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https://www.readbyqxmd.com/read/28726611/added-value-of-next-generation-sequencing-for-multilocus-sequence-typing-analysis-of-a-pneumocystis-jirovecii-pneumonia-outbreak1
#1
Elena Charpentier, Cécile Garnaud, Claire Wintenberger, Sébastien Bailly, Jean-Benjamin Murat, John Rendu, Patricia Pavese, Thibault Drouet, Caroline Augier, Paolo Malvezzi, Anne Thiébaut-Bertrand, Marie-Reine Mallaret, Olivier Epaulard, Muriel Cornet, Sylvie Larrat, Danièle Maubon
Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included...
August 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28708078/spatial-variation-of-soil-organic-carbon-and-total-nitrogen-in-the-coastal-area-of-mid-eastern-china
#2
Yan Xu, Lijie Pu, Qilin Liao, Ming Zhu, Xue Yu, Tianying Mao, Chenxing Xu
Soils play an important role in sequestrating atmospheric CO₂. Coastal tidal flats have been intensively reclaimed for food security and living spaces worldwide. We aimed to identify the changes of soil organic carbon (SOC) and total nitrogen (TN) following coastal reclamation and their spatial variation in the coastal area of mid-Eastern China to provide information for coastal cropland management. We measured SOC and TN of 463 soil samples in the coastal plain of mid-Eastern China. The results showed that SOC and TN increased highly from the uncultivated coastal tidal flat (2...
July 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28696720/bacterial-production-of-a-pederin-analogue-by-a-free-living-marine-alphaproteobacterium
#3
Carmen Schleissner, Librada M Cañedo, Pilar Rodríguez, Cristina Crespo, Paz Zúñiga, Ana Peñalver, Fernando de la Calle, Carmen Cuevas
The polyketide pederin family are cytotoxic compounds isolated from insects, lichen, and marine sponges. During the past decade, different uncultivable bacteria symbionts have been proposed as the real producers of these compounds, such as those found in insects, lichen, and marine sponges, and their trans-AT polyketide synthase gene clusters have been identified. Herein we report the isolation and biological activities of a new analogue of the pederin family, compound 1, from the culture of a marine heterotrophic alphaproteobacterium, Labrenzia sp...
July 11, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28687345/molecular-diversity-geographic-distribution-and-host-range-of-monocot-infecting-mastreviruses-in-africa-and-surrounding-islands
#4
Simona Kraberger, Salem Saumtally, Daniel Pande, Michel H R Khoodoo, Sonalall Dhayan, Asha Dookun-Saumtally, Dionne N Shepherd, Penelope Hartnady, Richard Atkinson, Francisco M Lakay, Britt Hanson, Devasha Redhi, Adérito L Monjane, Oliver P Windram, Matthew Walters, Sunday Oluwafemi, Jean Michel-Lett, Pierre Lefeuvre, Darren P Martin, Arvind Varsani
Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus...
July 4, 2017: Virus Research
https://www.readbyqxmd.com/read/28686606/plant-fed-versus-chemicals-fed-rhizobacteria-of-lucerne-plant-only-teabags-culture-media-not-only-increase-culturability-of-rhizobacteria-but-also-recover-a-previously-uncultured-lysobacter-sp-novosphingobium-sp-and-pedobacter-sp
#5
Nabil A Hegazi, Mohamed S Sarhan, Mohamed Fayez, Sascha Patz, Brian R Murphy, Silke Ruppel
In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR)...
2017: PloS One
https://www.readbyqxmd.com/read/28684155/novel-mastreviruses-identified-in-australian-wild-rice
#6
Simona Kraberger, Andrew D W Geering, Matthew Walters, Darren P Martin, Arvind Varsani
Most known mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland...
July 4, 2017: Virus Research
https://www.readbyqxmd.com/read/28677304/integrated-structural-biology-and-molecular-ecology-of-n-cycling-enzymes-from-ammonia-oxidizing-archaea
#7
Bradley B Tolar, Jonathan Herrmann, John R Bargar, Henry van den Bedem, Soichi Wakatsuki, Christopher A Francis
Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically-relevant ammonia oxidizers is unfortunately extremely limited...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28674200/the-deep-hot-biosphere-twenty-five-years-of-retrospection
#8
Daniel R Colman, Saroj Poudel, Blake W Stamps, Eric S Boyd, John R Spear
Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28658759/revisiting-the-utility-of-histopathological-examination-of-biopsy-a-necessity-in-microbiology
#9
Priyamvada Roy, Shukla Das, Sonal Sharma, Vaibhav Girotra, Neelima Gupta, Rumpa Saha, Iqbal Rajinder Kaur
INTRODUCTION: Culture is the gold standard, while potassium hydroxide mount is simplest technique used for diagnosis of fungal pathogens. Histopathological examination is the only definitive means to identify certain uncultivable fungi. AIM: To analyse role of histopathological examination and potassium hydroxide (KOH) mount for diagnosing fungal infections by correlating them with culture. MATERIALS AND METHODS: In this nine year retrospective study, all biopsy specimens submitted for microbiological examination were included...
May 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28648396/25-years-of-serving-the-community-with-ribosomal-rna-gene-reference-databases-and-tools
#10
Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, Wolfgang Ludwig
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis...
