Update: Looks like this is the main response from some of the researchers/authors I contacted about this (and its sister article): Preserving microbial diversity (2018): http://science.sciencemag.org/content/362/6410/33 — they seem to be in complete agreement. My concern is that single paper will be inadequate to stem the tide. Even the news coverage that paper got was terrible and only focused on one of the least important aspects — the “microbial Noah’s Ark”. The more important aspects are the immediate steps to stop and reverse (FMT) the extinction & societal consequences.

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I am someone disabled and bedridden from CFS. I’ve been following the microbiome literature for a few years because it seems likely to hold a cure. When I saw this “eat dirt” stuff it seemed like a misinterpretation of the literature, so I read three books by 4 microbiologists and one doctor, which advocated for this notion, to see what there was to it.

First:

“Let Them Eat Dirt Saving Your Child from an Oversanitized World (2016)” by B. Brett Finlay, PhD, and Marie-Claire Arrieta, PhD. My review.

Second:

“Eat dirt (2016)” by Dr Josh Axe. My review.

Third:

“Dirt is Good (2017)” by Jack Gilbert and Rob Knight. My review.

In summary, I now consider this to be closed and debunked. They are partially click-bait, massively contradictory, jump to conclusions, make unsupported statements, and misinterpret the literature. It seems clear to me that it stems from all 5 authors having deficits in various areas, and possibly being afraid of addressing the real issues — antibiotics, poor diet, lack of breastfeeding, and unhealthy people having kids.

Moreover, it’s “unfortunate” there are no consequences for PhDs and Doctors who spread this kind of dangerous misinformation.

In the past I have been on a raw diet, including raw meat & fermented raw meat, for a few years (would not recommend it), and have also been severely and permanently harmed from one antibiotic and then had another antibiotic save my life. So I am open to all sides.

What constitutes a healthy/ideal gut microbiome is largely unknown, as are the origins of the gut microbiome and the factors that shape it: http://HumanMicrobiome.info/origins

The fact that you can do permanent damage to the gut microbiome from a variety of things, including antibiotics, and that the only known way of anywhere-near-fully repairing the gut microbiome is FMT from someone young, in perfect health, who’s never taken an antibiotic or damaged their gut microbiome in anyway, plus what we know about the microbiome and aging, strongly suggests there is something very important being inherited during pregnancy/birth/breastfeeding which cannot be picked up from the environment.

Soil is contaminated with lead, which has a variety of detrimental health impacts, including neurological damage [1][2].

Fact vs opinion:

Nothing wrong with opinion, but many people seem to have problems with being able to read an article and distinguish between the two. It’s important to see if certain statements come with a citation. Often when they do not, the statement is opinion. Here are some examples:

This article is 100% unsubstantiated opinion: http://boostarz.com/2017/07/17/dirt-good-kids-need-exposure-germsaccording-new-research/

He “thinks” dirt is good: https://www.aol.com/article/lifestyle/2017/07/19/parents-stop-chasing-your-kids-around-with-hand-sanitizer/23038117/

Speculation, opinion, misinformation, jumping to conclusions, misinterpretations: https://health.usnews.com/wellness/family/articles/2016-12-27/how-germs-dirt-and-hookworms-can-boost-your-health

“I’m a sound believer” https://www.thealternativedaily.com/health-benefits-of-dirt

Informed people can tell from the URLs & web pages that these are low quality sources of information. The problem is that most of the population is not that informed, and these articles get various doctors and microbiologists to make supporting statements. Very convincing overall for most laypeople.

Another “eat dirt” headline where the article gives 0 supporting evidence: http://www.chicagotribune.com/lifestyles/health/sc-hlth-microbiome-1018-story.html

Another “dirt is good” clickbait title where nowhere in the video is that supported: https://www.youtube.com/watch?v=mlTFbuVvMU0

This excellent review:

Cleaning up the hygiene hypothesis (2017), by Megan Scudellari. The rise of allergy and autoimmune diseases is due to much more than rampant cleanliness. Is it time to throw out the hygiene hypothesis? Today, epidemiological, experimental, and molecular evidence support a different hypothesis: Early exposure to a diverse range of “friendly” microbes — not infectious pathogens — is necessary to train the human immune system to react appropriately to stimuli http://www.pnas.org/content/114/7/1433.full

There is one opinion sentence in it which “pro dirt” people used to justify perpetuating their position:

“We’re talking about a number of factors, not just one. It’s the diet, sanitation, antibiotic use, parasites, and more…”

That is an opinion statement. The data does not support that position, as you will see in this (and that) article.

