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The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. 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Chim. Acta Int. J. Clin. Chem."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Putignani, L., Oliva, S., Isoldi, S., Del Chierico, F., Carissimi, C., Laudadio, I., Cucchiara, S., and Stronati, L. (2021). Fecal and Mucosal Microbiota Profiling in Pediatric Inflammatory Bowel Diseases. Eur. J. Gastroenterol. Hepatol., 10.","DOI":"10.1097\/MEG.0000000000002050"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1136\/gutjnl-2016-312135","article-title":"Interplay of Host Genetics and Gut Microbiota Underlying the Onset and Clinical Presentation of Inflammatory Bowel Disease","volume":"67","author":"Imhann","year":"2018","journal-title":"Gut"},{"key":"ref_4","first-page":"1366","article-title":"Functional Analysis of Gut Microbiota and Immunoinflammation in Children with Autism Spectrum Disorders","volume":"51","author":"Carissimi","year":"2019","journal-title":"Dig. Liver Dis. Off. J. Ital. Soc. Gastroenterol. Ital. Assoc. Study Liver"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.tim.2015.05.006","article-title":"Infectious Asthma Triggers: Time to Revise the Hygiene Hypothesis?","volume":"23","author":"Webley","year":"2015","journal-title":"Trends Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.cell.2016.02.011","article-title":"Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk","volume":"165","author":"Zhu","year":"2016","journal-title":"Cell"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1111\/all.13389","article-title":"Early-Life Gut Microbiome and Egg Allergy","volume":"73","author":"Fazlollahi","year":"2018","journal-title":"Allergy"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The Human Microbiome Project","volume":"449","author":"Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Rowan-Nash, A.D., Korry, B.J., Mylonakis, E., and Belenky, P. (2019). Cross-Domain and Viral Interactions in the Microbiome. Microbiol. Mol. Biol. Rev., 83.","DOI":"10.1128\/MMBR.00044-18"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Pollock, J., Glendinning, L., Wisedchanwet, T., and Watson, M. (2018). The Madness of Microbiome: Attempting To Find Consensus \u201cBest Practice\u201d for 16S Microbiome Studies. Appl. Environ. Microbiol., 84.","DOI":"10.1128\/AEM.02627-17"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1089\/omi.2019.0073","article-title":"Next-Generation Metagenomics: Methodological Challenges and Opportunities","volume":"23","author":"Laudadio","year":"2019","journal-title":"Omics J. Integr. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1111\/apt.14280","article-title":"Review Article: The Human Intestinal Virome in Health and Disease","volume":"46","author":"Carding","year":"2017","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/nrmicro2853","article-title":"Going Viral: Next Generation Sequencing Applied to Human Gut Phage Populations","volume":"10","author":"Reyes","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"14250","DOI":"10.1073\/pnas.202488399","article-title":"Genomic Analysis of Uncultured Marine Viral Communities","volume":"99","author":"Breitbart","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1126\/science.1093857","article-title":"Environmental Genome Shotgun Sequencing of the Sargasso Sea","volume":"304","author":"Venter","year":"2004","journal-title":"Science"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"6220","DOI":"10.1128\/JB.185.20.6220-6223.2003","article-title":"Metagenomic Analyses of an Uncultured Viral Community from Human Feces","volume":"185","author":"Breitbart","year":"2003","journal-title":"J. Bacteriol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Zhang, T., Breitbart, M., Lee, W.H., Run, J.-Q., Wei, C.L., Soh, S.W.L., Hibberd, M.L., Liu, E.T., Rohwer, F., and Ruan, Y. (2005). RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses. PLOS Biol., 4.","DOI":"10.1371\/journal.pbio.0040003"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"12891","DOI":"10.1073\/pnas.0504666102","article-title":"Cloning of a Human Parvovirus by Molecular Screening of Respiratory Tract Samples","volume":"102","author":"Allander","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Vemuri, R., Shankar, E.M., Chieppa, M., Eri, R., and Kavanagh, K. (2020). Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths. Microorganisms, 8.","DOI":"10.3390\/microorganisms8040483"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Mukhopadhya, I., Segal, J.P., Carding, S.R., Hart, A.L., and Hold, G.L. (2019). The Gut Virome: The \u2018Missing Link\u2019 between Gut Bacteria and Host Immunity?. Ther. Adv. Gastroenterol., 12.","DOI":"10.1177\/1756284819836620"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1038\/nm.3950","article-title":"Early Life Dynamics of the Human Gut Virome and Bacterial Microbiome in Infants","volume":"21","author":"Lim","year":"2015","journal-title":"Nat. Med."