diverse microbiome found in isolated Amazons

[davey72]

Excerpt: The microbiome of an isolated tribe of hunter-gatherers in the Amazon contain the highest levels of bacterial diversity ever documented for humans, according to a study published in Science Advances this week. And despite never having been exposed to commercial antimicrobials, some of their resident microbes carry genes that confer resistance to manmade antibiotics. That means the ability to resist was there long before our drugs came along.

A growing body of evidence links westernization to the loss of bacterial diversity, though no one really knows whether diverse bacterial flora helps or harms health. By studying populations with little or no previous exposure to industrialized lifestyles, researchers hope to understand the makeup of microbiomes similar to that of our early ancestors, and in the process, see if there are benefits to hosting a rich, diverse microbial diversity.

For thousands of years, the Yanomami people lived (and still do live) a semi-nomadic, hunter-gatherer lifestyle in the Amazonian jungle. They were first contacted in the 1960s, and in 2008, an unmapped Yanomami village was spotted by an army helicopter in the High Orinoco state of southern Venezuela. The next year, researchers returned to collect mouth swabs, feces, and forearm skin samples from 34 villagers ages 4 through 50. Now, a large international team led by New York University’s Maria Dominguez-Bello have sequenced and analyzed the microbial DNA contained within.

Those samples revealed significantly higher bacterial diversity than samples collected from study participants in the U.S., as well as two non-Western groups with limited exposure thus far: Amazonian Guahibo Amerindians in Venezuela and residents of rural Malawian communities in southeast Africa. The microbiome of industrialized peoples are 40 percent less diverse, and even minimal exposure to Western medicines greatly decreased diversity as well. Some of the bacteria found at higher levels are known to be beneficial -- such as preventing kidney stones from forming.

Furthermore, despite having no exposure to commercial drugs, the fecal samples showed how the Yanomami harbored gut bacteria with functional genes that code for antibiotic resistance. These genes turned on in response to antibiotics, and in tests, they deactivated various natural, semi-synthetic, and synthetic drugs. “The silenced antibiotic-resistant genes show that you don't need exposure to antibiotics to possess antibiotic-resistant genes," Dominquez Bello says in a news release.

These genes may have come from an early exchange between human microbes and soil bacteria, which produce natural antibiotics to kill their competitors. In fact, most antibiotics developed in the 1940s and 1950s were derived from soil bacteria, "so, we would expect that natural resistance to antibiotics would emerge over millions of years of evolution," Washington University’s Gautam Dantas says. However, "it was alarming to find genes from the tribespeople that would deactivate these modern, synthetic drugs,” Dantas adds in a university statement. The work suggests that genes equipped to resist antibiotics may be a natural feature of the human microbiome.

-http://www.iflscience.com/health-and-medicine/tremendously-diverse-microbiome-found-hunter-gatherers-living-amazon

 

[riclapaz]

These genes may have come from an early exchange between human microbes and soil bacteria, which produce natural antibiotics to kill their competitors. In fact, most antibiotics developed in the 1940s and 1950s were derived from soil bacteria, "so, we would expect that natural resistance to antibiotics would emerge over millions of years of evolution," Washington University’s Gautam Dantas says. However, "it was alarming to find genes from the tribespeople that would deactivate these modern, synthetic drugs,” Dantas adds in a university statement. The work suggests that genes equipped to resist antibiotics may be a natural feature of the human microbiome.

Thanks for sharing davey72, reading this article, I remembered this Foxx shared:

I had never heard of soil based probiotics until I saw an acupuncturist who was also in the Paleo physicians network (http://paleophysiciansnetwork.com/), who recommended them to me. I took two pills a day of the brand Prescript-Assist for about two weeks as recommended by an Applied Kinesiologist, though I can't say I noticed any significant effects. Surprisingly, there doesn't seem to be many people talking about them as either good or bad and there aren't many articles on them. Here's the brand I used, which has many positive reviews and also a group of people who claimed that the soil based probiotic made them sick (varied reports of headache, bloating, constipation, nausea, diarrhea, auto-immune flare up, and stomach pain):

http://www.amazon.com/Prescript-Assist-Spectrum-Probiotic-Prebiotic-Complex/dp/B00JB2GOFI/

An article I found:

http://www.thebarefootgolfer.com/2013/03/22/soil-based-organisms-a-superior-probiotic/

Soil-Based Organisms – A Superior Probiotic?
March 22, 2013

Introduction
With the addition of this post on soil-based organisms as probiotics, I guess this can now be considered a series of posts on probiotics since I have written about them here and here already. I am also sure I will come across even more things to discuss with regards to probiotics in the future as they appear to be getting a good deal of attention in the research and medical community particularly as an alternative to antibiotics. This post however, will be a little different as I will not be writing about a specific condition, it will be a post about a specific type of probiotic. This type of probitic is one that I am considering as my next step in controlling my “minor” autoimmune condition (seasonal allergies). I have been reading a fair bit about this type of probiotic and have become very interested in its suggested ability to regulate the immune system and its antimicrobial properties.

