Microorganisms have inhabited the Earth for billions of years, long before humans appeared. Even though we have always been exposed to a large number of microorganisms in food, water, the air and on environmental surfaces, in recent times food processing, water purification and the widely held belief that the only good microbe is a dead one have dramatically reduced our exposure.

Scientists have hypothesized that reduced exposure to microorganisms in our diets might have come at a cost. That is, the fact that the immune system has to cope with the absence of non-harmful microorganisms with immune regulatory functions could contribute to the current rise in immune-mediated diseases such as autoimmune diseases, allergic diseases and asthma.

In this context, a group of scientists are now arguing that perhaps we need to go back to consuming large numbers of safe microorganisms every day as a means of preventing, limiting or ameliorating diseases linked to immune system dysfunction.

The early human diet, tied to agriculture and settlement in villages, included fermented foods as staples. However, as humans have gradually moved to a more industrialized lifestyle, the number of commensal microorganisms in our diet has decreased. That has led to reduced interaction between safe live microorganisms obtained from diet and the digestive and immune cells across the gastrointestinal tract, subsequently increasing the likelihood of chronic disease.

Thus, the idea that live microorganisms could provide health benefits seems plausible.

Although both fresh fruits and vegetables, along with fermented foods, contribute to the live microbes ingested by consumers, only fermented foods are considered to provide a major source of commensal microorganisms. For instance, it has been estimated that regular consumers of fermented foods may ingest up to 1011 colony-forming units per day.

The evidence supporting the inclusion of safe live microorganisms in diet to improve health comes mainly from randomized controlled trials on probiotics (including fermented foods that are a true source of probiotics, such as some fermented milks and kefirs) and associative studies on the health benefits of fermented foods.

Within fermented foods, yogurt has been widely studied as a means of improving lactose digestion in lactose maldigesters. Beyond yogurt’s known benefits for gastrointestinal health, human studies have also shown the role of yogurt as a marker of a healthier lifestyle and greater adherence to the Mediterranean Diet and its association with improved gut barrier function and improved metabolic and cardiovascular health.

While the majority of studies on probiotics in the form of supplements, drugs or fermented foods have been performed in populations with specific conditions, data on healthy populations are limited. This, in turn, hinders recommendations around ingesting live microbes (what levels and what microbes?) for the general healthy population.

The idea that consuming large numbers of safe bacteria is beneficial to preserving and restoring health has some supporting evidence in the most recent consensus on probiotics. But it is too early to establish a Recommended Dietary Allowance or Adequate Intake for microorganisms. As Colin Hill acknowledges in this open access article, the long-term assumption that it is easy for a microorganism to be bad but much less likely for it to have a positive impact on health is an obstacle to encouraging laypeople to consume high levels of safe microbes for health benefits.

With current levels of chronic diseases and gastrointestinal maladies related to the immune system and the gut microbiome so high, a microbial RDA idea is worth considering. In the meantime, the authors of this opinion article propose some go-to steps that will help inform dietary recommendations for living microorganisms.


  • Evaluating available evidence from dietary databases is the first step towards determining whether consuming living microorganisms provides quantifiable health benefits. One caveat of studies that have addressed the effect of consuming live microorganism-containing food on health outcomes is that they focused on specific probiotic strains rather than general live microorganism consumption.
  • Performing more randomized controlled trials on fermented foods containing live microorganisms: this research should control participants’ background diet and use questionnaires that determine the intake of live microorganisms. Different factors such as cooking methods and preservation (i.e., canned versus fresh) should be considered in human studies reporting on estimates of microbe consumption. That is currently a limitation of existing nutrition databases.
  • Collecting relevant data and confounders in studies exploring how consuming live microorganism-containing foods affect health outcomes. The foods contain a wide range of substrates beyond live microbes that could affect the relationship between fermented food intake and health or disease endpoints.



Marco ML, Hill C, Hutkins R, et al. Should there be a recommended daily intake of microbes? J Nutr. 2020; 150(12):3061-3067. doi: 10.1093/jn/nxaa323.

Hill C, Guarner F, Reid G, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014; 11(8):506-514. doi: 10.1038/nrgastro.2014.66.

Hill C. RDA for microbes – are you getting your daily dose? Biochem (Lond). 2018; 40(4):22-25. doi: 10.1042/BIO04004022.