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Gut Virome

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https://www.readbyqxmd.com/read/30065169/unprecedented-diversity-of-ssdna-phages-from-the-family-microviridae-detected-within-the-gut-of-a-protochordate-model-organism-ciona-robusta
#1
Alexandria Creasy, Karyna Rosario, Brittany A Leigh, Larry J Dishaw, Mya Breitbart
Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae . Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut...
July 31, 2018: Viruses
https://www.readbyqxmd.com/read/30010747/gut-microbial-and-metabolomic-profiles-after-fecal-microbiota-transplantation-in-pediatric-ulcerative-colitis-patients
#2
David J Nusbaum, Fengzhu Sun, Jie Ren, Zifan Zhu, Natalie Ramsy, Nicholas Pervolarakis, Sachin Kunde, Whitney England, Bei Gao, Oliver Fiehn, Sonia Michail, Katrine Whiteson
Ulcerative colitis is a chronic inflammatory disease of the colon that carries a significant disease burden in children. Therefore, new therapeutic approaches are being explored to help children living with this disease. Fecal microbiota transplantation (FMT) has been successful in some children with ulcerative colitis. However, the mechanism of its therapeutic effect in this patient population is not well understood. To characterize changes in gut microbial and metabolomic profiles after FMT, we performed 16S rRNA gene sequencing, shotgun metagenomic sequencing, virome analysis and untargeted metabolomics by gas chromatography-time of flight-mass spectrometry on stool samples collected before and after FMT from four children with ulcerative colitis who responded to this treatment...
September 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29933546/the-mammalian-intestinal-microbiome-composition-interaction-with-the-immune-system-significance-for-vaccine-efficacy-and-potential-for-disease-therapy
#3
REVIEW
Ulrich Desselberger
The mammalian gut is colonized by a large variety of microbes, collectively termed ‘the microbiome’. The gut microbiome undergoes rapid changes during the first few years of life and is highly variable in adulthood depending on various factors. With the gut being the largest organ of immune responses, the composition of the microbiome of the gut has been found to be correlated with qualitative and quantitative differences of mucosal and systemic immune responses. Animal models have been very useful to unravel the relationship between gut microbiome and immune responses and for the understanding of variations of immune responses to vaccination in different childhood populations...
June 21, 2018: Pathogens
https://www.readbyqxmd.com/read/29844669/responses-of-intestinal-virome-to-silver-nanoparticles-safety-assessment-by-classical-virology-whole-genome-sequencing-and-bioinformatics-approaches
#4
Kuppan Gokulan, Aschalew Z Bekele, Kenneth L Drake, Sangeeta Khare
Background: Effects of silver nanoparticles (AgNP) on the intestinal virome/phage community are mostly unknown. The working hypothesis of this study was that the exposure of pharmaceutical/nanomedicine and other consumer-use material containing silver ions and nanoparticles to the gastrointestinal tract may result in disturbance of the beneficial gut viruses/phages. Methods: This study assesses the impact of AgNP on the survival of individual bacteriophages using classical virology cultivation and electron microscopic techniques...
2018: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/29761040/viromes-of-one-year-old-infants-reveal-the-impact-of-birth-mode-on-microbiome-diversity
#5
Angela McCann, Feargal J Ryan, Stephen R Stockdale, Marion Dalmasso, Tony Blake, C Anthony Ryan, Catherine Stanton, Susan Mills, Paul R Ross, Colin Hill
Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity...
2018: PeerJ
https://www.readbyqxmd.com/read/29751830/amniotic-fluid-from-healthy-term-pregnancies-does-not-harbor-a-detectable-microbial-community
#6
Efrem S Lim, Cynthia Rodriguez, Lori R Holtz
Recent studies have conflicting data regarding the presence of intra-amniotic microbiota. Viral communities are increasingly recognized as important although overlooked components of the human microbiota. It is unknown if the developing fetus is exposed to a community of viruses (virome). Given the debate over the existence of an intra-amniotic microbial community and the importance of understanding how the infant gut is populated, we characterized the virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies using next-generation sequencing methods...