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.chom.2019.09.009","article-title":"The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific","volume":"26","author":"Shkoporov","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1038\/s41591-019-0405-7","article-title":"Metagenomic Analysis of Colorectal Cancer Datasets Identifies Cross-Cohort Microbial Diagnostic Signatures and a Link with Choline Degradation","volume":"25","author":"Thomas","year":"2019","journal-title":"Nat. Med."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41591-019-0406-6","article-title":"Meta-Analysis of Fecal Metagenomes Reveals Global Microbial Signatures That Are Specific for Colorectal Cancer","volume":"25","author":"Wirbel","year":"2019","journal-title":"Nat. Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-Omics of the Gut Microbial Ecosystem in Inflammatory Bowel Diseases","volume":"569","author":"Arze","year":"2019","journal-title":"Nature"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"4925","DOI":"10.1038\/s41388-020-1341-1","article-title":"Gut Microbiota Modulation: A Novel Strategy for Prevention and Treatment of Colorectal Cancer","volume":"39","author":"Fong","year":"2020","journal-title":"Oncogene"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/s41575-019-0204-0","article-title":"Translating the Gut Microbiome: Ready for the Clinic?","volume":"16","author":"Lynch","year":"2019","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.metabol.2017.04.014","article-title":"Examining the Gut Bacteriome, Virome, and Mycobiome in Glucose Metabolism Disorders: Are We on the Right Track?","volume":"73","author":"Stefanaki","year":"2017","journal-title":"Metabolism"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Hobbs, Z., and Abedon, S.T. (2016). Diversity of Phage Infection Types and Associated Terminology: The Problem with \u2019Lytic or Lysogenic\u2019. FEMS Microbiol. Lett., 363.","DOI":"10.1093\/femsle\/fnw047"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1053\/j.gastro.2009.02.076","article-title":"Rotaviruses: From Pathogenesis to Vaccination","volume":"136","author":"Greenberg","year":"2009","journal-title":"Gastroenterology"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1038\/s41385-019-0199-4","article-title":"Norovirus Encounters in the Gut: Multifaceted Interactions and Disease Outcomes","volume":"12","author":"Hassan","year":"2019","journal-title":"Mucosal Immunol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.jcv.2014.03.003","article-title":"Pediatric Parechovirus Infections","volume":"60","author":"Esposito","year":"2014","journal-title":"J. Clin. Virol. Off. Publ. Pan Am. Soc. Clin. Virol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.resmic.2008.04.006","article-title":"Viral Diversity and Dynamics in an Infant Gut","volume":"159","author":"Breitbart","year":"2008","journal-title":"Res. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1111\/pedi.12952","article-title":"Higher Frequency of Vertebrate-Infecting Viruses in the Gut of Infants Born to Mothers with Type 1 Diabetes","volume":"21","author":"Kim","year":"2020","journal-title":"Pediatr. Diabetes"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.chom.2019.01.019","article-title":"Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins","volume":"25","author":"Chou","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13100-017-0095-y","article-title":"Viral Communities of the Human Gut: Metagenomic Analysis of Composition and Dynamics","volume":"8","author":"Aggarwala","year":"2017","journal-title":"Mob. DNA"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Garmaeva, S., Sinha, T., Kurilshikov, A., Fu, J., Wijmenga, C., and Zhernakova, A. (2019). Studying the Gut Virome in the Metagenomic Era: Challenges and Perspectives. BMC Biol., 17.","DOI":"10.1186\/s12915-019-0704-y"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1016\/j.chom.2020.08.003","article-title":"The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut","volume":"28","author":"Gregory","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"E6166","DOI":"10.1073\/pnas.1706359114","article-title":"Intestinal Virome Changes Precede Autoimmunity in Type I Diabetes-Susceptible Children","volume":"114","author":"Zhao","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.chom.2018.06.005","article-title":"Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome","volume":"24","author":"Ferretti","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1186\/s40168-019-0766-7","article-title":"Discordant Transmission of Bacteria and Viruses from Mothers to Babies at Birth","volume":"7","author":"Maqsood","year":"2019","journal-title":"Microbiome"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/s41586-020-2192-1","article-title":"The Stepwise Assembly of the Neonatal Virome Is Modulated by Breastfeeding","volume":"581","author":"Liang","year":"2020","journal-title":"Nature"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.3389\/fmicb.2018.01162","article-title":"Shared and Distinct Features of Human Milk and Infant Stool Viromes","volume":"9","author":"Pannaraj","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s40168-017-0282-6","article-title":"Maternal Inheritance of Bifidobacterial Communities and Bifidophages in Infants through Vertical Transmission","volume":"5","author":"Duranti","year":"2017","journal-title":"Microbiome"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1093\/nutrit\/nuaa029","article-title":"The Human Milk Microbiome: Who, What, When, Where, Why, and How?","volume":"79","author":"Stinson","year":"2020","journal-title":"Nutr. Rev."