Applications of bacteriophages in precision engineering of the human gut microbiome

Abstract

As our understanding of the role of the gut microbiome in human diseases deepens, precision engineering of the gut microbiome using bacteriophages has gained significant attention. Herein, we review the recent advances in bacteriophage-mediated modulation of the gut microbiome, discuss approaches at the ecological and genetic levels, and summarize the challenges and strategies pertinent to each level of intervention. Drawing on the structural attributes of bacteriophages in the context of precision engineering, we examined the latest developments in the field of phage administration. Gaining a nuanced understanding of microbiome manipulation will yield tailored strategies and technologies. This could revolutionize the prevention and treatment of diseases linked to gut pathogens and offer new avenues for the therapeutic use of bacteriophages.11 Abbreviations: AAVs: adeno-associated viruses; AIEC: adherent-invasive Escherichia coli; BFT: Bacteroides fragilis toxin; CBE: cytosine base editor; CDI: Clostridium difficile infection; CRC: colorectal cancer; DDS: drug delivery system; DSBs: double-strand breaks; EHEC: enterohemorrhagic Escherichia coli; EMA: European Medicines Agency; EPC: egg phosphatidylcholine; ETBF: enterotoxigenic Bacteroides fragilis; FDA: Food and Drug Administration; FMT: fecal microbiota transplant; FVT: fecal virus transplantation; HDR: homology-directed repair; IBD: inflammatory bowel disease; IDANPs: iron-doped apatite nanoparticles; IND: investigational new drug; LPS: lipopolysaccharides; MOI: Multiplicity of infection; NAFLD: nonalcoholic fatty liver disease; NCDs: noncommunicable diseases; NTBF: non-toxigenic Bacteroides fragilis; PSC: primary sclerosing cholangitis; STEC: Shiga toxin-producing Escherichia coli

Keywords

• Bacteriophages
• Microbiome engineering
• Human gut microbiome