coli strains are nonpathogenic, several E. coli pathotypes exist that cause infection within and outside the gastrointestinal tract...
March 22, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28326685/hugonella-massiliensis-gen-nov-sp-nov-genome-sequence-and-description-of-a-new-strictly-anaerobic-bacterium-isolated-from-the-human-gut
#2
Ziena Elsawi, Amadou Hamidou Togo, Mamadou Beye, Grégory Dubourg, Claudia Andrieu, Nicholas Armsrtong, Magali Richez, Fabrizio di Pinto, Fadi Bittar, Noémie Labas, Pierre-Edouard Fournier, Didier Raoult, Saber Khelaifia
The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI-TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8(T) (=CSUR P2118 =  DSM 101782) from stool specimens collected from a 51-year-old obese French woman. Strain AT8(T) is a strictly anaerobic, nonmotile, nonspore-forming gram-positive coccus that do not exhibit catalase and oxidase activities...
March 21, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28318117/transcriptional-regulation-of-cpsq-mfpabc-and-mfpabc-by-calr%C3%A2-in-vibrio-parahaemolyticus
#3
He Gao, Lingyu Zhang, George Osei-Adjei, Wenhui Yang, Dongsheng Zhou, Xinxiang Huang, Huiying Yang, Zhe Yin, Yiquan Zhang
The cpsQ-mfpABC locus is transcribed as two operons, i.e., cpsQ-mfpABC and mfpABC, in Vibrio parahaemolyticus, and both of them are all required for biofilm formation. CalR belongs to the LysR-type transcriptional regulator family, and was originally identified as a repressor of the swarming motility and T3SS1 genes expression in V. parahaemolyticus. In the present work, a combination of qRT-PCR, primer extension, LacZ fusion expression, electrophoretic mobility shift assay, and DNase I footprinting assays were employed to elucidate the regulatory mechanisms of cpsQ-mfpABC and mfpABC by CalR...
March 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28318115/microbial-players-and-processes-involved-in-phytoplankton-bloom-utilization-in-the-water-column-of-a-fast-flowing-river-dominated-estuary
#4
Maria W Smith, Lydie Herfort, Caroline S Fortunato, Byron C Crump, Holly M Simon
Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3-μm prefilter and 0...
March 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28317294/comparative-genome-analysis-reveals-important-genetic-differences-among-serotype-o1-and-serotype-o2-strains-of-y-%C3%A2-ruckeri-and-provides-insights-into-host-adaptation-and-virulence
#5
Desirée Cascales, José A Guijarro, Ana I García-Torrico, Jessica Méndez
Despite the existence of a commercial vaccine routinely used to protect salmonids against Yersinia ruckeri, outbreaks still occur, mainly caused by nonmotile and lipase-negative strains (serotype O1 biotype 2). Moreover, epizootics caused by other uncommon serotypes have also been reported. At the moment, one of the main concerns for the aquaculture industry is the expanding range of hosts of this pathogen and the emergence of new biotypes and serotypes causing mortality in fish farms and against which the vaccine cannot protect...
March 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28303666/is-the-methanogenic-community-reflecting-the-methane-emissions-of-river-sediments-comparison-of-two-study-sites
#6
Prem Prashant Chaudhary, Martin Rulík, Martin Blaser
Studies on methanogenesis from freshwater sediments have so far primarily focused on lake sediments. To expand our knowledge on the community composition of methanogenic archaea in river sediments, we studied the abundance and diversity of methanogenic archaea at two localities along a vertical profile (top 50 cm) obtained from sediment samples from Sitka stream (the Czech Republic). In this study, we compare two sites which previously have been shown to have a 10-fold different methane emission. Archaeal and methanogen abundance were analyzed by real-time PCR and T-RFLP...
March 16, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28299913/endophytic-fungi-harbored-in-the-root-of-sophora-tonkinensis-gapnep-diversity-and-biocontrol-potential-against-phytopathogens
#7
Yu Qun Yao, Fang Lan, Yun Ming Qiao, Ji Guang Wei, Rong Shao Huang, Liang Bo Li
This work, for the first time, investigated the diversity of endophytic fungi harbored in the xylem and phloem of the root of Sophora tonkinensis Gapnep from three geographic localities with emphasis on the influence of the tissue type and geographic locality on endophytic fungal communities and their potential as biocontrol agents against phytopathogens of Panax notoginseng. A total of 655 fungal strains representing 47 taxa were isolated. Forty-two taxa (89.4%) were identified but not five taxa (10.6%) according to morphology and molecular phylogenetics...
