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https://www.readbyqxmd.com/read/29346651/bipartite-network-analysis-of-gene-sharings-in-the-microbial-world
#1
Eduardo Corel, Raphaël Méheust, Andrew K Watson, James O McInerney, Philippe Lopez, Eric Bapteste
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29339825/corallivory-and-the-microbial-debacle-in-two-branching-scleractinians
#2
Yvan Bettarel, Sébastien Halary, Jean-Christophe Auguet, Thanh Chi Mai, Ngoc Van Bui, Thierry Bouvier, Patrice Got, Corinne Bouvier, Sonia Monteil-Bouchard, Desnues Christelle
The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i...
January 16, 2018: ISME Journal
https://www.readbyqxmd.com/read/29304041/development-of-a-biosensor-protein-bullet-as-a-fluorescent-method-for-fast-detection-of-escherichia-coli-in-drinking-water
#3
Ignacio Gutiérrez-Del-Río, Laura Marín, Javier Fernández, María Álvarez San Millán, Francisco Javier Ferrero, Marta Valledor, Juan Carlos Campo, Natalia Cobián, Ignacio Méndez, Felipe Lombó
Drinking water can be exposed to different biological contaminants from the source, through the pipelines, until reaching the final consumer or industry. Some of these are pathogenic bacteria and viruses which may cause important gastrointestinal or systemic diseases. The microbiological quality of drinking water relies mainly in monitoring three indicator bacteria of faecal origin, Escherichia coli, Enterococcus faecalis and Clostridium perfringens, which serve as early sentinels of potential health hazards for the population...
2018: PloS One
https://www.readbyqxmd.com/read/29301542/monitoring-of-poyang-lake-water-for-sewage-contamination-using-human-enteric-viruses-as-an-indicator
#4
Hui Zhu, Fang Yuan, Zhaokang Yuan, Rong Liu, Fei Xie, Ling Huang, Xiaojun Liu, Xiaoqing Jiang, Jian Wang, Qunying Xu, Zhiqiang Shen, Donghan Liu, Ronghao Zhang, Yuanan Lu
BACKGROUND: Recreational water contaminated with fecal pollution poses a great public health concern, as fecal waste may cause serious waterborne illnesses. Current recreational water standards using fecal indicator bacteria (FIB) have their limitations for human protection especially in developing countries such as China. METHODS: To explore the potential use of enteric viruses as a potential indicator of fecal contamination, four viruses: norovirus geno-groups I and II, enteroviruses, and adenoviruses were tested in this study using molecular detection methods and sensitive RT-PC developed in the University of Hawaii...
January 5, 2018: Virology Journal
https://www.readbyqxmd.com/read/29299190/evaluation-of-microbiota-associated-with-herpesviruses-in-active-sites-of-generalized-aggressive-periodontitis
#5
Claudio Passariello, Pierangelo Gigola, Luca Testarelli, Monica Puttini, Serena Schippa, Stefano Petti
Aims: The present study aimed to investigate microbial patterns associated with disease progression and coinfection by different Herpesviruses in generalized aggressive periodontitis (GAP). Methods: Microbiological samples were obtained from active (AS) and non-active (n-AS) sites in 165 subjects affected by GAP and were analyzed for 40 bacterial species by the Checkerboard DNA-DNA Hybridization technique and for Herpes simplex 1 (HSV-1), Human Cytomegalovirus (CMV), and Epstein Bar virus (EBV) by PCR...
April 2017: Annali di Stomatologia
https://www.readbyqxmd.com/read/29297963/matrix-approach-to-the-simultaneous-detection-of-multiple-potato-pathogens-by-real-time-pcr
#6
M M Nikitin, N V Statsyuk, P A Frantsuzov, V G Dzhavakhiya, A G Golikov
AIM: Create a method for highly sensitive, selective, rapid, and easy-to-use detection and identification of economically significant potato pathogens, including viruses, bacteria and oomycetes, be it single pathogen, or a range of various pathogens occurring simultaneously. METHODS AND RESULTS: Test-systems for real-time PCR, operating in the unified amplification regime, have been developed for Phytophthora infestans, Pectobacterium atrosepticum, Dickeya dianthicola, Dickeya solani, Ralstonia solanacearum, Pectobacterium carotovorum, Clavibacter michiganensis subsp...
