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Can’t see the forest for the microbes


Cryotube-wielding scientists are the latest in a long line of researchers studying hunter-gatherer groups throughout the world that seek balance between the prying nature of research and the rights and respect of indigenous cultures. In a timely discussion, Dominguez-Bello and others[1] foretell of a future where mining the microbial richness of native peoples is probable, but must be undertaken with the highest ethical standards and with specific consideration to the native cultures with regards to equitable outcomes that may result from commercialization. It’s imperative we do no harm at any level in the process.

But as researchers contemplate and ply the translational potential of often extraordinarily diverse hunter-gatherer microbiomes in the context of important ethical considerations, we should be careful not to miss the trees for the microbes. By this I mean the regional (microbial) species pool that is the source of the rich microbial diversity that draws us to minimally impacted cultures in the first place.

As discussed in a post last week, working amongst the Hadza hunter-gatherers of Tanzania for the last few years has brought front and center the intimate – and seasonal – relationship humans evolved microbes on the landscape. With each animal killed, microbes are given the opportunity to move from one species to the next – so long as they can find a suitable niche. With each berry that is plucked from a bush or tuber dug from beneath the microbial-rich ground, each and every act of a foragers lifestyle keeps the Hadza – and presumably our common hominid ancestors – connected to an extensive regional species pool.[2]

As researchers muse about the therapeutic possibilities of novel species and small molecules that may recover co-evolved interactions lost in the industrialized west, perhaps our greatest reciprocal action as researchers working with native peoples who seek to maintain their way of life in the face of increasing anthropogenic pressure, would be to characterize and acknowledge the regional species pool in their microbial health and the loss of ours. While much is made of diet, antibiotics and niceties of the developed world as environmental filters (species sorting) resulting in our degraded western microbiomes, we need not forget how closely linked microbial richness in native peoples is embedded in the integrity of the biological systems they inhabit.

As 50% of the worlds population is living in biodiversity-degraded urban settings characterized by a compounding torrent of environmental filters yoked to westernization lifestyles, the microbial-rich Hadza gut is trying to tell us we can’t turn the tide on the cascade of microbial species extinctions in our own guts unless we take on the root cause of our current inner ecological disaster and their impending one.

In the absence of protecting the microbiota of the Hadza and other remote groups through legislation similar to the U.S. Endangered Species Act or international frameworks such as that provided by the Convention on International Trade in Endangered Species of Wild Fauna and Flora – which is an argument that could and should be made – perhaps bio-banking in the form of larger biomass (poo) collection during fieldwork to go with extensive environmental sampling that should be the foundation of all future work among native peoples might be considered. In other words, if we don’t safeguard for humanity the extraordinary microbial diversity the Hadza and other minimally impacted indigenous cultures harbor – either through bio-banking (with permission) of larger samples for future scientists or outright protection from encroachment from pastoralist and other groups – then our knowledge of how we might recover lost species of microbes that all humans co-evolved with be lost forever.

Going beyond the swab would place missing microbes in the western gut firmly in the wheelhouse of ecological theory and the ongoing ecological calamity that is the modern world. For native peoples, a more broad ecological approach by researchers to understanding their local microbial diversity might provide another arrow in the quiver in their struggle to protect their lands and way of life.



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  1. Dominguez-Bello, M.G., et al., Ethics of exploring the microbiome of native peoples. Nature Microbiology, 2016. 1: p. 16097.
  2. Cornell, H.V. and S.P. Harrison, What Are Species Pools and When Are They Important? Annual Review of Ecology, Evolution, and Systematics, 2014. 45(1): p. 45-67.



  1. In the last sentence of the first paragraph, the term implicit is used. I think you mean “imperative”.

  2. I know what you are receiving from the Hadza, but I don’t know what the Hadza are getting for helping you. What is your contribution to bettering their lives.?

