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https://www.readbyqxmd.com/read/28647822/devosia-nitraria-sp-nov-a-novel-species-isolated-from-the-roots-of-nitraria-sibirica-in-china
#1
Lin Xu, Yong Zhang, Nicholas Read, Shuangjiang Liu, Ville-Petri Friman
An aerobic, Gram-stain negative, short rod-shaped and motile strain, 36-5-1(T), was isolated from the roots of Nitraria sibirica in Zhangye city, Gansu province, north-west of China. Phylogenetic analysis based on the 16S rRNA gene sequence and two housekeeping genes (glnA and atpD) indicated that the strain represents a novel species closely related to the Devosia, Rhizobium and Devosia genera with 98.3, 96.2 and 91.1% similarities, respectively. The strain 36-5-1(T) contained Q-10 as the predominant ubiquinone and 16:0 (36...
June 24, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28647620/the-mitogenome-phylogeny-of-adephaga-coleoptera
#2
Alejandro López-López, Alfried P Vogler
The beetle suborder Adephaga consists of several aquatic ('Hydradephaga') and terrestrial ('Geadephaga') families whose relationships remain poorly known. In particular, the position of Cicindelidae (tiger beetles) appears problematic, as recent studies have found them either within the Hydradephaga based on mitogenomes, or together with several unlikely relatives in Geadephaga based on 18S rRNA genes. We newly sequenced nine mitogenomes of representatives of Cicindelidae and three ground beetles (Carabidae), and conducted phylogenetic analyses together with 29 existing mitogenomes of Adephaga...
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28647619/molecular-phylogeny-of-the-achatinoidea-mollusca-gastropoda
#3
Ian Kendrich Fontanilla, Fred Naggs, Christopher Mark Wade
This study presents a multi-gene phylogenetic analysis of the Achatinoidea and provides an initial basis for a taxonomic revaluation of family level groups within the superfamily. A total of 5028 nucleotides from the nuclear rRNA, actin and histone 3 genes and the 1(st) and 2(nd) codon positions of the mitochondrial cytochrome c oxidase subunit I gene were sequenced from 24 species, representing six currently recognised families. Results from maximum likelihood, neighbour joining, maximum parsimony and Bayesian inference trees revealed that, of currently recognised families, only the Achatinidae are monophyletic...
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28647582/comparison-of-sequencing-the-d2-region-of-the-large-subunit-ribosomal-rna-gene-microseq%C3%A2-versus-the-internal-transcribed-spacer-its-regions-using-two-public-databases-for-identification-of-common-and-uncommon-clinically-relevant-fungal-species
#4
S Arbefeville, A Harris, P Ferrieri
CONTEXT: Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. OBJECTIVE: The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data...
June 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28647499/complete-sequence-and-characterization-of-the-mitochondrial-genome-of-diphyllobothrium-stemmacephalum-the-type-species-of-genus-diphyllobothrium-cestoda-diphyllobothriidae-using-next-generation-sequencing
#5
Hiroshi Yamasaki, Shinji Izumiyama, Tomoyoshi Nozaki
We first constructed and characterized the complete mitochondrial genome (mitogenome) sequence of Diphyllobothrium stemmacephalum, the type species of genus Diphyllobothrium, using next generation sequencing (NGS). The mitogenome of D. stemmacephalum was 13,716bp, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 longer intergenic non-coding regions, and has features common to mitogenomes of other cestodes. Although it has been accepted that tRNA for serine (trnS2(UCN)) in Platyhelminthes lacks a D arm, the trnS2(UCN) of D...
June 21, 2017: Parasitology International
https://www.readbyqxmd.com/read/28647397/actinomyces-radicidentis-and-actinomyces-haliotis-coccoid-actinomyces-species-isolated-from-the-human-oral-cavity
#6
Rolf Claesson, Ulf Sjögren, Anders Esberg, Malin Brundin, Margareta Granlund
There are few reports on the bacterial species Actinomyces radicidentis in the literature. In this study, putative A. radicidentis isolates were collected from 16 root canal samples from 601 examined patients. The isolates were examined by biochemical tests, 16S rRNA gene sequencing, Arbitrarily-primed (AP-) PCR, antibiotic susceptibility testing, and MALDI-TOF analyses. In parallel, two A. radicidentis reference strains and two putative A. radicidentis isolates from United Kingdom were tested. Sixteen of the 18 isolates were confirmed as A...
June 21, 2017: Anaerobe
https://www.readbyqxmd.com/read/28647304/phylogenies-of-symbiotic-genes-of-bradyrhizobium-symbionts-of-legumes-of-economic-and-environmental-importance-in-brazil-support-the-definition-of-the-new-symbiovars-pachyrhizi-and-sojae
#7
Jakeline Renata Marçon Delamuta, Pâmela Menna, Renan Augusto Ribeiro, Mariangela Hungria
Bradyrhizobium comprises most tropical symbiotic nitrogen-fixing strains, but the correlation between symbiotic and core genes with host specificity is still unclear. In this study, the phylogenies of the nodY/K and nifH genes of 45 Bradyrhizobium strains isolated from legumes of economic and environmental importance in Brazil (Arachis hypogaea, Acacia auriculiformis, Glycine max, Lespedeza striata, Lupinus albus, Stylosanthes sp. and Vigna unguiculata) were compared to 16S rRNA gene phylogeny and genetic diversity by rep-PCR...