March 15, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28294553/nitric-oxide-enhanced-shiga-toxin-production-was-regulated-by-fur-and-reca-in-enterohemorrhagic-escherichia-coli-o157
#8
Kimitoshi Ichimura, Takeshi Shimizu, Akio Matsumoto, Shinichiro Hirai, Eiji Yokoyama, Hiroki Takeuchi, Kinnosuke Yahiro, Masatoshi Noda
Enterohemorrhagic Escherichia coli (EHEC) produces Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2). Nitric oxide (NO), which acts as an antimicrobial defense molecule, was found to enhance the production of Stx1 and Stx2 in EHEC under anaerobic conditions. Although EHEC O157 has two types of anaerobic NO reductase genes, an intact norV and a deleted norV, in the deleted norV-type EHEC, a high concentration of NO (12-29 μmol/L, maximum steady-state concentration) is required for enhanced Stx1 production and a low concentration of NO (~12 μmol/L, maximum steady-state concentration) is sufficient for enhanced Stx2 production under anaerobic conditions...
March 15, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28296357/antibacterial-antifungal-and-antiviral-effects-of-three-essential-oil-blends
#9
Amandine Brochot, Angèle Guilbot, Laïla Haddioui, Christine Roques
New agents that are effective against common pathogens are needed particularly for those resistant to conventional antimicrobial agents. Essential oils (EOs) are known for their antimicrobial activity. Using the broth microdilution method, we showed that (1) two unique blends of Cinnamomum zeylanicum, Daucus carota, Eucalyptus globulus and Rosmarinus officinalis EOs (AB1 and AB2; cinnamon EOs from two different suppliers) were active against the fourteen Gram-positive and -negative bacteria strains tested, including some antibiotic-resistant strains...
March 14, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28296352/the-role-of-inoculum-and-reactor-configuration-for-microbial-community-composition-and-dynamics-in-mainstream-partial-nitritation-anammox-reactors
#10
Shelesh Agrawal, Søren M Karst, Eva M Gilbert, Harald Horn, Per H Nielsen, Susanne Lackner
Implementation of partial nitritation anammox (PNA) in the mainstream (municipal wastewater treatment) is still under investigation. Microbial community structure and reactor type can influence the performance of PNA reactor; yet, little is known about the role of the community composition of the inoculum and the reactor configuration under mainstream conditions. Therefore, this study investigated the community structure of inocula of different origin and their consecutive community dynamics in four different lab-scale PNA reactors with 16S rRNA gene amplicon sequencing...
March 10, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28256808/farm-level-survey-of-spore-forming-bacteria-on-four-dairy-farms-in-the-waikato-region-of-new-zealand
#11
Tanushree B Gupta, Gale Brightwell
The aim of our study was to determine the occurrence and diversity of economically important spore-forming bacteria in New Zealand dairy farm systems. Farm dairy effluent (FDE) collected from Waikato dairy farms were tested for the presence of spore-forming bacteria, using a new culture-based methodology followed by genomic analysis. An enrichment step in which samples were inoculated in cooked meat glucose starch broth under anaerobic conditions, aided in the differential isolation of Bacillus and Clostridium species...
March 3, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28251842/the-first-description-of-a-hormone-sensitive-lipase-from-a-basidiomycete-structural-insights-and-biochemical-characterization-revealed-bjerkandera-adusta-baestb-as-a-novel-esterase
#12
María Del Rayo Sánchez-Carbente, Ramón Alberto Batista-García, Ayixón Sánchez-Reyes, Angela Escudero-Garcia, Catalina Morales-Herrera, Laura I Cuervo-Soto, Leidys French-Pacheco, Arline Fernández-Silva, Carlos Amero, Edmundo Castillo, Jorge Luis Folch-Mallol
The heterologous expression and characterization of a Hormone-Sensitive Lipases (HSL) esterase (BaEstB) from the Basidiomycete fungus Bjerkandera adusta is reported for the first time. According to structural analysis, amino acid similarities and conservation of particular motifs, it was established that this enzyme belongs to the (HSL) family. The cDNA sequence consisted of 969 nucleotides, while the gene comprised 1133, including three introns of 57, 50, and 57 nucleotides. Through three-dimensional modeling and phylogenetic analysis, we conclude that BaEstB is an ortholog of the previously described RmEstB-HSL from the phylogenetically distant fungus Rhizomucor miehei...
March 1, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28244230/confocal-laser-scanning-scanning-electron-and-transmission-electron-microscopy-investigation-of-enterococcus-faecalis-biofilm-degradation-using-passive-and-active-sodium-hypochlorite-irrigation-within-a-simulated-root-canal-model
#13
Saifalarab A Mohmmed, Morgana E Vianna, Matthew R Penny, Stephen T Hilton, Nicola Mordan, Jonathan C Knowles
Root canal irrigation is an important adjunct to control microbial infection. The aim of this study was to investigate the effect of 2.5% (wt/vol) sodium hypochlorite (NaOCl) agitation on the removal, killing, and degradation of Enterococcus faecalis biofilm. A total of 45 root canal models were manufactured using 3D printing with each model comprising an 18 mm length simulated root canal of apical size 30 and taper 0.06. E. faecalis biofilms were grown on the apical 3 mm of the models for 10 days. A total of 60 s of 9 ml of 2...