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"McCann, A., Ryan, F.J., Stockdale, S.R., Dalmasso, M., Blake, T., Ryan, C.A., Stanton, C., Mills, S., Ross, P.R., and Hill, C. (2018). Viromes of One Year Old Infants Reveal the Impact of Birth Mode on Microbiome Diversity. PeerJ, 6.","DOI":"10.7717\/peerj.4694"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"17004","DOI":"10.1038\/nmicrobiol.2017.4","article-title":"Dynamics of the Human Gut Microbiome in Inflammatory Bowel Disease","volume":"2","author":"Halfvarson","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1038\/nrgastro.2017.88","article-title":"Gut Microbiota and IBD: Causation or Correlation?","volume":"14","author":"Ni","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.jaci.2019.11.003","article-title":"The Microbiome and Inflammatory Bowel Disease","volume":"145","author":"Glassner","year":"2020","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.iac.2018.08.008","article-title":"Early-Onset Inflammatory Bowel Disease","volume":"39","author":"Kelsen","year":"2019","journal-title":"Immunol. Allergy Clin. N. Am."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Nusbaum, D.J., Sun, F., Ren, J., Zhu, Z., Ramsy, N., Pervolarakis, N., Kunde, S., England, W., Gao, B., and Fiehn, O. (2018). Gut Microbial and Metabolomic Profiles after Fecal Microbiota Transplantation in Pediatric Ulcerative Colitis Patients. FEMS Microbiol. Ecol., 94.","DOI":"10.1093\/femsec\/fiy133"},{"key":"ref_52","first-page":"1419","article-title":"Metagenomic Analysis of Microbiome in Colon Tissue from Subjects with Inflammatory Bowel Diseases Reveals Interplay of Viruses and Bacteria","volume":"21","author":"Wang","year":"2015","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1097\/MPG.0000000000002140","article-title":"Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease","volume":"68","author":"Fernandes","year":"2019","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/ecco-jcc\/jjaa094","article-title":"Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease","volume":"14","author":"Liang","year":"2020","journal-title":"J. Crohns Colitis"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.cell.2015.01.002","article-title":"Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease","volume":"160","author":"Norman","year":"2015","journal-title":"Cell"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.1001\/jama.2013.6285","article-title":"Seroconversion to Multiple Islet Autoantibodies and Risk of Progression to Diabetes in Children","volume":"309","author":"Ziegler","year":"2013","journal-title":"JAMA"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.gde.2018.01.006","article-title":"Genetics of Type 1 Diabetes","volume":"50","author":"Robertson","year":"2018","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1002\/(SICI)1096-9071(199706)52:2<121::AID-JMV1>3.0.CO;2-5","article-title":"Detection of Coxsackie B Virus RNA Sequences in Whole Blood Samples from Adult Patients at the Onset of Type I Diabetes Mellitus","volume":"52","author":"Hober","year":"1997","journal-title":"J. Med. Virol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.2337\/diabetes.49.8.1314","article-title":"Enterovirus Infection as a Risk Factor for Beta-Cell Autoimmunity in a Prospectively Observed Birth Cohort: The Finnish Diabetes Prediction and Prevention Study","volume":"49","author":"Korpela","year":"2000","journal-title":"Diabetes"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.2337\/db14-1370","article-title":"Detection of a Low-Grade Enteroviral Infection in the Islets of Langerhans of Living Patients Newly Diagnosed with Type 1 Diabetes","volume":"64","author":"Krogvold","year":"2015","journal-title":"Diabetes"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"d35","DOI":"10.1136\/bmj.d35","article-title":"Enterovirus Infection and Type 1 Diabetes Mellitus: Systematic Review and Meta-Analysis of Observational Molecular Studies","volume":"342","author":"Yeung","year":"2011","journal-title":"BMJ"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1038\/nm0798-781","article-title":"Diabetes Induced by Coxsackie Virus: Initiation by Bystander Damage and Not Molecular Mimicry","volume":"4","author":"Horwitz","year":"1998","journal-title":"Nat. Med."