The Microbiome: 100 Trillion Guests

Chapter summary

The microbiome is about 100 trillion bacteria, fungi and archaea, weighing roughly 2kg, that live on and in us.
For a century microbes were seen only as a cause of disease. In the past decade they have been recognised as partners.
They play a role in nutrition, obesity, allergies, autoimmunity and even gender bias in disease.
Most people carry the same basic set of bacteria through life.

In 2013, over 200 scientists from 80 institutions sequenced the microbiome of 242 healthy adults, sampling skin, mouth, nose, gut and vagina.
Skin and vaginal sites showed less diversity than the mouth and gut. The mouth alone holds several hundred species, and each tooth is its own ecosystem.
Gut bacteria include E. coli, mostly harmless, although some strains cause disease. Mouth bacteria form plaque and make acids that cause tooth decay.
Obesity: Ridaura (2013) transferred gut bacteria from twins, one lean and one obese, into mice. The mice took on the lean or obese traits, and bacteria from the lean donor could reverse the obese pattern.
Diversity: In 300 Danes, those with more diverse gut bacteria showed fewer signs of metabolic syndrome.
Gender bias: Markle and colleagues found that microbes affect sex hormone levels, which may explain why some autoimmune diseases are more common in women.
Malnutrition: In kwashiorkor, one child may be malnourished while a sibling is not. Breast milk and the microbiome are part of the answer.
Allergies: Professor Hans Bisgaard’s study of over 400 children found less bacterial diversity in infancy raised the risk of allergy by school age. Babies born by caesarean meet fewer bacteria and develop more allergies.

Supporters: Probiotics are sold to replace bacteria lost after antibiotics and help digestion. Drug discovery from microbial molecules is a long-term hope.
The author’s caution: The science is early. He suggests learning to live with the microbiome and not “messing with it”. The biggest practical improvement comes from cutting sugar and simple carbohydrates.
Cleanliness: It is open whether antibacterial mouthwash and very clean homes do harm. Do not take this as advice to ignore hygiene.

The effect of a diet depends on a person’s genes and bacteria, and the bacteria are shaped partly by diet.
Past nutrient studies may have been confounded by microbiome differences.
Reports suggest autoimmune conditions can be managed by diet, perhaps through the microbiome.

Kostic, A., Howitt, M. and Garrett, W. (2013) Exploring host-microbiota interactions in animal models and humans. Genes and Development 27:701-718.
Ridaura, V. et al. (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341:1241214.
Flak, M., Neves, J. and Blumberg, R. (2013) Welcome to the microgenderome. Science 339:1044-1045.
Markle, J. et al. (2013) Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science 339:1084-1088.
Gordon, J. et al. (2012) The human gut microbiota and undernutrition. Sci Transl Med 4:137ps12.
Smith, M. et al. (2013) Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science.
Bisgaard, H. (2011) Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. J Allergy Clin Immunol.