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Gut Virome

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https://read.qxmd.com/read/30763537/virome-diversity-correlates-with-intestinal-microbiome-diversity-in-adult-monozygotic-twins
#1
J Leonardo Moreno-Gallego, Shao-Pei Chou, Sara C Di Rienzi, Julia K Goodrich, Timothy D Spector, Jordana T Bell, Nicholas D Youngblut, Ian Hewson, Alejandro Reyes, Ruth E Ley
The virome is one of the most variable components of the human gut microbiome. Within twin pairs, viromes have been shown to be similar for infants, but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the vast virome diversity is unclear. Here, we examine the relationship between microbiome and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles are unique to each individual, are dominated by Caudovirales and Microviridae, and exhibit a small core that includes crAssphage...
February 13, 2019: Cell Host & Microbe
https://read.qxmd.com/read/30741981/higher-abundance-of-enterovirus-a-species-in-the-gut-of-children-with-islet-autoimmunity
#2
Ki Wook Kim, Jessica L Horton, Chi Nam Ignatius Pang, Komal Jain, Preston Leung, Sonia R Isaacs, Rowena A Bull, Fabio Luciani, Marc R Wilkins, Jacki Catteau, W Ian Lipkin, William D Rawlinson, Thomas Briese, Maria E Craig
Enteroviruses (EVs) are prime candidate environmental triggers of islet autoimmunity (IA), with potential as vaccine targets for type 1 diabetes prevention. However, the use of targeted virus detection methods and the selective focus on EVs by most studies increases the risk for substantial investigation bias and an overestimated association between EV and type 1 diabetes. Here we performed comprehensive virome-capture sequencing to examine all known vertebrate-infecting viruses without bias in 182 specimens (faeces and plasma) collected before or at seroconversion from 45 case children with IA and 48 matched controls...
February 11, 2019: Scientific Reports
https://read.qxmd.com/read/30691529/choice-of-assembly-software-has-a-critical-impact-on-virome-characterisation
#3
Thomas D S Sutton, Adam G Clooney, Feargal J Ryan, R Paul Ross, Colin Hill
BACKGROUND: The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members...
January 28, 2019: Microbiome
https://read.qxmd.com/read/30674646/gut-virome-analysis-of-cameroonians-reveals-high-diversity-of-enteric-viruses-including-potential-interspecies-transmitted-viruses
#4
Claude Kwe Yinda, Emiel Vanhulle, Nádia Conceição-Neto, Leen Beller, Ward Deboutte, Chenyan Shi, Stephen Mbigha Ghogomu, Piet Maes, Marc Van Ranst, Jelle Matthijnssens
Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact...
January 23, 2019: MSphere
https://read.qxmd.com/read/30621339/bacteriocins-and-bacteriophages-therapeutic-weapons-for-gastrointestinal-diseases
#5
REVIEW
Loris Riccardo Lopetuso, Maria Ernestina Giorgio, Angela Saviano, Franco Scaldaferri, Antonio Gasbarrini, Giovanni Cammarota
Bacteriocins are bactericidal peptides, ribosomally synthesized, with an inhibitory activity against diverse groups of undesirable microorganisms. Bacteriocins are produced by both gram-positive and gram-negative bacteria, and to a lesser extent by some archaea. Bacteriophages are viruses that are able to infect bacterial cells and force them to produce viral components, using a lytic or lysogenic cycle. They constitute a large community in the human gut called the phageome, the most abundant part of the gut virome...
January 6, 2019: International Journal of Molecular Sciences
https://read.qxmd.com/read/30578857/the-gut-microbiome-in-food-allergy
#6
REVIEW
William Zhao, Hsi-En Ho, Supinda Bunyavanich
OBJECTIVE: To review observational human, murine, and interventional trial studies that have examined the gut microbiome in food allergy, and to provide perspective on future investigations in this field. DATA SOURCES: A review of the published literature was performed with PubMed, and clinical studies catalogued at ClinicalTrials.gov were also reviewed. STUDY SELECTIONS: The most recent relevant studies, seminal works, and topical clinical trials were selected...
December 19, 2018: Annals of Allergy, Asthma & Immunology
https://read.qxmd.com/read/30574559/finer-scale-phylosymbiosis-insights-from-insect-viromes
#7
Brittany A Leigh, Sarah R Bordenstein, Andrew W Brooks, Aram Mikaelyan, Seth R Bordenstein
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness (e.g., beta diversity relationships) of host-associated microbial communities parallels the phylogeny of the host species. Representing the most abundant biological entities on the planet and common members of the animal-associated microbiome, viruses can be influential members of host-associated microbial communities that may recapitulate, reinforce, or ablate phylosymbiosis. Here we sequence the metagenomes of purified viral communities from three different parasitic wasp Nasonia species, one cytonuclear introgression line of Nasonia , and the flour moth outgroup Ephestia kuehniella...