January 3, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29287070/a-diagnostic-and-epidemiologic-investigation-of-acute-febrile-illness-afi-in-kilombero-tanzania
#7
Christine Hercik, Leonard Cosmas, Ondari D Mogeni, Newton Wamola, Wanze Kohi, Victor Omballa, Melvin Ochieng, Shirley Lidechi, Juma Bonventure, Caroline Ochieng, Clayton Onyango, Barry S Fields, Sayoki Mfinanga, Joel M Montgomery
INTRODUCTION: In low-resource settings, empiric case management of febrile illness is routine as a result of limited access to laboratory diagnostics. The use of comprehensive fever syndromic surveillance, with enhanced clinical microbiology, advanced diagnostics and more robust epidemiologic investigation, could enable healthcare providers to offer a differential diagnosis of fever syndrome and more appropriate care and treatment. METHODS: We conducted a year-long exploratory study of fever syndrome among patients ≥ 1 year if age, presenting to clinical settings with an axillary temperature of ≥37...
2017: PloS One
https://www.readbyqxmd.com/read/29284418/the-aetiologies-of-central-nervous-system-infections-in-hospitalised-cambodian-children
#8
Paul Turner, Kuong Suy, Le Van Tan, Pora Sar, Thyl Miliya, Nguyen Thi Thu Hong, Vu Thi Ty Hang, Nguyen Thi Han Ny, Sona Soeng, Nicholas P J Day, H Rogier van Doorn, Claudia Turner
BACKGROUND: Central nervous system (CNS) infections are an important cause of childhood morbidity and mortality. The aetiologies of these potentially vaccine-preventable infections have not been well established in Cambodia. METHODS: We did a one year prospective study of children hospitalised with suspected CNS infection at Angkor Hospital for Children, Siem Reap. Cerebrospinal fluid specimens (CSF) samples underwent culture, multiplex PCR and serological analysis to identify a range of bacterial and viral pathogens...
December 29, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29237789/community-acquired-pneumonia-in-children-the-challenges-of-microbiological-diagnosis
#9
C M C Rodrigues, H Groves
Community-acquired pneumonia (CAP) is the leading cause of mortality in children under five years of age, globally. To improve the management of CAP, we must distinguish CAP from other common paediatric conditions and develop better diagnostic methods to detect the causative organism, so to best direct appropriate resources in both industrialised and developing countries. Here, we review the diagnostic modalities available for identifying viruses and bacteria in the upper and lower respiratory tract of children, with a discussion of their utility and limitations in diagnosing CAP in children...
December 13, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29153181/a-100-year-review-microbiology-and-safety-of-milk-handling
#10
Kathryn J Boor, Martin Wiedmann, Sarah Murphy, Sam Alcaine
Microbes that may be present in milk can include pathogens, spoilage organisms, organisms that may be conditionally beneficial (e.g., lactic acid bacteria), and those that have not been linked to either beneficial or detrimental effects on product quality or human health. Although milk can contain a full range of organisms classified as microbes (i.e., bacteria, viruses, fungi, and protozoans), with few exceptions (e.g., phages that affect fermentations, fungal spoilage organisms, and, to a lesser extent, the protozoan pathogens Cryptosporidium and Giardia) dairy microbiology to date has focused predominantly on bacteria...
December 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29150768/toe-web-intertrigo-in-kaposi-s-sarcoma-patients-a-microbiological-study-in-a-large-cohort-of-patients
#11
G Nazzaro, A Tourlaki, B Scoppio, A Restelli, A Grancini, L Brambilla
Kaposi 's sarcoma (KS) is a rare multifocal angioproliferative disease associated with human herpes virus 8 (HHV-8) infection, characterized by cutaneous nodules or plaques especially on the lower limbs. Some skin modifications, such as chronic lymphedema, plantar hyperkeratosis and interdigital desquamation, may be associated with consequent impairment of the local immunosurveillance and increased risk of some bacterial or mycotic infections. With the objective of evaluating if bacterial or mycotic infections in KS patients are supported by different microorganisms compared to control patients, we performed an observational retrospective study, comparing positive cultural swabs of interdigital intertrigo of KS patients with positive cultural swabs of interdigital intertrigo of patients admitted to our dermatologic unit during the last 10 years...
November 17, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29132426/comment-on-a-re-assessment-of-the-safety-of-silver-in-household-water-treatment-rapid-systematic-review-of-mammalian-in-vivo-genotoxicity-studies
#12
EDITORIAL
Daniele Lantagne, Justine Rayner, Anjuliee Mittelman, Kurt Pennell
We wish to thank Fewtrell, Majuru, and Hunter for their article highlighting genotoxic risks associated with the use of particulate silver for primary drinking water treatment. The recent promotion of colloidal silver products for household water treatment in developing countries is problematic due to previously identified concerns regarding manufacturing quality and questionable advertising practices, as well as the low efficiency of silver nanoparticles to treat bacteria, viruses, and protozoa in source waters...
