Kathie A Mihindukulasuriya1, Ruben A T Mars2, Abigail J Johnson3, Tonya Ward4, Sambhawa Priya5, Heather R Lekatz2, Krishna R Kalari6, Lindsay Droit1, Tenghao Zheng7, Ran Blekhman5, Mauro D'Amato8, Gianrico Farrugia2, Dan Knights9, Scott A Handley10, Purna C Kashyap11. 1. Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri. 2. Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota. 3. Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota. 4. BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota. 5. Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota. 6. Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota. 7. School of Biological Sciences, Monash University, Clayton, Victoria, Australia. 8. Gastrointestinal Genetics Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain. 9. Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota. Electronic address: dknights@umn.edu. 10. Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri. Electronic address: shandley@wustl.edu. 11. Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Medicine and Physiology, Mayo Clinic, Rochester, Minnesota. Electronic address: kashyap.purna@mayo.edu.
Abstract
BACKGROUND & AIMS: The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS. METHODS: We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets. RESULTS: We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses). CONCLUSIONS: We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.
BACKGROUND & AIMS: The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS. METHODS: We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets. RESULTS: We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses). CONCLUSIONS: We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.
Authors: Ruben A T Mars; Yi Yang; Tonya Ward; Mo Houtti; Sambhawa Priya; Heather R Lekatz; Xiaojia Tang; Zhifu Sun; Krishna R Kalari; Tal Korem; Yogesh Bhattarai; Tenghao Zheng; Noam Bar; Gary Frost; Abigail J Johnson; Will van Treuren; Shuo Han; Tamas Ordog; Madhusudan Grover; Justin Sonnenburg; Mauro D'Amato; Michael Camilleri; Eran Elinav; Eran Segal; Ran Blekhman; Gianrico Farrugia; Jonathan R Swann; Dan Knights; Purna C Kashyap Journal: Cell Date: 2020-09-10 Impact factor: 41.582
Authors: Peter J Walker; Stuart G Siddell; Elliot J Lefkowitz; Arcady R Mushegian; Evelien M Adriaenssens; Donald M Dempsey; Bas E Dutilh; Balázs Harrach; Robert L Harrison; R Curtis Hendrickson; Sandra Junglen; Nick J Knowles; Andrew M Kropinski; Mart Krupovic; Jens H Kuhn; Max Nibert; Richard J Orton; Luisa Rubino; Sead Sabanadzovic; Peter Simmonds; Donald B Smith; Arvind Varsani; Francisco Murilo Zerbini; Andrew J Davison Journal: Arch Virol Date: 2020-11 Impact factor: 2.574
Authors: F A Bastiaan von Meijenfeldt; Ksenia Arkhipova; Diego D Cambuy; Felipe H Coutinho; Bas E Dutilh Journal: Genome Biol Date: 2019-10-22 Impact factor: 13.583