Defining the human gut host-phage network through single-cell viral tagging

Area of Science:

• Microbiology
• Virology
• Genomics

Background:

• Viral discovery is rapidly advancing through culture-independent sequencing.
• Identifying hosts for newly discovered viruses is crucial for understanding microbial ecosystems.
• Existing methods often require virus or host cultivation, limiting discovery.

Purpose of the Study:

• To adapt and demonstrate a viral tagging approach for identifying host-phage pairings without cultivation.
• To investigate virus-host interactions within the human fecal microbiome.
• To assess the potential for cross-reactivity and its implications for therapies like fecal microbiota transplantation.

Main Methods:

• Utilized fluorescently labeled viruses to tag bacterial hosts.
• Employed single-cell sorting to isolate host-phage pairs.
• Performed genome amplification and high-throughput sequencing to identify both viral and bacterial partners.

Main Results:

• Successfully identified 363 unique host-phage pairings, predominantly subject-specific.
• Characterized previously unknown viruses associated with known bacterial hosts.
• Observed limited evidence of phages targeting multiple bacterial species, suggesting a minor role in inter-species horizontal gene transfer.
• Noted significant cross-reactivity between phages and bacteria across different individuals.

Conclusions:

• The viral tagging method effectively identifies host-phage interactions in complex microbiomes.
• The human gut harbors a vast number of uncharacterized viruses with specific host ranges.
• Phages may not be primary drivers of inter-species gene transfer in the gut.
• Cross-reactivity has significant implications for fecal microbiota transplantation efficacy and safety.