Enteric Virome Research Articles

Identification and characterization of a novel Enterococcus bacteriophage with potential to ameliorate murine colitis

Increase of the enteric bacteriophages (phage), components of the enteric virome, has been associated with the development of inflammatory bowel diseases. However, little is known about how a given phage contributes to the regulation of intestinal inflammation. In this study, we isolated a new phage associated with Enterococcus gallinarum, named phiEG37k, the level of which was increased in C57BL/6 mice with colitis development. We found that, irrespective of the state of inflammation, over 95% of the E. gallinarum population in the mice contained phiEG37k prophage within their genome and the phiEG37k titers were proportional to that of E. gallinarum in the gut. To explore whether phiEG37k impacts intestinal homeostasis and/or inflammation, we generated mice colonized either with E. gallinarum with or without the prophage phiEG37k. We found that the mice colonized with the bacteria with phiEG37k produced more Mucin 2 (MUC2) that serves to protect the intestinal epithelium, as compared to those colonized with the phage-free bacteria. Consistently, the former mice were less sensitive to experimental colitis than the latter mice. These results suggest that the newly isolated phage has the potential to protect the host by strengthening mucosal integrity. Our study may have clinical implication in further understanding of how bacteriophages contribute to the gut homeostasis and pathogenesis.

Insights into Gastrointestinal Virome: Etiology and Public Exposure

Recycled wastewater is widely used owing to the potential shortage of water resources for drinking purposes, recreational activities, and irrigation. However, gut microbiomes of both human beings and animals negatively affect this water quality. Wastewater contamination is continuously monitored, using fecal contamination indicators or microbial source tracking approaches, to oppose arising enteric infections. Viral gastroenteritis is considered a principal manifestation of waterborne pathogenic virome-mediated infections, which are mainly transmitted via the fecal-oral route. Furthermore, acquired enteric viromes are the common cause of infantile acute diarrhea. Moreover, public exposure to wastewater via wastewater discharge or treated wastewater reuse has led to a significant surge of public health concerns. In this review, we discussed the etiology of waterborne enteric viromes, notably gastrointestinal virus infections, and public exposure to municipal wastewater. Conclusively, the early human virome is affected mainly by birth mode, dietary behavior, and maternal health, and could provide a signature of disease incidence, however, more virome diversification is acquired in adulthood. A multi-phase treatment approach offered an effective means for the elimination of wastewater reuse mediated public risks. The insights highlighted in this paper offer essential information for defining probable etiologies and assessing risks related to exposure to discharged or reused wastewater.

Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome

The contributions of the viral component of the microbiome-the virome-to the development of innate and adaptive immunity are largely unknown. Here, we systematically defined the host response in mice to a panel of eukaryotic enteric viruses representing six different families. Infections with most of these viruses were asymptomatic in the mice, the magnitude and duration of which was dependent on the microbiota. Flow cytometric and transcriptional profiling of mice mono-associated with these viruses unveiled general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine, as well as numerous viral-strain-specific responses that persisted. Comparison with a dataset derived from analogous bacterial mono-association in mice identified bacterial species that evoke an immune response comparable with the viruses we examined. These results expand an understanding of the immune space occupied by the enteric virome and underscore the importance of viral exposure events.

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

BackgroundCoronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.MethodsWe enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.ResultsPatients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.ConclusionsBoth enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19.DSYBHuMJfnq5gtf9T4pKWxVideo .

The dark side of the gut: Virome-host interactions in intestinal homeostasis and disease.

The diverse enteric viral communities that infect microbes and the animal host collectively constitute the gut virome. Although recent advances in sequencing and analysis of metaviromes have revealed the complexity of the virome and facilitated discovery of new viruses, our understanding of the enteric virome is still incomplete. Recent studies have uncovered how virome-host interactions can contribute to beneficial or detrimental outcomes for the host. Understanding the complex interactions between enteric viruses and the intestinal immune system is a prerequisite for elucidating their role in intestinal diseases. In this review, we provide an overview of the enteric virome composition and summarize recent findings about how enteric viruses are sensed by and, in turn, modulate host immune responses during homeostasis and disease.

Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States.

The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.

Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses.

Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (n = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The Reoviridae family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the Picornaviridae family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. Astroviridae (astroviruses) and Caliciviridae (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.

Temporal Landscape of Human Gut Virome in SARS-CoV-2 Infection and Severity

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts.SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as virome) that play a role in regulating host immunity and pathophysiology.Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All study subjects had faecal specimens sampled at inclusion. Blood specimens were sampled for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serially faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome respectively. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Findings: Patients with COVID-19 showed underrepresentation of P epper mild mottle virus (RNA virus) and multiple bacteriophage lineage s (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome dysbiosis persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Human faecal baseline abundance of 9 virus species (1 RNA virus, Pepper chlorotic spot virus, and 8 DNA virus species) inversely correlated with disease severity of COVID-19. These viruses were also inversely associated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 9 COVID-19 severity-associated virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects. Interpretation: Both enteric RNA and DNA viromes were perturbed in COVID-19, which prolonged even after disease resolution. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age partly explains that older subjects are prone to severe and unfavorable COVID-19 outcomes. Our data altogether highlight the significance of human gut virome in COVID-19 disease course and potentially therapeutics.Funding Statement: This work was supported by The D. H. Chen Foundation, Center for Gut Microbiota Research (Faculty of Medicine, The Chinese University of Hong Kong) and Health and Medical Research Fund (Hong Kong, China).Declaration of Interests: None.Ethics Approval Statement: This study was approved by the Joint Chinese University of Hong Kong–New Territories East Cluster Clinical Research Ethics Committees (Reference number: 2020.076). All subjects provided informed consent to participate in this study and agreed for publication of the research results.

Genetic heterogeneity of canine bufaviruses.

Canine bufavirus (CBuV) is a protoparvovirus, genetically related to human and non-human primate bufaviruses and distantly related to canine parvovirus type 2 (CPV-2). CBuV was initially identified from young dogs with respiratory signs but subsequent studies revealed that this virus is also a common component of the canine enteric virome. In this survey, by assessing archival and recent collections of dogs faecal samples, CBuV DNA was detected with a higher prevalence rate (8.8%) in animals with enteritis than in control animals (5.0%), although this difference was not statistically significant. The rate of co-infections with other enteric viruses in diarrhoeic dogs was high (84.6%), mostly in association with canine parvovirus CPV-2 (90.1%). The complete ORF2 gene was determined in five samples, and the nearly full-length genome was reconstructed for three strains, 62/2017/ITA, 9AS/2005/ITA and 35/2018/ITA. Upon sequence comparison, the viruses appeared highly conserved in the NS1 (97.2%-97.9% nt and 97.5%-98.1% aa identities). In the complete VP2 coding region, three strains were similar to the prototype viruses (99.7-99.8 nt and 99.6%-99.8% aa) whilst strains 9AS/2005/ITA and 35/2016/ITA were distantly related (87.6%-89.3% nt and 93.9%-95.1% aa identities). Interestingly, genetic diversification occurred downstream conserved regions such as the VP1/VP2 splicing signals and/or the G-rich motif in the N terminus of the VP2, suggesting a potential recombination nature. Upon phylogenetic analysis, the two divergent CBuV strains formed a distinct cluster/genotype.

Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome

BackgroundChanges in the enteric microbiota have been suggested to contribute to gastrointestinal diseases, including irritable bowel syndrome. Most of the published work is on bacterial dysbiosis with meager data on the role of the virome in irritable bowel syndrome and other gastrointestinal diseases. In the current study, we therefore aimed to investigate the viral community composition of the gut and test for potential dysbiosis linked to irritable bowel syndrome.ResultsA metagenomics analysis on fecal samples of 50 individuals — 30 of whom met the Rome IV criteria for IBS and 20 healthy controls— was conducted. There was a noticeable alteration in viral taxa observed in association with irritable bowel syndrome when compared to healthy individuals — where some eukaryotic viral taxa noticeably prevail over others. We observed a significant decrease in the diversity and abundance of enteric virome particularly in eukaryotic viruses of Megavirales in patients with irritable bowel syndrome.ConclusionsThese findings shed light on a new hypothesis that the alteration of the viral taxa contributes to the pathogenesis of irritable bowel syndrome and related symptoms, and therefore, pave the way for developing a new diagnostic biomarker or anti-viral drugs for the treatment of irritable bowel syndrome.