November 2018: MSystems
https://read.qxmd.com/read/30472682/enteric-fungal-microbiota-dysbiosis-and-ecological-alterations-in-colorectal-cancer
#8
Olabisi Oluwabukola Coker, Geicho Nakatsu, Rudin Zhenwei Dai, William Ka Kei Wu, Sunny Hei Wong, Siew Chien Ng, Francis Ka Leung Chan, Joseph Jao Yiu Sung, Jun Yu
OBJECTIVES: Bacteriome and virome alterations are associated with colorectal cancer (CRC). Nevertheless, the gut fungal microbiota in CRC remains largely unexplored. We aimed to characterise enteric mycobiome in CRC. DESIGN: Faecal shotgun metagenomic sequences of 184 patients with CRC, 197 patients with adenoma and 204 control subjects from Hong Kong were analysed (discovery cohort: 73 patients with CRC and 92 control subjects; validation cohort: 111 patients with CRC, 197 patients with adenoma and 112 controls from Hong Kong)...
November 24, 2018: Gut
https://read.qxmd.com/read/30459201/diagnostic-potential-and-interactive-dynamics-of-the-colorectal-cancer-virome
#9
Geoffrey D Hannigan, Melissa B Duhaime, Mack T Ruffin, Charlie C Koumpouras, Patrick D Schloss
Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome...
November 20, 2018: MBio
https://read.qxmd.com/read/30449316/biology-and-taxonomy-of-crass-like-bacteriophages-the-most-abundant-virus-in-the-human-gut
#10
Emma Guerin, Andrey Shkoporov, Stephen R Stockdale, Adam G Clooney, Feargal J Ryan, Thomas D S Sutton, Lorraine A Draper, Enrique Gonzalez-Tortuero, R Paul Ross, Colin Hill
CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb...
November 14, 2018: Cell Host & Microbe
https://read.qxmd.com/read/30429469/%C3%AE-crass001-represents-the-most-abundant-bacteriophage-family-in-the-human-gut-and-infects-bacteroides-intestinalis
#11
Andrey N Shkoporov, Ekaterina V Khokhlova, C Brian Fitzgerald, Stephen R Stockdale, Lorraine A Draper, R Paul Ross, Colin Hill
CrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (ΦCrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host...
November 14, 2018: Nature Communications
https://read.qxmd.com/read/30356736/immunological-tolerance-and-function-associations-between-intestinal-bacteria-probiotics-prebiotics-and-phages
#12
REVIEW
Luis Vitetta, Gemma Vitetta, Sean Hall
Post-birth there is a bacterial assault on all mucosal surfaces. The intestinal microbiome is an important participant in health and disease. The pattern of composition and concentration of the intestinal microbiome varies greatly. Therefore, achieving immunological tolerance in the first 3-4 years of life is critical for maintaining health throughout a lifetime. Probiotic bacteria are organisms that afford beneficial health effects to the host and in certain instances may protect against the development of disease...
2018: Frontiers in Immunology
https://read.qxmd.com/read/30302521/alterations-in-the-diversity-and-composition-of-mice-gut-microbiota-by-lytic-or-temperate-gut-phage-treatment
#13
Hong-Duo Bao, Mao-da Pang, Ademola Olaniran, Xu-Hui Zhang, Hui Zhang, Yan Zhou, Li-Chang Sun, Stefan Schmidt, Ran Wang
Phages, the most abundant species in the mammalian gut, have numerous advantages as biocontrol agent over antibiotics. In this study, mice were orally treated with the lytic gut phage PA13076 (group B), the temperate phage BP96115 (group C), no phage (group A), or streptomycin (group D) over 31 days. At the end of the experiment, fecal microbiota diversity and composition was determined and compared using high-throughput sequencing of the V3-V4 hyper-variable region of the 16S rRNA gene and virus-like particles (VLPs) were quantified in feces...
October 9, 2018: Applied Microbiology and Biotechnology
https://read.qxmd.com/read/30252582/metagenomic-analysis-of-intestinal-mucosa-revealed-a-specific-eukaryotic-gut-virome-signature-in-early-diagnosed-inflammatory-bowel-disease
#14
Federica Ungaro, Luca Massimino, Federica Furfaro, Valeria Rimoldi, Laurent Peyrin-Biroulet, Silvia D'Alessio, Silvio Danese
Intestinal dysbiosis is one of the causes underlying the pathogenesis of inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD). Besides bacteria, microbiota comprises both prokaryotic and eukaryotic viruses, that together compose the gut virome. Few works have defined the viral composition of stools, while the virome populating intestinal mucosae from early-diagnosed IBD patients has never been studied. Here we show that, by in-depth metagenomic analysis of RNA-Seq data obtained from gut mucosae of young treatment-naïve patients, early-diagnosed for CD and UC, and from healthy subjects (Ctrl), UC patients display significantly higher levels of eukaryotic Hepadnaviridae transcripts by comparison with both Ctrl and CD patients, whereas CD patients show increased abundance of Hepeviridae versus Ctrl...
