keyword
MENU ▼
Read by QxMD icon Read
search

virome

keyword
https://www.readbyqxmd.com/read/28790203/the-in-feed-antibiotic-carbadox-induces-phage-gene-transcription-in-the-swine-gut-microbiome
#1
Timothy A Johnson, Torey Looft, Andrew J Severin, Darrell O Bayles, Daniel J Nasko, K Eric Wommack, Adina Howe, Heather K Allen
Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28780905/virome-comparisons-in-wild-diseased-and-healthy-captive-giant-pandas
#2
Wen Zhang, Shixing Yang, Tongling Shan, Rong Hou, Zhijian Liu, Wang Li, Lianghua Guo, Yan Wang, Peng Chen, Xiaochun Wang, Feifei Feng, Hua Wang, Chao Chen, Quan Shen, Chenglin Zhou, Xiuguo Hua, Li Cui, Xutao Deng, Zhihe Zhang, Dunwu Qi, Eric Delwart
BACKGROUND: The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS: Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals...
August 7, 2017: Microbiome
https://www.readbyqxmd.com/read/28780492/known-unknowns-how-might-the-persistent-herpesvirome-shape-immunity-and-aging
#3
REVIEW
Janko Nikolich-Zugich, Felicia Goodrum, Kenneth Knox, Megan J Smithey
The microbial community that colonizes all living organisms is gaining appreciation for its contributions to both physiologic and pathogenic processes. The virome, a subset of the overall microbiome, large and diverse, including viruses that persistently inhabit host cells, endogenous viral elements genomically or epigenomically integrated into cells, and viruses that infect the other (bacterial, protozoan, fungal, and archaeal) microbiome phylla. These viruses live in the organism for its life, and therefore are to be considered part of the aging process experienced by the organism...
August 3, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28765570/characterization-and-diversity-of-phages-infecting-aeromonas-salmonicida-subsp-salmonicida
#4
Antony T Vincent, Valérie E Paquet, Alex Bernatchez, Denise M Tremblay, Sylvain Moineau, Steve J Charette
Phages infecting Aeromonas salmonicida subsp. salmonicida, the causative agent of the fish disease furunculosis, have been isolated for decades but very few of them have been characterized. Here, the host range of 12 virulent phages, including three isolated in the present study, was evaluated against a panel of 65 A. salmonicida isolates, including representatives of the psychrophilic subspecies salmonicida, smithia, masoucida, and the mesophilic subspecies pectinolytica. This bacterial set also included three isolates from India suspected of being members of a new subspecies...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28759053/the-eukaryotic-gut-virome-in-hematopoietic-stem-cell-transplantation-new-clues-in-enteric-graft-versus-host-disease
#5
Jérôme Legoff, Matthieu Resche-Rigon, Jerome Bouquet, Marie Robin, Samia N Naccache, Séverine Mercier-Delarue, Scot Federman, Erik Samayoa, Clotilde Rousseau, Prescillia Piron, Nathalie Kapel, François Simon, Gérard Socié, Charles Y Chiu
Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0...
July 31, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28755263/phage-host-associations-in-a-full-scale-activated-sludge-plant-during-sludge-bulking
#6
Ruyin Liu, Rong Qi, Juan Wang, Yu Zhang, Xinchun Liu, Simona Rossetti, Valter Tandoi, Min Yang
Sludge bulking, a notorious microbial issue in activated sludge plants, is always accompanied by dramatic changes in the bacterial community. Despite large numbers of phages in sludge systems, their responses to sludge bulking and phage-host associations during bulking are unknown. In this study, high-throughput sequencing of viral metagenomes and bacterial 16S rRNA genes were employed to characterize viral and bacterial communities in a sludge plant under different sludge conditions (sludge volume index (SVI) of 180, 132, and 73 ml/g)...
July 29, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28743462/bacteriophages-in-the-human-gut-our-fellow-travelers-throughout-life-and-potential-biomarkers-of-heath-or-disease
#7
REVIEW
Babak Bakhshinejad, Saeedeh Ghiasvand
The gastrointestinal (GI) tract is populated by a huge variety of viruses. Bacterial viruses (bacteriophages) constitute the largest and the most unrecognized part of virome. The total bacteriophage community of the human gut is called phageome. Phages colonize the gut from the earliest moments of life and become our fellow travelers throughout life. Phageome seems to be unique to each individual and shows a high degree of interpersonal variation. In the healthy gut, a vast majority of phages have a lysogenic lifestyle...
July 22, 2017: Virus Research
https://www.readbyqxmd.com/read/28732571/examining-the-gut-bacteriome-virome-and-mycobiome-in-glucose-metabolism-disorders-are-we-on-the-right-track
#8
REVIEW
Charikleia Stefanaki, Melpomeni Peppa, George Mastorakos, George P Chrousos
Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living "organ" that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism...
August 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28724557/the-human-virome-implications-for-clinical-practice-in-transplantation-medicine
#9
Susanna K Tan, David A Relman, Benjamin A Pinsky
Advances in DNA sequencing technology have provided an unprecedented opportunity to study the human virome. Transplant recipients and other immunocompromised hosts are at particular risk for developing virus-related pathology; thus, the impact of the virome on health and disease may be even more relevant in this population. Here we discuss technical considerations in studying the human virome, the current literature on the virome in transplant recipients, and near future applications of sequence-based findings that can further our understanding of viruses in transplantation medicine...