Toll-like receptor 7 protects against intestinal inflammation and restricts the development of tissue-resident memory CD8+ T cells

Abstract The maintenance of intestinal homeostasis depends on a complex interaction between microbiota, intestinal epithelial barrier, and the immune system. Alteration in of one of these components could lead to the development of inflammatory bowel diseases (IBD). Norovirus infection of mice with a mutation in the Crohn’s disease susceptibility gene Atg16L1 induces intestinal inflammation. Moreover, persistent norovirus infection leads to intestinal virus-specific CD8+ T cells responses. However, the role of the enteric virome in IBD is still poorly understood. Toll-like receptor 7 (TLR7) recognizes single-stranded RNA viruses. Here, we investigate the role of TLR7 in intestinal homeostasis and inflammation. At steady state, Tlr7−/− mice have an approx. 10-fold increase in small and large intestinal lamina propria (LP) granzyme B+ tissue-resident memory (Trm) CD8+ T cells compared to WT mice (WT: 5.5, Tlr7−/−: 59.5 %, p < 0.005), reminiscent of persistent norovirus infection. Furthermore, Tlr7−/− mice were more susceptible to dextran sulfate sodium (DSS) colitis with more severe inflammation (Histoscore: WT: 7.6, Tlr7−/−: 12.7, p < 0.005), increased disease activity index (WT: 5.5, Tlr7−/−: 7.4, p < 0.05), and increased secretion of IFNg (WT: 5.2, Tlr7−/−: 24.2 ng/ml, p < 0.005) and TNFα (WT: 108.6, Tlr7−/−: 191.8 pg/ml, p < 0.05). Increased colonic inflammation was associated with increased LP Trm CD8+ T cells (WT: 3.9, Tlr7−/−: 42.0 %, p < 0.005). Our data shows that TLR7-deficiency promotes the development of LP Trm CD8+ T cells and increases susceptibility to DSS colitis. In conclusion, TLR7 plays an important role in maintaining immune response to intestinal viruses and protects against development of colitis.

Abstract PR03: Functional characterization of the enteric animal virome as mediator of host health

Abstract The enteric virome includes viruses that infect eukaryotic cells in the gut and is one constituent of the mammalian microbiome. Although best known for causing acute diarrheal disease, many of these viruses cause subclinical infections, and indeed are often detected in asymptomatic individuals. The consequences of harboring these viruses are unclear. We recently demonstrated that norovirus mono-colonization promotes the development of the intestinal architecture and the mucosal immune system of germ-free mice in a manner similar to symbiotic bacteria and can protect against models of chemical and microbial injury. It is unclear whether this symbiotic virus-host relationship is a unique feature of murine norovirus strain CR6 colonization. Here, we examined the extent to which members of the eukaryotic enteric virome contribute to the state of the host health. Examination of 10 enteric DNA and RNA viruses representing 6 viral families capable of spreading through the fecal-oral route revealed that many establish a prolonged infection, which often is not limited to the intestinal tissues, in the absence of visible disease after oral inoculation. Further histologic analysis of the small intestinal and colonic tissues confirmed no pathogenic effects on the intestinal tissues. To evaluate the direct impact of asymptomatic viral infections independently from the bacterial microbiome, we performed RNA-seq on intestinal tissues and a comprehensive flow cytometry analysis of intestinal and extraintestinal organs, assessing over 20 immune cell subsets and their cytokine production capacity, following viral mono-colonization of germ-free mice. We found profound effects exerted by the enteric viruses on the immune system in all the tissues tested. In addition to confirming anticipated consequences of viral infection such as expansions of Th1 cells and effector memory T cells, we identified novel virus-specific responses, such as norovirus-induced expansion of type 1 regulatory T cells and parvovirus-mediated induction of regulatory T cells. Interestingly, intestinal T cells and innate lymphoid cells from almost all the virome-colonized mice were more predisposed towards the production of proinflammatory Th1 cytokines, such as IFNγ, and of Il22. An increase in the IL22 signature was also detected in the intestinal transcriptome of virome-colonized mice, suggesting that the virome members support the production of this cytokine already at the steady-state level. Of note, only a few viruses were inducing a type I interferon signature in the tissues, suggesting that pathways other than type I interferon mediate the virome effects on the host. Taken together, these data demonstrate that multiple members of the enteric virome can contribute to the development and function of the mucosal immune system. This abstract is also being presented as Poster A13. Citation Format: Simone Dallari, Thomas Heaney, Adriana Rosas-Villegas, Ken Cadwell. Functional characterization of the enteric animal virome as mediator of host health [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr PR03.