September 25, 2018: Gut Microbes
https://read.qxmd.com/read/30181300/the-intestinal-virome-and-immunity
#15
REVIEW
Jessica A Neil, Ken Cadwell
The composition of the human microbiome is considered a major source of interindividual variation in immunity and, by extension, susceptibility to diseases. Intestinal bacteria have been the major focus of research. However, diverse communities of viruses that infect microbes and the animal host cohabitate the gastrointestinal tract and collectively constitute the gut virome. Although viruses are typically investigated as pathogens, recent studies highlight a relationship between the host and animal viruses in the gut that is more akin to host-microbiome interactions and includes both beneficial and detrimental outcomes for the host...
September 15, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://read.qxmd.com/read/30169455/enteric-virome-and-bacterial-microbiota-in-children-with-ulcerative-colitis-and-crohn-disease
#16
Melissa A Fernandes, Sofia G Verstraete, Tung G Phan, Xutao Deng, Emily Stekol, Brandon LaMere, Susan V Lynch, Melvin B Heyman, Eric Delwart
OBJECTIVES: We examined the fecal virome and bacterial community composition of children with Crohn disease (CD), ulcerative colitis (UC), and healthy controls to test the hypothesis that unique patterns of viral organisms and/or presence of bacterial pathogens may be identified that could contribute to the pathogenesis of pediatric inflammatory bowel disease (IBD). METHODS: Fecal samples from 24 children (mean 12.2 years) with CD (n = 7) or UC (n = 5) and similar aged controls (n = 12) were processed to determine individual viromes...
January 2019: Journal of Pediatric Gastroenterology and Nutrition
https://read.qxmd.com/read/30128999/diversity-analysis-in-viral-metagenomes
#17
Jorge Francisco Vázquez-Castellanos
Viruses are the most abundant and diverse biological entity in the earth. Nowadays, there are several viral metagenomes from different ecological niches which have been used to characterize new viral particles and to determine their diversity. However, viral metagenomic data have the disadvantage to be high-dimensional compositional and sparse. This type of data renders many of the conventional multivariate statistical analyses inoperative. Fortunately, different libraries and statistical packages have been developed to deal with this problem and perform the different ecological and statistical analyses...
2018: Methods in Molecular Biology
https://read.qxmd.com/read/30128992/viral-genome-isolation-from-human-faeces-for-succession-assessment-of-the-human-gut-virome
#18
David Mayo-Muñoz
Despite the important role of the microbiota in the human gastrointestinal tract (GIT) and its impact on life-long health, the successional process through which this microbial community develops during infancy is still poorly understood. Specially, little is known about how the amount and type of viruses present in the GIT, i.e., the virome, varies throughout this period and about the role this collection of viruses may play in the assembly of the GIT microbiota.The patterns of taxonomic change of the GIT viral community can be analyzed in a birth cohort of infants during the first year of life...
2018: Methods in Molecular Biology
https://read.qxmd.com/read/30128991/netovir-modular-approach-to-customize-sample-preparation-procedures-for-viral-metagenomics
#19
Nádia Conceição-Neto, Kwe Claude Yinda, Marc Van Ranst, Jelle Matthijnssens
The democratization of next-generation sequencing (NGS) technologies has enabled scientists to explore the diversity of microbial life in various ecological niches in an unpreceded depth. The role of viruses as a key player in health and disease is becoming increasingly clear. To address the need for an up scalable, reproducible protocol to purify RNA and DNA viruses from a sample, we describe our optimized method. The Novel Enrichment Technique Of Viromes (NetoVIR) allows researchers to attain a fast, reproducible, and high-throughput sample preparation protocol for NGS gut viromics studies...
2018: Methods in Molecular Biology
https://read.qxmd.com/read/30128989/extraction-and-purification-of-viruses-from-fecal-samples-for-metagenome-and-morphology-analyses
#20
Josué L Castro-Mejía, Ling Deng, Finn K Vogensen, Alejandro Reyes, Dennis S Nielsen
The human enteric virome consists of endogenous retro elements and viruses that infect the host and members of the gut microbiome (GM). Mounting evidence suggests that the gut virome plays a central role in maintaining homeostasis and via the GM influences immunology of the host. To thoroughly characterize the gut virome, it is often very useful to first separate and concentrate extracellular viral-like particles (eVLPs) enabling an integrative characterization of them. Here, we describe a detailed protocol for extraction and concentration of the viral fraction from fecal samples based on a polyethylene glycol precipitation (PEG) approach...
2018: Methods in Molecular Biology
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