May 11, 2018: Microbiome
https://www.readbyqxmd.com/read/29719871/a-prospective-metagenomic-and-metabolomic-analysis-of-the-impact-of-exercise-and-or-whey-protein-supplementation-on-the-gut-microbiome-of-sedentary-adults
#7
Owen Cronin, Wiley Barton, Peter Skuse, Nicholas C Penney, Isabel Garcia-Perez, Eileen F Murphy, Trevor Woods, Helena Nugent, Aine Fanning, Silvia Melgar, Eanna C Falvey, Elaine Holmes, Paul D Cotter, Orla O'Sullivan, Michael G Molloy, Fergus Shanahan
Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in the diversity, composition, and functional profiles of microbial populations in the gut have been described in cross-sectional studies of habitual athletes. However, this relationship is also affected by changes in diet, such as changes in dietary and supplementary protein consumption, that coincide with exercise. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption...
May 2018: MSystems
https://www.readbyqxmd.com/read/29689266/alterations-in-enteric-virome-are-associated-with-colorectal-cancer-and-survival-outcomes
#8
Geicho Nakatsu, Haokui Zhou, William Ka Kei Wu, Sunny Hei Wong, Olabisi Oluwabukola Coker, Zhenwei Dai, Xiangchun Li, Chun-Ho Szeto, Naoki Sugimura, Thomas Yuen-Tung Lam, Allen Chi-Shing Yu, Xiansong Wang, Zigui Chen, Martin Chi-Sang Wong, Siew Chien Ng, Matthew Tak Vai Chan, Paul Kay Sheung Chan, Francis Ka Leung Chan, Joseph Jao-Yiu Sung, Jun Yu
BACKGROUND & AIMS: Patients with colorectal cancer (CRC) have a different gut microbiome signature than individuals without CRC. Little is known about the viral component of CRC-associated microbiome. We aimed to identify and validate viral taxonomic markers of CRC that might be used in detection of the disease or predicting outcome. METHODS: We performed shotgun metagenomic analyses of viromes of fecal samples from 74 patients with CRC (cases) and 92 individuals without CRC (controls) in Hong Kong (discovery cohort)...
August 2018: Gastroenterology
https://www.readbyqxmd.com/read/29670252/urbanization-and-the-gut-microbiota-in-health-and-inflammatory-bowel-disease
#9
REVIEW
Tao Zuo, Michael A Kamm, Jean-Frédéric Colombel, Siew C Ng
In the 21st century, urbanization represents a major demographic shift in developed and developing countries. Rapid urbanization in the developing world has been associated with an increasing incidence of several autoimmune diseases, including IBD. Patients with IBD exhibit a decrease in the diversity and richness of the gut microbiota, while urbanization attenuates the gut microbial diversity and might have a role in the pathogenesis of IBD. Environmental exposures during urbanization, including Westernization of diet, increased antibiotic use, pollution, improved hygiene status and early-life microbial exposure, have been shown to affect the gut microbiota...
July 2018: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/29668682/biogeography-and-environmental-conditions-shape-bacteriophage-bacteria-networks-across-the-human-microbiome
#10
Geoffrey D Hannigan, Melissa B Duhaime, Danai Koutra, Patrick D Schloss
Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body...
April 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29615108/phages-infecting-faecalibacterium-prausnitzii-belong-to-novel-viral-genera-that-help-to-decipher-intestinal-viromes
#11
Jeffrey K Cornuault, Marie-Agnès Petit, Mahendra Mariadassou, Leandro Benevides, Elisabeth Moncaut, Philippe Langella, Harry Sokol, Marianne De Paepe
BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases...
April 3, 2018: Microbiome
https://www.readbyqxmd.com/read/29570694/enteric-virome-sensing-its-role-in-intestinal-homeostasis-and-immunity
#12
REVIEW
Rebecca N Metzger, Anne B Krug, Katharina Eisenächer
Pattern recognition receptors (PRRs) sensing commensal microorganisms in the intestine induce tightly controlled tonic signaling in the intestinal mucosa, which is required to maintain intestinal barrier integrity and immune homeostasis. At the same time, PRR signaling pathways rapidly trigger the innate immune defense against invasive pathogens in the intestine. Intestinal epithelial cells and mononuclear phagocytes in the intestine and the gut-associated lymphoid tissues are critically involved in sensing components of the microbiome and regulating immune responses in the intestine to sustain immune tolerance against harmless antigens and to prevent inflammation...