February 28, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28229558/microbial-diversity-of-a-full-scale-uasb-reactor-applied-to-poultry-slaughterhouse-wastewater-treatment-integration-of-16s-rrna-gene-amplicon-and-shotgun-metagenomic-sequencing
#14
Tiago Palladino Delforno, Gileno Vieira Lacerda Júnior, Melline F Noronha, Isabel K Sakamoto, Maria Bernadete A Varesche, Valéria M Oliveira
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset...
February 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28217917/a-comprehensive-phylogenetic-analysis-of-copper-transporting-p1b-atpases-from-bacteria-of-the-rhizobiales-order-uncovers-multiplicity-diversity-and-novel-taxonomic-subtypes
#15
Ciro Cubillas, Fabiola Miranda-Sánchez, Antonio González-Sánchez, José Pedro Elizalde, Pablo Vinuesa, Susana Brom, Alejandro García-de Los Santos
The ubiquitous cytoplasmic membrane copper transporting P1B-1 and P1B-3 -type ATPases pump out Cu(+) and Cu(2+) , respectively, to prevent cytoplasmic accumulation and avoid toxicity. The presence of five copies of Cu-ATPases in the symbiotic nitrogen-fixing bacteria Sinorhizobium meliloti is remarkable; it is the largest number of Cu(+) -transporters in a bacterial genome reported to date. Since the prevalence of multiple Cu-ATPases in members of the Rhizobiales order is unknown, we performed an in silico analysis to understand the occurrence, diversity and evolution of Cu(+) -ATPases in members of the Rhizobiales order...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28217901/the-choice-of-the-dna-extraction-method-may-influence-the-outcome-of-the-soil-microbial-community-structure-analysis
#16
Sylwia Zielińska, Piotr Radkowski, Aleksandra Blendowska, Agnieszka Ludwig-Gałęzowska, Joanna M Łoś, Marcin Łoś
Metagenomics approaches and recent improvements in the next-generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28215046/genome-resolved-metagenomics-of-a-bioremediation-system-for-degradation-of-thiocyanate-in-mine-water-containing-suspended-solid-tailings
#17
Sumayah F Rahman, Rose S Kantor, Robert Huddy, Brian C Thomas, Andries W van Zyl, Susan T L Harrison, Jillian F Banfield
Thiocyanate (SCN(-) ) is a toxic compound that forms when cyanide (CN(-) ), used to recover gold, reacts with sulfur species. SCN(-) -degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory-based reactors operated without suspended solids...
February 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28213899/human-influence-and-biotic-homogenization-drive-the-distribution-of-escherichia-coli-virulence-genes-in-natural-habitats
#18
Adriana Cabal, Joaquin Vicente, Julio Alvarez, Jose Angel Barasona, Mariana Boadella, Lucas Dominguez, Christian Gortazar
Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs). We used a quantitative real-time PCR (qPCR) for the direct detection and quantification of the genus-specific gene uidA, nine E...
February 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28173636/identification-and-characterization-of-a-novel-fusobacterium-nucleatum-adhesin-involved-in-physical-interaction-and-biofilm-formation-with-streptococcus-gordonii
#19
Bruno P Lima, Wenyuan Shi, Renate Lux
To successfully colonize the oral cavity, bacteria must directly or indirectly adhere to available oral surfaces. Fusobacterium nucleatum plays an important role in oral biofilm community development due to its broad adherence abilities, serving as a bridge between members of the oral biofilm that cannot directly bind to each other. In our efforts to characterize the molecular mechanisms utilized by F. nucleatum to physically bind to key members of the oral community, we investigated the involvement of F. nucleatum outer membrane proteins in its ability to bind to the pioneer biofilm colonizer, Streptococcus gordonii...
February 7, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28173613/illumina-sequencing-based-analysis-of-sediment-bacteria-community-in-different-trophic-status-freshwater-lakes
#20
Yu Wan, Xiaohong Ruan, Yaping Zhang, Rongfu Li
Sediment bacterial community is the main driving force for nutrient cycling and energy transfer in aquatic ecosystem. A thorough understanding of the community's spatiotemporal variation is critical for us to understand the mechanisms of cycling and transfer. Here, we investigated the sediment bacterial community structures and their relations with environmental factors, using Lake Taihu as a model system to explore the dependence of biodiversity upon trophic level and seasonality. To combat the limitations of conventional techniques, we employed Illumina MiSeq Sequencing and LeFSe cladogram to obtain a more comprehensive view of the bacterial taxonomy and their variations of spatiotemporal distribution...
February 7, 2017: MicrobiologyOpen
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