In Chris Kresser’s most recent Revolution Health Radio episode, he talked about The Old Friends hypothesis of chronic disease and autoimmunity and the introduction of what is called soil-based organism probiotics. The bacteria in this type of probiotic is not the common Lactobacillus type you commonly hear about, they are actually bacteria commonly found in soil. Eeeeewwww…you mean eating dirt is good for me. Well, it seems the short answer is yes. Now just so you are aware, probiotics containing soil based organisms are not actually dirt, they have simply cultured the bacteria strains that are commonly found in dirt, and only the ones that are not pathogenic.

The Old Friends Hypothesis – Overview
So this is actually pretty interesting stuff. Chris Kresser, in his radio show linked to above, provides a description of this hypothesis as well, and quotes a book called An Epidemic of Absence:

You can check out a summary of the book here. Ultimately, the argument that is presented is that the human species did not evolve in the absence of microorganisms (ie, bacteria and parasites). In reality, we likely evolved together in a symbiosis of sorts, the outcome of which being that we likely, in many ways, rely on the presence of microorganisms in our body, even certain organisms that may be considered pathogenic or parasitic. Really cool stuff right?

Some of you may have heard of what I think is called the hygiene theory? Anyway, it goes something like this: Our immune system has evolved to fight off intruders like viruses and pathogenic bacteria; however, in developed countries, and particularly in countries obsessed over sterilization (think hand sanitizer), we are no longer exposed to the same amount and/or type of such microorganisms, leading to our immune system attacking other things instead (like our own body or inhaled pollen). This may be oversimplified but I gave it my best shot.

Based on reading reviews of the above noted book, a slightly different hypothesis is that the presence of microorganisms in our body and our immune system support each other and if we take one of the supports away (take away the presence of microorganisms) the other one falls (our immune system). In other words the presence of microorganisms in our body seems to provide proper immune system regulation. Again, pretty cool. I will note that I have not read this book, but I will in the very near future. The summary also mentions that it dives into a theory about how allergies can be traced back to inflammatory responses in mothers. I always thought it was my parents fault 

Soil-Based Organisms – Probiotics:
So, some of the microorganisms referred to above would be those found in soil, with the theory that we probably haven’t washed our food and hands 20 million times a day until fairly recently in human history, so we likely ate some dirt, albeit not handfuls at a time. This really got me thinking, and Chris advised that he finds a soil-based probiotic called Prescript-Assist helpful for some of his patients. For me that meant I was going to try and do a bit of research and write something about this. I guess it’s my way of learning.

I started looking for local places that sold a soil-based probiotics and had some trouble doing so. However, I did come across some articles on the possible dangers of taking such a product. Some blogs out there were saying that soil-based probiotics can make you sick, or even cause death…Yikes, time to look further into this one right? It seems that there is limited scientific articles out there on soil based probiotics, but the ones that I found had some positive information for me.

Unfortunately, this article (1) only has the abstract available and I couldn’t track down the full paper. It looks promising based on the fact that it is indicating that a soil based probiotic product has been shown to be beneficial in immune regulation and reducing symptoms in a number of autoimmune conditions, including allergies. At the same time, the abstract was a bit confusing and I couldn’t determine if it was a study on one individual or a review study of sorts.

With regards to IBS specifically, there are two studies (2, 3) that have shown beneficial effects of Prescript-Assist on IBS symptoms. One study was 2 weeks in duration, and the other was a 1 year extension of the first 2 week study.

A specific soil-based bacteria bacillus clausii, was shown to significantly and safely reduce the duration of respiratory infections in children (4). Two literature reviews (5, 6) have indicated that a soil-based bacteria (certain strains of bacillus) have positive effects on certain conditions do to immune regulating and antimicrobial properties.

On a safety note, it appears as though there has been very minimal reports of negative effects of soil-based probiotics (5, 6, 7, 8), so they do appear quite safe based on reading the noted studies. However, the warning in these studies that is given is that some bacillus strains are pathogenic and can cause illness, although these strains don’t seem to be used in probiotic products. Another note is that the studies I looked at mainly deal with bacillus strains of soil-based organisms only, and most soil based probiotics have many strains of bacteria in them (please don’t quote me on that since I haven’t read all soil-based product labels).