March 23, 2018: Viruses
https://www.readbyqxmd.com/read/29402305/assessment-of-the-gorilla-gut-virome-in-association-with-natural-simian-immunodeficiency-virus-infection
#13
Mirela D'arc, Carolina Furtado, Juliana D Siqueira, Héctor N Seuánez, Ahidjo Ayouba, Martine Peeters, Marcelo A Soares
BACKGROUND: Simian immunodeficiency viruses (SIVs) of chimpanzees and gorillas from Central Africa crossed the species barrier at least four times giving rise to human immunodeficiency virus type 1 (HIV-1) groups M, N, O and P. The paradigm of non-pathogenic lentiviral infections has been challenged by observations of naturally infected chimpanzees with SIVcpz associated with a negative impact on their life span and reproduction, CD4+ T-lymphocyte loss and lymphoid tissue destruction...
February 5, 2018: Retrovirology
https://www.readbyqxmd.com/read/29378882/bacteriophages-of-the-urinary-microbiome
#14
Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J Wolfe, Catherine Putonti
Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses...
April 1, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29203935/viral-enteritis-in-calves
#15
REVIEW
Diego E Gomez, J Scott Weese
A complex community of bacteria, viruses, fungi, protists, and other microorganisms inhabit the gastrointestinal tract of calves and play important roles in gut health and disease. The viral component of the microbiome (the virome) is receiving increasing attention for its role in neonatal calf diarrhea (NCD). Rotavirus and coronavirus have for a long time been associated with NCD and commercial vaccines have been produced against these agents. Recently, several other viruses which may play a role in diarrhea have been discovered in calf fecal samples, mostly by sequence-based methods...
December 2017: Canadian Veterinary Journal. la Revue Vétérinaire Canadienne
https://www.readbyqxmd.com/read/29179741/dietary-energy-drives-the-dynamic-response-of-bovine-rumen-viral-communities
#16
Christopher L Anderson, Matthew B Sullivan, Samodha C Fernando
BACKGROUND: Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen...
November 28, 2017: Microbiome
https://www.readbyqxmd.com/read/29155033/the-gut-virome-of-the-protochordate-model-organism-ciona-intestinalis-subtype-a
#17
Brittany A Leigh, Anni Djurhuus, Mya Breitbart, Larry J Dishaw
The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members...
January 15, 2018: Virus Research
https://www.readbyqxmd.com/read/29133882/discovery-of-an-expansive-bacteriophage-family-that-includes-the-most-abundant-viruses-from-the-human-gut
#18
Natalya Yutin, Kira S Makarova, Ayal B Gussow, Mart Krupovic, Anca Segall, Robert A Edwards, Eugene V Koonin
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery 1-3 . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome 4 . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study...
January 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29026445/viral-communities-of-the-human-gut-metagenomic-analysis-of-composition-and-dynamics
#19
REVIEW
Varun Aggarwala, Guanxiang Liang, Frederic D Bushman
BACKGROUND: The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. MAIN BODY: Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28982318/virome-and-inflammasomes-a-finely-tuned-balance-with-important-consequences-for-the-host-health
#20
Giulia Freer, Fabrizio Maggi, Mauro Pistello
The virome is a multifaceted network of viruses inhabiting humans in health and disease. The virome forms a conspicuous portion of the so-called microbiome. Massive amount of data recently emerging demonstrates that the microbiome, once generically referred to as human (or animal) flora, is not a static entity but closely reflects what we eat, how and where we live, what we do, and many other unexpected variables. Composition, location, and amount of the microbiome have a direct impact on innate and adaptive host immune defences...
October 5, 2017: Current Medicinal Chemistry
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