Enteric Virome and Carcinogenesis in the Gut.

Colorectal cancer (CRC) is a leading cause of cancer-related deaths in both the USA and the world. Recent research has demonstrated the involvement of the gut microbiota in CRC development and progression. Microbial biomarkers of disease have focused primarily on the bacterial component of the microbiome; however, the viral portion of the microbiome, consisting of both bacteriophages and eukaryotic viruses, together known as the virome, has been lesser studied. Here we review the recent advancements in high-throughput sequencing (HTS) technologies and bioinformatics, which have enabled scientists to better understand how viruses might influence the development of colorectal cancer. We discuss the contemporary findings revealing modulations in the virome and their correlation with CRC development and progression. While a variety of challenges still face viral HTS detection in clinical specimens, we consider herein numerous next steps for future basic and clinical research. Clinicians need to move away from a single infectious agent model for disease etiology by grasping new, more encompassing etiological paradigms, in which communities of various microbial components interact with each other and the host. The reporting and indexing of patient health information, socioeconomic data, and other relevant metadata will enable identification of predictive variables and covariates of viral presence and CRC development. Altogether, the virome has a more profound role in carcinogenesis and cancer progression than once thought, and viruses, specific for either human cells or bacteria, are clinically relevant in understanding CRC pathology, patient prognosis, and treatment development.

Viral Hormones: Expanding Dimensions in Endocrinology.

Viruses have developed different mechanisms to manipulate their hosts, including the process of viral mimicry in which viruses express important host proteins. Until recently, examples of viral mimicry were limited to mimics of growth factors and immunomodulatory proteins. Using a comprehensive bioinformatics approach, we have shown that viruses possess the DNA/RNA with potential to encode 16 different peptides with high sequence similarity to human peptide hormones and metabolically important regulatory proteins. We have characterized one of these families, the viral insulin/IGF-1-like peptides (VILPs), which we identified in four members of the Iridoviridae family. VILPs can bind to human insulin and IGF-1 receptors and stimulate classic postreceptor signaling pathways. Moreover, VILPs can stimulate glucose uptake in vitro and in vivo and stimulate DNA synthesis. DNA sequences of some VILP-carrying viruses have been identified in the human enteric virome. In addition to VILPs, sequences with homology to 15 other peptide hormones or cytokines can be identified in viral DNA/RNA sequences, some with a very high identity to hormones. Recent data by others has identified a peptide that resembles and mimics α-melanocyte-stimulating hormone's anti-inflammatory effects in in vitro and in vivo models. Taken together, these studies reveal novel mechanisms of viral and bacterial pathogenesis in which the microbe can directly target or mimic the host endocrine system. These findings also introduce the concept of a system of microbial hormones that provides new insights into the evolution of peptide hormones, as well as potential new roles of microbial hormones in health and disease.

The Revival of the Battle between David and Goliath in the Enteric Viruses and Microbiota Struggle: Potential Implication for Celiac Disease.

The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the microbial community structure and activity. Dysbiosis is associated with numerous chronic human diseases. Since the virome can impact microbial genetics and behavior, understanding its biology, composition, cellular cycle, regulation, mode of action and potential beneficial or hostile activities can change the present paradigm of the cross-talks in the luminal gut compartment. Celiac disease is a frequent autoimmune disease in which viruses can play a role in disease development. Based on the current knowledge on the enteric virome, in relation to celiac disease pathophysiological evolvement, the current review summarizes the potential interphases between the two. Exploring and understanding the role of the enteric virome in gluten-dependent enteropathy might bring new therapeutic strategies to change the luminal eco-event for the patient’s benefit.