June 22, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28630471/candidatus-mycoplasma-girerdii-replicates-diversifies-and-co-occurs-with-trichomonas-vaginalis-in-the-oral-cavity-of-a-premature-infant
#11
Elizabeth K Costello, Christine L Sun, Erica M Carlisle, Michael J Morowitz, Jillian F Banfield, David A Relman
Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis)...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28625077/microbiome-and-microbial-biofilm-profiles-of-peri-implantitis-a-systematic-review
#12
Gloria Inés Lafaurie, María Alejandra Sabogal, Diana Marcela Castillo, María Victoria Rincón, Luz Amparo Gómez, Yamil Augusto Lesmes, Leandro Chambrone
BACKGROUND: This systematic review assesses the microbiological profiles of peri-implantitis, periodontitis and healthy implants based on studies that evaluated microbial biofilms and entire microbiomes to establish their similarities and differences. METHODS: The Medical Literature Analysis and Retrieval System Online, via PubMed, EMBASE (Excerpta Medica Database) and Cochrane Central Register of Controlled Trials (CENTRAL) were searched without language restrictions through July 30, 2016...
June 19, 2017: Journal of Periodontology
https://www.readbyqxmd.com/read/28618189/comparative-genomics-of-the-dna-damage-inducible-network-in-the-patescibacteria
#13
Miquel Sánchez-Osuna, Jordi Barbé, Ivan Erill
Metagenomics provide unprecedented insights into the genetic diversity of uncultivated bacteria inhabiting natural environments. Recent surveys have uncovered a major radiation of candidate phyla encompassing the Patescibacteria superphylum. Patescibacteria have small genomes and a presumed symbiotic or parasitic lifestyle, but the difficulty in culturing representative members constrains the characterization of behavioral and adaptive traits. Here we combine in silico and in vitro approaches to characterize the SOS transcriptional response to DNA damage in the Patescibacteria superphylum...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28604068/comparison-of-the-effects-of-poultry-manure-and-its-biochar-on-barley-growth-in-petroleum-contaminated-soils
#14
Maryam Barati, Fereshteh Bakhtiari, Dariush Mowla, Sedigheh Safarzadeh
This study was conducted to evaluate and compare the effectiveness of two organic amendments (poultry manure (PM) and poultry manure biochar (PMB)) for the degradation of petroleum hydrocarbons in contaminated soils by barley plant at three levels of total petroleum hydrocarbons (TPHs) during 5 month under greenhouse conditions. TPHs removal efficiency and microbial respiration were shown to be higher at soil cultivated plant than uncultivated soil and in lowest level of contamination rather than other levels of contamination and at organic amendment treatment than unamended soil...
June 12, 2017: International Journal of Phytoremediation
https://www.readbyqxmd.com/read/28594267/a-plant-pathogenic-bacterium-exploits-the-tricarboxylic-acid-cycle-metabolic-pathway-of-its-insect-vector
#15
Nabil Killiny, Yasser Nehela, Faraj Hijaz, Christopher I Vincent
Huanglongbing in citrus is caused by a phloem-limited, uncultivable, gram-negative α-proteobacterium, Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by the phloem-sucking insect, Diaphorina citri (Hemiptera: Liviidae), in a persistent, circulative, and propagative manner. In this study, we investigated the metabolomic and respiration rates changes in D. citri upon infection with CLas using gas chromatography-mass spectrometry (GC-MS) and gas exchange analysis. The level of glycine, L-serine, L-threonine, and gamma-amino butyric acid were higher in CLas-infected D...
June 8, 2017: Virulence
https://www.readbyqxmd.com/read/28591840/novel-approaches-in-function-driven-single-cell-genomics
#16
Devin F R Doud, Tanja Woyke
Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology...
June 7, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28553195/characterization-of-the-cultivable-gut-microflora-in-wild-caught-%C3%A2-mediterranean-fish-species
#17
Ahmad Jammal, Michel Bariche, Heinrich Zu Dohna, Zakaria Kambris
BACKGROUND: Microflora of the gastrointestinal tract plays important roles in food digestion, nutrient absorption and in host defense against ingested pathogens. Several studies have focused on the microflora of farmed fishes, but the gut flora of wild fishes remains poorly characterized. The aim of this work was to provide an overview of the bacteria colonizing the gut of wild-caught fishes and to determine whether some bacterial species can be pathogenic. RESULTS: We isolated cultivable bacteria from fifteen wild-caught Mediterranean fish species corresponding to different habitat, diet and origin...
May 2017: Current Nutrition and Food Science
https://www.readbyqxmd.com/read/28504576/is-the-role-of-human-female-reproductive-tract-microbiota-underestimated
#18
D Kamińska, M Gajecka
An issue that is currently undergoing extensive study is the influence of human vaginal microbiota (VMB) on the health status of women and their neonates. Healthy women are mainly colonised with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners; however, other bacteria may be elements of the VMB, particularly in women with bacterial vaginosis. The implementation of culture-independent molecular methods in VMB characterisation, especially next-generation sequencing, have provided new information regarding bacterial diversity in the vagina, revealing a large number of novel, fastidious, and/or uncultivated bacterial species...
May 15, 2017: Beneficial Microbes
https://www.readbyqxmd.com/read/28502120/gut-microbial-communities-of-american-pikas-ochotona-princeps-evidence-for-phylosymbiosis-and-adaptations-to-novel-diets
#19
Kevin D Kohl, Johanna Varner, Jennifer L Wilkening, M Denise Dearing
1.Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. 2.We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences...
May 14, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28493460/single-cell-genomics-reveals-pyrrolysine-encoding-potential-in-members-of-uncultivated-archaeal-candidate-division-msbl1
#20
Yue Guan, Mohamed F Haroon, Intikhab Alam, James G Ferry, Ulrich Stingl
Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea...
May 10, 2017: Environmental Microbiology Reports
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