Correction MEDICAL SCIENCES Correction for “Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D. Kostic, Tiffany W. Poon, Hera Vlamakis, Heli Siljander, Taina Härkönen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Jorma Ilonen, David Wang, Mikael Knip, Ramnik J. Xavier, and Herbert W. Virgin, which was first published July 10, 2017; 10.1073/pnas.1706359114 (Proc Natl Acad Sci USA 114: E6166–E6175). The authors wish to note the following: “After publication, we discovered that certain patient-related information in the spreadsheets placed online had information that could conceiv- ably be used to identify, or at least narrow down, the identity of children whose fecal samples were studied. The article has been updated online to remove these potential privacy concerns. These changes do not alter the conclusions of the paper.” Published under the PNAS license. Published online November 19, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1817913115 E11426 | PNAS | November 27, 2018 | vol. 115 | no. 48 www.pnas.org Downloaded by guest on September 26, 2021 Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children Guoyan Zhaoa,1, Tommi Vatanenb,c, Lindsay Droita, Arnold Parka, Aleksandar D. Kosticb,2, Tiffany W. Poonb, Hera Vlamakisb, Heli Siljanderd,e, Taina Härkönend,e, Anu-Maaria Hämäläinenf, Aleksandr Peetg,h, Vallo Tillmanng,h, Jorma Iloneni, David Wanga,j, Mikael Knipd,e,k,l, Ramnik J. Xavierb,m, and Herbert W. Virgina,1 aDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; bInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142; cDepartment of Information and Computer Science, Aalto University School of Science, 02150 Espoo, Finland; dChildren’s Hospital, University of Helsinki and Helsinki University Central Hospital, 00290 Helsinki, Finland; eResearch Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland; fJorvi Hospital, Helsinki Hospital, 02740 Espoo, Finland; gChildren’s Clinic of Tartu University Hospital, 50406 Tartu, Estonia; hDepartment of Pediatrics, University of Tartu, 50090 Tartu, Estonia; iImmunogenetics Laboratory, University of Turku and Turku University Hospital, FI-20520 Turku, Finland; jDepartment of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110; kFolkhälsan Research Center, 00290 Helsinki, Finland; lTampere Center for Child Health Research, Tampere University Hospital, 33520 Tampere, Finland; and mCenter for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 Contributed by Herbert W. Virgin, June 7, 2017 (sent for review April 17, 2017; reviewed by Mya Breitbart and Julie A. Segre) Viruses have long been considered potential triggers of autoimmune viruses, whereas in other cases, disease-associated changes in diseases. Here we defined the intestinal virome from birth to the bacteriophages have been identified. Studies in mice clearly doc- development of autoimmunity in children at risk for type 1 diabetes ument that virus infection can trigger damage to the islets (13–16). (T1D). A total of 220 virus-enriched preparations from serially collected Furthermore, intestinal eukaryotic viruses have been implicated in fecal samples from 11 children (cases) who developed serum autoan- triggering human T1D, based mostly on seroepidemiologic studies tibodies associated with T1D (of whom five developed clinical T1D) of responses to one or a few candidate viruses (17–19). However, were compared with samples from controls. Intestinal viromes of case in another study, no changes in the virome were detected for subjects were less diverse than those of controls. Among eukaryotic 3–9 mo before the development of autoimmunity (20). In a recent viruses, we identified significant enrichment of Circoviridae-related study, CrAssphage, a human bacteriophage, was correlated with sequences in samples from controls in comparison with cases. Entero- Bacteroides dorei, but a direct association of this virus with islet virus, kobuvirus, parechovirus, parvovirus, and rotavirus sequences autoimmunity was not observed (21). Importantly, although it were frequently detected but were not associated with autoimmu- generally has been assumed that viruses cause harm by triggering nity. For bacteriophages, we found higher Shannon diversity and rich- diseases, studies in animal models show that virus infection is not ness in controls compared with cases and observed that changes in necessarily harmful and can provide symbiotic benefits (22–24), the intestinal virome over time differed between cases and controls. and actually may offer protection from the development of T1D Using Random Forests analysis, we