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nrendo.2016.30","article-title":"Viral Infections in Type 1 Diabetes Mellitus\u2014Why the \u03b2 Cells?","volume":"12","author":"Eizirik","year":"2016","journal-title":"Nat. Rev. Endocrinol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"930","DOI":"10.2337\/dc14-2490","article-title":"Gut Virome Sequencing in Children with Early Islet Autoimmunity","volume":"38","author":"Oikarinen","year":"2015","journal-title":"Diabetes Care"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.1038\/s41598-018-38368-8","article-title":"Higher Abundance of Enterovirus A Species in the Gut of Children with Islet Autoimmunity","volume":"9","author":"Kim","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"2654","DOI":"10.3389\/fimmu.2019.02654","article-title":"Norovirus Changes Susceptibility to Type 1 Diabetes by Altering Intestinal Microbiota and Immune Cell Functions","volume":"10","author":"Pearson","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1038\/s41591-019-0667-0","article-title":"Prospective Virome Analyses in Young Children at Increased Genetic Risk for Type 1 Diabetes","volume":"25","author":"Vehik","year":"2019","journal-title":"Nat. Med."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"9685","DOI":"10.1038\/s41598-019-46087-x","article-title":"Type 1 Diabetes: An Association Between Autoimmunity, the Dynamics of Gut Amyloid-Producing E. Coli and Their Phages","volume":"9","author":"Tetz","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Briese, T., Kapoor, A., Mishra, N., Jain, K., Kumar, A., Jabado, O.J., and Lipkin, W.I. (2015). Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis. mBio, 6.","DOI":"10.1128\/mBio.01491-15"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"(2021, April 12). Enhanced Virome Sequencing Using Targeted Sequence Capture. Available online: https:\/\/genome.cshlp.org\/content\/25\/12\/1910.","DOI":"10.1101\/gr.191049.115"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1126\/science.1229000","article-title":"Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor","volume":"339","author":"Smith","year":"2013","journal-title":"Science"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"26051","DOI":"10.1038\/srep26051","article-title":"Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition","volume":"6","author":"Million","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Blanton, L.V., Charbonneau, M.R., Salih, T., Barratt, M.J., Venkatesh, S., Ilkaveya, O., Subramanian, S., Manary, M.J., Trehan, I., and Jorgensen, J.M. (2016). Gut Bacteria That Prevent Growth Impairments Transmitted by Microbiota from Malnourished Children. Science, 351.","DOI":"10.1126\/science.aad3311"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1126\/science.aad8588","article-title":"Lactobacillus Plantarum Strain Maintains Growth of Infant Mice during Chronic Undernutrition","volume":"351","author":"Schwarzer","year":"2016","journal-title":"Science"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"11941","DOI":"10.1073\/pnas.1514285112","article-title":"Gut DNA Viromes of Malawian Twins Discordant for Severe Acute Malnutrition","volume":"112","author":"Reyes","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Desai, C., Handley, S.A., Rodgers, R., Rodriguez, C., Ordiz, M.I., Manary, M.J., and Holtz, L.R. (2020). Growth Velocity in Children with Environmental Enteric Dysfunction Is Associated with Specific Bacterial and Viral Taxa of the Gastrointestinal Tract in Malawian Children. PLoS Negl. Trop. Dis., 14.","DOI":"10.1371\/journal.pntd.0008387"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.chom.2020.01.004","article-title":"Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner","volume":"27","author":"Khan","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1016\/S1473-3099(18)30362-1","article-title":"Estimates of the Global, Regional, and National Morbidity, Mortality, and Aetiologies of Diarrhoea in 195 Countries: A Systematic Analysis for the Global Burden of Disease Study 2016","volume":"18","author":"Troeger","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/S0140-6736(17)32152-9","article-title":"Global, Regional, and National Age-Sex Specific Mortality for 264 Causes of Death, 1980\u20132016: A Systematic Analysis for the Global Burden of Disease Study 2016","volume":"390","author":"Naghavi","year":"2017","journal-title":"Lancet"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"3427","DOI":"10.1128\/JCM.01589-12","article-title":"Nearly Constant Shedding of Diverse Enteric Viruses by Two Healthy Infants","volume":"50","author":"Kapusinszky","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Mogotsi, M.T., Mwangi, P.N., Bester, P.A., Mphahlele, M.J., Seheri, M.L., O\u2019Neill, H.G., and Nyaga, M.M. (2020). Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses. Viruses, 12.","DOI":"10.3390\/v12111260"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1002\/jmv.24711","article-title":"Multiplex RT-PCR for Rapid Detection of Viruses Commonly Causing Diarrhea in Pediatric Patients","volume":"89","author":"Thongprachum","year":"2017","journal-title":"J. Med. Virol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"11024","DOI":"10.1128\/JVI.01427-12","article-title":"Acute Diarrhea in West African Children: Diverse Enteric Viruses and a Novel Parvovirus Genus","volume":"86","author":"Phan","year":"2012","journal-title":"J. Virol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.3201\/eid2006.131430","article-title":"Novel Human Bufavirus Genotype 3 in Children with Severe Diarrhea, Bhutan","volume":"20","author":"Yahiro","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"965.e1","DOI":"10.1016\/j.cmi.2015.06.006","article-title":"Bufavirus Genotype 3 in Turkish Children with Severe Diarrhoea","volume":"21","author":"Altay","year":"2015","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1007\/s00705-015-2441-z","article-title":"Bufavirus in Fecal Specimens of Patients with and without Diarrhea in Thailand","volume":"160","author":"Chieochansin","year":"2015","journal-title":"Arch. Virol."