PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults

Abstract

The gut microbiota is increasingly recognized as an important modulator of human health. As such, there is a growing need to identify effective means of selectively modifying gut microbial communities. Bacteriophages, which were briefly utilized as clinical antimicrobials in the early 20th century, present an opportunity to selectively reduce populations of undesirable microorganisms. However, whether intentional consumption of specific bacteriophages affects overall gut ecology is not yet known. Using a commercial cocktail of Escherichia coli-targeting bacteriophages, we examined their effects on gut microbiota and markers of intestinal and systemic inflammation in a healthy human population. In a double-blinded, placebo-controlled crossover trial, normal to overweight adults consumed bacteriophages for 28 days. Stool and blood samples were collected and used to examine inflammatory markers, lipid metabolism, and gut microbiota. Reductions in fecal E. coli loads were observed with phage consumption. However, there were no significant changes to alpha and beta diversity parameters, suggesting that consumed phages did not globally disrupt the microbiota. However, specific populations were altered in response to treatment, including increases in members of the butyrate-producing genera Eubacterium and a decreased proportion of taxa most closely related to Clostridium perfringens. Short-chain fatty acid production, inflammatory markers, and lipid metabolism were largely unaltered, but there was a small but significant decrease in circulating interleukin-4 (Il-4). Together, these data demonstrate the potential of bacteriophages to selectively reduce target organisms without global disruption of the gut community.

Keywords: bacteriophage; cytokines; gastrointestinal; gut microbiota; inflammation; short-chain fatty acid.

Conflict of interest statement

Funding was provided by Deerland Enzymes to the Think Healthy Group, Inc., through an unrestricted educational grant. T.C.W. is the Principal and CEO of the Think Healthy Group, Inc., a food science and nutrition consulting firm dedicated to advancing cutting-edge research and public health through engagement with industry, academia, government, media, and nongovernmental organizations. All conflicts can be found on his website at www.drtaylorwallace.com. Deerland Enzymes played no role in the study design, data collection, analysis, or interpretation and presentation of results. All other authors declare no conflicts of interest.

Figures

Figure 1

(A) Relative abundance of bacterial phyla detected in stool samples at baseline and after 28days for both phage (treatment) and placebo study periods. No significant differences were detected by analysis of covariance (ANCOVA) at p < 0.05. (B) Principle coordinates analysis (PCoA) with nonmetric dimensional scaling of species-level Bray–Curtis distances. Stress = 0.191; perMANOVA (1000 permutations) Pr (>F) = 0.996.

Figure 2

(A) Percent of total reads represented by amplicon sequence variants (ASVs) mapping to Escherichia. coli for each treatment and time point. (B) Change in E. coli levels from baseline values after treatment or placebo consumption. Data represents only individuals with baseline E. coli levels (n = 21). Error bars represent SEM.

Figure 3

Using Spearman’s rank, several ASVs were found to be significantly negatively correlated (red bars) or positively correlated (blue bars) with E. coli ASVs. Significant values were considered q < 0.10.

Figure 4

Using a negative binomial generalized linear model (GLM) (EdgeR), we identified several taxa that significantly (q < 0.10) differed from placebo levels after 28days of phage consumption. Red bars represent taxa reduced with phage treatment, and blue bars represent taxa that were increased.