November 13, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/29090481/utility-of-flexible-bronchoscopy-with-polymerase-chain-reaction-in-the-diagnosis-and-management-of-pulmonary-infiltrates-in-allogeneic-hsct-patients
#13
Fei-Fei Tang, Xiao-Su Zhao, Lan-Ping Xu, Xiao-Hui Zhang, Yu-Hong Chen, Xiao-Dong Mo, Kai-Yan Liu, Xiao-Jun Huang
OBJECTIVES: Pulmonary infiltrates in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients are potentially life-threatening and require early diagnosis and treatment. We aimed to retrospectively explore the clinical efficacy of polymerase chain reaction (PCR) in conjunction with flexible bronchoscopy (FB) in allo-HSCT patients with pulmonary infiltrates. PATIENTS AND METHODS: We retrospectively reviewed all patients undergoing FB after allo-HSCT at the Peking University Institute of Hematology from January 2013 to December 2016...
November 1, 2017: Clinical Transplantation
https://www.readbyqxmd.com/read/29074195/presence-of-enteric-viruses-bioaccumulation-and-stability-in-anomalocardia-brasiliana-clams-gmelin-1791
#14
Doris Sobral Marques Souza, Ana Ferreira Ávila Dominot, Vanessa Moresco, Célia Regina Monte Barardi
Bivalve mollusks are filter feeders and may accumulate human pathogens in their tissues. Many studies demonstrated human diseases associated with bivalve consumption, especially oysters. Anomalocardia brasiliana clams are distributed along the Brazilian coastal area and are an exotic ingredient for some typical dishes in Brazil. Even though there are several reports describing the contamination of oysters and mussels with human pathogens, there is a lack of studies reporting contamination of A. brasiliana with human pathogens...
August 12, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29051394/evolution-on-rugged-adaptive-landscapes
#15
Uri Obolski, Yoav Ram, Lilach Hadany
Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors on the genetic space. How would a population evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930's by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes...
October 20, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/29045616/potential-impact-of-global-climate-change-on-benthic-deep-sea-microbes
#16
Roberto Danovaro, Cinzia Corinaldesi, Antonio Dell Anno, Eugenio Rastelli
Benthic deep-sea environments are the largest ecosystem on Earth, covering approximately 65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH), and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor)...
October 13, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29040428/understanding-the-promises-and-hurdles-of-metagenomic-next-generation-sequencing-as-a-diagnostic-tool-for-infectious-diseases
#17
Patricia J Simner, Steven Miller, Karen C Carroll
Agnostic metagenomic next-generation sequencing (mNGS) has emerged as a promising single, universal pathogen detection method for infectious diseases diagnostics. This methodology allows for identification and genomic characterization of bacteria, fungi, parasites and viruses without the need for a priori knowledge of a specific pathogen directly from clinical specimens. Although there are increasing reports of mNGS successes, several hurdles need to be addressed, such as differentiation of colonization from infection, extraneous sources of nucleic acid, method standardization, and data storage, protection, analysis, and interpretation...
October 12, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29022247/persistent-norovirus-contamination-of-groundwater-supplies-in-two-waterborne-outbreaks
#18
Ari Kauppinen, Tarja Pitkänen, Ilkka T Miettinen
Microbiological contamination of groundwater supplies causes waterborne outbreaks worldwide. In this study, two waterborne outbreaks related to microbiological contamination of groundwater supplies are described. Analyses of pathogenic human enteric viruses (noroviruses and adenoviruses), fecal bacteria (Campylobacter spp. and Salmonella spp.), and indicator microbes (E. coli, coliform bacteria, intestinal enterococci, Clostridium perfringens, heterotrophic plate count, somatic and F-specific coliphages) were conducted in order to reveal the cause of the outbreaks and to examine the effectiveness of the implemented management measures...
October 11, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/28904380/transfer-of-labile-organic-matter-and-microbes-from-the-ocean-surface-to-the-marine-aerosol-an-experimental-approach
#19
Eugenio Rastelli, Cinzia Corinaldesi, Antonio Dell'Anno, Marco Lo Martire, Silvestro Greco, Maria Cristina Facchini, Matteo Rinaldi, Colin O'Dowd, Darius Ceburnis, Roberto Danovaro
Surface ocean bubble-bursting generates aerosols composed of microscopic salt-water droplets, enriched in marine organic matter. The organic fraction profoundly influences aerosols' properties, by scattering solar radiations and nucleating water particles. Still little is known on the biochemical and microbiological composition of these organic particles. In the present study, we experimentally simulated the bursting of bubbles at the seawater surface of the North-Eastern Atlantic Ocean, analysing the organic materials and the diversity of the bacteria in the source-seawaters and in the produced aerosols...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28898207/shotgun-metagenomics-from-sampling-to-analysis
#20
REVIEW
Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman, Nicola Segata
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed...
September 12, 2017: Nature Biotechnology
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