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Ayouni, S., Estienney, M., Hammami, S., Neji Guediche, M., Pothier, P., Aouni, M., Belliot, G., and de Rougemont, A. (2016). Cosavirus, Salivirus and Bufavirus in Diarrheal Tunisian Infants. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0162255"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.3201\/eid2007.140190","article-title":"New Viruses in Idiopathic Human Diarrhea Cases, the Netherlands","volume":"20","author":"Smits","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1007\/s00705-016-2756-4","article-title":"The Fecal Virome of South and Central American Children with Diarrhea Includes Small Circular DNA Viral Genomes of Unknown Origin","volume":"161","author":"Phan","year":"2016","journal-title":"Arch. Virol."},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Yinda, C.K., Vanhulle, E., Concei\u00e7\u00e3o-Neto, N., Beller, L., Deboutte, W., Shi, C., Ghogomu, S.M., Maes, P., Van Ranst, M., and Matthijnssens, J. (2019). Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses. mSphere, 4.","DOI":"10.1128\/mSphere.00585-18"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"18599","DOI":"10.1038\/s41598-019-55216-5","article-title":"First Identification of Mammalian Orthoreovirus Type 3 by Gut Virome Analysis in Diarrheic Child in Brazil","volume":"9","author":"Rosa","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/s00005-018-0520-z","article-title":"Celiac Disease Autoimmunity","volume":"66","author":"Lorite","year":"2018","journal-title":"Arch. Immunol. Ther. Exp. (Warsz.)"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1136\/gut.28.8.995","article-title":"Evidence for the Role of a Human Intestinal Adenovirus in the Pathogenesis of Coeliac Disease","volume":"28","author":"Kagnoff","year":"1987","journal-title":"Gut"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"l231","DOI":"10.1136\/bmj.l231","article-title":"Enterovirus as Trigger of Coeliac Disease: Nested Case-Control Study within Prospective Birth Cohort","volume":"364","author":"Kahrs","year":"2019","journal-title":"BMJ"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1007\/s12026-013-8420-0","article-title":"A Subset of Anti-Rotavirus Antibodies Directed against the Viral Protein VP7 Predicts the Onset of Celiac Disease and Induces Typical Features of the Disease in the Intestinal Epithelial Cell Line T84","volume":"56","author":"Dolcino","year":"2013","journal-title":"Immunol. Res."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.aah5298","article-title":"Reovirus Infection Triggers Inflammatory Responses to Dietary Antigens and Development of Celiac Disease","volume":"356","author":"Bouziat","year":"2017","journal-title":"Science"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1111\/j.1572-0241.2006.00741.x","article-title":"Rotavirus Infection Frequency and Risk of Celiac Disease Autoimmunity in Early Childhood: A Longitudinal Study","volume":"101","author":"Stene","year":"2006","journal-title":"Off. J. Am. Coll. Gastroenterol. ACG"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1136\/gutjnl-2019-319809","article-title":"Metagenomics of the Faecal Virome Indicate a Cumulative Effect of Enterovirus and Gluten Amount on the Risk of Coeliac Disease Autoimmunity in Genetically at Risk Children: The TEDDY Study","volume":"69","author":"Lindfors","year":"2020","journal-title":"Gut"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s40168-019-0626-5","article-title":"Choice of Assembly Software Has a Critical Impact on Virome Characterisation","volume":"7","author":"Sutton","year":"2019","journal-title":"Microbiome"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1136\/gutjnl-2019-319067","article-title":"Giant Oversights in the Human Gut Virome","volume":"69","author":"Sutton","year":"2020","journal-title":"Gut"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/j.chom.2019.10.009","article-title":"Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease","volume":"26","author":"Clooney","year":"2019","journal-title":"Cell Host Microbe"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/8\/4127\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:48:50Z","timestamp":1760161730000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/8\/4127"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,16]]},"references-count":101,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,4]]}},"alternative-id":["ijms22084127"],"URL":"https:\/\/doi.org\/10.3390\/ijms22084127","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,16]]}}}