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The Future of the Microbiome in Public Health

Rapid advances in research on the human microbiome are leading to new insights on the role of our body’s microorganisms in healthy development and aging, while shedding light on how factors such as diet and the built environment shapes our microbiomes, with potential long-term health consequences. Cross-sectoral conversations between microbiome researchers and public health leaders will help ensure that this emerging evidence can be integrated into our health system, while at the same time identify areas where more research is needed.

On May 1, 2019, members of CIFAR’s program in Humans and the Microbiome participated in an interactive panel discussion at Public Health 2019, the annual conference of the Canadian Public Health Association. The panelists presented key insights on how the human microbiome shapes health and disease across the lifespan, as well as the implications of shifting societal and cultural practices on the microbiome and in turn health. Through discussions with session participants, they explored how emerging evidence in these areas could inform the development of key public health programs, practices and policies.

Key Insights

  • An estimated 50% of cells in the human body are microorganisms, with potentially 150 times more microbial genes than human genes. This collection of microbial genomes (i.e., the microbiome) is amenable to change, presenting a possible way to modify diseases in humans. While public health has traditionally focused on the dangers of pathogenic microbes, less than 1% of bacteria associated with humans are pathogens, and even many of these are not necessarily harmful to us.
  • Antibiotics are essential medicines that have saved millions of lives, but there are health consequences to their long-term use, including emerging antimicrobial resistance. There is growing evidence from studies in both animal models and human populations that early-life antibiotics use is associated with the rise of chronic diseases such as obesity.
  • Microbes in our bodies play important roles in training our immune systems. The hygiene hypothesis suggests that the increased prevalence of allergies and inflammatory diseases in Western societies may be a result of decreased early childhood exposure to a diversity of microorganisms. Compared to urban Western populations, communities with “non-Western” lifestyles tend to have more diverse microbiomes and generally lower rates of chronic disease.
  • Our built environment may affect the diversity of our microbial communities and hence our health. For example, in advanced economies of the West, people spend 90% or more of their daily lives indoors — a condition that is vastly different from much of human history. Researchers are investigating what aspects of the living environment of non-Western populations, such as hunter-gatherer communities, may have a role in establishing healthy microbiomes.
  • Vaginal birth gives babies their first set of microorganisms, most of which are required to metabolize certain breast milk components that are otherwise indigestible by humans. There are differences between the microbiomes of babies born through vaginal birth and C-section, and the latter can be shifted towards the former by swabbing with vaginal microbial flora. However, it remains controversial whether vaginal swabbing should be put into wide clinical practice.
  • Between birth and age 3, there are major increases in the number and diversity of the gut microbiome that are important for later life. This is the most malleable period in the development of the gut microbial community, and when factors such as the built environment and antibiotics use can have strong effects. The microbiome tends to remain stable after age 3, with notable exceptions during illness, change in diet, travel or pregnancy.
  • Microbial diversity tends to decrease as people age. Individuals who develop aging-related disorders such as Alzheimer’s or Parkinson’s exhibit distinct microbiome changes, but the clinical utility of this correlation for prediction or treatment requires further study.
  • Diet – the type of food we eat, meal times, or the use of probiotics – have a major impact on the composition and function of our gut microbiomes. But individuals’ responses to such dietary factors vary, and may be shaped by their personal microbial diversity.
  • Microorganisms in the gut are part of a “gut-brain axis” that may have mental health implications. They produce metabolites that closely resemble neurotransmitters and may exert effects on the central nervous system. Studies in rodents suggest that behaviours like anxiety are highly impacted by microbial metabolites, but such effects are difficult to study in humans.

Priorities and Next Steps

  • While researchers have catalogued many of the microbial strains in our body and discovered a number of strong correlations with health and disease, developing a mechanistic understanding of the function of individual strains and how they interact will greatly inform the development of future microbiome-based health interventions.
  • Much current research on microbiomes are focused on bacteria. The role of other organisms such as viruses (including the bacteriophages that parasitize these bacteria), fungi and worms is becoming another area of active investigation.
  • Microorganisms may be a route by which environmental factors, social determinants of health and health inequities become embodied in health outcomes. The microbiome may thus provide a low-tech, low-cost way to intervene and address certain health disparities.


  • Eran Elinav, Weizmann Institute of Science / CIFAR
  • Corinne Maurice, McGill University / CIFAR
  • Melissa Melby, University of Delaware / CIFAR

Further Reading

The Human Microbiome & Public Health: Supporting Healthy Development and Aging (event brief)
The Microbiome in Human Health (event brief)
Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features (recent publication from Elinav lab)
Antibiotic treatment in infancy can hasten the onset of type-1 diabetes in mice (research brief)
Yeast found in the gut linked to asthma (news article on recent research from the lab of Brett Finlay, co-director of the Humans & the Microbiome program)
Q & A: Let Them Eat Dirt (interview with Brett Finlay about his 2016 book)

For more information, contact Amy CookSenior Director, Knowledge Mobilization.

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