Ceren Simsek

Ulcerative colitis (UC) is an inflammatory bowel disease characterized by recurrent colonic inflammation. Standard treatments focus on controlling inflammation but remain ineffective for one-third of patients. This underscores the need for alternative approaches, such as fecal microbiota transplantation (FMT), which transfers healthy donor microbiota to patients. The role of viruses in this process, however, remains underexplored. To address this, we analyzed the gut virome using metagenomic sequencing of enriched viral particles from 320 longitudinal fecal samples of 44 patients enrolled in the RESTORE-UC FMT trial. Patients were treated with FMTs from healthy donors (allogenic, treatment) or themselves (autologous, control). We found that colonic inflammation, both its presence and location, had a greater impact on the gut virome than FMT itself. In autologous FMT patients, the virome was unstable and showed rapid divergence over time, a phenomenon we termed virome drift. In allogenic FMT patients, the virome temporarily shifted toward the healthy donor, lasting up to 5 weeks and primarily driven by microviruses. Notably, two distinct virome configurations were identified and linked to either healthy donors or patients. In conclusion, inflammation strongly affects the gut virome in UC patients, which may lead to instability and obstruct the engraftment of allogeneic FMT.

Inflammatory bowel disease [IBD] is a major debilitating disease. Recently, the gut microbiota has gained attention as an important factor involved in the pathophysiology of IBD. As a complement to the established bacterial ‘enterotypes’ associated with IBD, we focused here on viruses. We investigated the intestinal virome of IBD patients undergoing biological therapy for the presence of virome configurations associated with IBD, and to uncover how those configurations are associated with therapeutic success. Viral-like particle enrichment followed by deep sequencing was performed on 432 faecal samples from 181 IBD patients starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into ‘viral community types’, respectively. Patients were stratified based on unsupervised clustering into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated with the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Crassvirales and Malgrandaviricetes phages. During post-interventional analysis, endoscopic outcome was associated with gut virome composition. Remitting UC patients had a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Pre-interventional analyses also identified five novel phages associated with treatment success. This study proposed two gut virome configurations that may be involved in the pathophysiology of IBD. Interestingly, those viral configurations are further associated with therapeutic success, suggesting a potential clinical relevance.

Objective: IBD patients have an altered gut virome composition; however, the relationship to disease is unknown. Our aim is to investigate the existence of viral community types and assess the impact of therapeutic outcome (and other covariates) on the gut virome. Design: Viral particle enrichment followed by deep sequencing (1.52 TB) was performed on 432 faecal samples from 181 IBD patients (CD=126;UC=55) starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures determined covariates of the virome composition and condensed the gut virota into viral community types. Results: IBD patients were stratified based on unsupervised machine learning into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Ca udoviricetes [non-CrAss] phages and was associated to the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Caudoviricetes [ Cr Ass] and M algrandaviricetes phages. Gut virome variation was explained by patients’ individuality (75.8%), disease location (1.4%), age (0.5%) and faecal moisture (0.3%), with diagnosis not showing a non-redundant effect. Endoscopic outcome (0.5%) was accompanied by gut virome shifts in UC. Non-remitting UC, but not CD, patients revealed a high percentage of community type CA, a low diversity, and a high lysogenic potential. During pre-interventional analysis, we discovered five novel phages with a predictive value for therapeutic outcome. Conclusion: The gut virota shows the existence of distinct virome configurations that are associated with endoscopic outcome, and community typing could be a valuable tool to improve our understanding about IBD subtypes, pathology, and activity. Significance of this study: What is already known on this subject? Bacterial community typing (‘enterotyping’) is an established practice to stratify individuals based on their bacteriome composition IBD pathology is repeatedly associated with alterations in the gut virome reflected by a high Caudovirales and low Microviridae abundance IBD pathology is associated with a shift in phage lifestyle towards a highly lysogenic state of the gut virome What are the new findings? Viral community types exist and could stratify individuals based on their gut virome composition in a large prospective multi-therapeutic IBD cohort Viral community types could be associated to the dysbiotic Bact2-enterotype Endoscopic outcome (remission/non-remission) was a significant covariate of the gut virome composition post-intervention and could be associated with viral community types in UC patients Non-remitting UC patients revealed a low diversity and a high abundance of lysogenic phages We discovered five novel phages (e.g., novel CrAss-like phage) associated with predicting treatment success How might it impact the clinical practice in the foreseeable future? Viral community types could be a valuable tool to investigate IBD pathology and to differentiate between IBD subtypes and disease activity Viral community typing might distinguish a healthy gut from a dysbiotic gut virome Clinical studies should validate phages as predictive biomarkers in IBD patients starting therapy

Despite the global use of rotavirus vaccines, vaccine breakthrough cases remain a pediatric health problem. In this study, we investigated suspected rotavirus vaccine breakthrough cases using next-generation sequencing (NGS)-based viral metagenomics ( n = 102) and a panel of semiquantitative reverse transcription-PCR (RT-qPCR) ( n = 92) targeting known enteric pathogens.

The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens.

Bats host many viruses pathogenic to humans, and increasing evidence suggests that Rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America and Africa were PCR-positive for RVA and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, including evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite varying levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses. Importance: The increased research on bat coronaviruses after SARS-CoV and MERS-CoVallowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general and bats in particular, for global preparedness against emerging viral pathogens. The current effort to characterize bat rotavirus strains from 3 continents shed light on the vast genetic diversity of rotaviruses and also hinted at a bat origin for several atypical rotaviruses in humans and animals, implying that zoonoses of bat rotaviruses might occur more frequently than currently realized.