Lengthy, well-cited article about fermented foods & probiotics by microbiologist researcher: https://www.sciencebasedmedicine.org/everything-you-always-wanted-to-know-about-fermented-foods/

They do a great job providing sources for most of the claims, but they then make some claims which are not backed by the literature, and no sources are provided since they don’t exist. Such as “fermented foods can restore normal gut microbiota after antibiotics”. Article has additional issues with lack of distinguishing between strains/host-native strains.

There are numerous citations for my positions and statements in this wiki maintained by me, but I’m happy to get others or point to specific ones if asked. I use a wiki because it’s not feasible to cite 10–20 studies to support one statement/position: http://HumanMicrobiome.info/intro

Diversity:

A large part of the argument seemed to be based on gut microbiome diversity being beneficial — http://HumanMicrobiome.info#Diet — and thus we have less diverse gut microbiomes due to over-sanitation and not eating dirt as our ancestors would have.

The mechanistic link between health and gut microbiota diversity (2018): https://www.nature.com/articles/s41598-018-20141-6 — “more efficient systems and redundancy”

In reality, the literature shows that gut microbiome diversity comes from diet, not eating dirt. See wiki diet link above and:

First snapshot of Inuit gut microbiome shows similarities to Western microbiome (2017): https://eurekalert.org/pub_releases/2017-01/asfm-fso122916.php — http://msphere.asm.org/content/2/1/e00297-16

The Inuit gut microbiome is dynamic over time and shaped by traditional foods (2017): http://cancerdiscovery.aacrjournals.org/content/early/2017/11/14/2159-8290.CD-NB2017-162

So, the Inuit, who live the sanitation free life, have similar microbiomes due to similar diet.

Hadza gut microbiome is dependent on diet and thus shifts with seasonal changes in diet: https://www.nytimes.com/2017/08/24/science/gut-bacteria-hadza-diet-health.html

Hunter-gatherers’ (Hadza) seasonal gut-microbe diversity loss echoes our permanent one: https://www.sciencedaily.com/releases/2017/08/170824141231.htm — http://www.pbs.org/newshour/rundown/gut-microbes-found-hunter-gatherers-shift-seasons/ — http://science.sciencemag.org/content/357/6353/802

Vaginal seeding:

A part of the “eat dirt” ethos.

It seems illogical for microbes smeared on the skin to colonize the infant gut, but somehow a large amount of people were convinced this was the case. The current evidence suggests this is misguided: http://HumanMicrobiome.info/maternity

And that the infant gut microbiome may begin prior to birth: http://HumanMicrobiome.info/origins

Misinterpretation:

“Many have simplified this concept to ‘dirty environments help build one’s immune system, thus dirt is good, clean homes are bad’. This isn’t an accurate representation of the science.” https://archive.fo/8ljtn#selection-835.0-835.1

2018 PBS documentary covers the fact that the Amish have fewer allergies (around 24:00), but they admit they are still trying to figure out why. http://www.pbs.org/video/nova-wonders-whats-living-in-you-fnbfuy/

What the studies do support is general exposure to a wild life environment, and inhaling a natural and healthy air, that likely includes various microbial and dirt particles.

“The results so far suggest that simply inhaling M. vaccae — you get a dose just by taking a walk in the wild or rooting around in the garden — could help elicit a jolly state of mind. Lowry says." http://discovermagazine.com/2007/jul/raw-data-is-dirt-the-new-prozac — https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868963/

“Breathing in, playing in, and digging in dirt may be good for your health” — soil bacteria injected into lungs: https://qz.com/993258/dirt-has-a-microbiome-and-it-may-double-as-an-antidepressant/ This is also based on one single organism. “Dirt” contains innumerable types.

This 2013 study “Cohabiting family members share microbiota with one another and with their dogs” https://elifesciences.org/articles/00458 got a lot of press but was often misrepresented. It showed a greater sharing of skin microbiota, rather than gut.

There is a significant amount of flat out misinformation spread on low quality sites, such as:

“Study links super-clean homes to obese children http://www.kxxv.com/story/39125259/study-links-super-clean-homes-to-obese-children” — Wrong! This was a correlation study that showed eco-friendly cleaning products were associated with lower obesity, which could be caused by a variety of things unrelated to “super clean homes”.

