Microbes, Immunity and Health

June 23rd, 2020 | Posted in Info

Diseases of the immune system have increased over the last few decades in urban environments. The hygiene hypothesis suggests that immune mediated diseases may be linked to reduced contact with the soil and the natural environment whilst living in over sanitised environments and being overly clean. These all affect the balance of micro-organisms that live on us and in us and play a key role in our health.

See blog post on One Health for more information about the role of the soil in health and disease.

Here we will look at the factors that affect the microbiota and the consequences for health.

The Importance of Microbes

The human body contains many types of microorganisms including bacteria, viruses, fungi, and protozoa, which are collectively known as the microbiota. The microbiome is defined as microorganisms and their genomes (1). These microorganisms contain about 100 times more genes than the human genome. The microbiota affects the development and function of all organ systems in the body, and contributes to adaptation and evolution. It also has a protective effect against pathogenic microorganisms and toxins.

Factors that affect microbiota diversity include:

  • diet
  • use of antibiotics and other medicines
  • use of alcohol and other drugs
  • exposure to the natural environment
  • pregnancy
  • age
  • genetics
  • infections
  • exposure to toxins
  • physical activity
  • stress
  • parental microbiotas impact on the health of their children
  • season – there are seasonal fluctuations in the composition of the microbiota (2)

The microbiota plays a role in many aspects of health including:

  • development and regulation of the immune system
  • digestion of food
  • metabolic and endocrine (hormonal) pathways
  • brain function and behaviour
  • epigenetic modification
  • production of vitamins, such as B12 and K
  • metabolism of toxins

Urbanisation and Health

Exposure to environmental microbes increases microbiota diversity which is beneficial to health. For example, growing up in microbe-rich environments, such as traditional farms, has been shown to have protective effects on children’s health.

Global comparisons reveal a decrease in gut microbiota diversity attributed to Western diets, lifestyle practices such as caesarian section, antibiotic use, formula-feeding of infants, and sanitation of the living environment. The loss of soil biodiversity due to urbanization could also have major consequences for health (3).

Studies have shown that the lack of microbiota diversity may be implicated in:

  • Autoimmune diseases including type 1 diabetes, rheumatism and muscular dystrophy.
  • Chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma.
  • Other conditions such as cancer, depression, stress, autism, and Alzheimer’s disease (1).

Traditional Lifestyles and the Microbiota

The study of traditional populations provides an insight into the microbes that co-evolved with humans unperturbed by industrialization. Research into the microbiota of the Hadza hunter-gatherers of Tanzania found seasonal shifts in types of bacterial, diversity, and carbohydrate utilization by the microbiota. When compared to the microbiota composition from other populations around the world, the Hadza microbiota shares bacterial families with other traditional societies that are rarely seen in people in industrialized nations (4).

Soil, Skin Health and the Immune System

A recent study found that contact with microbiologically diverse natural substances such as soil and plant based material for just a short amount of time immediately increased, at least temporarily, the diversity of skin microbiota. It may be that soil and plant based matter could be used to modify the skin microbiome, and eventually, in the treatment of other disorders of the immune system (5).


Spend time in nature and get your hands in the soil whenever you can. Oh, and avoid using harsh chemicals around the home and don’t wash too often!

See blog post Benefits of Exercise and COVID-19 to find out about how exercise may be of particular importance in protecting ourselves against the effects of the coronavirus.


1. Biosci Microbiota Food Health 2020;39(2):23-32. Interaction of the Microbiota With the Human Body in Health and Diseases. Altves S et al.

2. BMC Microbiol 2020 Apr 21;20(1):100. Seasonal Variation in Gut Microbiota Composition: Cross-Sectional Evidence From Ukrainian Population. Koliada A et al.

3. Front Microbiol 2017 Oct 6;8:1935. Linking the Gut Microbial Ecosystem With the Environment: Does Gut Health Depend on Where We Live? Tasnim N et al.

4. Gut Microbes . 2019;10(2):216-227. Links Between Environment, Diet, and the Hunter-Gatherer Microbiome. Fragianakis G et al.

5. Microbiologyopen 2019 Mar;8(3):e00645. Short-term Direct Contact With Soil and Plant Materials Leads to an Immediate Increase in Diversity of Skin Microbiota. Gronroos M et al.