June 7, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28647233/evaluation-of-bacterial-pathogen-diversity-abundance-and-health-risks-in-urban-recreational-water-by-amplicon-next-generation-sequencing-and-quantitative-pcr
#8
Qijia Cui, Tingting Fang, Yong Huang, Peiyan Dong, Hui Wang
The microbial quality of urban recreational water is of great concern to public health. The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks. To assess the levels of bacterial pathogens and health risks in urban recreational water, we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year. The pathogen diversity revealed by 16S rRNA gene targeted next-generation sequencing (NGS) showed that 16 of 40 genera and 13 of 76 reference species were present...
July 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/28647123/zinc-solubilizing-bacillus-spp-potential-candidates-for-biofortification-in-maize
#9
Muhammad Zahid Mumtaz, Maqshoof Ahmad, Moazzam Jamil, Tanveer Hussain
Bioaugmentation of Zn solubilizing rhizobacteria could be a sustainable intervention to increase bioavailability of Zn in soil which can be helpful in mitigation of yield loss and malnutrition of zinc. In present study, a number of pure rhizobacterial colonies were isolated from maize rhizosphere and screened for their ability to solubilize zinc oxide. These isolates were screened on the basis of zinc and phosphate solubilization, IAA production, protease production, catalase activity and starch hydrolysis...
September 2017: Microbiological Research
https://www.readbyqxmd.com/read/28646792/bacterial-profile-in-human-atherosclerotic-plaques
#10
Annika Lindskog Jonsson, Frida Fåk Hållenius, Rozita Akrami, Elias Johansson, Per Wester, Conny Arnerlöv, Fredrik Bäckhed, Göran Bergström
BACKGROUND AND AIMS: Several studies have confirmed the presence of bacterial DNA in atherosclerotic plaques, but its contribution to plaque stability and vulnerability is unclear. In this study, we investigated whether the bacterial plaque-profile differed between patients that were asymptomatic or symptomatic and whether there were local differences in the microbial composition within the plaque. METHODS: Plaques were removed by endarterectomy from asymptomatic and symptomatic patients and divided into three different regions known to show different histological vulnerability: A, upstream of the maximum stenosis; B, site for maximum stenosis; C, downstream of the maximum stenosis...
June 8, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28646634/marinisporobacter-balticus-gen-nov-sp-nov-desulfosporosinus-nitroreducens-sp-nov-and-desulfosporosinus-fructosivorans-sp-nov-new-spore-forming-bacteria-isolated-from-subsurface-sediments-of-the-baltic-sea
#11
Verona Vandieken, Helge Niemann, Bert Engelen, Heribert Cypionka
Four novel Gram-stain-positive, endospore-forming bacteria of the order Clostridiales were isolated from subsurface sediments sampled during International Ocean Discovery Program Expedition 347 to the Baltic Sea. One strain (59.4MT) grew as an obligate heterotroph by aerobic respiration and anaerobically by fermentation. Optimum growth was observed with 0.5 % NaCl at 25 °C and pH 7.0-7.3. Analysis of 16S rRNA gene sequences of 59.4MT revealed Alkaliphilus transvaalensis (92.3 % identity), Candidatus Geosporobacter ferrireducens (92...
June 20, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28646633/reclassification-of-flexibacter-tractuosus-nbrc-15981t-as-marivirga-harenae-sp-nov-in-the-family-flammeovirgaceae
#12
Yuki Muramatsu, Yuki Kamakura, Mai Takahashi, Yasuyoshi Nakagawa
Flexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa. Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids...
June 9, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28646380/isolation-selection-and-biological-characterization-research-of-highly-effective-electricigens-from-mfcs-for-phenol-degradation
#13
Guo Wei, Du Xia, Wang Li-Li, Yan Hong
The microbial fuel cells (MFCs) are recognized to be highly effective for the biodegradation of phenol. For isolating the phenol-degrading bacteria, the sample containing 500 mg/L phenol was collected from the MFCs. The strain (WL027) was identified basing on the 16S rRNA gene analysis and phylogenetic analysis as Bacillus cereus. The effects of pH, temperature, concentrations of phenol, heavy metal ions, and salt on the growth of strain as well as the degradation of phenol have been carefully studied. The WL027-strain exhibited favorable tolerance for the metal cations including Cr(2+), Co(2+), Pb(2+), and Cu(2+) with the concentration of 0...
June 23, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28646338/chemotherapy-induced-gastrointestinal-toxicity-is-associated-with-changes-in-serum-and-urine-metabolome-and-fecal-microbiota-in-male-sprague-dawley-rats
#14
Richard A Forsgård, Vannina G Marrachelli, Katri Korpela, Rafael Frias, Maria Carmen Collado, Riitta Korpela, Daniel Monleon, Thomas Spillmann, Pia Österlund
PURPOSE: Chemotherapy-induced gastrointestinal toxicity (CIGT) is a complex process that involves multiple pathophysiological mechanisms. We have previously shown that commonly used chemotherapeutics 5-fluorouracil, oxaliplatin, and irinotecan damage the intestinal mucosa and increase intestinal permeability to iohexol. We hypothesized that CIGT is associated with alterations in fecal microbiota and metabolome. Our aim was to characterize these changes and examine how they relate to the severity of CIGT...