    • Good Q. Every Hadza that participates in the study provides informed consent. I have to admit when we first launched the study 3 years ago it was not clear what the Hadza would gain from our activities – as we did not know what we would learn from our work. I guess its the same thing the decades of anthropological work strains to answer as well (note the Hadza host a steady stream of researchers every year). It’s hard to imagine how a Hadza would gain anything from a peer-reviewed article on optimal foraging theory even if the Hadza contributed data to the study. So I get the delima faced by anthropologist. People often assume that our study is medical in nature – which it is not. It’s more of an ecological project. We are simply interested in how a free-living human population – that is still minimally impacted by industrialization – acquires microbes through social networks and the environment. This year we are launching a project whereby we visit various Hadza camps throughout the region we have worked with in order to present a nighttime power point presentation of our findings to date with local interpreters. (As odd as it sounds, very few researchers who visit the Hadza do this simple thing). As you can imagine, trying to articulate our sometimes complicated results will be a challenge. But with the help of organizations like TZ_based UCRT and others, we are excited about how this will turn out. But back to your original Q: after several years of data collection its hard to put a finger on what the Hadza get in return. However, we do provide funds for a regional Hadza medical fund – and have done so for years. We donate monies to Hadza that are pursuing an education in many of the regions boarding schools. We’ve also provided funds and other support for a Hadza man that is attending law school! We also provide support in many other ways. However, I think the biggest contribution we will make to the Hadza is playing a more prominent role in providing (microbial) evidence of why their lands should be protected from encroaching pastoralist. It’s becoming increasingly clear that the health of their ecosystem is directly related to their gut health.

  3. How much of this diversity that exists in the Hadza microbiome is the result of species that are just passing through vs. resident species the bloom and die off based on diet and other factors? In other words, if you transplanted a sample from a hadza to a westerner, how much diversity would be lost over time just due to lack of ongoing environmental exposure? It seems to me that the ongoing exposure to microbes in food, water, activities, environment, etc. is crucial to a diverse microbiome….

    As someone focused on developing my own microbiome diversity, diet only take me so far down the road… Supplementation only adds a little…. Seems like ongoing and diverse exposure (wild foods, getting dirty, swimming in natural bodies of water, etc.) is a missing ingredient that is rarely emphasized as a critical component

  4. I am glad your project continues. Every email message I’ve read from the project has been important and enlightening. Thank you for doing key research and providing perspective.

  5. Hi Jeff my four year old was diagnosed with type 1 diabetes in November 2015 after a course of Erythromycin macrolide anitbiotics which was prescribed by the local doctor for an ear ache. The doctors hand them out like lollies without any warning as to any side effects. My son had his first round of antibiotics when he was 1 week old for a possibly infected unbilical cord which could possibly have been treated differently and he has had several rounds since then. I have been reading everything I can about diabetes type 1 since then which includes recent research that links pulsed broad spectrum use of antibiotics on mice that can cause diabetes. There is also previous research that links diabetes type 1 with environmental factors such as early antibiotics use particularly where there was 5 or more rounds, bovine milk, nitrates in the water and distance from the equator (ie lack of vitamin D), Given that its an autoimmune disease and the research is saying 80% of a persons immunity is from their gut it seems to me that decimating the native diversity of the gut through repeated antibiotic use reduces a child’s immunity and leaves them susceptible to develop type 1 diabetes. Erythromycin can directly damage the pancreas (not mentioned by the local doctor) but apart from that doctors don’t actually know how antibiotics work they just know some things it does. So you have doctors over prescribing antibiotics which they don’t understand how it affects the body or the affect it has on the gut bacteria which they don’t understand either. As long as the doctors and the pharmaceutical companies are making money everyone seems happy. Except me I’m mad as hell! I’m a lawyer and I would love nothing more to make a class action. Not because I want the money but because I think the doctors are grossly negligent and its about time someone did something about it. I don’t know many people with type 1 diabetes but I would really like to know if anyone else thinks there is a link between type 1 diabetes and antibiotics. I know of one other case where a 15 month old baby developed type 1 diabetes after finishing a course of antibiotics. The doctors will say type 1 diabetes results from a virus however thats their default line when they have no clue. I have been following your research which I find absolutely fascinating. Keep up the good work!

