Hundreds of New Viruses Discovered in Human Gut Microbiome

Strategic Insights -

A groundbreaking international study, led by Professor Jeremy J. Barr and Associate Professor Sam Forster, has identified hundreds of new viruses living inside bacteria within the human gut. These viruses, known as bacteriophages, are capable of reshaping the gut microbiome and potentially influencing gut health and disease progression. The study, published in Nature, employed a large-scale, culture-based approach to isolate and study temperate bacteriophages in the human gut, revealing surprising discoveries about the role of Stevia and human gut cells in activating dormant viruses.

Key Takeaways:

  • The study identified 252 bacterial isolates from the human microbiome, sourced from the Australian Microbiome Culture Collection (AusMiCC), which contained hundreds of new viruses.
  • Stevia, a common plant-based sugar substitute, was found to be a leading activator for gut phages, along with compounds released by the human gut cells.
  • The study revealed that most gut bacteriophages are dormant, with only a small fraction capable of being activated under the tested conditions.
  • When exposed to human gut cells, the activation rate of these viruses jumped significantly, suggesting a direct role of human biology in shaping the viral landscape of the gut.
  • The team used CRISPR-based genetic engineering to identify mutations in viral genes that prevent activation, offering insight into how some gut viruses become permanently dormant.
  • The research has significant implications for health translation, providing the opportunity to develop microbiome therapeutics for diseases such as inflammatory bowel disease and cancers.
  • The study lays the groundwork for future applications in synthetic biology, biotechnology, and microbiome therapeutics, decoding the viral dark matter of the human gut.

Statistics:

  • 252 bacterial isolates from the human microbiome were sourced from the Australian Microbiome Culture Collection (AusMiCC).
  • Ten diverse compounds, foods, and conditions were used to treat the isolates.
  • Stevia was a leading activator for gut phages, along with compounds released by human gut cells.
  • 99.9% of gut bacteriophages were found to be dormant under the tested conditions.
  • When exposed to human gut cells, the activation rate of these viruses jumped to 50.6%.

Sources:

  • Professor Jeremy J. Barr, Monash University's School of Biological Sciences, and Associate Professor Sam Forster, Hudson Institute of Medical Research.
  • Australian Microbiome Culture Collection (AusMiCC).
  • Nature, DOI: 10.1038/s41586-025-09614-7.