Refers to the paper: http://science.sciencemag.org/content/351/6275/aad3311?rss=1

This answer explains why eating one’s way to health-associated microbiota isn’t as simple as it sounds.

Healthy microbiota itself remains undefined. What’s optimal for one may cause disease in another. After all, during her years as a cook, Asymptomatic carrier – Wikipedia Mary Mallon – Wikipedia, popularly known as Typhoid Mary, spread typhoid in her wake without ever suffering its ill-effects herself (1). One of several sources that supply human microbiota, diet is just more tractable in being more within an individual’s control, and even there, our knowledge of microbiota is still far too preliminary to assert much with confidence.

Many other factors, some of them beyond a child’s control, are involved in assembling our microbiota. For example, an individual can’t control whether they were born full-term or not, by vaginal delivery or C-section, got fed breast milk or not, experienced modern sanitation from birth or not, each of which profoundly shapes initial human microbiota colonization.

Are such early-life influences inalterable, being imprinted for life or modifiable? While that’s still unknown, the notion of keystone or starter species, that those species that colonize first create a milieu that favors specific other microbes to follow, suggests the former may be more likely (2, 3).

Birth mode changes microbial colonization & influences long-term health: Epidemiology suggests a child born by C-section may experience long-term adverse outcomes such as higher risk of allergy (4). Such a child acquires microbes from mother’s skin and the environment of its birth surroundings rather than from the mother’s birth canal. Presumably C-section bypasses optimal microbial colonization.

Sanitation: People born into modern sanitation and piped chlorinated water supply have a fundamentally altered microbial ecosystem compared to their forebears and to those still lacking modern sanitation. Unbeknonwnst to us, multitudes of microbes that inhabited our bodies lifelong through the course of evolution vanished from our immediate environments with the advent of modern sanitation and chlorinated water. This profound change altered ecosystems of large swaths of human populations over the course of the 20th century, what Moises Velasquez-Manoff calls ‘An Epidemic of Absence‘ (5).

An illustrative example, in 1947, well into the modern sanitation era, ~36% of Europeans were still estimated to carry helminths such as Enterobius vermicularis (pinworm), Trichuris trichuria and Ascaris lumbricoides (6). However, by 2002, pinworm had become rare in European populations (7). Meantime, numerous epidemiological studies have picked up an association between harboring helminths and extremely reduced rates of allergies (2, 3, 8, 9, 10). Inverse associations of helminth carriage with autoimmunities such as Multiple sclerosis – Wikipedia (MS) and inflammatory conditions such as Inflammatory bowel disease – Wikipedia (IBD) are also now well-known (11).

Again, modern sanitation-related microbial disappearances are becoming more, not less, widespread, and several generations of humans have already been born into vastly microbially depleted environments over the course of the 20th century till date.

Lifestyle Factors: Sterile wipes and washes, and modern soaps and detergents fundamentally alter skin microbiota. After all, such products can’t distinguish pathogens from microbes used to inhabiting our skins over eons, can they?

Specific microbes such as Bifidobacterium longum – Wikipedia reach neonates’ guts through breast milk (12). The mid-20th century fad of feeding babies formula obviously inadvertently severed an association forged across evolutionary time (10). Consequence? We’re still muddling our way through a full accounting of the cost.

Avoidance of dirt and mud has been increasingly fetishized in recent times and yet numerous health benefits can be ascribed to close encounters with the millgram quantities of largely harmless microbes such as Mycobacterium vaccae – Wikipedia found therein (13).

Could such microbiota changes even be reversed or their consequences mitigated by greater microbial exposures later in life? Value of diet-based prescriptions, whatever those might be, hinges on the answer to that still open question.


1. Tirumalai Kamala’s answer to Does an asymptomatic disease induce immunity?

2. Tirumalai Kamala’s answer to Is there any strong research about the effects of increased exposure to pathogens from grouping children in settings like day care centers or schools?

3. Tirumalai Kamala’s answer to Do you think there is sufficient evidence for the “hygiene hypothesis”?

4. Tirumalai Kamala’s answer to Is giving birth in water bad for the development of the child’s immune system?

5. An Epidemic of Absence: A New Way of Understanding Allergies and Autoimmune Diseases Reprint, Moises Velasquez-Manoff – Amazon.com

6. Stoll, Norman R. “This wormy world.” The Journal of parasitology 33.1 (1947): 1-18.).

7. Gale, E. “A missing link in the hygiene hypothesis?.” Diabetologia 45.4 (2002): 588-594. A missing link in the hygiene hypothesis?

8. Tirumalai Kamala’s answer to What are some examples of animals in the natural environment exposing themselves to some variant of weak pathogens to enhance their immunity?

9. Tirumalai Kamala’s answer to How might parasites turn out to be good for their hosts?

10. Tirumalai Kamala’s answer to What ramifications has current research on the human microbiome yielded (besides pre- and probiotics)?

11. Rook, Graham AW. “Hygiene hypothesis and autoimmune diseases.” Clinical reviews in allergy & immunology 42.1 (2012): 5-15. https://pdfs.semanticscholar.org…

12. http://www.cell.com/cell-chemica…

13. Rook, G. A. W. “99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: Darwinian medicine and the ‘hygiene’or ‘old friends’ hypothesis.” Clinical & Experimental Immunology 160.1 (2010): 70-79. http://onlinelibrary.wiley.com/d…