July 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28724405/environmental-drivers-of-viral-community-composition-in-antarctic-soils-identified-by-viromics
#10
Evelien M Adriaenssens, Rolf Kramer, Marc W Van Goethem, Thulani P Makhalanyane, Ian Hogg, Don A Cowan
BACKGROUND: The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS: Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28713847/next-generation-sequencing-of-the-dna-virome-from-fecal-samples
#11
Cynthia L Monaco, Douglas S Kwon
Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand displacement amplified (MDA) and fragmented; and 4) libraries are constructed and sequenced using Illumina Miseq. Subsequent sequence analysis for viral sequence identification should be sensitive but stringent...
March 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28713358/aquarium-viromes-viromes-of-human-managed-aquatic-systems
#12
Yiseul Kim, William Van Bonn, Tiong G Aw, Joan B Rose
An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28698277/deep-sea-hydrothermal-vent-viruses-compensate-for-microbial-metabolism-in-virus-host-interactions
#13
Tianliang He, Hongyun Li, Xiaobo Zhang
Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28696303/intestinal-virome-changes-precede-autoimmunity-in-type-i-diabetes-susceptible-children
#14
Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D Kostic, Tiffany W Poon, Hera Vlamakis, Heli Siljander, Taina Härkönen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Jorma Ilonen, David Wang, Mikael Knip, Ramnik J Xavier, Herbert W Virgin
Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls...
July 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28677677/marine-viruses-discovered-via-metagenomics-shed-light-on-viral-strategies-throughout-the-oceans
#15
Felipe H Coutinho, Cynthia B Silveira, Gustavo B Gregoracci, Cristiane C Thompson, Robert A Edwards, Corina P D Brussaard, Bas E Dutilh, Fabiano L Thompson
Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter...
July 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28672885/characterization-of-sinorhizobium-sp-lm21-prophages-and-virus-encoded-dna-methyltransferases-in-the-light-of-comparative-genomic-analyses-of-the-sinorhizobial-virome
#16
Przemyslaw Decewicz, Monika Radlinska, Lukasz Dziewit
The genus Sinorhizobium/Ensifer mostly groups nitrogen-fixing bacteria that create root or stem nodules on leguminous plants and transform atmospheric nitrogen into ammonia, which improves the productivity of the plants. Although these biotechnologically-important bacteria are commonly found in various soil environments, little is known about their phages. In this study, the genome of Sinorhizobium sp. LM21 isolated from a heavy-metal-contaminated copper mine in Poland was investigated for the presence of prophages and DNA methyltransferase-encoding genes...
June 26, 2017: Viruses
https://www.readbyqxmd.com/read/28671295/characterization-of-the-nasopharyngeal-viral-microbiome-from-children-with-community-acquired-pneumonia-but-negative-for-luminex-xtag-respiratory-viral-panel-assay-detection
#17
Lili Xu, Yun Zhu, Lili Ren, Baoping Xu, Chunyan Liu, Zhengde Xie, Kunling Shen
In the present study, 50 nasopharyngeal swabs from children with community-acquired pneumonia (CAP) but negative for 18 common respiratory viruses, as measured by the Luminex xTAG Respiratory Viral Panel Assay, were subjected to multiplex metagenomic analyses using a next-generation sequencing platform. Taxonomic analysis showed that all sequence reads could be assigned to a specific species. An average of 95.13% were assigned to the Bacteria kingdom, whereas only 0.72% were potentially virus derived. This snapshot of the respiratory tract virome revealed most viral reads to be respiratory tract related, classified into four known virus families: Paramyxoviridae, Herpesviridae, Anelloviridae, and Polyomaviridae...
July 3, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28663745/viromes-as-genetic-reservoir-for-the-microbial-communities-in-aquatic-environments-a-focus-on-antimicrobial-resistance-genes
#18
Stefano Colombo, Stefania Arioli, Eros Neri, Giulia Della Scala, Giorgio Gargari, Diego Mora
Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28659484/case-control-comparison-of-enteric-viromes-in-captive-rhesus-macaques-with-acute-or-idiopathic-chronic-diarrhea
#19
Beatrix Kapusinszky, Amir Ardeshir, Usha Mulvaney, Xutao Deng, Eric Delwart
Diarrhea is the major cause of non-research associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, a form of human inflammatory bowel disease. To test for viral etiologies we characterized and compared the fecal virome from 32 healthy, 31 with acute diarrhea, and 29 with ICD animals. The overall fraction of eukaryotic viral reads was 0.063% for the healthy group, 0...
June 28, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28651630/maternal-inheritance-of-bifidobacterial-communities-and-bifidophages-in-infants-through-vertical-transmission
#20
Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Federica Armanini, Francesca Turroni, Kieran James, Pamela Ferretti, Valentina Gorfer, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Moreno Zolfo, Alice Viappiani, Edoardo Pasolli, Ilaria Bariletti, Rosarita Canto, Rosanna Clementi, Marina Cologna, Tiziana Crifò, Giuseppina Cusumano, Sabina Fedi, Stefania Gottardi, Claudia Innamorati, Caterina Masè, Daniela Postai, Daniela Savoi, Massimo Soffiati, Saverio Tateo, Anna Pedrotti, Nicola Segata, Douwe van Sinderen, Marco Ventura
BACKGROUND: The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS: The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses...
June 26, 2017: Microbiome
keyword
keyword
29595
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"