UC Merced

The human intestinal microbiome is a complex, dynamic consortium of bacteria, viruses, archaea, and protists, that play a crucial role in maintaining host physiology through nutrient absorption, protection against pathogens, and regulating host immunity. The viral component of the microbiome, or virome, is composed of eukaryotic and prokaryotic viruses, including viruses that infect human cells, viruses that infect microbes (such as bacteria, fungi, and archaea), and plant viruses that are primarily derived from the environment and diet. Although the bacterial component of the intestinal microbiome has been extensively studied, emerging research has shown that alterations in the enteric virome have been reported in a variety of diseases including colorectal cancer, inflammatory bowel disease, obesity, and type I diabetes. Bacteriophages are the dominant component of the enteric virome. These viruses infect bacteria and play a crucial role in shaping bacterial communities in mammalian systems. However, our understanding of how they directly impact health and disease is limited. Bacteriophages in healthy human intestines are predominantly temperate double-stranded DNA Caudovirales or single-stranded DNA (ssDNA) Microviridae. Metagenomic analysis has shown that patients with Crohn’s disease (CD) and ulcerative colitis (UC) have a greater abundance of Caudovirales bacteriophages and fewer Microviridae bacteriophages within their intestines, indicating that bacteriophage populations are altered in these disease states. However, the ability of bacteriophages to directly stimulate human intestinal epithelial cells has not been extensively explored. Intestinal bacteriophages consist of temperate phages located within bacterial genomes and free lytic bacteriophages associated with intestinal mucus during the steady state. However, a recent study reported the detection and characterization of novel filamentous bacteriophage (or inoviruses) from intestinal commensal bacteria. Filamentous bacteriophages have been implicated in diseases caused by bacterial pathogens Pseudomonas aeruginosa, Neisseria meningitidis, and Vibrio cholerae. Despite the abundance and presence of bacteriophages in the mucosa, few studies have been conducted on their direct impact on intestinal epithelial cells. The focus of my research is to investigate the intestinal epithelial responses to bacteriophages. We found that filamentous bacteriophages M13 and Fd induced dose-dependent IL-8 expression in the human intestinal epithelial cell line HT-29 to a greater degree than their lytic counterparts T4 and ϕX174 did. We also found that M13, but not Fd, reduced bacterial internalization in HT-29 cells. This led us to investigate whether M13 could induce antiviral and antimicrobial responses in these cells. M13 upregulated type I and III IFN expression and augmented short-chain fatty acid (SCFA)-mediated LL-37 expression in HT-29 cells. Taken together, our data established that bacteriophages can directly stimulate human intestinal epithelial cells. These results provide new insights into the complex interactions between bacteriophages and intestinal mucosa, which may underlie disease pathogenesis.