Interaction with mammalian enteric viruses alters outer membrane vesicle production and content by commensal bacteria

Abstract

Intestinal commensal bacteria contribute to maintaining gut homeostasis. Disruptions to the commensal flora are linked to the development and persistence of disease. The importance of these organisms is further demonstrated by the widespread ability of enteric viruses to exploit commensal bacteria to enhance viral infection. These viruses interact directly with commensal bacteria, and while the impact of this interaction on viral infection is well described for several viruses, the impact on the commensal bacteria has yet to be explored. In this article, we demonstrate, for the first time, that enteric viruses alter the gene expression and phenotype of individual commensal bacteria. Human and murine norovirus interaction with bacteria resulted in genome‐wide differential gene expression and marked changes in the surface architecture of the bacterial cells. Furthermore, the interaction of the virus with bacteria led to increased production of smaller outer membrane vesicles (OMVs). Enhanced production of smaller vesicles was also observed when noroviruses were incubated with other commensal bacteria, indicating a potentially broad impact of norovirus interaction. The vesicle production observed in the in vivo model followed a similar trend where an increased quantity of smaller bacterial vesicles was observed in stool collected from virus‐infected mice compared to mock‐infected mice. Furthermore, changes in vesicle size were linked to changes in protein content and abundance, indicating that viral binding induced a shift in the mechanism of the OMV biogenesis. Collectively, these data demonstrate that enteric viruses induce specific changes in bacterial gene expression, leading to changes in bacterial extracellular vesicle production that can potentially impact host responses to infection.

Glucose Reduces Norovirus Binding to Enterobacter cloacae and Alters Gene Expression of Bacterial Surface Structures in a Growth Phase Dependent Manner

“…We also examined changes in the expression of these bacterial genes during HNoV binding. Unlike MNV, HNoV did not significantly alter the expression of the targeted genes, however, the trends in gene expression were, in some cases, similar to MNV and were also consistent with previous RNA-seq analysis [ 12 ]. The observed differential impacts on gene expression between these viruses may be connected to the differing methods by which each type of norovirus attaches to the bacteria.…”

“…To further explore this hypothesis that glucose is reducing the expression of key bacterial surface structures, we measured the expression of genes associated with bacterial surface structures previously associated with norovirus interactions (e.g., the flagellum and the outer membrane) [ 1 , 20 ]. We have previously found that norovirus interactions with E. cloacae significantly alters the expression of genes associated with the bacterial outer and trans membranes [ 12 ]. We also know that MNV binding to bacteria is variable, with 10% to 20% of bacteria remaining unbound by MNV following incubation with the virus, which may impact the consistency of gene expression data found in each replicate [ 20 ].…”

“…A previous study has shown that MNV primarily attaches to the bacterial outer membrane [ 20 ], while HNoV displays more extensive binding to both the outer membrane and bacterial appendages [ 1 , 9 ]. Furthermore, previous work demonstrated that, while both viruses induce genome-wide changes in bacterial gene expression, they only share about one-third of the differentially regulated genes in common, indicating that these viruses alter bacterial gene expression in different manners [ 12 ]. In addition to binding proteinaceous structures like the outer membrane and flagella, HNoVs have been shown to bind prolifically to carbohydrate-based structures (i.e., HGBAs) on the bacterial cell surface [ 1 ], and it may be that this virus more significantly alters the expression of genes associated with the production of carbohydrate-based structure.…”

“…Not only do commensal bacteria alter norovirus infection, but norovirus interactions with these bacteria induce changes in bacterial gene expression and physiology [ 12 ]. Specifically, norovirus interactions with E. cloacae significantly alter the expression of genes associated with the bacterial membrane, leading to increased expression of bacterial appendages on the cell surface and increased membrane ruffling.…”

Role of Microbiota in Viral Infections and Pathological Progression

“…This is accompanied by marked changes in the intestinal microbiota due to the infection. Noroviruses are reported in animal studies and in vitro studies on the interaction between the virus and the microbiota during infection [ 20 ]. In vitro experiments have shown that human noroviruses can infect B cells in the presence of bacteria coated with histo-blood group antigens.…”