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Gut Virome

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
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
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
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 enteric virome and bacterial community composition of children with Crohn's 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...
August 30, 2018: Journal of Pediatric Gastroenterology and Nutrition
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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