Host-native vs environmental:

There is a major difference between host-native microbes that have been evolving alongside us for hundreds, if not thousands/millions of years, vs non-native environmental microbes. Yes, we’ve been killing these off with antimicrobials and junk diets, yes you should be alarmed. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850918/

The literature indicates the important microbes are the known beneficial, native ones passed down generationally from breast feeding, vaginal birth, possibly the womb, and early healthy diet (resource selection & shaping), and these are very different from ones you pick up environmentally via poor sanitation practices. It’s very probable that these host-native microbes prevent detrimental impacts from environmental microbes, IE: dirt. http://HumanMicrobiome.info/maternity

The evolution of host-symbiont dependence (2017): http://dx.doi.org/10.1038/NCOMMS15973 — https://archive.fo/6I7aa Bacteria passed between generations benefits you more than others. “Bacteria passed straight to children have more healthcare benefits than if they are transmitted via the surrounding environment”.

Many more “host-native” citations in this probiotic guide: http://HumanMicrobiome.info/probiotic-guide

Commensals cause inflammatory reaction in the absence of keystone minority microbes: https://around.uoregon.edu/content/oregon-study-suggests-some-gut-microbes-may-be-keystones-health

Subsets of highly connected “keystone” taxa, generally comprising 1–5% of community richness, explained community turnover better than using all taxa: http://www.biorxiv.org/content/early/2017/07/03/159087

Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics (2018): https://www.biorxiv.org/node/110194.full — low abundant species can be more metabolically active compared to others.

Specific vaginal lactobacilli suppress the inflammation induced by lipopolysaccharide stimulation through downregulation of toll-like receptor 4 expression in human embryonic intestinal epithelial cells: https://www.jstage.jst.go.jp/article/bmfh/36/1/36_16-011/_article

“environmentally obtained microbiota can also be very diverse and therefore play either beneficial or detrimental roles within the gut” (2018): https://sci-hub.tw/https://www.sciencedirect.com/science/article/pii/S0034528818300109

Mouse Microbiomes Are Mostly Inherited. Transmission modes of the mammalian gut microbiota (Oct 2018). The microbiota of the two mouse lineages remained distinct even after 10 generations. Most microbiota genera transmitted vertically. Those taxa that transmitted horizontally through the shared environment of the animal facility tended to be those that include pathogens. https://www.the-scientist.com/news-opinion/mouse-microbiomes-are-mostly-inherited-64998

Twin studies where one twin is healthy and the other has dysbiosis indicates an environmental source of the dysbiosis. Interesting example with Mo Farah and his twin brother.

One of the biggest revelations is the fact that dysbiosis increases with age and is a big part of the aging process, and these “diseases of old age” can be corrected by fixing the dysbiosis. If eating dirt & other environmental microbes was good for you, then you’d expect to see people get healthier as they age (since they’d be collecting more and more environmental microbes), which isn’t the case. http://HumanMicrobiome.info/aging

Inflammation, But Not Telomere Length, Predicts Successful Ageing at Extreme Old Age (2018). Inflammation is the prime candidate amongst potential determinants of mortality, capability and cognition up to extreme old age. Chronic systemic inflammation becomes increasingly associated with risk of death, loss of cognitive function and increasing dependency. https://www.ebiomedicine.com/article/S2352-3964(15)30081-5/fulltext

The Hadza essentially do FMT from animals they eat https://archive.fo/RQMVv and certainly pick up many helminths, parasites, and pathogens. Is there a net benefit? From what I’ve seen it’s not known, and not possible to know yet due to limitations in current knowledge & techniques. But they also don’t use antibiotics, have a natural whole foods diet, breast feed, and have vaginal births. And unhealthy ones die off (~20% of Hadza children die young http://humanfoodproject.com/please-pass-microbes/) instead of being saved by modern medicine (often via devastation of the gut microbiome with antibiotics) and then going on to have more unhealthy kids with inherited damaged microbiomes.

The discussion section of this 2014 review paper “Rural and urban microbiota — To be or not to be?” provides excellent related info on gut microbiome, FMT, and donor selection: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4153773/

Environmental impacts do exist:

Many citations in the previous links.

Others: https://archive.fo/V15aA#selection-903.0-903.1

But we don’t currently know the extent or impact/importance.

Infectious disease:

When I first heard about this “eat dirt” stuff, it seemed analogous to aspects of the anti-vaccine movement, in that people have forgotten what it was like before vaccines. Similarly, it seems people have forgotten how prolific certain microbial illnesses used to be (and still are in many 3rd world countries due to poor sanitation).

There are a plethora of known pathogens (such as various herpes viruses) that have been linked to numerous chronic illnesses. We know for sure that a variety of microbes cause disease and we can transfer disease states via FMT. Additionally, the current evidence strongly suggests that microbial pathogens that are currently undetected play a major role in dysbiosis and most diseases beyond current medical capabilities. IBD, Alzheimer’s, and “autoimmune” diseases are some examples.