In the end, since the bacterial content of each product differs, who knows how accurate labeling of these products are, and the fact that some soil based bacteria can lead to illness, I decided that it was my best bet to seek out a qualified practitioner to suggest something for me. Thus, I have an appointment scheduled with a naturopath next week and soil-based probiotics will be a topic for me during this appointment. Given the reports of the effectiveness of these products on autoimmune conditions with what appears to be minimal, if any, risk of illness, I am very eager for this appointment and to start a product of this type. I must regulate my immune system, and hopefully soil-based probiotics will be the regulators 

Remember, I am not a healthcare practitioner, I am simply communicating what I have researched and read on my own, and what I have decided to try for myself. Hope this is helpful and interesting. I would like to hear if anyone who may read this has ever used a soil based probiotic and what their experience with it was.

Sincerely,

The Barefoot Golfer


References:
1.) http://www.ncbi.nlm.nih.gov/pubmed/11365013
2.) http://www.ncbi.nlm.nih.gov/pubmed/17692729
3.) http://www.ncbi.nlm.nih.gov/pubmed/16117982
4.) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1936284/
5.) http://www.ncbi.nlm.nih.gov/pubmed/16102604
6.) http://www.ncbi.nlm.nih.gov/pubmed/21315976
7.) http://www.ncbi.nlm.nih.gov/pubmed/22121830
8.) http://www.ncbi.nlm.nih.gov/pubmed/18312567

Here's the only thing I could find from Chris Kresser, aside from the radio show linked in the above article:

https://chriskresserlac-shopify.helpjuice.com/questions/47699-Prescript-Assist-and-*spore-forming-organisms*

Prescript-Assist and *spore forming organisms*
There is a lot of confusion about this topic. Jini Patel has raised concerns about soil-based organisms (SBOs) in this article , based on claims made by Natasha Trevnev, the founder of Natren (a company that sells lactic acid-based probiotics). Most of the objections raised in the article are either technically inaccurate or outdated by current research. It has become clear through DNA sequencing of the gut microbiota that the human gut has a makeup of bacteria similar to or already of SBO origin. From an evolutionary perspective, it's likely that we were exposed to SBOs to a much larger degree than we are now, due to the industrialization of agriculture and food distribution, and changes in soil quality and diversity.

The term "spore former" refers to microflora that can form spores that are biologically active, i.e. reproduce in the spore form, and are highly resistant to the environment and cause disease. Endospore formers, on the other hand, are biologically inactive and remain that way until environmental conditions allow resuming normal forms. Prescript Assist does have endospore formers, but they simply pass out of the system if they ever form in the gut of any mammal.

The Relman-Stanford group studies have shown that SBOs are more numerous in the gut than lactic acid microflora, and that the microflora resident in the healthy mucosa of the gut differ considerably from what is present in fecal material (which tends to have higher numbers of lactobacilli and bifidobacteria).

Finally,Prescript-Assist microflora are recognized Class 1 Etiological Agents, non-toxic, non-pathogenic, from independently maintained lines -- this is well documented in both of the Clinical Therapeutics Articles. More than a decade of use as a supplement has revealed no adverse effects and/or side-effects [including reportedly patients with impaired immune systems], as well as the initial demonstrations with repeated consumptions of doses amounting to 500X that recommended for ordinarily daily use with no ill effect.

There's at least one main dissenting opinion on the topic of soil based probiotics that I found:

http://fixyourgut.com/hso-probiotics-part-3-prescript-assist/

HSO’s Part 3 – I Do Not Recommend Prescript Assist
May 16, 2014
John Brisson


Want to learn all about HSOs? Get a copy of Fix Your Gut.

Everyone in the natural health community loves Prescript Assist, I guess I am a lone wolf. From Sisson,1 to Asprey,2 to Kresser,3 everyone believes that Prescript Assist or HSO’s are the best things since sliced gluten free bread.

The sad thing is most of the time I agree with Kresser, but this time I cannot stand behind one of my mentors.

But why is that?

Well, in theory Prescript Assist appears to be perfect HSO supplement. The supplement is heat and shelf stable, and most of the HSO’s are encapsulated in either endospores or make their own biofilms so you know it will survive your stomach acid and propagate freely in the large intestine.

Kresser goes as far as to say that the HSO’s found in Prescript Assist are:4

“Finally, Prescript-Assist microflora are recognized Class 1 Etiological Agents, non-toxic, non-pathogenic, from independently maintained lines — this is well documented in both of the Clinical Therapeutics Articles. More than a decade of use as a supplement has revealed no adverse effects and/or side-effects [including reportedly patients with impaired immune systems], as well as the initial demonstrations with repeated consumptions of doses amounting to 500X that recommended for ordinarily daily use with no ill effect.”

