The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study

Abstract

Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.

Keywords: human microbiome; metagenomics; noroviruses.

FIG 1

Alpha and beta diversities of prechallenge microbiomes were different between asymptomatic and symptomatic individuals. Alpha diversity of asymptomatic microbiomes showed (A) lower Shannon diversity (not significant) and (B) significantly higher Simpson diversity than for symptomatic microbiomes (*, P < 0.01) based on extracted 16S rRNA reads. Microbiomes show some separation according to Bray-Curtis distances of extracted 16S rRNA genes (C) and Mash distances (D) in NMDS plots. ANOSIM test results are provided for each NMDS.

FIG 2

Taxa differentially abundant between symptomatic and asymptomatic individuals at the prechallenge time point (T = 0) using 16S rRNA reads extracted from metagenomes. Taxa enriched in the asymptomatic baseline microbiomes were largely members of the class Bacteroidia (phylum Bacteroidetes) but also included two gammaproteobacterial taxa. Most of the taxa enriched in the symptomatic microbiomes belonged to the class Clostridia in the phylum Firmicutes. Each taxon is labeled at the highest resolved taxonomic level, followed by phylum and class in parentheses. The linear discriminant analysis (LDA) score (log 10) of each taxon is represented by the horizontal bars, with red and green bars indicating taxa enriched in microbiomes from asymptomatic and symptomatic study subjects, respectively.

FIG 3

Relative abundances of processes and genes that differentiated the asymptomatic and symptomatic individuals. (A) Representation of each second-order KEGG category. (B) All 26 significantly different individual genes (KOs) between the two outcome groups.

FIG 4

Whole-community similarity over the infection period, with the challenge administered on day 1 (black dashed line). Solid lines represent the Mash distance of whole metagenomes over time and reveal a shift away from time zero (baseline) coinciding with the increase in norovirus titer (dashed lines). As virus titers decrease, Mash distances initially drop, with those for two of three individuals rising again in later time points.

FIG 5

Genes that differed significantly (corrected P < 0.05) in copy number/genome between MAGs that increased (purple) or decreased (orange) following the viral challenge. Functions enriched in “decrease” MAGs included proteins involved in carbohydrate metabolism and signal transduction, while functions enriched in “increase” MAGs were largely hypothetical. The highest-level functional category is provided by a color bar on the y axis (“hypothetical” refers to uncategorized KEGG annotations, i.e., “not included in pathway or BRITE”).