  6. In terms of what you can do for the Hadza, tell them the story of Henrietta Lacks.
    Make sure they understand the value of what they possess and make sure they sell their shit for what it’s worth so they can decide how they want their own futures to roll out.

  7. Hi Jeff,
    I just finished watching your video on YouTube. In it, you mention that “whole grains may be promoting the growth of inflammatory bacteria. This brings to mind a research report I found on the NCBI website. It was a well written research report, 38 pages, and it made the claim that Glycophosate, plus it’s surfactants, were killing our good bacteria, and not harming our bad bacteria. Also, it was being connected with the rise in gluten intolerance.

    So,,,,,,, it might be the Roundup ready wheat, etc and the chemical residues disrupting the shiitake pathway of our good bacteria, that is the real culprit behind our suspicions about whole grains. Food-for-thought at least.

    I want to say, I am very impressed with your work Jeff !

    I realize that we will continue to study the human microbiome over the next ten years, and learn many good things. But,,,,,,,, if that’s all we do, we squander an important time frame in stopping the harm that we do to the microbiome, almost everywhere we look.
    I encourage you and your acquaintances to meet with the NIH and discuss how to eliminate products that are causing harm to the microbiome :
    1. reducing the number of antibiotic prescriptions given by medical professionals. I think this needs to be a priority in 2017. We must not continue to cause damage to the microbiomes of unsuspecting people, via antibiotics, when they are not absolutely necessary. It is a huge mistake, one that we can correct. The NIH needs to educate all medical professionals about the human microbiome, how important it is to our health, and how we need to reduce the number of antibiotics prescribed, whenever practical or possible.

    2. Asking the NIH and the FDA to reduce, year by year, the levels of added sugars in processed foods. In five years we need to reduce our sugar consumption to 1/8th of what it is now. We can study this to death, but if we fail to act, we continue the damage to the health of unsuspecting people. We have to face the fact that the average American has lost 40% of this diversity, so the average person is already sick, and sugar compounds the problem by then feeding our bad bacteria.

    3. Ask the NIH to re-examine the use of mouthwash, and toothpaste, and if they cause harm to the oral microbiome, as well as the subsequent microbiomes. We also need to eliminate chlorine, at the tap. While it is valuable in our pipes for preventing disease, it is harmful to our good bacteria, when we drink it, and when we bathe in it.

    4. I am convinced there is a role that the oral microbiome plays in establishing anaerobic bacteria in the large intestine. When we use chlorinated water, mouthwash, and toothpaste we may be disrupting this natural process, without realizing it. There are anaerobic bacteria, in the oral microbiome. Where else to we get anaerobic bacteria to populate our gut microbiome, unless it is our oral microbiome ?

    5. Please, encourage your colleagues to write/visit the NIH and ask them to re-examine the many products we are exposed to that could be potentially harming our good bacteria. We have approved a long list of products, without testing whether they cause harm to our microbiome. We need to change this in 2017. We need to stop the harm. How will we know if our dietary interventions, probiotics, FMTs, etc. are truly effective, unless we first eliminate the other harmful mistakes/products in our lives that cause harm ? It is a mistake to keep studying the microbiome, while we continue to unwittingly cause harm. First do no harm.

    Please, reach out to others and convince them to meet with the NIH.

  8. I think it is great that you are studying this tribe and their hopefully ‘undamaged’ microbiome.

    What do you think about taking steps in the US to : 1. reduce the prescribing of antibiotics, by health care providers ? Since we know that antibiotics are harmful, thanks to the great work by Dr. Martin Blaser, do you think this is something worthy of accomplishing in 2017 ?

    2. What do you think about the use of antibacterials in teething rings for babies ?
    There are around 700 products with antibacterials in them, still being produced. Do you think this is cause for concern since antibiotics wreck havoc on the flora of the microbiome ?

  9. HI Jeff; Love what you are doing out there. Imperative stuff. But … you left me hanging terribly after the insertion of the over sized turkey baster. The essay just stopped. And I had no idea of the outcome of the transplant. Was there a dramatic change.? Was it perceptible within yourself as a health /mood change? Did it change back to your prior state quickly? Or not? Pray tell … most curious.

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