June 23, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28646313/domestic-wastewater-treatment-by-constructed-wetlands-enhanced-with-bioremediating-rhizobacteria
#15
Irina Salgado, Herlen Cárcamo, María Elena Carballo, Mario Cruz, María Del Carmen Durán
Constructed wetlands (CWs) offer several advantages for treating waters; however, the successful application of these systems remains a challenge. Practical solutions to pollution through CWs remain incipient because wetlands are still studied as "black boxes"; further studies are required regarding the involvement of rhizosphere bacteria in the removal of pollutants. This research focused on increasing the performance of CWs treatment systems for the removal of inorganic and organic pollutants from domestic wastewater, by the application of native bioremediating rhizobacteria...
June 23, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28646202/the-microbiome-of-endophytic-wood-colonizing-bacteria-from-pine-trees-as-affected-by-pine-wilt-disease
#16
Diogo Neves Proença, Romeu Francisco, Susanne Kublik, Anne Schöler, Gisle Vestergaard, Michael Schloter, Paula V Morais
Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646175/ribosome-rna-profiling-to-quantify-ovarian-development-and-identify-sex-in-fish
#17
Zhi-Gang Shen, Hong Yao, Liang Guo, Xiao-Xia Li, Han-Ping Wang
Terminologies of ovary development, by somewhat subjective describing and naming main changes of oocytes, have been criticized for confusing and inconsistency of terms and classifications, and the incurred consequences impede communication among researchers. In the present work, we developed regression between ovary development and three ribosome RNA (rRNA) indexes, namely 5S rRNA percent, 18S rRNA percent, and 5S-18S rRNA ratio, using close relationship between volume percent of primary growth stage oocytes or gonadosomatic index and rRNA content, demonstrating species-specific quantification of ovary development can be established in species with either synchronous and asynchronous oogenesis...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28645701/effect-of-phosphate-solubilizing-bacteria-on-phosphorus-dynamics-and-the-bacterial-community-during-composting-of-sugarcane-industry-waste
#18
German A Estrada-Bonilla, Cintia M Lopes, Ademir Durrer, Paulo R L Alves, Nicolle Passaglia, Elke J B N Cardoso
Sugarcane processing generates a large quantity of residues, such as filter cake and ashes, which are sometimes composted prior to their amendment in soil. However, important issues still have to be addressed on this subject, such as the description of bacterial succession that occurs throughout the composting process and the possibilities of using phosphate-solubilizing bacteria (PSB) during the process to improve phosphorus (P) availability in the compost end product. Consequently, this study evaluated the bacterial diversity and P dynamics during the composting process when inoculated with Pseudomonas aeruginosa PSBR12 and Bacillus sp...
June 7, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28645313/molecular-investigation-and-phylogeny-of-anaplasmataceae-species-infecting-domestic-animals-and-ticks-in-corsica-france
#19
Mustapha Dahmani, Bernard Davoust, Djamel Tahir, Didier Raoult, Florence Fenollar, Oleg Mediannikov
BACKGROUNDS: Corsica is a French island situated in the Mediterranean Sea. The island provides suitable natural conditions to study disease ecology, especially tick-borne diseases and emerging diseases in animals and ticks. The family Anaplasmataceae is a member of the order Rickettsiales; it includes the genera Anaplasma, Ehrlichia, Neorickettsia and Wolbachia. Anaplasmosis and ehrlichiosis traditionally refer to diseases caused by obligate intracellular bacteria of the genera Anaplasma and Ehrlichia...
June 23, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28645307/aberrant-intestinal-microbiota-due-to-il-1-receptor-antagonist-deficiency-promotes-il-17-and-tlr4-dependent-arthritis
#20
Rebecca Rogier, Thomas H A Ederveen, Jos Boekhorst, Harm Wopereis, Jose U Scher, Julia Manasson, Sanne J C M Frambach, Jan Knol, Johan Garssen, Peter M van der Kraan, Marije I Koenders, Wim B van den Berg, Sacha A F T van Hijum, Shahla Abdollahi-Roodsaz
BACKGROUND: Perturbation of commensal intestinal microbiota has been associated with several autoimmune diseases. Mice deficient in interleukin-1 receptor antagonist (Il1rn (-/-) mice) spontaneously develop autoimmune arthritis and are susceptible to other autoimmune diseases such as psoriasis, diabetes, and encephalomyelitis; however, the mechanisms of increased susceptibility to these autoimmune phenotypes are poorly understood. We investigated the role of interleukin-1 receptor antagonist (IL-1Ra) in regulation of commensal intestinal microbiota, and assessed the involvement of microbiota subsets and innate and adaptive mucosal immune responses that underlie the development of spontaneous arthritis in Il1rn (-/-) mice...
June 23, 2017: Microbiome
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