Well, I’ll be damned Prescript Assist is the safest HSO supplement known to mankind!

Too bad for Prescript Assist and Kresser insurmountable scientific data proves otherwise.

The Problems with Prescript Assist



Most HSO’s in Prescript Assist are unknown if they are part of normal human flora or have non-existent human studies and research of safety. More information about the interaction between these HSO’s and their human hosts might be known once the human microbiome project5 is completed, but for now it is truly unknown if any of these bacteria makeup your biome.

You might be asking yourself what is so wrong with that?

The main issue is that using any bacteria or yeast with unknown pathogenic capabilities in healthy and especially sick people is just asking for trouble. Without research, we simply don’t know what these organisms are capable of doing in the human body.


HSO’s That Are Not Considered Normal Human Flora or Have Non-Existent Human Interaction Research in Prescript Assist6

Azospirillum brasiliense
Azospirillum lipoferum
Bacillus brevis
Bacillus marcerans
Bacillus pumilus
Bacillus polymyxa
Bacteroides lipolyticum
Bacteroides succinogenes
Kurthia zopfii
Myrothecium verrucaria
Pseudomonas calcis
Pseudomonas denitrificans
Pseudomonas glathei
Streptomyces fradiae
Streptomyces cellulosae
Streptomyces griseoflavus


Remember when Kresser mentioned that the HSO’s in Prescript Assist were non-pathogenic, and no side effects, or illness have ever been reported from the HSO’s found in the product. Yeah, well I guess he didn’t do a lot of research before he made that statement.



Documented Opportunistic HSO’s in Prescript Assist



Acinetobacter calcoaceticus7 8 9 10
Bacillus subtilis11
Phanerochaete chrysosporium12
Pseudomonas fluorescens13 14


All of these listed HSO’s are known to cause opportunistic infections in humans. Pseudomonas fluorescens has even been implicated as the cause of Crohn’s disease (I believe that it is a coinfection instead of being the direct cause.)

These bacterium are able to produce endospores and biofilm which make them harder to eliminate if they become opportunistic. It is a lot easier to eliminate opportunistic Lactobacillus acidophilus then Pseudomonas fluorescens.

I hope you now understand why I cannot recommend any of my clients supplement Prescript Assist, and I hope you take my research and do some investigating of the supplement on your own.


http://www.marksdailyapple.com/definitive-guide-to-primal-supplementation/#axzz31t4SchA6 ↩
http://www.bulletproofexec.com/the-red-meat-scapegoat-the-new-york-times-carnitine-heart-disease-and-science/ ↩
http://store.chriskresser.com/products/prescript-assist-probiotic ↩
https://chriskresserlac-shopify.helpjuice.com/questions/47699-Prescript-Assist-and-*spore-forming-organisms* ↩
http://commonfund.nih.gov/hmp/index ↩
http://www.prescript-assist.com/ ↩
http://www.ncbi.nlm.nih.gov/pubmed/846390 ↩
http://www.ncbi.nlm.nih.gov/pubmed/362918 ↩
http://link.springer.com/article/10.1007%2FBF01643394#page-1 ↩
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC172888/ ↩
http://fixyourgut.com/hso-probiotics-part-2-danger-supplementing-bacillus-subtilis/ ↩
http://onlinelibrary.wiley.com/doi/10.1002/rcr2.31/abstract ↩
http://www.gutpathogens.com/content/2/1/16 ↩
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC133002/ ↩

He raises some good points and I don't think I'm qualified to dissect the specific technicalities of the individual strains to determine if the data is accurate or not. And unfortunately I haven't found much data from other well known bloggers on the topic. It has been recommended in the paleo sphere a number of times (I found some recommendations on Paleo Hacks) and the reviews on Amazon are generally pretty positive. I didn't experience any perceived negative effects, but no significant positive ones either. It's possible that I simply didn't notice any effects in either direction as I took them some months ago and the effects may have been small. The negative reviews on Amazon are hard to evaluate because we have no idea what the diets of the people who had negative reactions to the supplement are or other factors that might contribute to their having a negative reaction.

I think these may be worthy of more investigation and experimentation, but it may be wise to proceed with caution.

I agree with Foxx, is an interesting research topic, unfortunately I have not succeeded in finding some more information. :/

 

[davey72]

That is interesting. I remember hearing somewhere when i was a kid that clean soil was good for you and consumi g some good for digestion.