Both conventional stool/blood testing, and commercial 16s testing, have severe limitations and test for a tiny amount of pathogens: http://HumanMicrobiome.info#Testing

The fact that you can do FMT from a diseased human to an animal and induce the same problems in the animal proves that it is not simply a matter of “missing microbes” but rather pathogens at play. http://aem.asm.org/content/early/2018/04/30/AEM.00434-18.abstract

Both a sterile environment and FMT build resistance against TRALI (Transfusion Related Acute Lung Injury) in mice. But TRALI was also transferrable with FMT (2018): https://www.news-medical.net/news/20180711/Study-reveals-link-between-gastrointestinal-flora-and-acute-lung-injury-after-blood-transfusions.aspx

Pretty alarming use of routine antibiotics but gives a different perspective from an environment of poor sanitation. Infant Deaths Fall Sharply in Africa With Routine Antibiotics (azithromycin): https://www.nytimes.com/2018/04/25/health/africa-infant-mortality-antibiotic.html

There are numerous instances of “bacterial overgrowth” being the cause of diseases. Examples: [1] [2].

Many microbes are very harmful and can trigger dysbiosis, short term and long term. Practicing poor hygiene is playing russian roulette. One example is that being in the forest is pretty much agreed upon to be very healthy [1]. Yet you can catch life-threatening illnesses such as lyme disease very easily in that environment.

Just like indiscriminate poop eating is not going to get you a successful FMT, the same applies for environmental microbes. Poop from someone very healthy can have huge benefits, yet eating out of a toilet or stool from someone unhealthy could be fatal. And obviously that unhealthy person picked up their problematic microbes from the environment. My experience & knowledge of FMT concludes that it’s extremely easy to pick up pathogens and very hard to pick up anything beneficial.

A large part of the “eat dirt/dirt is good” stuff seems to revolve around one asthma finding. There’s no evidence that people who live on farms or in less than sanitary conditions are all-around healthier due to eating dirt. It’s a myopic viewpoint. So people advocating poor hygiene based on that are basically telling you that getting asthma is worse than potentially fatal infectious diseases.

Disentangling complex parasite interactions: Protection against cerebral malaria by one helminth species is jeopardized by co-infection with another (2018): https://doi.org/10.1371/journal.pntd.0006483

You may want to read the relevant book “This is your brain on parasites (2016)”.

List of recent studies & articles related to infectious disease, strongly contradicting the “eat dirt” and associated anti-hygiene notions: https://archive.fo/aurWP

Antibiotics:

Antibiotics are extremely harmful, and their harms are likely currently underappreciated.

http://HumanMicrobiome.info/Intro#more-effects-of-antibiotics

http://HumanMicrobiome.info/maternity#antibiotics

Poor hygiene, including dirt eating, is likely to increase the chance of someone picking up an infection/pathogen and thus needing/taking antibiotics.

The tremendous amount of individual reports of antibiotics doing severe long-term harms makes it rational to question whether studies that show a “revert back to normal” some time after stopping, are adequately measuring the important things. One example is Rifaximin, which is said to cause beneficial shifts in the gut microbiome to an increased bifido count. Yet many people on IBS forums report very similar, severe and long term detriments (including myself): https://archive.is/qgWWS

FDA warns against “fluoroquinolone” class of antibiotics (2016): https://www.idstewardship.com/common-antibiotics-flagged-for-debilitating-toxicities/ “The warning was prompted by disabling and potentially irreversible side effects that have been tied to fluoroquinolone use”

And other drugs can have bactericide effects: Non-antibiotic drugs promote antibiotic resistance. These accidental bactericides included proton-pump inhibitors such as omeprazole, calcium-channel blockers, antihistamines, painkillers and antipsychotics. (2018): https://www.nature.com/articles/nature25979

There is no support for these harms to be reversible with eating dirt. The research even suggests FMT might not be able to completely undo the harms:

Immune Responses to Broad-Spectrum Antibiotic Treatment and Fecal Microbiota Transplantation in Mice (2017): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395657/

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake (2010): https://genome.cshlp.org/content/20/10/1411.long

Animals/pets live the “eat dirt” lifestyle yet suffer the same short and long term consequences from antibiotics: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054061/

This recent study seems to completely prove me right and them wrong:

“expansion of a certain species of house dust fungus (Wallemia mellicola) can occur in the intestines of mice after they are treated with antibiotics and exposed to the fungus. By contrast, mice with an intact and healthy intestinal microbiota resist this expansion. After expansion of this fungal population, the mice are more prone to develop asthma-like inflammation in their lungs when exposed to allergens” https://www.eurekalert.org/pub_releases/2018-09/p-gfe091318.php

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So when can we expect the 5 authors mentioned in the beginning of this article to submit retractions?