title: Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice.
abstract: To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. The contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.
authors.affiliation: Iowa State University, Ames, IA, USA.|Argonne National Laboratory, Argonne, IL, USA.
authors.forename: Adina
authors.initials: A
authors.lastname: Howe
authors.affiliation: Department of Medicine, University of Chicago, Chicago, IL, USA.
authors.forename: Daina L
authors.initials: DL
authors.lastname: Ringus
authors.affiliation: Iowa State University, Ames, IA, USA.
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: Williams
authors.affiliation: Department of Medicine, University of Chicago, Chicago, IL, USA.
authors.forename: Zi-Ning
authors.initials: ZN
authors.lastname: Choo
authors.affiliation: Argonne National Laboratory, Argonne, IL, USA.
authors.forename: Stephanie M
authors.initials: SM
authors.lastname: Greenwald
authors.affiliation: Argonne National Laboratory, Argonne, IL, USA.|Department of Medicine, University of Chicago, Chicago, IL, USA.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Owens
authors.affiliation: Department of Medicine, University of Chicago, Chicago, IL, USA.
authors.forename: Maureen L
authors.initials: ML
authors.lastname: Coleman
authors.affiliation: Argonne National Laboratory, Argonne, IL, USA.|Department of Medicine, University of Chicago, Chicago, IL, USA.
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.affiliation: Department of Medicine, University of Chicago, Chicago, IL, USA.
authors.forename: Eugene B
authors.initials: EB
authors.lastname: Chang
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification; D020451:Contig Mapping; D004032:Diet; D004041:Dietary Fats; D004043:Dietary Fiber; D019422:Dietary Sucrose; D005260:Female; D005767:Gastrointestinal Diseases / Q000382:microbiology* / Q000821:virology*; D000069196:Gastrointestinal Microbiome; D007422:Intestines / Q000382:microbiology; D054892:Metagenome; D051379:Mice; D008810:Mice, Inbred C57BL; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014780:Viruses / Q000145:classification
chemical_list: D004041:Dietary Fats; D004043:Dietary Fiber; D019422:Dietary Sucrose; D012336:RNA, Ribosomal, 16S