identified disease-associated viral (25, 26). Thus, an evaluation of the virome in children at risk for bacteriophage contigs after subtraction of age-associated contigs. T1D might have the potential to identify viruses associated with These disease-associated contigs were statistically linked to specific either disease risk or protection from disease. In this study, we components of the bacterial microbiome. Thus, changes in the intes- defined the RNA and DNA intestinal virome of children before tinal virome preceded autoimmunity in this cohort. Specific compo- the development of autoimmunity and identified changes in the nents of the virome were both directly and inversely associated with virome potentially associated with protection against or develop- the development of human autoimmune disease. ment of this human autoimmune disease. virome | microbiome | Circoviridae | type 1 diabetes | bacteriophages Significance he microbiome contains multiple types of organisms, including Type 1 diabetes (T1D) is a major autoimmune disease with in- Tbacteria, archaea, fungi, and eukaryotic organisms, as well as creasing incidence in recent years. In this study, we found that the the viruses that infect both the host and other members of the intestinal viromes of cases were less diverse than those of con- microbiome (1). Changes in various components of the micro- trols. We identified eukaryotic viruses and bacteriophage contigs biome have been observed in association with multiple human that are associated with the presence or absence of autoimmu- diseases (1–4). Prominent among diseases that are influenced by nity. These viruses provide targets for future mechanistic studies microorganisms is type 1 diabetes (T1D), a disease involving an to differentiate causal and incidental associations between the autoimmune attack on the insulin-secreting beta cells of the pan- virome and protection against the development of T1D. creatic islets of Langerhans. Changes in intestinal bacteria have been linked to the development of T1D in some studies (5, 6). Author contributions: G.Z., D.W., R.J.X., and H.W.V. designed research; G.Z., L.D., and A. Park performed research; G.Z., T.V., A.D.K., T.W.P., H.V., H.S., T.H., A.-M.H., A. Peet, V.T., J.I., and Some common observations include increased abundance of the M.K. contributed new reagents/analytic tools; G.Z. analyzed data; and G.Z. and H.W.V. wrote Bacteroides genus (7–9) and reduced abundance of butyrate- the paper. producing bacteria (7, 10). In a study that included 11 seroposi- Reviewers: M.B., University of South Florida; and J.A.S., National Human Genome tive children from Finland and Estonia, of whom 4 progressed to Research Institute. T1D, Kostic et al. demonstrated a reduction in bacterial diversity Conflict of interest statement: M.K. serves as an advisor to Vactech Oyj and Provention among the cases (11). These changes emerged after the appearance Bio, Inc. of autoantibodies that are predictive of T1D (11), potentially sug- Data deposition: The CRESS DNA virus genomic sequences have been deposited in the gesting that intestinal bacteria might be involved in the progression GenBank database (accession nos. MF118166–MF118169). Raw data have been deposited in the Sequence Read Archive (accession no. PRJNA387903). from beta-cell autoimmunity to clinical disease rather than in the 1To whom correspondence may be addressed. Email: [email protected] or virgin@wustl. initiation of the disease process (6). edu. Changes in intestinal viruses have been observed in patients with 2 Present address: Pathophysiology and Molecular Pharmacology Section, Joslin Diabetes inflammatory bowel disease and AIDS (2–4, 12), indicating that Center, Boston, MA 02215. changes in the virome can be associated with infectious and in- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. flammatory diseases. In some cases, these changes involve eukaryotic 1073/pnas.1706359114/-/DCSupplemental. E6166–E6175 | PNAS | Published online July 10, 2017 www.pnas.org/cgi/doi/10.1073/pnas.1706359114 Results viral sequences, which accounted for 0.04–93.17% of deduplicated PNAS PLUS Cohort and Sample Sequencing. To characterize the intestinal virome sequences. There were no significant differences in the total num- and its relationship to T1D disease susceptibility, we studied se- ber of sequences, the number of quality-controlled unique sequences, quential fecal samples from a well-characterized prospective lon- or the percentage of eukaryotic viral sequences between cases and gitudinal study of infants at risk for T1D (11).