Functional characterization of the enteric animal virome

Abstract The enteric virome includes viruses that infect eukaryotic cells in the gut and is one constituent of the mammalian microbiome. Although best known for causing acute diarrheal disease, many of these viruses are detected in asymptomatic individuals. The immune consequence of harboring these viruses is unclear. We recently demonstrated that norovirus infection promotes the development of the mucosal immune system in mice in a manner similar to symbiotic bacteria, and can protect against models of chemical and microbial injury. These results are reminiscent of findings from the microbiome field demonstrating that intestinal colonization by individual bacterial species directs the differentiation of the immune system. Here, we examined the extent to which the eukaryotic enteric virome contributes to the state of the host immune system. Examination of 10 enteric DNA and RNA viruses, representing 6 viral families, revealed that many establish prolonged infection in the absence of disease. To evaluate the immunological impact of these viral infections that occurs independently of other members of the microbiome, we performed a comprehensive flow cytometry analysis of several organs following infection of germ-free mice that assessed over 20 immune cell subsets and their capacity for cytokine production. We found profound effects of enteric viral infection in all the tissues tested, showing strain-specific responses, such as norovirus-induced expansion of type 1 regulatory T cells, and commonly shared ones, such as the increased potential of colonic T cells to produce Il-22. Taken together, these data demonstrate that enteric virome members contribute to the immune status of the host.

Viral species richness and composition in young children with loose or watery stool in Ethiopia

BackgroundStool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.MethodsWe examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.ResultsOf 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman’s r = − 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).ConclusionsIn conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.

1118. Viral Species Richness and Composition in Young Children With Loose or Watery Stool in Ethiopia

BackgroundStool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.MethodsWe examine the pediatric enteric virome across stool consistency to evaluate differences in richness and community composition using fecal samples collected from children participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.ResultsOf 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The mean age of children with stool samples was 2.7 years old. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman’s r = −0.45, P = 0.013).The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95% CI 3.9, 7.7).ConclusionWe documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition. Our results suggest that loose or watery stool, as measured by the mBSFS-C, may signal enteric viral infection in young children. Additional studies are warranted to confirm these findings.Disclosures All authors: No reported disclosures.

The fecal virome of red-crowned cranes

The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus “Chapparvovirus”, and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.Electronic supplementary materialThe online version of this article (10.1007/s00705-018-4037-x) contains supplementary material, which is available to authorized users.

Enteric virome of Ethiopian children participating in a clean water intervention trial.

BackgroundThe enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial.Methodology/principal findingsFecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well. Feces from these villages were then analyzed in 29 sample pools using viral metagenomics. A total of 127 different viruses belonging to 3 RNA and 3 DNA viral families were detected. Picornaviridae family sequence reads were the most commonly found, originating from 14 enterovirus and 6 parechovirus genotypes plus multiple members of four other picornavirus genera (cosaviruses, saliviruses, kobuviruses, and hepatoviruses). Picornaviruses with nearly identical capsid VP1 were detected in different pools reflecting recent spread of these viral strains. Next in read frequencies and positive pools were sequences from the Caliciviridae family including noroviruses GI and GII and sapoviruses. DNA viruses from multiple genera of the Parvoviridae family were detected (bocaviruses 1–4, bufavirus 3, and dependoparvoviruses), together with four species of adenoviruses and common anelloviruses shedding. RNA in the order Picornavirales and CRESS-DNA viral genomes, possibly originating from intestinal parasites or dietary sources, were also characterized. No significant difference was observed between the number of mammalian viruses shed from children from villages with and without a new water well.ConclusionsWe describe an approach to estimate the efficacy of potentially virus transmission-reducing interventions and the first complete (DNA and RNA viruses) description of the enteric viromes of East African children. A wide diversity of human enteric viruses was found in both intervention and control groups. Mammalian enteric virome diversity was not reduced in children from villages with a new water well. This population-based sampling also provides a baseline of the enteric viruses present in Northern Ethiopia against which to compare future viromes.