Slumdog Microbiome More Diverse

I was recently invited to put together a series of slides – or webinar – for a national supermarket chain on things their customers could do to improve the health of their gut microbiome. Once I got past the obvious first few slides that recommend they might spend a little less time in national supermarket chains and get some someone smarter than me to do this webinar, I listed what I think is the most important – and most counterintuitive recommendation that was still in keeping with my only half-kidding slides up until this point – move to a slum in Bangladesh.

As researchers plumb the gut of an increasing number non-western, or so-called developing regions or nations throughout the world, an interesting pattern is emerging. Not unexpected, different populations harbor different combinations of bacteria – on their skin, and in their bowels – but they also have a greater overall diversity of bacteria as well. When it comes to our inner ecosystem, our kick-it-and-see western diet and lifestyle experiment may not only be removing some important members all together (think wide spread use of antibiotics, for example), but reducing our gut microbiomes ability to defend itself (and us) against opportunistic pathogens (some domestic, some foreign) and reducing its overall metabolic output (more on this in a minute).

12273263_mA recent study comparing healthy children from the slums of Bangladesh with children in the U.S. is adding to a growing body of literature that suggests we may be getting a little too clean for our own good. In this study they collected stool samples from six healthy Bangladeshi children (ages 8-13), four healthy U.S. children (ages 10-14), and four Bangladeshi adults (ages 18-41). rDNA pyrosequencing was performed on all the samples, which provided a detail of the microbes present and their abundance in each of the samples. In addition, they also wanted to see how the gut microbiome changed overtime, so they collected monthly samples for five months from four of the six Bangladeshi children and for six months from all four U.S. children.

Overall, the Bangladeshi children harbored a greater diversity of gut bacteria than did their U.S. counterparts. This finding is similar to that reported between children living in a rural African village in Burkina Faso when compared to children in Italy.  This same diversity disparity is also noted between Venezuelan Amazonas and rural Malawians when compared to U.S. populations – of all ages. In addition, while the kiddos in the U.S. carried some bacterial genera (n=3) not seen in the Bangladeshi kids, the Bangladeshi kids carried many more (n=13) not found in the U.S. children.

The diet between the two populations could not be more different. In the U.S., the children consume much more protein and fat from animal resources, while the kids in Bangladesh rarely eat meat, but have a diet based on lentils, bread and rice. The researchers also speculate the U.S. kids have a more diverse diet, though detailed dietary information was not collected as part of the study.

What was potentially more interesting was how the gut microbiome changed over time. In short, the Bangladeshi kids showed greater diversity from month to month (from the baseline of the original sample) than did the U.S. kids – that is, they were more stable-like.

The take home from this small, but interesting study is potentially profound. While the researchers are quick to point out that the “causal relationships underlying the composition changes” are difficult to pinpoint, genetics, diet and lifestyle all likely play a role. From the perspective of an ecologist, and more specifically a microbial ecologists, diversity is something you want in an ecosystem. Greater diversity is associated with resilience, or the microbiomes ability to deal with such things as opportunistic pathogens or perturbations from diet. A less biodiverse gut microbiome may handle your five-donut binge at the office, or your bottle and half of red wine one night, instead of your usual two glasses, very differently. Dietary pulses or longer term shifts in diet, like antibiotics, are perturbations that can shift the composition of your gut microbiome and reduce diversity, as some species become more dominant under the perturbation.

The greater month-to-month variability in bacteria in the Bangladeshi kids is not likely attributable to antibiotics or wide shifts in diet. It is likely the continuous and “intensive exposure” to a diversity of microbes in their environment due to varying unhygienic conditions found in the slum that is driving the diversity. The potential greater exposure to large swaths of diverse people and animals contribute as well – something that has been lost in more western societies.

Infectious disease and associated gastroenteritis can be rampant (and deadly) in developing countries, revealing that the factors that shape microbial diversity and ones susceptibility to disease are complex. But the emerging themes of diversity and our ancestral lifestyle of constant exposure to the natural world and its myriad of wonderful (but sometimes harmful) microbes, will likely dominate our discussions of health and well being in the decades to come. Or, at least I hope so.


**Note if you are curious what’s in your gut, you can join Phase II of the American Gut project.

16 Comments Add yours

  1. Alan says:

    I think that you misspoke–“Bangladeshi kids showed greater diversity from month to month (from the baseline of the original sample) than did the U.S. kids – that is, they were more stable-like.”

    From the abstract of Lin et al. 2013–“Furthermore, community membership and structure in Bangladeshi
    children was significantly less stable month-to-month than U.S. children”

    More change in microbiome structure through time, not “more stable-like”.

    Thank you for the link and post. Very interesting. I may need to travel!

    1. Jeff Leach says:

      Good catch Alan. I fixed. Much appreciated.

  2. Hi Jeff, I have recently come across the works of this guy:

    and have started to read one of his books. Are you familiar with his work? If so, I’m curious if you have an opinion on todays studies like the ones you mention above compared to Bechamps ideas. Its interesting to read these things and also very confusing. Thanks!

    1. Jeff Leach says:

      Thanks Shawn. Don’t really follow him. Looks interesting however. Thanks for sharing.

      1. What is most interesting is that I think if his theories are actually correct it would change the meaning of the results of our tests. I believe there are more people that continued his work, but I have not gotten that far. His book is a tough read.

  3. Lucy says:

    I wonder if the higher amounts of sugar in the western diet don’t play a big role in this as well as the other factors mentioned.

  4. Jeff – I’m from that human culture that wants to believe that the human gut biome is maintained (and, for some people, created) by pro and pre biotics in the human diet. In fact we like to believe that human beings have an instinct for creating ferments to feed or develop their gut biome. I know that typical American diet lacks both the ferments and the pro biotic foods that keep the gut flora humming. What I didn’t see in your article above was any mention of traditional foods those dirty slum kids may have in their diets. Of course, I didn’t see any other explanation for the differences, either, so, I guess my question is: do you rule out the value of traditional fermented foods to create and maintain a diverse gut community? (In other words, is the onlly way I can build the health of my gut biome to eat a healthy person’s poop? (There’s some hope for the later given a study I recently heard of that proves that every inch of NYC is contaminated with human fecal matter.)) Thanks, Jeff -Allan

    1. Jeff Leach says:

      according to the researchers, the kids were not consuming fermented foods.

  5. AlexP says:

    In a healthy human family, extended family and social circle, sharing pets, hugs, kisses and other simpler skin-to-skin contact, lots of bacteria must be passed around. I wonder if this is the reason that people living alone are more likely to have an abbreviated life span, that their microbiomes are more limited and less likely to be renewed or reinvigorated by human social contact. Of course, I imagine that pets ameliorate some of that effect, but if the pet is also isolated, what then?

    I look forward to seeing the undoubtedly fascinating results of further research into the human microbiome.

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